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from rdkit import Chem
from rdkit.Chem import rdPartialCharges
import collections
def _isCallable(thing):
return (hasattr(collections,'Callable') and isinstance(thing,collections.Callable)) or \
hasattr(thing,'__call__')
_descList=[]
def _setupDescriptors(namespace):
global _descList,descList
from rdkit.Chem import GraphDescriptors,MolSurf,Lipinski,Fragments,Crippen
from rdkit.Chem.EState import EState_VSA
mods = [GraphDescriptors,MolSurf,EState_VSA,Lipinski,Crippen,Fragments]
otherMods = [Chem]
for nm,thing in namespace.items():
if nm[0]!='_' and _isCallable(thing):
_descList.append((nm,thing))
others = []
for mod in otherMods:
tmp = dir(mod)
for name in tmp:
if name[0] != '_':
thing = getattr(mod,name)
if _isCallable(thing):
others.append(name)
for mod in mods:
tmp = dir(mod)
for name in tmp:
if name[0] != '_' and name[-1] != '_' and name not in others:
# filter out python reference implementations:
if name[:2]=='py' and name[2:] in tmp:
continue
thing = getattr(mod,name)
if _isCallable(thing):
namespace[name]=thing
_descList.append((name,thing))
descList=_descList
from rdkit.Chem import rdMolDescriptors as _rdMolDescriptors
MolWt = lambda *x,**y:_rdMolDescriptors._CalcMolWt(*x,**y)
MolWt.version=_rdMolDescriptors._CalcMolWt_version
MolWt.__doc__="""The average molecular weight of the molecule
>>> MolWt(Chem.MolFromSmiles('CC'))
30.07
>>> MolWt(Chem.MolFromSmiles('[NH4+].[Cl-]'))
53.49...
"""
HeavyAtomMolWt=lambda x:MolWt(x,True)
HeavyAtomMolWt.__doc__="""The average molecular weight of the molecule ignoring hydrogens
>>> HeavyAtomMolWt(Chem.MolFromSmiles('CC'))
24.02...
>>> HeavyAtomMolWt(Chem.MolFromSmiles('[NH4+].[Cl-]'))
49.46
"""
HeavyAtomMolWt.version="1.0.0"
ExactMolWt = lambda *x,**y:_rdMolDescriptors.CalcExactMolWt(*x,**y)
ExactMolWt.version=_rdMolDescriptors._CalcExactMolWt_version
ExactMolWt.__doc__="""The exact molecular weight of the molecule
>>> ExactMolWt(Chem.MolFromSmiles('CC'))
30.04...
>>> ExactMolWt(Chem.MolFromSmiles('[13CH3]C'))
31.05...
"""
def NumValenceElectrons(mol):
""" The number of valence electrons the molecule has
>>> NumValenceElectrons(Chem.MolFromSmiles('CC'))
14.0
>>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)O'))
18.0
>>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)[O-]'))
18.0
>>> NumValenceElectrons(Chem.MolFromSmiles('C(=O)'))
12.0
"""
tbl = Chem.GetPeriodicTable()
accum = 0.0
for atom in mol.GetAtoms():
accum += tbl.GetNOuterElecs(atom.GetAtomicNum())
accum -= atom.GetFormalCharge()
accum += atom.GetTotalNumHs()
return accum
NumValenceElectrons.version="1.0.0"
def NumRadicalElectrons(mol):
""" The number of radical electrons the molecule has
(says nothing about spin state)
>>> NumRadicalElectrons(Chem.MolFromSmiles('CC'))
0.0
>>> NumRadicalElectrons(Chem.MolFromSmiles('C[CH3]'))
0.0
>>> NumRadicalElectrons(Chem.MolFromSmiles('C[CH2]'))
1.0
>>> NumRadicalElectrons(Chem.MolFromSmiles('C[CH]'))
2.0
>>> NumRadicalElectrons(Chem.MolFromSmiles('C[C]'))
3.0
"""
accum = 0.0
for atom in mol.GetAtoms():
accum += atom.GetNumRadicalElectrons()
return accum
NumRadicalElectrons.version="1.0.0"
def _ChargeDescriptors(mol,force=False):
if not force and hasattr(mol,'_chargeDescriptors'):
return mol._chargeDescriptors
chgs = rdPartialCharges.ComputeGasteigerCharges(mol)
minChg=500.
maxChg=-500.
for at in mol.GetAtoms():
chg = float(at.GetProp('_GasteigerCharge'))
minChg = min(chg,minChg)
maxChg = max(chg,maxChg)
res = (minChg,maxChg)
mol._chargeDescriptors=res
return res
def MaxPartialCharge(mol,force=False):
_,res = _ChargeDescriptors(mol,force)
return res
MaxPartialCharge.version="1.0.0"
def MinPartialCharge(mol,force=False):
res,_ = _ChargeDescriptors(mol,force)
return res
MinPartialCharge.version="1.0.0"
def MaxAbsPartialCharge(mol,force=False):
v1,v2 = _ChargeDescriptors(mol,force)
return max(abs(v1),abs(v2))
MaxAbsPartialCharge.version="1.0.0"
def MinAbsPartialCharge(mol,force=False):
v1,v2 = _ChargeDescriptors(mol,force)
return min(abs(v1),abs(v2))
MinAbsPartialCharge.version="1.0.0"
from rdkit.Chem.EState.EState import MaxEStateIndex,MinEStateIndex,MaxAbsEStateIndex,MinAbsEStateIndex
_setupDescriptors(locals())
#------------------------------------
#
# doctest boilerplate
#
def _test():
import doctest,sys
return doctest.testmod(sys.modules["__main__"],optionflags=doctest.ELLIPSIS)
if __name__ == '__main__':
import sys
failed,tried = _test()
sys.exit(failed)
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""" SMARTS definitions for the publically available MACCS keys
and a MACCS fingerprinter
I compared the MACCS fingerprints generated here with those from two
other packages (not MDL, unfortunately). Of course there are
disagreements between the various fingerprints still, but I think
these definitions work pretty well. Some notes:
1) most of the differences have to do with aromaticity
2) there's a discrepancy sometimes because the current RDKit
definitions do not require multiple matches to be distinct. e.g. the
SMILES C(=O)CC(=O) can match the (hypothetical) key O=CC twice in my
definition. It's not clear to me what the correct behavior is.
3) Some keys are not fully defined in the MDL documentation
4) Two keys, 125 and 166, have to be done outside of SMARTS.
5) Key 1 (ISOTOPE) isn't defined
Rev history:
2006 (gl): Original open-source release
May 2011 (gl): Update some definitions based on feedback from Andrew Dalke
"""
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
from rdkit import DataStructs
# these are SMARTS patterns corresponding to the MDL MACCS keys
smartsPatts={
1:('?',0), # ISOTOPE
#2:('[#104,#105,#106,#107,#106,#109,#110,#111,#112]',0), # atomic num >103 Not complete
2:('[#104]',0), # limit the above def'n since the RDKit only accepts up to #104
3:('[#32,#33,#34,#50,#51,#52,#82,#83,#84]',0), # Group IVa,Va,VIa Rows 4-6
4:('[Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr]',0), # actinide
5:('[Sc,Ti,Y,Zr,Hf]',0), # Group IIIB,IVB (Sc...)
6:('[La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu]',0), # Lanthanide
7:('[V,Cr,Mn,Nb,Mo,Tc,Ta,W,Re]',0), # Group VB,VIB,VIIB
8:('[!#6;!#1]1~*~*~*~1',0), # QAAA@1
9:('[Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt]',0), # Group VIII (Fe...)
10:('[Be,Mg,Ca,Sr,Ba,Ra]',0), # Group IIa (Alkaline earth)
11:('*1~*~*~*~1',0), # 4M Ring
12:('[Cu,Zn,Ag,Cd,Au,Hg]',0), # Group IB,IIB (Cu..)
13:('[#8]~[#7](~[#6])~[#6]',0), # ON(C)C
14:('[#16]-[#16]',0), # S-S
15:('[#8]~[#6](~[#8])~[#8]',0), # OC(O)O
16:('[!#6;!#1]1~*~*~1',0), # QAA@1
17:('[#6]#[#6]',0), #CTC
18:('[#5,#13,#31,#49,#81]',0), # Group IIIA (B...)
19:('*1~*~*~*~*~*~*~1',0), # 7M Ring
20:('[#14]',0), #Si
21:('[#6]=[#6](~[!#6;!#1])~[!#6;!#1]',0), # C=C(Q)Q
22:('*1~*~*~1',0), # 3M Ring
23:('[#7]~[#6](~[#8])~[#8]',0), # NC(O)O
24:('[#7]-[#8]',0), # N-O
25:('[#7]~[#6](~[#7])~[#7]',0), # NC(N)N
26:('[#6]=;@[#6](@*)@*',0), # C$=C($A)$A
27:('[I]',0), # I
28:('[!#6;!#1]~[CH2]~[!#6;!#1]',0), # QCH2Q
29:('[#15]',0),# P
30:('[#6]~[!#6;!#1](~[#6])(~[#6])~*',0), # CQ(C)(C)A
31:('[!#6;!#1]~[F,Cl,Br,I]',0), # QX
32:('[#6]~[#16]~[#7]',0), # CSN
33:('[#7]~[#16]',0), # NS
34:('[CH2]=*',0), # CH2=A
35:('[Li,Na,K,Rb,Cs,Fr]',0), # Group IA (Alkali Metal)
36:('[#16R]',0), # S Heterocycle
37:('[#7]~[#6](~[#8])~[#7]',0), # NC(O)N
38:('[#7]~[#6](~[#6])~[#7]',0), # NC(C)N
39:('[#8]~[#16](~[#8])~[#8]',0), # OS(O)O
40:('[#16]-[#8]',0), # S-O
41:('[#6]#[#7]',0), # CTN
42:('F',0), # F
43:('[!#6;!#1;!H0]~*~[!#6;!#1;!H0]',0), # QHAQH
44:('[!#1;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#35;!#53]',0), # OTHER
45:('[#6]=[#6]~[#7]',0), # C=CN
46:('Br',0), # BR
47:('[#16]~*~[#7]',0), # SAN
48:('[#8]~[!#6;!#1](~[#8])(~[#8])',0), # OQ(O)O
49:('[!+0]',0), # CHARGE
50:('[#6]=[#6](~[#6])~[#6]',0), # C=C(C)C
51:('[#6]~[#16]~[#8]',0), # CSO
52:('[#7]~[#7]',0), # NN
53:('[!#6;!#1;!H0]~*~*~*~[!#6;!#1;!H0]',0), # QHAAAQH
54:('[!#6;!#1;!H0]~*~*~[!#6;!#1;!H0]',0), # QHAAQH
55:('[#8]~[#16]~[#8]',0), #OSO
56:('[#8]~[#7](~[#8])~[#6]',0), # ON(O)C
57:('[#8R]',0), # O Heterocycle
58:('[!#6;!#1]~[#16]~[!#6;!#1]',0), # QSQ
59:('[#16]!:*:*',0), # Snot%A%A
60:('[#16]=[#8]',0), # S=O
61:('*~[#16](~*)~*',0), # AS(A)A
62:('*@*!@*@*',0), # A$!A$A
63:('[#7]=[#8]',0), # N=O
64:('*@*!@[#16]',0), # A$A!S
65:('c:n',0), # C%N
66:('[#6]~[#6](~[#6])(~[#6])~*',0), # CC(C)(C)A
67:('[!#6;!#1]~[#16]',0), # QS
68:('[!#6;!#1;!H0]~[!#6;!#1;!H0]',0), # QHQH (&...) SPEC Incomplete
69:('[!#6;!#1]~[!#6;!#1;!H0]',0), # QQH
70:('[!#6;!#1]~[#7]~[!#6;!#1]',0), # QNQ
71:('[#7]~[#8]',0), # NO
72:('[#8]~*~*~[#8]',0), # OAAO
73:('[#16]=*',0), # S=A
74:('[CH3]~*~[CH3]',0), # CH3ACH3
75:('*!@[#7]@*',0), # A!N$A
76:('[#6]=[#6](~*)~*',0), # C=C(A)A
77:('[#7]~*~[#7]',0), # NAN
78:('[#6]=[#7]',0), # C=N
79:('[#7]~*~*~[#7]',0), # NAAN
80:('[#7]~*~*~*~[#7]',0), # NAAAN
81:('[#16]~*(~*)~*',0), # SA(A)A
82:('*~[CH2]~[!#6;!#1;!H0]',0), # ACH2QH
83:('[!#6;!#1]1~*~*~*~*~1',0), # QAAAA@1
84:('[NH2]',0), #NH2
85:('[#6]~[#7](~[#6])~[#6]',0), # CN(C)C
86:('[C;H2,H3][!#6;!#1][C;H2,H3]',0), # CH2QCH2
87:('[F,Cl,Br,I]!@*@*',0), # X!A$A
88:('[#16]',0), # S
89:('[#8]~*~*~*~[#8]',0), # OAAAO
90:('[$([!#6;!#1;!H0]~*~*~[CH2]~*),$([!#6;!#1;!H0;R]1@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~[R]1@[R]@[CH2;R]1)]',0), # QHAACH2A
91:('[$([!#6;!#1;!H0]~*~*~*~[CH2]~*),$([!#6;!#1;!H0;R]1@[R]@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~[R]1@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~*~[R]1@[R]@[CH2;R]1)]',0), # QHAAACH2A
92:('[#8]~[#6](~[#7])~[#6]',0), # OC(N)C
93:('[!#6;!#1]~[CH3]',0), # QCH3
94:('[!#6;!#1]~[#7]',0), # QN
95:('[#7]~*~*~[#8]',0), # NAAO
96:('*1~*~*~*~*~1',0), # 5 M ring
97:('[#7]~*~*~*~[#8]',0), # NAAAO
98:('[!#6;!#1]1~*~*~*~*~*~1',0), # QAAAAA@1
99:('[#6]=[#6]',0), # C=C
100:('*~[CH2]~[#7]',0), # ACH2N
101:('[$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1)]',0), # 8M Ring or larger. This only handles up to ring sizes of 14
102:('[!#6;!#1]~[#8]',0), # QO
103:('Cl',0), # CL
104:('[!#6;!#1;!H0]~*~[CH2]~*',0), # QHACH2A
105:('*@*(@*)@*',0), # A$A($A)$A
106:('[!#6;!#1]~*(~[!#6;!#1])~[!#6;!#1]',0), # QA(Q)Q
107:('[F,Cl,Br,I]~*(~*)~*',0), # XA(A)A
108:('[CH3]~*~*~*~[CH2]~*',0), # CH3AAACH2A
109:('*~[CH2]~[#8]',0), # ACH2O
110:('[#7]~[#6]~[#8]',0), # NCO
111:('[#7]~*~[CH2]~*',0), # NACH2A
112:('*~*(~*)(~*)~*',0), # AA(A)(A)A
113:('[#8]!:*:*',0), # Onot%A%A
114:('[CH3]~[CH2]~*',0), # CH3CH2A
115:('[CH3]~*~[CH2]~*',0), # CH3ACH2A
116:('[$([CH3]~*~*~[CH2]~*),$([CH3]~*1~*~[CH2]1)]',0), # CH3AACH2A
117:('[#7]~*~[#8]',0), # NAO
118:('[$(*~[CH2]~[CH2]~*),$(*1~[CH2]~[CH2]1)]',1), # ACH2CH2A > 1
119:('[#7]=*',0), # N=A
120:('[!#6;R]',1), # Heterocyclic atom > 1 (&...) Spec Incomplete
121:('[#7;R]',0), # N Heterocycle
122:('*~[#7](~*)~*',0), # AN(A)A
123:('[#8]~[#6]~[#8]',0), # OCO
124:('[!#6;!#1]~[!#6;!#1]',0), # QQ
125:('?',0), # Aromatic Ring > 1
126:('*!@[#8]!@*',0), # A!O!A
127:('*@*!@[#8]',1), # A$A!O > 1 (&...) Spec Incomplete
128:('[$(*~[CH2]~*~*~*~[CH2]~*),$([R]1@[CH2;R]@[R]@[R]@[R]@[CH2;R]1),$(*~[CH2]~[R]1@[R]@[R]@[CH2;R]1),$(*~[CH2]~*~[R]1@[R]@[CH2;R]1)]',0), # ACH2AAACH2A
129:('[$(*~[CH2]~*~*~[CH2]~*),$([R]1@[CH2]@[R]@[R]@[CH2;R]1),$(*~[CH2]~[R]1@[R]@[CH2;R]1)]',0), # ACH2AACH2A
130:('[!#6;!#1]~[!#6;!#1]',1), # QQ > 1 (&...) Spec Incomplete
131:('[!#6;!#1;!H0]',1), # QH > 1
132:('[#8]~*~[CH2]~*',0), # OACH2A
133:('*@*!@[#7]',0), # A$A!N
134:('[F,Cl,Br,I]',0), # X (HALOGEN)
135:('[#7]!:*:*',0), # Nnot%A%A
136:('[#8]=*',1), # O=A>1
137:('[!C;!c;R]',0), # Heterocycle
138:('[!#6;!#1]~[CH2]~*',1), # QCH2A>1 (&...) Spec Incomplete
139:('[O;!H0]',0), # OH
140:('[#8]',3), # O > 3 (&...) Spec Incomplete
141:('[CH3]',2), # CH3 > 2 (&...) Spec Incomplete
142:('[#7]',1), # N > 1
143:('*@*!@[#8]',0), # A$A!O
144:('*!:*:*!:*',0), # Anot%A%Anot%A
145:('*1~*~*~*~*~*~1',1), # 6M ring > 1
146:('[#8]',2), # O > 2
147:('[$(*~[CH2]~[CH2]~*),$([R]1@[CH2;R]@[CH2;R]1)]',0), # ACH2CH2A
148:('*~[!#6;!#1](~*)~*',0), # AQ(A)A
149:('[C;H3,H4]',1), # CH3 > 1
150:('*!@*@*!@*',0), # A!A$A!A
151:('[#7;!H0]',0), # NH
152:('[#8]~[#6](~[#6])~[#6]',0), # OC(C)C
153:('[!#6;!#1]~[CH2]~*',0), # QCH2A
154:('[#6]=[#8]',0), # C=O
155:('*!@[CH2]!@*',0), # A!CH2!A
156:('[#7]~*(~*)~*',0), # NA(A)A
157:('[#6]-[#8]',0), # C-O
158:('[#6]-[#7]',0), # C-N
159:('[#8]',1), # O>1
160:('[C;H3,H4]',0), #CH3
161:('[#7]',0), # N
162:('a',0), # Aromatic
163:('*1~*~*~*~*~*~1',0), # 6M Ring
164:('[#8]',0), # O
165:('[R]',0), # Ring
166:('?',0), # Fragments FIX: this can't be done in SMARTS
}
maccsKeys = None
def _InitKeys(keyList,keyDict):
""" *Internal Use Only*
generates SMARTS patterns for the keys, run once
"""
assert len(keyList) == len(keyDict.keys()),'length mismatch'
for key in keyDict.keys():
patt,count = keyDict[key]
if patt != '?':
try:
sma = Chem.MolFromSmarts(patt)
except:
sma = None
if not sma:
print('SMARTS parser error for key #%d: %s'%(key,patt))
else:
keyList[key-1] = sma,count
def _pyGenMACCSKeys(mol,**kwargs):
""" generates the MACCS fingerprint for a molecules
**Arguments**
- mol: the molecule to be fingerprinted
- any extra keyword arguments are ignored
**Returns**
a _DataStructs.SparseBitVect_ containing the fingerprint.
>>> m = Chem.MolFromSmiles('CNO')
>>> bv = GenMACCSKeys(m)
>>> tuple(bv.GetOnBits())
(24, 68, 69, 71, 93, 94, 102, 124, 131, 139, 151, 158, 160, 161, 164)
>>> bv = GenMACCSKeys(Chem.MolFromSmiles('CCC'))
>>> tuple(bv.GetOnBits())
(74, 114, 149, 155, 160)
"""
global maccsKeys
if maccsKeys is None:
maccsKeys = [(None,0)]*len(smartsPatts.keys())
_InitKeys(maccsKeys,smartsPatts)
ctor=kwargs.get('ctor',DataStructs.SparseBitVect)
res = ctor(len(maccsKeys)+1)
for i,(patt,count) in enumerate(maccsKeys):
if patt is not None:
if count==0:
res[i+1] = mol.HasSubstructMatch(patt)
else:
matches = mol.GetSubstructMatches(patt)
if len(matches) > count:
res[i+1] = 1
elif (i+1)==125:
# special case: num aromatic rings > 1
ri = mol.GetRingInfo()
nArom=0
res[125]=0
for ring in ri.BondRings():
isArom=True
for bondIdx in ring:
if not mol.GetBondWithIdx(bondIdx).GetIsAromatic():
isArom=False
break
if isArom:
nArom+=1
if nArom>1:
res[125]=1
break
elif (i+1)==166:
res[166]=0
# special case: num frags > 1
if len(Chem.GetMolFrags(mol))>1:
res[166]=1
return res
GenMACCSKeys = rdMolDescriptors.GetMACCSKeysFingerprint
FingerprintMol = rdMolDescriptors.GetMACCSKeysFingerprint
#------------------------------------
#
# doctest boilerplate
#
def _test():
import doctest,sys
return doctest.testmod(sys.modules["__main__"])
if __name__ == '__main__':
import sys
failed,tried = _test()
sys.exit(failed)
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"path": "rdkit/Chem/MACCSkeys.py",
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"size": "11266",
"license": "bsd-3-clause",
"hash": -340494744810183800,
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"ratio": 1.9264705882352942,
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"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.3883243178335294,
"avg_score": null,
"num_lines": null
} |
""" functionality for drawing trees on sping canvases
"""
from rdkit.sping import pid as piddle
import math
class VisOpts(object):
circRad = 10
minCircRad = 4
maxCircRad = 16
circColor = piddle.Color(0.6,0.6,0.9)
terminalEmptyColor = piddle.Color(.8,.8,.2)
terminalOnColor = piddle.Color(0.8,0.8,0.8)
terminalOffColor = piddle.Color(0.2,0.2,0.2)
outlineColor = piddle.transparent
lineColor = piddle.Color(0,0,0)
lineWidth = 2
horizOffset = 10
vertOffset = 50
labelFont = piddle.Font(face='helvetica',size=10)
highlightColor = piddle.Color(1.,1.,.4)
highlightWidth = 2
visOpts = VisOpts()
def CalcTreeNodeSizes(node):
"""Recursively calculate the total number of nodes under us.
results are set in node.totNChildren for this node and
everything underneath it.
"""
children = node.GetChildren()
if len(children) > 0:
nHere = 0
nBelow=0
for child in children:
CalcTreeNodeSizes(child)
nHere = nHere + child.totNChildren
if child.nLevelsBelow > nBelow:
nBelow = child.nLevelsBelow
else:
nBelow = 0
nHere = 1
node.nExamples = len(node.GetExamples())
node.totNChildren = nHere
node.nLevelsBelow = nBelow+1
def _ExampleCounter(node,min,max):
if node.GetTerminal():
cnt = node.nExamples
if cnt < min: min = cnt
if cnt > max: max = cnt
else:
for child in node.GetChildren():
provMin,provMax = _ExampleCounter(child,min,max)
if provMin < min: min = provMin
if provMax > max: max = provMax
return min,max
def _ApplyNodeScales(node,min,max):
if node.GetTerminal():
if max!=min:
loc = float(node.nExamples - min)/(max-min)
else:
loc = .5
node._scaleLoc = loc
else:
for child in node.GetChildren():
_ApplyNodeScales(child,min,max)
def SetNodeScales(node):
min,max = 1e8,-1e8
min,max = _ExampleCounter(node,min,max)
node._scales=min,max
_ApplyNodeScales(node,min,max)
def DrawTreeNode(node,loc,canvas,nRes=2,scaleLeaves=False,showPurity=False):
"""Recursively displays the given tree node and all its children on the canvas
"""
try:
nChildren = node.totNChildren
except AttributeError:
nChildren = None
if nChildren is None:
CalcTreeNodeSizes(node)
if not scaleLeaves or not node.GetTerminal():
rad = visOpts.circRad
else:
scaleLoc = getattr(node, "_scaleLoc", 0.5)
rad = visOpts.minCircRad + node._scaleLoc*(visOpts.maxCircRad-visOpts.minCircRad)
x1 = loc[0] - rad
y1 = loc[1] - rad
x2 = loc[0] + rad
y2 = loc[1] + rad
if showPurity and node.GetTerminal():
examples = node.GetExamples()
nEx = len(examples)
if nEx:
tgtVal = int(node.GetLabel())
purity = 0.0
for ex in examples:
if int(ex[-1])==tgtVal:
purity += 1./len(examples)
else:
purity = 1.0
deg = purity*math.pi
xFact = rad*math.sin(deg)
yFact = rad*math.cos(deg)
pureX = loc[0]+xFact
pureY = loc[1]+yFact
children = node.GetChildren()
# just move down one level
childY = loc[1] + visOpts.vertOffset
# this is the left-hand side of the leftmost span
childX = loc[0] - ((visOpts.horizOffset+visOpts.circRad)*node.totNChildren)/2
for i in range(len(children)):
# center on this child's space
child = children[i]
halfWidth = ((visOpts.horizOffset+visOpts.circRad)*child.totNChildren)/2
childX = childX + halfWidth
childLoc = [childX,childY]
canvas.drawLine(loc[0],loc[1],childLoc[0],childLoc[1],
visOpts.lineColor,visOpts.lineWidth)
DrawTreeNode(child,childLoc,canvas,nRes=nRes,scaleLeaves=scaleLeaves,
showPurity=showPurity)
# and move over to the leftmost point of the next child
childX = childX + halfWidth
if node.GetTerminal():
lab = node.GetLabel()
cFac = float(lab)/float(nRes-1)
if hasattr(node,'GetExamples') and node.GetExamples():
theColor = (1.-cFac)*visOpts.terminalOffColor + cFac*visOpts.terminalOnColor
outlColor = visOpts.outlineColor
else:
theColor = (1.-cFac)*visOpts.terminalOffColor + cFac*visOpts.terminalOnColor
outlColor = visOpts.terminalEmptyColor
canvas.drawEllipse(x1,y1,x2,y2,
outlColor,visOpts.lineWidth,
theColor)
if showPurity:
canvas.drawLine(loc[0],loc[1],pureX,pureY,piddle.Color(1,1,1),2)
else:
theColor = visOpts.circColor
canvas.drawEllipse(x1,y1,x2,y2,
visOpts.outlineColor,visOpts.lineWidth,
theColor)
# this does not need to be done every time
canvas.defaultFont=visOpts.labelFont
labelStr = str(node.GetLabel())
strLoc = (loc[0] - canvas.stringWidth(labelStr)/2,
loc[1]+canvas.fontHeight()/4)
canvas.drawString(labelStr,strLoc[0],strLoc[1])
node._bBox = (x1,y1,x2,y2)
def CalcTreeWidth(tree):
try:
tree.totNChildren
except AttributeError:
CalcTreeNodeSizes(tree)
totWidth = tree.totNChildren * (visOpts.circRad+visOpts.horizOffset)
return totWidth
def DrawTree(tree,canvas,nRes=2,scaleLeaves=False,allowShrink=True,showPurity=False):
dims = canvas.size
loc = (dims[0]/2,visOpts.vertOffset)
if scaleLeaves:
#try:
# l = tree._scales
#except AttributeError:
# l = None
#if l is None:
SetNodeScales(tree)
if allowShrink:
treeWid = CalcTreeWidth(tree)
while treeWid > dims[0]:
visOpts.circRad /= 2
visOpts.horizOffset /= 2
treeWid = CalcTreeWidth(tree)
DrawTreeNode(tree,loc,canvas,nRes,scaleLeaves=scaleLeaves,
showPurity=showPurity)
def ResetTree(tree):
tree._scales = None
tree.totNChildren = None
for child in tree.GetChildren():
ResetTree(child)
def _simpleTest(canv):
from Tree import TreeNode as Node
root = Node(None,'r',label='r')
c1 = root.AddChild('l1_1',label='l1_1')
c2 = root.AddChild('l1_2',isTerminal=1,label=1)
c3 = c1.AddChild('l2_1',isTerminal=1,label=0)
c4 = c1.AddChild('l2_2',isTerminal=1,label=1)
DrawTreeNode(root,(150,visOpts.vertOffset),canv)
if __name__ == '__main__':
from rdkit.sping.PIL.pidPIL import PILCanvas
canv = PILCanvas(size=(300,300),name='test.png')
_simpleTest(canv)
canv.save()
| {
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"path": "rdkit/ML/DecTree/TreeVis.py",
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"size": "6400",
"license": "bsd-3-clause",
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"ratio": 3.063666826232647,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.9018011882622234,
"avg_score": 0.04097473872208241,
"num_lines": 224
} |
""" functionality for drawing trees on sping canvases
"""
from rdkit.sping import pid as piddle
import math
class VisOpts(object):
circRad = 10
minCircRad = 4
maxCircRad = 16
circColor = piddle.Color(0.6, 0.6, 0.9)
terminalEmptyColor = piddle.Color(.8, .8, .2)
terminalOnColor = piddle.Color(0.8, 0.8, 0.8)
terminalOffColor = piddle.Color(0.2, 0.2, 0.2)
outlineColor = piddle.transparent
lineColor = piddle.Color(0, 0, 0)
lineWidth = 2
horizOffset = 10
vertOffset = 50
labelFont = piddle.Font(face='helvetica', size=10)
highlightColor = piddle.Color(1., 1., .4)
highlightWidth = 2
visOpts = VisOpts()
def CalcTreeNodeSizes(node):
"""Recursively calculate the total number of nodes under us.
results are set in node.totNChildren for this node and
everything underneath it.
"""
children = node.GetChildren()
if len(children) > 0:
nHere = 0
nBelow = 0
for child in children:
CalcTreeNodeSizes(child)
nHere = nHere + child.totNChildren
if child.nLevelsBelow > nBelow:
nBelow = child.nLevelsBelow
else:
nBelow = 0
nHere = 1
node.nExamples = len(node.GetExamples())
node.totNChildren = nHere
node.nLevelsBelow = nBelow + 1
def _ExampleCounter(node, min, max):
if node.GetTerminal():
cnt = node.nExamples
if cnt < min:
min = cnt
if cnt > max:
max = cnt
else:
for child in node.GetChildren():
provMin, provMax = _ExampleCounter(child, min, max)
if provMin < min:
min = provMin
if provMax > max:
max = provMax
return min, max
def _ApplyNodeScales(node, min, max):
if node.GetTerminal():
if max != min:
loc = float(node.nExamples - min) / (max - min)
else:
loc = .5
node._scaleLoc = loc
else:
for child in node.GetChildren():
_ApplyNodeScales(child, min, max)
def SetNodeScales(node):
min, max = 1e8, -1e8
min, max = _ExampleCounter(node, min, max)
node._scales = min, max
_ApplyNodeScales(node, min, max)
def DrawTreeNode(node, loc, canvas, nRes=2, scaleLeaves=False, showPurity=False):
"""Recursively displays the given tree node and all its children on the canvas
"""
try:
nChildren = node.totNChildren
except AttributeError:
nChildren = None
if nChildren is None:
CalcTreeNodeSizes(node)
if not scaleLeaves or not node.GetTerminal():
rad = visOpts.circRad
else:
scaleLoc = getattr(node, "_scaleLoc", 0.5)
rad = visOpts.minCircRad + node._scaleLoc * (visOpts.maxCircRad - visOpts.minCircRad)
x1 = loc[0] - rad
y1 = loc[1] - rad
x2 = loc[0] + rad
y2 = loc[1] + rad
if showPurity and node.GetTerminal():
examples = node.GetExamples()
nEx = len(examples)
if nEx:
tgtVal = int(node.GetLabel())
purity = 0.0
for ex in examples:
if int(ex[-1]) == tgtVal:
purity += 1. / len(examples)
else:
purity = 1.0
deg = purity * math.pi
xFact = rad * math.sin(deg)
yFact = rad * math.cos(deg)
pureX = loc[0] + xFact
pureY = loc[1] + yFact
children = node.GetChildren()
# just move down one level
childY = loc[1] + visOpts.vertOffset
# this is the left-hand side of the leftmost span
childX = loc[0] - ((visOpts.horizOffset + visOpts.circRad) * node.totNChildren) / 2
for i in range(len(children)):
# center on this child's space
child = children[i]
halfWidth = ((visOpts.horizOffset + visOpts.circRad) * child.totNChildren) / 2
childX = childX + halfWidth
childLoc = [childX, childY]
canvas.drawLine(loc[0], loc[1], childLoc[0], childLoc[1], visOpts.lineColor, visOpts.lineWidth)
DrawTreeNode(child, childLoc, canvas, nRes=nRes, scaleLeaves=scaleLeaves, showPurity=showPurity)
# and move over to the leftmost point of the next child
childX = childX + halfWidth
if node.GetTerminal():
lab = node.GetLabel()
cFac = float(lab) / float(nRes - 1)
if hasattr(node, 'GetExamples') and node.GetExamples():
theColor = (1. - cFac) * visOpts.terminalOffColor + cFac * visOpts.terminalOnColor
outlColor = visOpts.outlineColor
else:
theColor = (1. - cFac) * visOpts.terminalOffColor + cFac * visOpts.terminalOnColor
outlColor = visOpts.terminalEmptyColor
canvas.drawEllipse(x1, y1, x2, y2, outlColor, visOpts.lineWidth, theColor)
if showPurity:
canvas.drawLine(loc[0], loc[1], pureX, pureY, piddle.Color(1, 1, 1), 2)
else:
theColor = visOpts.circColor
canvas.drawEllipse(x1, y1, x2, y2, visOpts.outlineColor, visOpts.lineWidth, theColor)
# this does not need to be done every time
canvas.defaultFont = visOpts.labelFont
labelStr = str(node.GetLabel())
strLoc = (loc[0] - canvas.stringWidth(labelStr) / 2, loc[1] + canvas.fontHeight() / 4)
canvas.drawString(labelStr, strLoc[0], strLoc[1])
node._bBox = (x1, y1, x2, y2)
def CalcTreeWidth(tree):
try:
tree.totNChildren
except AttributeError:
CalcTreeNodeSizes(tree)
totWidth = tree.totNChildren * (visOpts.circRad + visOpts.horizOffset)
return totWidth
def DrawTree(tree, canvas, nRes=2, scaleLeaves=False, allowShrink=True, showPurity=False):
dims = canvas.size
loc = (dims[0] / 2, visOpts.vertOffset)
if scaleLeaves:
#try:
# l = tree._scales
#except AttributeError:
# l = None
#if l is None:
SetNodeScales(tree)
if allowShrink:
treeWid = CalcTreeWidth(tree)
while treeWid > dims[0]:
visOpts.circRad /= 2
visOpts.horizOffset /= 2
treeWid = CalcTreeWidth(tree)
DrawTreeNode(tree, loc, canvas, nRes, scaleLeaves=scaleLeaves, showPurity=showPurity)
def ResetTree(tree):
tree._scales = None
tree.totNChildren = None
for child in tree.GetChildren():
ResetTree(child)
def _simpleTest(canv):
from Tree import TreeNode as Node
root = Node(None, 'r', label='r')
c1 = root.AddChild('l1_1', label='l1_1')
c2 = root.AddChild('l1_2', isTerminal=1, label=1)
c3 = c1.AddChild('l2_1', isTerminal=1, label=0)
c4 = c1.AddChild('l2_2', isTerminal=1, label=1)
DrawTreeNode(root, (150, visOpts.vertOffset), canv)
if __name__ == '__main__':
from rdkit.sping.PIL.pidPIL import PILCanvas
canv = PILCanvas(size=(300, 300), name='test.png')
_simpleTest(canv)
canv.save()
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"path": "rdkit/ML/DecTree/TreeVis.py",
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"hash": -8702271723224396000,
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"ratio": 3.037089871611983,
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"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.4197650385111983,
"avg_score": null,
"num_lines": null
} |
""" functionality for drawing trees on sping canvases
"""
import math
from rdkit.sping import pid as piddle
class VisOpts(object):
circRad = 10
minCircRad = 4
maxCircRad = 16
circColor = piddle.Color(0.6, 0.6, 0.9)
terminalEmptyColor = piddle.Color(.8, .8, .2)
terminalOnColor = piddle.Color(0.8, 0.8, 0.8)
terminalOffColor = piddle.Color(0.2, 0.2, 0.2)
outlineColor = piddle.transparent
lineColor = piddle.Color(0, 0, 0)
lineWidth = 2
horizOffset = 10
vertOffset = 50
labelFont = piddle.Font(face='helvetica', size=10)
highlightColor = piddle.Color(1., 1., .4)
highlightWidth = 2
visOpts = VisOpts()
def CalcTreeNodeSizes(node):
"""Recursively calculate the total number of nodes under us.
results are set in node.totNChildren for this node and
everything underneath it.
"""
children = node.GetChildren()
if len(children) > 0:
nHere = 0
nBelow = 0
for child in children:
CalcTreeNodeSizes(child)
nHere = nHere + child.totNChildren
if child.nLevelsBelow > nBelow:
nBelow = child.nLevelsBelow
else:
nBelow = 0
nHere = 1
node.nExamples = len(node.GetExamples())
node.totNChildren = nHere
node.nLevelsBelow = nBelow + 1
def _ExampleCounter(node, min, max):
if node.GetTerminal():
cnt = node.nExamples
if cnt < min:
min = cnt
if cnt > max:
max = cnt
else:
for child in node.GetChildren():
provMin, provMax = _ExampleCounter(child, min, max)
if provMin < min:
min = provMin
if provMax > max:
max = provMax
return min, max
def _ApplyNodeScales(node, min, max):
if node.GetTerminal():
if max != min:
loc = float(node.nExamples - min) / (max - min)
else:
loc = .5
node._scaleLoc = loc
else:
for child in node.GetChildren():
_ApplyNodeScales(child, min, max)
def SetNodeScales(node):
min, max = 1e8, -1e8
min, max = _ExampleCounter(node, min, max)
node._scales = min, max
_ApplyNodeScales(node, min, max)
def DrawTreeNode(node, loc, canvas, nRes=2, scaleLeaves=False, showPurity=False):
"""Recursively displays the given tree node and all its children on the canvas
"""
try:
nChildren = node.totNChildren
except AttributeError:
nChildren = None
if nChildren is None:
CalcTreeNodeSizes(node)
if not scaleLeaves or not node.GetTerminal():
rad = visOpts.circRad
else:
scaleLoc = getattr(node, "_scaleLoc", 0.5)
rad = visOpts.minCircRad + node._scaleLoc * (visOpts.maxCircRad - visOpts.minCircRad)
x1 = loc[0] - rad
y1 = loc[1] - rad
x2 = loc[0] + rad
y2 = loc[1] + rad
if showPurity and node.GetTerminal():
examples = node.GetExamples()
nEx = len(examples)
if nEx:
tgtVal = int(node.GetLabel())
purity = 0.0
for ex in examples:
if int(ex[-1]) == tgtVal:
purity += 1. / len(examples)
else:
purity = 1.0
deg = purity * math.pi
xFact = rad * math.sin(deg)
yFact = rad * math.cos(deg)
pureX = loc[0] + xFact
pureY = loc[1] + yFact
children = node.GetChildren()
# just move down one level
childY = loc[1] + visOpts.vertOffset
# this is the left-hand side of the leftmost span
childX = loc[0] - ((visOpts.horizOffset + visOpts.circRad) * node.totNChildren) / 2
for i in range(len(children)):
# center on this child's space
child = children[i]
halfWidth = ((visOpts.horizOffset + visOpts.circRad) * child.totNChildren) / 2
childX = childX + halfWidth
childLoc = [childX, childY]
canvas.drawLine(loc[0], loc[1], childLoc[0], childLoc[1], visOpts.lineColor, visOpts.lineWidth)
DrawTreeNode(child, childLoc, canvas, nRes=nRes, scaleLeaves=scaleLeaves, showPurity=showPurity)
# and move over to the leftmost point of the next child
childX = childX + halfWidth
if node.GetTerminal():
lab = node.GetLabel()
cFac = float(lab) / float(nRes - 1)
if hasattr(node, 'GetExamples') and node.GetExamples():
theColor = (1. - cFac) * visOpts.terminalOffColor + cFac * visOpts.terminalOnColor
outlColor = visOpts.outlineColor
else:
theColor = (1. - cFac) * visOpts.terminalOffColor + cFac * visOpts.terminalOnColor
outlColor = visOpts.terminalEmptyColor
canvas.drawEllipse(x1, y1, x2, y2, outlColor, visOpts.lineWidth, theColor)
if showPurity:
canvas.drawLine(loc[0], loc[1], pureX, pureY, piddle.Color(1, 1, 1), 2)
else:
theColor = visOpts.circColor
canvas.drawEllipse(x1, y1, x2, y2, visOpts.outlineColor, visOpts.lineWidth, theColor)
# this does not need to be done every time
canvas.defaultFont = visOpts.labelFont
labelStr = str(node.GetLabel())
strLoc = (loc[0] - canvas.stringWidth(labelStr) / 2, loc[1] + canvas.fontHeight() / 4)
canvas.drawString(labelStr, strLoc[0], strLoc[1])
node._bBox = (x1, y1, x2, y2)
def CalcTreeWidth(tree):
try:
tree.totNChildren
except AttributeError:
CalcTreeNodeSizes(tree)
totWidth = tree.totNChildren * (visOpts.circRad + visOpts.horizOffset)
return totWidth
def DrawTree(tree, canvas, nRes=2, scaleLeaves=False, allowShrink=True, showPurity=False):
dims = canvas.size
loc = (dims[0] / 2, visOpts.vertOffset)
if scaleLeaves:
# try:
# l = tree._scales
# except AttributeError:
# l = None
# if l is None:
SetNodeScales(tree)
if allowShrink:
treeWid = CalcTreeWidth(tree)
while treeWid > dims[0]:
visOpts.circRad /= 2
visOpts.horizOffset /= 2
treeWid = CalcTreeWidth(tree)
DrawTreeNode(tree, loc, canvas, nRes, scaleLeaves=scaleLeaves, showPurity=showPurity)
def ResetTree(tree):
tree._scales = None
tree.totNChildren = None
for child in tree.GetChildren():
ResetTree(child)
def _simpleTest(canv):
from .Tree import TreeNode as Node
root = Node(None, 'r', label='r')
c1 = root.AddChild('l1_1', label='l1_1')
c2 = root.AddChild('l1_2', isTerminal=1, label=1)
c3 = c1.AddChild('l2_1', isTerminal=1, label=0)
c4 = c1.AddChild('l2_2', isTerminal=1, label=1)
DrawTreeNode(root, (150, visOpts.vertOffset), canv)
if __name__ == '__main__':
from rdkit.sping.PIL.pidPIL import PILCanvas
canv = PILCanvas(size=(300, 300), name='test.png')
_simpleTest(canv)
canv.save()
| {
"repo_name": "rvianello/rdkit",
"path": "rdkit/ML/DecTree/TreeVis.py",
"copies": "11",
"size": "6394",
"license": "bsd-3-clause",
"hash": 5713088176838420000,
"line_mean": 26.9213973799,
"line_max": 100,
"alpha_frac": 0.6598373475,
"autogenerated": false,
"ratio": 3.0375296912114016,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 1,
"avg_score": 0.01823990198679555,
"num_lines": 229
} |
""" primitive license handler
License file format:
(lines beginning with # are ignored)
Expiration_Date: <expiration date of license>
Verification: <verification code>
Date format: day-month-year
The verification code is used to ensure that the date
has not been tampered with
"""
import sha,base64,time,exceptions
EXPIRED=-1
BADMODULE=0
class LicenseError(exceptions.Exception):
pass
# this is a base64 encoding of the string "RD License Manager"
# it's done this way to provide minimal security (by preventing
# a simple run of "strings")
_salt='UkQgTGljZW5zZSBNYW5hZ2Vy\n'
#
# Verification strings are constructed using the SHA
# digest of the message formed from:
# 1) the results of base64 decoding _salt (defined above)
# 2) the text of the Expiration Date
# 3) the string representation of the int form of the
# time.mktime() date corresponding to the Expiration Date
def _Verify(lines):
verifier = sha.new(base64.decodestring(_salt))
inL = lines[0]
if inL == '':
raise LicenseError,'EOF hit parsing license file'
if inL.find('Expiration_Date:')==-1:
raise LicenseError,'bad license file format'
dText = inL.split(':')[-1].strip()
verifier.update(dText)
try:
dateComponents = map(int,dText.split('-'))
except:
dateComponents = []
if len(dateComponents) != 3:
raise LicenseError,'bad date format in license file'
day,month,year = dateComponents
pos = 1
for line in lines:
if line.find('Modules:')!=-1:
break
if line.find('Modules:') != -1:
modules = line.split(':')[-1].strip().upper().split(',')
#modules = ','.join([x.strip() for x in modules.split(',')])
else:
modules = ''
pos = 1
inL = lines[pos]
while pos < len(lines) and inL.find('Verification:')==-1:
pos += 1
inL = lines[pos]
if inL == '':
raise LicenseError,'EOF hit parsing license file'
if inL.find('Verification:')==-1:
raise LicenseError,'bad license file format'
vText = inL.split(':')[-1].strip()
expDate = int(time.mktime((year,month,day,
0,0,0,
0,0,0)))
verifier.update(str(expDate))
verifier.update(','.join(modules))
if verifier.hexdigest() != vText:
raise LicenseError,'verification of license file failed'
# ok, the license file has not been tampered with... proceed
return expDate,modules
def _CheckDate(expDate):
year,month,day,h,m,s,w,d,dst = time.gmtime()
newD = int(time.mktime((year,month,day,
0,0,0,
0,0,0)))
if expDate > newD:
return 1
else:
return 0
def CheckLicenseFile(filename):
try:
inF = open(filename,'r')
except IOError:
raise LicenseError,'License file %s could not be opened'%(filename)
lines = []
for line in inF.readlines():
if len(line) and line[0] != '#':
lines.append(line.strip())
expDate,modules = _Verify(lines)
if not _CheckDate(expDate):
return EXPIRED
def CheckLicenseString(text,checkModule=None):
lines = text.split('\n')
expDate,modules = _Verify(lines)
if not _CheckDate(expDate):
return EXPIRED
if checkModule:
if checkModule.upper() not in modules:
return BADMODULE
return 1
if __name__ == '__main__':
import sys
if len(sys.argv)>1:
for nm in sys.argv[1:]:
print nm,CheckLicenseFile(nm),CheckLicenseString(open(nm,'r').read())
| {
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"path": "rdkit/utils/Licensing.py",
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"few_assignments": false,
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""" Basic EState definitions
"""
from __future__ import print_function
import numpy
from rdkit import Chem
def GetPrincipleQuantumNumber(atNum):
if atNum<=2: return 1
elif atNum <= 10: return 2
elif atNum <= 18: return 3
elif atNum <= 36: return 4
elif atNum <= 54: return 5
elif atNum <= 86: return 6
else: return 7
def EStateIndices(mol,force=1):
""" returns a tuple of EState indices for the molecule
Reference: Hall, Mohney and Kier. JCICS _31_ 76-81 (1991)
"""
if not force and hasattr(mol,'_eStateIndices'):
return mol._eStateIndices
tbl = Chem.GetPeriodicTable()
nAtoms = mol.GetNumAtoms()
Is = numpy.zeros(nAtoms,numpy.float)
for i in range(nAtoms):
at = mol.GetAtomWithIdx(i)
atNum = at.GetAtomicNum()
d = at.GetDegree()
if d>0:
h = at.GetTotalNumHs()
dv = tbl.GetNOuterElecs(atNum)-h
N = GetPrincipleQuantumNumber(atNum)
Is[i] = (4./(N*N) * dv + 1)/d
dists = Chem.GetDistanceMatrix(mol,useBO=0,useAtomWts=0)
dists += 1
accum = numpy.zeros(nAtoms,numpy.float)
for i in range(nAtoms):
for j in range(i+1,nAtoms):
p = dists[i,j]
if p < 1e6:
tmp = (Is[i]-Is[j])/(p*p)
accum[i] += tmp
accum[j] -= tmp
res = accum+Is
mol._eStateIndices=res
return res
EStateIndices.version='1.0.0'
def MaxEStateIndex(mol,force=1):
return max(EStateIndices(mol,force));
MaxEStateIndex.version="1.0.0"
def MinEStateIndex(mol,force=1):
return min(EStateIndices(mol,force));
MinEStateIndex.version="1.0.0"
def MaxAbsEStateIndex(mol,force=1):
return max([abs(x) for x in EStateIndices(mol,force)]);
MaxAbsEStateIndex.version="1.0.0"
def MinAbsEStateIndex(mol,force=1):
return min([abs(x) for x in EStateIndices(mol,force)]);
MinAbsEStateIndex.version="1.0.0"
if __name__ =='__main__':
smis = ['CCCC','CCCCC','CCCCCC','CC(N)C(=O)O','CC(N)C(=O)[O-].[Na+]']
for smi in smis:
m = Chem.MolFromSmiles(smi)
print(smi)
inds = EStateIndices(m)
print('\t',inds)
| {
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"has_no_keywords": false,
"few_assignments": false,
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""" Basic EState definitions
"""
from __future__ import print_function
import numpy
from rdkit import Chem
def GetPrincipleQuantumNumber(atNum):
""" Get principal quantum number for atom number """
if atNum <= 2:
return 1
elif atNum <= 10:
return 2
elif atNum <= 18:
return 3
elif atNum <= 36:
return 4
elif atNum <= 54:
return 5
elif atNum <= 86:
return 6
else:
return 7
def EStateIndices(mol, force=True):
""" returns a tuple of EState indices for the molecule
Reference: Hall, Mohney and Kier. JCICS _31_ 76-81 (1991)
"""
if not force and hasattr(mol, '_eStateIndices'):
return mol._eStateIndices
tbl = Chem.GetPeriodicTable()
nAtoms = mol.GetNumAtoms()
Is = numpy.zeros(nAtoms, numpy.float)
for i in range(nAtoms):
at = mol.GetAtomWithIdx(i)
atNum = at.GetAtomicNum()
d = at.GetDegree()
if d > 0:
h = at.GetTotalNumHs()
dv = tbl.GetNOuterElecs(atNum) - h
N = GetPrincipleQuantumNumber(atNum)
Is[i] = (4. / (N * N) * dv + 1) / d
dists = Chem.GetDistanceMatrix(mol, useBO=0, useAtomWts=0)
dists += 1
accum = numpy.zeros(nAtoms, numpy.float)
for i in range(nAtoms):
for j in range(i + 1, nAtoms):
p = dists[i, j]
if p < 1e6:
tmp = (Is[i] - Is[j]) / (p * p)
accum[i] += tmp
accum[j] -= tmp
res = accum + Is
mol._eStateIndices = res
return res
EStateIndices.version = '1.0.0'
def MaxEStateIndex(mol, force=1):
return max(EStateIndices(mol, force))
MaxEStateIndex.version = "1.0.0"
def MinEStateIndex(mol, force=1):
return min(EStateIndices(mol, force))
MinEStateIndex.version = "1.0.0"
def MaxAbsEStateIndex(mol, force=1):
return max([abs(x) for x in EStateIndices(mol, force)])
MaxAbsEStateIndex.version = "1.0.0"
def MinAbsEStateIndex(mol, force=1):
return min([abs(x) for x in EStateIndices(mol, force)])
MinAbsEStateIndex.version = "1.0.0"
def _exampleCode():
""" Example code for calculating E-state indices """
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
for smi in smis:
m = Chem.MolFromSmiles(smi)
print(smi)
inds = EStateIndices(m)
print('\t', inds)
if __name__ == '__main__': # pragma: nocover
_exampleCode()
| {
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"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.5940630306638428,
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} |
""" Basic EState definitions
"""
import numpy
from rdkit import Chem
def GetPrincipleQuantumNumber(atNum):
if atNum<=2: return 1
elif atNum <= 10: return 2
elif atNum <= 18: return 3
elif atNum <= 36: return 4
elif atNum <= 54: return 5
elif atNum <= 86: return 6
else: return 7
def EStateIndices(mol,force=1):
""" returns a tuple of EState indices for the molecule
Reference: Hall, Mohney and Kier. JCICS _31_ 76-81 (1991)
"""
if not force and hasattr(mol,'_eStateIndices'):
return mol._eStateIndices
tbl = Chem.GetPeriodicTable()
nAtoms = mol.GetNumAtoms()
Is = numpy.zeros(nAtoms,numpy.float)
for i in range(nAtoms):
at = mol.GetAtomWithIdx(i)
atNum = at.GetAtomicNum()
d = at.GetDegree()
if d>0:
h = at.GetTotalNumHs()
dv = tbl.GetNOuterElecs(atNum)-h
N = GetPrincipleQuantumNumber(atNum)
Is[i] = (4./(N*N) * dv + 1)/d
dists = Chem.GetDistanceMatrix(mol,useBO=0,useAtomWts=0)
dists += 1
accum = numpy.zeros(nAtoms,numpy.float)
for i in range(nAtoms):
for j in range(i+1,nAtoms):
p = dists[i,j]
if p < 1e6:
tmp = (Is[i]-Is[j])/(p*p)
accum[i] += tmp
accum[j] -= tmp
res = accum+Is
mol._eStateIndices=res
return res
EStateIndices.version='1.0.0'
if __name__ =='__main__':
smis = ['CCCC','CCCCC','CCCCCC','CC(N)C(=O)O','CC(N)C(=O)[O-].[Na+]']
for smi in smis:
m = Chem.MolFromSmiles(smi)
print smi
inds = EStateIndices(m)
print '\t',inds
| {
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""" contains a class to store parameters for and results from
Composite building
"""
from rdkit import RDConfig
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbModule
def SetDefaults(runDetails):
""" initializes a details object with default values
**Arguments**
- details: (optional) a _CompositeRun.CompositeRun_ object.
If this is not provided, the global _runDetails will be used.
**Returns**
the initialized _CompositeRun_ object.
"""
runDetails.nRuns = 1
runDetails.nModels = 10
runDetails.outName = ''
runDetails.badName = ''
runDetails.splitRun = 0
runDetails.splitFrac = 0.7
runDetails.lockRandom = 0
runDetails.randomActivities = 0
runDetails.shuffleActivities = 0
runDetails.replacementSelection = 0
#
# Tree Parameters
#
runDetails.useTrees = 1
runDetails.pruneIt = 0
runDetails.lessGreedy = 0
runDetails.limitDepth = -1
runDetails.recycleVars = 0
runDetails.randomDescriptors = 0 # toggles growing of random forests
#
# KNN Parameters
#
runDetails.useKNN = 0
runDetails.knnDistFunc = ''
runDetails.knnNeighs = 0
#
# SigTree Parameters
#
runDetails.useSigTrees = 0
runDetails.useCMIM = 0
runDetails.allowCollections = False
#
# Naive Bayes Classifier Parameters
#
runDetails.useNaiveBayes = 0
runDetails.mEstimateVal = -1.0
runDetails.useSigBayes = 0
# #
# # SVM Parameters
# #
# runDetails.useSVM = 0
# runDetails.svmKernel = SVM.radialKernel
# runDetails.svmType = SVM.cSVCType
# runDetails.svmGamma = None
# runDetails.svmCost = None
# runDetails.svmWeights = None
# runDetails.svmDataType = 'float'
# runDetails.svmDegree = 3
# runDetails.svmCoeff = 0.0
# runDetails.svmEps = 0.001
# runDetails.svmNu = 0.5
# runDetails.svmCache = 40
# runDetails.svmShrink = 1
# runDetails.svmDataType='float'
runDetails.bayesModel = 0
runDetails.dbName = ''
runDetails.dbUser = RDConfig.defaultDBUser
runDetails.dbPassword = RDConfig.defaultDBPassword
runDetails.dbWhat = '*'
runDetails.dbWhere = ''
runDetails.dbJoin = ''
runDetails.qTableName = ''
runDetails.qBounds = []
runDetails.qBoundCount = ''
runDetails.activityBounds = []
runDetails.activityBoundsVals = ''
runDetails.detailedRes = 0
runDetails.noScreen = 0
runDetails.threshold = 0.0
runDetails.filterFrac = 0.0
runDetails.filterVal = 0.0
runDetails.modelFilterVal = 0.0
runDetails.modelFilterFrac = 0.0
runDetails.internalHoldoutFrac = 0.3
runDetails.pickleDataFileName = ''
runDetails.startAt = None
runDetails.persistTblName = ''
runDetails.randomSeed = (23, 42)
runDetails.note = ''
return runDetails
class CompositeRun:
""" class to store parameters for and results from Composite building
This class has a default set of fields which are added to the database.
By default these fields are stored in a tuple, so they are immutable. This
is probably what you want.
"""
fields = (("rundate", "varchar(32)"),
("dbName", "varchar(200)"),
("dbWhat", "varchar(200)"),
("dbWhere", "varchar(200)"),
("dbJoin", "varchar(200)"),
("tableName", "varchar(80)"),
("note", "varchar(120)"),
("shuffled", "smallint"),
("randomized", "smallint"),
("overall_error", "float"),
("holdout_error", "float"),
("overall_fraction_dropped", "float"),
("holdout_fraction_dropped", "float"),
("overall_correct_conf", "float"),
("overall_incorrect_conf", "float"),
("holdout_correct_conf", "float"),
("holdout_incorrect_conf", "float"),
("overall_result_matrix", "varchar(256)"),
("holdout_result_matrix", "varchar(256)"),
("threshold", "float"),
("splitFrac", "float"),
("filterFrac", "float"),
("filterVal", "float"),
("modelFilterVal", "float"),
("modelFilterFrac", "float"),
("nModels", "int"),
("limitDepth", "int"),
("bayesModels", "int"),
("qBoundCount", "varchar(3000)"),
("activityBoundsVals", "varchar(200)"),
("cmd", "varchar(500)"),
("model", DbModule.binaryTypeName), )
def _CreateTable(self, cn, tblName):
""" *Internal Use only*
"""
names = map(lambda x: x.strip().upper(), cn.GetTableNames())
if tblName.upper() not in names:
curs = cn.GetCursor()
fmt = []
for name, value in self.fields:
fmt.append('%s %s' % (name, value))
fmtStr = ','.join(fmt)
curs.execute('create table %s (%s)' % (tblName, fmtStr))
cn.Commit()
else:
heads = [x.upper() for x in cn.GetColumnNames()]
curs = cn.GetCursor()
for name, value in self.fields:
if name.upper() not in heads:
curs.execute('alter table %s add %s %s' % (tblName, name, value))
cn.Commit()
def Store(self, db='models.gdb', table='results', user='sysdba', password='masterkey'):
""" adds the result to a database
**Arguments**
- db: name of the database to use
- table: name of the table to use
- user&password: connection information
"""
cn = DbConnect(db, table, user, password)
curs = cn.GetCursor()
self._CreateTable(cn, table)
cols = []
vals = []
for name, _ in self.fields:
try:
v = getattr(self, name)
except AttributeError:
pass
else:
cols.append('%s' % name)
vals.append(v)
nToDo = len(vals)
qs = ','.join([DbModule.placeHolder] * nToDo)
vals = tuple(vals)
cmd = 'insert into %s (%s) values (%s)' % (table, ','.join(cols), qs)
curs.execute(cmd, vals)
cn.Commit()
def GetDataSet(self, **kwargs):
""" Returns a MLDataSet pulled from a database using our stored
values.
"""
from rdkit.ML.Data import DataUtils
data = DataUtils.DBToData(self.dbName, self.tableName, user=self.dbUser,
password=self.dbPassword, what=self.dbWhat, where=self.dbWhere,
join=self.dbJoin, **kwargs)
return data
def GetDataSetInfo(self, **kwargs):
""" Returns a MLDataSet pulled from a database using our stored
values.
"""
conn = DbConnect(self.dbName, self.tableName)
res = conn.GetColumnNamesAndTypes(join=self.dbJoin, what=self.dbWhat, where=self.dbWhere)
return res
| {
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"ratio": 3.585239085239085,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.9702374486839085,
"avg_score": null,
"num_lines": null
} |
""" contains a class to store parameters for and results from
Composite building
"""
from rdkit import RDConfig
from rdkit.Dbase.DbConnection import DbConnect
from rdkit import DataStructs
from rdkit.Dbase import DbModule
##from rdkit.ML.SVM import SVMClassificationModel as SVM
def SetDefaults(runDetails):
""" initializes a details object with default values
**Arguments**
- details: (optional) a _CompositeRun.CompositeRun_ object.
If this is not provided, the global _runDetails will be used.
**Returns**
the initialized _CompositeRun_ object.
"""
runDetails.nRuns = 1
runDetails.nModels = 10
runDetails.outName = ''
runDetails.badName = ''
runDetails.splitRun = 0
runDetails.splitFrac = 0.7
runDetails.lockRandom = 0
runDetails.randomActivities = 0
runDetails.shuffleActivities = 0
runDetails.replacementSelection = 0
#
# Tree Parameters
#
runDetails.useTrees = 1
runDetails.pruneIt = 0
runDetails.lessGreedy = 0
runDetails.limitDepth = -1
runDetails.recycleVars = 0
runDetails.randomDescriptors = 0 # toggles growing of random forests
#
# KNN Parameters
#
runDetails.useKNN = 0
runDetails.knnDistFunc = ''
runDetails.knnNeighs = 0
#
# SigTree Parameters
#
runDetails.useSigTrees = 0
runDetails.useCMIM = 0
runDetails.allowCollections = False
#
# Naive Bayes Classifier Parameters
#
runDetails.useNaiveBayes = 0
runDetails.mEstimateVal = -1.0
runDetails.useSigBayes = 0
## #
## # SVM Parameters
## #
## runDetails.useSVM = 0
## runDetails.svmKernel = SVM.radialKernel
## runDetails.svmType = SVM.cSVCType
## runDetails.svmGamma = None
## runDetails.svmCost = None
## runDetails.svmWeights = None
## runDetails.svmDataType = 'float'
## runDetails.svmDegree = 3
## runDetails.svmCoeff = 0.0
## runDetails.svmEps = 0.001
## runDetails.svmNu = 0.5
## runDetails.svmCache = 40
## runDetails.svmShrink = 1
## runDetails.svmDataType='float'
runDetails.bayesModel = 0
runDetails.dbName = ''
runDetails.dbUser = RDConfig.defaultDBUser
runDetails.dbPassword = RDConfig.defaultDBPassword
runDetails.dbWhat = '*'
runDetails.dbWhere = ''
runDetails.dbJoin = ''
runDetails.qTableName = ''
runDetails.qBounds = []
runDetails.qBoundCount = ''
runDetails.activityBounds = []
runDetails.activityBoundsVals = ''
runDetails.detailedRes = 0
runDetails.noScreen = 0
runDetails.threshold = 0.0
runDetails.filterFrac = 0.0
runDetails.filterVal = 0.0
runDetails.modelFilterVal = 0.0
runDetails.modelFilterFrac = 0.0
runDetails.internalHoldoutFrac = 0.3
runDetails.pickleDataFileName = ''
runDetails.startAt = None
runDetails.persistTblName = ''
runDetails.randomSeed = (23, 42)
runDetails.note = ''
return runDetails
class CompositeRun:
""" class to store parameters for and results from Composite building
This class has a default set of fields which are added to the database.
By default these fields are stored in a tuple, so they are immutable. This
is probably what you want.
"""
fields = (\
("rundate","varchar(32)"),
("dbName","varchar(200)"),
("dbWhat","varchar(200)"),
("dbWhere","varchar(200)"),
("dbJoin","varchar(200)"),
("tableName","varchar(80)"),
("note","varchar(120)"),
("shuffled","smallint"),
("randomized","smallint"),
("overall_error","float"),
("holdout_error","float"),
("overall_fraction_dropped","float"),
("holdout_fraction_dropped","float"),
("overall_correct_conf","float"),
("overall_incorrect_conf","float"),
("holdout_correct_conf","float"),
("holdout_incorrect_conf","float"),
("overall_result_matrix","varchar(256)"),
("holdout_result_matrix","varchar(256)"),
("threshold","float"),
("splitFrac","float"),
("filterFrac","float"),
("filterVal","float"),
("modelFilterVal", "float"),
("modelFilterFrac", "float"),
("nModels","int"),
("limitDepth","int"),
("bayesModels","int"),
("qBoundCount","varchar(3000)"),
("activityBoundsVals","varchar(200)"),
("cmd","varchar(500)"),
("model",DbModule.binaryTypeName),
)
def _CreateTable(self, cn, tblName):
""" *Internal Use only*
"""
names = map(lambda x: x.strip().upper(), cn.GetTableNames())
if tblName.upper() not in names:
curs = cn.GetCursor()
fmt = []
for name, value in self.fields:
fmt.append('%s %s' % (name, value))
fmtStr = ','.join(fmt)
curs.execute('create table %s (%s)' % (tblName, fmtStr))
cn.Commit()
else:
heads = [x.upper() for x in cn.GetColumnNames()]
curs = cn.GetCursor()
for name, value in self.fields:
if name.upper() not in heads:
curs.execute('alter table %s add %s %s' % (tblName, name, value))
cn.Commit()
def Store(self, db='models.gdb', table='results', user='sysdba', password='masterkey'):
""" adds the result to a database
**Arguments**
- db: name of the database to use
- table: name of the table to use
- user&password: connection information
"""
cn = DbConnect(db, table, user, password)
curs = cn.GetCursor()
self._CreateTable(cn, table)
cols = []
vals = []
for name, typ in self.fields:
try:
v = getattr(self, name)
except AttributeError:
pass
else:
cols.append('%s' % name)
vals.append(v)
nToDo = len(vals)
qs = ','.join([DbModule.placeHolder] * nToDo)
vals = tuple(vals)
cmd = 'insert into %s (%s) values (%s)' % (table, ','.join(cols), qs)
curs.execute(cmd, vals)
cn.Commit()
def GetDataSet(self, **kwargs):
""" Returns a MLDataSet pulled from a database using our stored
values.
"""
from rdkit.ML.Data import DataUtils
data = DataUtils.DBToData(self.dbName, self.tableName, user=self.dbUser,
password=self.dbPassword, what=self.dbWhat, where=self.dbWhere,
join=self.dbJoin, **kwargs)
return data
def GetDataSetInfo(self, **kwargs):
""" Returns a MLDataSet pulled from a database using our stored
values.
"""
from rdkit.Dbase.DbConnection import DbConnect
conn = DbConnect(self.dbName, self.tableName)
res = conn.GetColumnNamesAndTypes(join=self.dbJoin, what=self.dbWhat, where=self.dbWhere)
return res
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""" contains SMARTS definitions and calculators for EState atom types
defined in: Hall and Kier JCICS _35_ 1039-1045 (1995) Table 1
"""
from rdkit import Chem
_rawD = [
('sLi','[LiD1]-*'),
('ssBe','[BeD2](-*)-*'),
('ssssBe','[BeD4](-*)(-*)(-*)-*'),
('ssBH', '[BD2H](-*)-*'),
('sssB', '[BD3](-*)(-*)-*'),
('ssssB','[BD4](-*)(-*)(-*)-*'),
('sCH3', '[CD1H3]-*'),
('dCH2', '[CD1H2]=*'),
('ssCH2','[CD2H2](-*)-*'),
('tCH', '[CD1H]#*'),
('dsCH', '[CD2H](=*)-*'),
('aaCH', '[C,c;D2H](:*):*'),
('sssCH','[CD3H](-*)(-*)-*'),
('ddC', '[CD2H0](=*)=*'),
('tsC', '[CD2H0](#*)-*'),
('dssC', '[CD3H0](=*)(-*)-*'),
('aasC', '[C,c;D3H0](:*)(:*)-*'),
('aaaC', '[C,c;D3H0](:*)(:*):*'),
('ssssC','[CD4H0](-*)(-*)(-*)-*'),
('sNH3', '[ND1H3]-*'),
('sNH2', '[ND1H2]-*'),
('ssNH2','[ND2H2](-*)-*'),
('dNH', '[ND1H]=*'),
('ssNH', '[ND2H](-*)-*'),
('aaNH', '[N,nD2H](:*):*'),
('tN', '[ND1H0]#*'),
('sssNH','[ND3H](-*)(-*)-*'),
('dsN', '[ND2H0](=*)-*'),
('aaN', '[N,nD2H0](:*):*'),
('sssN', '[ND3H0](-*)(-*)-*'),
('ddsN', '[ND3H0](~[OD1H0])(~[OD1H0])-,:*'), # mod
('aasN', '[N,nD3H0](:*)(:*)-,:*'), # mod
('ssssN','[ND4H0](-*)(-*)(-*)-*'),
('sOH','[OD1H]-*'),
('dO', '[OD1H0]=*'),
('ssO','[OD2H0](-*)-*'),
('aaO','[O,oD2H0](:*):*'),
('sF','[FD1]-*'),
('sSiH3', '[SiD1H3]-*'),
('ssSiH2','[SiD2H2](-*)-*'),
('sssSiH','[SiD3H1](-*)(-*)-*'),
('ssssSi','[SiD4H0](-*)(-*)(-*)-*'),
('sPH2', '[PD1H2]-*'),
('ssPH', '[PD2H1](-*)-*'),
('sssP', '[PD3H0](-*)(-*)-*'),
('dsssP', '[PD4H0](=*)(-*)(-*)-*'),
('sssssP','[PD5H0](-*)(-*)(-*)(-*)-*'),
('sSH', '[SD1H1]-*'),
('dS', '[SD1H0]=*'),
('ssS', '[SD2H0](-*)-*'),
('aaS', '[S,sD2H0](:*):*'),
('dssS', '[SD3H0](=*)(-*)-*'),
('ddssS','[SD4H0](~[OD1H0])(~[OD1H0])(-*)-*'), # mod
('sCl', '[ClD1]-*'),
('sGeH3', '[GeD1H3](-*)'),
('ssGeH2','[GeD2H2](-*)-*'),
('sssGeH','[GeD3H1](-*)(-*)-*'),
('ssssGe','[GeD4H0](-*)(-*)(-*)-*'),
('sAsH2', '[AsD1H2]-*'),
('ssAsH', '[AsD2H1](-*)-*'),
('sssAs', '[AsD3H0](-*)(-*)-*'),
('sssdAs', '[AsD4H0](=*)(-*)(-*)-*'),
('sssssAs','[AsD5H0](-*)(-*)(-*)(-*)-*'),
('sSeH', '[SeD1H1]-*'),
('dSe', '[SeD1H0]=*'),
('ssSe', '[SeD2H0](-*)-*'),
('aaSe', '[SeD2H0](:*):*'),
('dssSe', '[SeD3H0](=*)(-*)-*'),
('ddssSe','[SeD4H0](=*)(=*)(-*)-*'),
('sBr','[BrD1]-*'),
('sSnH3', '[SnD1H3]-*'),
('ssSnH2','[SnD2H2](-*)-*'),
('sssSnH','[SnD3H1](-*)(-*)-*'),
('ssssSn','[SnD4H0](-*)(-*)(-*)-*'),
('sI','[ID1]-*'),
('sPbH3', '[PbD1H3]-*'),
('ssPbH2','[PbD2H2](-*)-*'),
('sssPbH','[PbD3H1](-*)(-*)-*'),
('ssssPb','[PbD4H0](-*)(-*)(-*)-*'),
]
esPatterns=None
def BuildPatts(rawV=None):
""" Internal Use Only
"""
global esPatterns,_rawD
if rawV is None:
rawV = _rawD
esPatterns = [None]*len(rawV)
for i,(name,sma) in enumerate(rawV):
try:
patt = Chem.MolFromSmarts(sma)
except:
sys.stderr.write('WARNING: problems with pattern %s (name: %s), skipped.\n'%(sma,name))
else:
esPatterns[i] = name,patt
def TypeAtoms(mol):
""" assigns each atom in a molecule to an EState type
**Returns:**
list of tuples (atoms can possibly match multiple patterns) with atom types
"""
if esPatterns is None:
BuildPatts()
nAtoms = mol.GetNumAtoms()
res = [None]*nAtoms
for name,patt in esPatterns:
matches = mol.GetSubstructMatches(patt,uniquify=0)
for match in matches:
idx = match[0]
if res[idx] is None:
res[idx] = [name]
elif name not in res[idx]:
res[idx].append(name)
for i,v in enumerate(res):
if v is not None:
res[i] = tuple(v)
else:
res[i] = ()
return res
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""" contains SMARTS definitions and calculators for EState atom types
defined in: Hall and Kier JCICS _35_ 1039-1045 (1995) Table 1
"""
from rdkit import Chem
_rawD = [
('sLi', '[LiD1]-*'),
('ssBe', '[BeD2](-*)-*'),
('ssssBe', '[BeD4](-*)(-*)(-*)-*'),
('ssBH', '[BD2H](-*)-*'),
('sssB', '[BD3](-*)(-*)-*'),
('ssssB', '[BD4](-*)(-*)(-*)-*'),
('sCH3', '[CD1H3]-*'),
('dCH2', '[CD1H2]=*'),
('ssCH2', '[CD2H2](-*)-*'),
('tCH', '[CD1H]#*'),
('dsCH', '[CD2H](=*)-*'),
('aaCH', '[C,c;D2H](:*):*'),
('sssCH', '[CD3H](-*)(-*)-*'),
('ddC', '[CD2H0](=*)=*'),
('tsC', '[CD2H0](#*)-*'),
('dssC', '[CD3H0](=*)(-*)-*'),
('aasC', '[C,c;D3H0](:*)(:*)-*'),
('aaaC', '[C,c;D3H0](:*)(:*):*'),
('ssssC', '[CD4H0](-*)(-*)(-*)-*'),
('sNH3', '[ND1H3]-*'),
('sNH2', '[ND1H2]-*'),
('ssNH2', '[ND2H2](-*)-*'),
('dNH', '[ND1H]=*'),
('ssNH', '[ND2H](-*)-*'),
('aaNH', '[N,nD2H](:*):*'),
('tN', '[ND1H0]#*'),
('sssNH', '[ND3H](-*)(-*)-*'),
('dsN', '[ND2H0](=*)-*'),
('aaN', '[N,nD2H0](:*):*'),
('sssN', '[ND3H0](-*)(-*)-*'),
('ddsN', '[ND3H0](~[OD1H0])(~[OD1H0])-,:*'), # mod
('aasN', '[N,nD3H0](:*)(:*)-,:*'), # mod
('ssssN', '[ND4H0](-*)(-*)(-*)-*'),
('sOH', '[OD1H]-*'),
('dO', '[OD1H0]=*'),
('ssO', '[OD2H0](-*)-*'),
('aaO', '[O,oD2H0](:*):*'),
('sF', '[FD1]-*'),
('sSiH3', '[SiD1H3]-*'),
('ssSiH2', '[SiD2H2](-*)-*'),
('sssSiH', '[SiD3H1](-*)(-*)-*'),
('ssssSi', '[SiD4H0](-*)(-*)(-*)-*'),
('sPH2', '[PD1H2]-*'),
('ssPH', '[PD2H1](-*)-*'),
('sssP', '[PD3H0](-*)(-*)-*'),
('dsssP', '[PD4H0](=*)(-*)(-*)-*'),
('sssssP', '[PD5H0](-*)(-*)(-*)(-*)-*'),
('sSH', '[SD1H1]-*'),
('dS', '[SD1H0]=*'),
('ssS', '[SD2H0](-*)-*'),
('aaS', '[S,sD2H0](:*):*'),
('dssS', '[SD3H0](=*)(-*)-*'),
('ddssS', '[SD4H0](~[OD1H0])(~[OD1H0])(-*)-*'), # mod
('sCl', '[ClD1]-*'),
('sGeH3', '[GeD1H3](-*)'),
('ssGeH2', '[GeD2H2](-*)-*'),
('sssGeH', '[GeD3H1](-*)(-*)-*'),
('ssssGe', '[GeD4H0](-*)(-*)(-*)-*'),
('sAsH2', '[AsD1H2]-*'),
('ssAsH', '[AsD2H1](-*)-*'),
('sssAs', '[AsD3H0](-*)(-*)-*'),
('sssdAs', '[AsD4H0](=*)(-*)(-*)-*'),
('sssssAs', '[AsD5H0](-*)(-*)(-*)(-*)-*'),
('sSeH', '[SeD1H1]-*'),
('dSe', '[SeD1H0]=*'),
('ssSe', '[SeD2H0](-*)-*'),
('aaSe', '[SeD2H0](:*):*'),
('dssSe', '[SeD3H0](=*)(-*)-*'),
('ddssSe', '[SeD4H0](=*)(=*)(-*)-*'),
('sBr', '[BrD1]-*'),
('sSnH3', '[SnD1H3]-*'),
('ssSnH2', '[SnD2H2](-*)-*'),
('sssSnH', '[SnD3H1](-*)(-*)-*'),
('ssssSn', '[SnD4H0](-*)(-*)(-*)-*'),
('sI', '[ID1]-*'),
('sPbH3', '[PbD1H3]-*'),
('ssPbH2', '[PbD2H2](-*)-*'),
('sssPbH', '[PbD3H1](-*)(-*)-*'),
('ssssPb', '[PbD4H0](-*)(-*)(-*)-*'),
]
esPatterns = None
def BuildPatts(rawV=None):
""" Internal Use Only
"""
global esPatterns, _rawD
if rawV is None:
rawV = _rawD
esPatterns = [None] * len(rawV)
for i, (name, sma) in enumerate(rawV):
patt = Chem.MolFromSmarts(sma)
if patt is None:
sys.stderr.write('WARNING: problems with pattern %s (name: %s), skipped.\n' % (sma, name))
else:
esPatterns[i] = name, patt
def TypeAtoms(mol):
""" assigns each atom in a molecule to an EState type
**Returns:**
list of tuples (atoms can possibly match multiple patterns) with atom types
"""
if esPatterns is None:
BuildPatts()
nAtoms = mol.GetNumAtoms()
res = [None] * nAtoms
for name, patt in esPatterns:
matches = mol.GetSubstructMatches(patt, uniquify=0)
for match in matches:
idx = match[0]
if res[idx] is None:
res[idx] = [name]
elif name not in res[idx]:
res[idx].append(name)
for i, v in enumerate(res):
if v is not None:
res[i] = tuple(v)
else:
res[i] = ()
return res
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"""
unit testing code for the SD file handling stuff
"""
import os
import tempfile
import unittest
from rdkit import Chem
from rdkit import RDConfig
from rdkit.six import next
class TestCase(unittest.TestCase):
def setUp(self):
self.fName = os.path.join(RDConfig.RDDataDir, 'NCI', 'first_200.props.sdf')
with open(self.fName, 'r') as inf:
inD = inf.read()
self.nMolecules = inD.count('$$$$')
def assertMolecule(self, mol, i):
""" Assert that we have a valid molecule """
self.assertIsNotNone(mol, 'read %d failed' % i)
self.assertGreater(mol.GetNumAtoms(), 0, 'no atoms in mol %d' % i)
def test_SDMolSupplier(self):
# tests reads using a file name (file contains 200 molecules)
supp = Chem.SDMolSupplier(self.fName)
# Can use as an iterator
for i in range(10):
mol = next(supp)
self.assertMolecule(mol, i)
# Can access directly
i = 100
mol = supp[i - 1]
self.assertMolecule(mol, i)
# We can access the number of molecules
self.assertEqual(len(supp), self.nMolecules, 'bad supplier length')
# We know the number and can still access directly
i = 12
mol = supp[i - 1]
self.assertMolecule(mol, i)
# Get an exception if we access an invalid number
with self.assertRaises(IndexError):
_ = supp[self.nMolecules] # out of bound read must fail
# and we can access with negative numbers
mol1 = supp[len(supp) - 1]
mol2 = supp[-1]
self.assertEqual(Chem.MolToSmiles(mol1), Chem.MolToSmiles(mol2))
def test_SDWriter(self):
# tests writes using a file name
supp = Chem.SDMolSupplier(self.fName)
_, outName = tempfile.mkstemp('.sdf')
writer = Chem.SDWriter(outName)
m1 = next(supp)
writer.SetProps(m1.GetPropNames())
for m in supp:
writer.write(m)
writer.flush()
writer.close()
# The writer does not have an explicit "close()" so need to
# let the garbage collector kick in to close the file.
writer = None
with open(outName, 'r') as inf:
outD = inf.read()
# The file should be closed, but if it isn't, and this
# is Windows, then the unlink() can fail. Wait and try again.
try:
os.unlink(outName)
except Exception:
import time
time.sleep(1)
try:
os.unlink(outName)
except Exception:
pass
self.assertEqual(self.nMolecules, outD.count('$$$$'), 'bad nMols in output')
# def _testStreamRoundtrip(self):
# inD = open(self.fName).read()
# supp = Chem.SDMolSupplier(self.fName)
# outName = tempfile.mktemp('.sdf')
# writer = Chem.SDWriter(outName)
# _ = next(supp)
# for m in supp:
# writer.write(m)
# writer.flush()
# writer = None
# outD = open(outName, 'r').read()
# try:
# os.unlink(outName)
# except Exception:
# import time
# time.sleep(1)
# try:
# os.unlink(outName)
# except Exception:
# pass
# assert inD.count('$$$$') == outD.count('$$$$'), 'bad nMols in output'
# io = StringIO(outD)
# supp = Chem.SDMolSupplier(stream=io)
# outD2 = supp.Dump()
# assert outD2.count('$$$$') == len(supp), 'bad nMols in output'
# assert outD2.count('$$$$') == outD.count('$$$$'), 'bad nMols in output'
# assert outD2 == outD, 'bad outd'
# def _testLazyDataRoundtrip(self):
# inD = open(self.fName).read()
# supp = Chem.SDMolSupplier(self.fName)
# outName = tempfile.mktemp('.sdf')
# writer = Chem.SDWriter(outName)
# _ = next(supp)
# for m in supp:
# writer.write(m)
# writer.flush()
# writer = None
# outD = open(outName, 'r').read()
# try:
# os.unlink(outName)
# except Exception:
# import time
# time.sleep(1)
# try:
# os.unlink(outName)
# except Exception:
# pass
# assert inD.count('$$$$') == outD.count('$$$$'), 'bad nMols in output'
# supp = Chem.SDMolSupplier.LazySDMolSupplier(inD=outD)
# outD2 = supp.Dump()
# assert outD2.count('$$$$') == len(supp), 'bad nMols in output'
# assert outD2.count('$$$$') == outD.count('$$$$'), 'bad nMols in output'
# assert outD2 == outD, 'bad outd'
# def _testLazyIter(self):
# " tests lazy reads using the iterator interface "
# supp = Chem.SDMolSupplier.LazySDMolSupplier(fileN=self.fName)
#
# nDone = 0
# for mol in supp:
# assert mol, 'read %d failed' % nDone
# assert mol.GetNumAtoms(), 'no atoms in mol %d' % nDone
# nDone += 1
# assert nDone == 200, 'bad number of molecules: %d' % (nDone)
#
# l = len(supp)
# assert l == 200, 'bad supplier length: %d' % (l)
#
# i = 12
# m = supp[i - 1]
# assert m, 'back index %d failed' % i
# assert m.GetNumAtoms(), 'no atoms in mol %d' % i
#
# try:
# m = supp[201]
# except IndexError:
# fail = 1
# else:
# fail = 0
# assert fail, 'out of bound read did not fail'
if __name__ == '__main__': # pragma: nocover
unittest.main()
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"""unit testing code for the SD file handling stuff
"""
import unittest,sys,os
from rdkit import RDConfig
from rdkit import Chem
import tempfile
from cStringIO import StringIO
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
self.fName = os.path.join(RDConfig.RDDataDir,'NCI','first_200.props.sdf')
def _testReader(self):
" tests reads using a file name "
supp = Chem.SDMolSupplier(self.fName)
for i in range(10):
m = supp.next()
assert m,'read %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
i = 100
m = supp[i-1]
assert m,'read %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
l = len(supp)
assert l == 200,'bad supplier length: %d'%(l)
i = 12
m = supp[i-1]
assert m,'back index %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
try:
m = supp[201]
except IndexError:
fail = 1
else:
fail = 0
assert fail,'out of bound read did not fail'
def test_Writer(self):
" tests writes using a file name "
inD = open(self.fName,'r').read()
supp = Chem.SDMolSupplier(self.fName)
outName = tempfile.mktemp('.sdf')
writer = Chem.SDWriter(outName)
m1 = supp.next()
writer.SetProps(m1.GetPropNames())
for m in supp:
writer.write(m)
writer.flush()
writer = None
outD = open(outName,'r').read()
try:
os.unlink(outName)
except:
import time
time.sleep(1)
try:
os.unlink(outName)
except:
pass
assert inD.count('$$$$')==outD.count('$$$$'),'bad nMols in output'
def _testStreamRoundtrip(self):
inD = open(self.fName).read()
supp = Chem.SDMolSupplier(self.fName)
outName = tempfile.mktemp('.sdf')
writer = Chem.SDWriter(outName)
m1 = supp.next()
for m in supp:
writer.write(m)
writer.flush()
writer = None
outD = open(outName,'r').read()
try:
os.unlink(outName)
except:
import time
time.sleep(1)
try:
os.unlink(outName)
except:
pass
assert inD.count('$$$$')==outD.count('$$$$'),'bad nMols in output'
io = StringIO(outD)
supp = Chem.SDMolSupplier(stream=io)
outD2 = supp.Dump()
assert outD2.count('$$$$')==len(supp),'bad nMols in output'
assert outD2.count('$$$$')==outD.count('$$$$'),'bad nMols in output'
assert outD2==outD,'bad outd'
def _testLazyDataRoundtrip(self):
inD = open(self.fName).read()
supp = Chem.SDMolSupplier(self.fName)
outName = tempfile.mktemp('.sdf')
writer = Chem.SDWriter(outName)
m1 = supp.next()
for m in supp:
writer.write(m)
writer.flush()
writer = None
outD = open(outName,'r').read()
try:
os.unlink(outName)
except:
import time
time.sleep(1)
try:
os.unlink(outName)
except:
pass
assert inD.count('$$$$')==outD.count('$$$$'),'bad nMols in output'
supp = SDMolSupplier.LazySDMolSupplier(inD=outD)
outD2 = supp.Dump()
assert outD2.count('$$$$')==len(supp),'bad nMols in output'
assert outD2.count('$$$$')==outD.count('$$$$'),'bad nMols in output'
assert outD2==outD,'bad outd'
def _testLazyIter(self):
" tests lazy reads using the iterator interface "
supp = SDMolSupplier.LazySDMolSupplier(fileN=self.fName)
nDone = 0
for mol in supp:
assert mol,'read %d failed'%i
assert mol.GetNumAtoms(),'no atoms in mol %d'%i
nDone += 1
assert nDone==200,'bad number of molecules: %d'%(nDone)
l = len(supp)
assert l == 200,'bad supplier length: %d'%(l)
i = 12
m = supp[i-1]
assert m,'back index %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
try:
m = supp[201]
except IndexError:
fail = 1
else:
fail = 0
assert fail,'out of bound read did not fail'
if __name__ == '__main__':
unittest.main()
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"size": "4271",
"license": "bsd-3-clause",
"hash": -1353290518686127600,
"line_mean": 24.4226190476,
"line_max": 77,
"alpha_frac": 0.6019667525,
"autogenerated": false,
"ratio": 3.1497050147492627,
"config_test": true,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.4751671767249263,
"avg_score": null,
"num_lines": null
} |
""" tools for interacting with chemdraw
"""
from __future__ import print_function
import string,tempfile,os,time
try:
import pythoncom
from win32com.client import gencache,Dispatch,constants
import win32com.client.gencache
cdxModule = win32com.client.gencache.EnsureModule("{5F646AAB-3B56-48D2-904C-A68D7989C251}", 0, 7, 0)
except Exception:
cdxModule = None
_cdxVersion=0
raise ImportError("ChemDraw version (at least version 7) not found.")
else:
_cdxVersion=7
if cdxModule:
from win32com.client import Dispatch
import win32gui
import re
cdApp = None
theDoc = None
theObjs = None
selectItem = None
cleanItem = None
centerItem = None
def StartChemDraw(visible=True,openDoc=False,showDoc=False):
""" launches chemdraw """
global cdApp,theDoc,theObjs,selectItem,cleanItem,centerItem
if cdApp is not None:
# if called more than once, do a restart
holder = None
selectItem = None
cleanItem = None
centerItem = None
theObjs = None
theDoc = None
cdApp = None
cdApp = Dispatch('ChemDraw.Application')
if openDoc:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
else:
theDoc = None
selectItem = cdApp.MenuBars(1).Menus(2).MenuItems(8)
cleanItem = cdApp.MenuBars(1).Menus(5).MenuItems(6)
if _cdxVersion == 6:
centerItem = cdApp.MenuBars(1).Menus(4).MenuItems(1)
else:
centerItem = cdApp.MenuBars(1).Menus(4).MenuItems(7)
if visible:
cdApp.Visible=1
if theDoc and showDoc:
theDoc.Activate()
def ReactivateChemDraw(openDoc=True,showDoc=True):
global cdApp,theDoc,theObjs
cdApp.Visible=1
if openDoc:
theDoc = cdApp.Documents.Add()
if theDoc and showDoc:
theDoc.Activate()
theObjs = theDoc.Objects
# ------------------------------------------------------------------
# interactions with Chemdraw
# ------------------------------------------------------------------
def CDXConvert(inData,inFormat,outFormat):
"""converts the data passed in from one format to another
inFormat should be one of the following:
chemical/x-cdx chemical/cdx
chemical/x-daylight-smiles chemical/daylight-smiles
chemical/x-mdl-isis chemical/mdl-isis
chemical/x-mdl-molfile chemical/mdl-molfile
chemical/x-mdl-rxn chemical/mdl-rxn
chemical/x-mdl-tgf chemical/mdl-tgf
chemical/x-questel-F1
chemical/x-questel-F1-query
outFormat should be one of the preceding or:
image/x-png image/png
image/x-wmf image/wmf
image/tiff
application/postscript
image/gif
"""
global theObjs,theDoc
if cdApp is None:
StartChemDraw()
if theObjs is None:
if theDoc is None:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
theObjs.SetData(inFormat,inData,pythoncom.Missing)
outD = theObjs.GetData(outFormat)
theObjs.Clear()
return outD
def CDXClean(inData,inFormat,outFormat):
"""calls the CDXLib Clean function on the data passed in.
CDXLib_Clean attempts to clean (prettify) the data before
doing an output conversion. It can be thought of as CDXConvert++.
CDXClean supports the same input and output specifiers as CDXConvert
(see above)
"""
global cdApp,theDoc,theObjs,selectItem,cleanItem
if cdApp is None:
StartChemDraw()
if theObjs is None:
if theDoc is None:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
theObjs.SetData(inFormat,inData,pythoncom.Missing)
theObjs.Select()
cleanItem.Execute()
outD = theObjs.GetData(outFormat)
theObjs.Clear()
return outD
def CDXDisplay(inData,inFormat='chemical/cdx',clear=1):
""" displays the data in Chemdraw """
global cdApp,theDoc,theObjs,selectItem,cleanItem,centerItem
if cdApp is None:
StartChemDraw()
try:
theDoc.Activate()
except Exception:
ReactivateChemDraw()
theObjs = theDoc.Objects
if clear:
theObjs.Clear()
theObjs.SetData(inFormat,inData,pythoncom.Missing)
return
def CDXGrab(outFormat='chemical/x-mdl-molfile'):
""" returns the contents of the active chemdraw document
"""
global cdApp,theDoc
if cdApp is None:
res = ""
else:
cdApp.Visible=1
if not cdApp.ActiveDocument:
ReactivateChemDraw()
try:
res = cdApp.ActiveDocument.Objects.GetData(outFormat)
except Exception:
res = ""
return res
def CloseChemdraw():
""" shuts down chemdraw
"""
global cdApp
try:
cdApp.Quit()
except Exception:
pass
Exit()
def Exit():
""" destroys our link to Chemdraw
"""
global cdApp
cdApp = None
def SaveChemDrawDoc(fileName='save.cdx'):
"""force chemdraw to save the active document
NOTE: the extension of the filename will determine the format
used to save the file.
"""
d = cdApp.ActiveDocument
d.SaveAs(fileName)
def CloseChemDrawDoc():
"""force chemdraw to save the active document
NOTE: the extension of the filename will determine the format
used to save the file.
"""
d = cdApp.ActiveDocument
d.Close()
def RaiseWindowNamed(nameRe):
# start by getting a list of all the windows:
cb = lambda x,y: y.append(x)
wins = []
win32gui.EnumWindows(cb,wins)
# now check to see if any match our regexp:
tgtWin = -1
for win in wins:
txt = win32gui.GetWindowText(win)
if nameRe.match(txt):
tgtWin=win
break
if tgtWin>=0:
win32gui.ShowWindow(tgtWin,1)
win32gui.BringWindowToTop(tgtWin)
def RaiseChemDraw():
e = re.compile('^ChemDraw')
RaiseWindowNamed(e)
try:
from PIL import Image
from io import StringIO
def SmilesToPilImage(smilesStr):
"""takes a SMILES string and returns a PIL image using chemdraw
"""
return MolToPilImage(smilesStr,inFormat='chemical/daylight-smiles',outFormat='image/gif')
def MolToPilImage(dataStr,inFormat='chemical/daylight-smiles',outFormat='image/gif'):
"""takes a molecule string and returns a PIL image using chemdraw
"""
# do the conversion...
res = CDXConvert(dataStr,inFormat,outFormat)
dataFile = StringIO(str(res))
img = Image.open(dataFile).convert('RGB')
return img
except ImportError:
def SmilesToPilImage(smilesStr):
print('You need to have PIL installed to use this functionality')
return None
def MolToPilImage(dataStr,inFormat='chemical/daylight-smiles',outFormat='image/gif'):
print('You need to have PIL installed to use this functionality')
return None
# ------------------------------------------------------------------
# interactions with Chem3D
# ------------------------------------------------------------------
c3dApp = None
def StartChem3D(visible=0):
""" launches Chem3D """
global c3dApp
c3dApp = Dispatch('Chem3D.Application')
if not c3dApp.Visible:
c3dApp.Visible = visible
def CloseChem3D():
""" shuts down Chem3D """
global c3dApp
c3dApp.Quit()
c3dApp = None
availChem3DProps = ('DipoleMoment','BendEnergy','Non14VDWEnergy','StericEnergy',
'StretchBendEnergy','StretchEnergy','TorsionEnergy','VDW14Energy')
def Add3DCoordsToMol(data,format,props={}):
""" adds 3D coordinates to the data passed in using Chem3D
**Arguments**
- data: the molecular data
- format: the format of _data_. Should be something accepted by
_CDXConvert_
- props: (optional) a dictionary used to return calculated properties
"""
global c3dApp
if c3dApp is None:
StartChem3D()
if format != 'chemical/mdl-molfile':
molData = CDXClean(data,format,'chemical/mdl-molfile')
else:
molData = data
molFName = tempfile.mktemp('.mol')
open(molFName,'wb+').write(molData)
doc = c3dApp.Documents.Open(molFName)
if not doc:
print('cannot open molecule')
raise ValueError('No Molecule')
# set up the MM2 job
job = Dispatch('Chem3D.MM2Job')
job.Type=1
job.DisplayEveryIteration=0
job.RecordEveryIteration=0
# start the calculation...
doc.MM2Compute(job)
# and wait for it to finish
while doc.ComputeStatus in [0x434f4d50,0x50454e44]:
pass
#outFName = tempfile.mktemp('.mol')
# this is horrible, but apparently Chem3D gets pissy with tempfiles:
outFName = os.getcwd()+'/to3d.mol'
doc.SaveAs(outFName)
# generate the properties
for prop in availChem3DProps:
props[prop] = eval('doc.%s'%prop)
doc.Close(0)
os.unlink(molFName)
c3dData = open(outFName,'r').read()
gone = 0
while not gone:
try:
os.unlink(outFName)
except Exception:
time.sleep(.5)
else:
gone = 1
return c3dData
def OptimizeSDFile(inFileName,outFileName,problemFileName='problems.sdf',
restartEvery=20):
""" optimizes the structure of every molecule in the input SD file
**Arguments**
- inFileName: name of the input SD file
- outFileName: name of the output SD file
- problemFileName: (optional) name of the SD file used to store molecules which
fail during the optimization process
- restartEvery: (optional) Chem3D will be shut down and restarted
every _restartEvery_ molecules to try and keep core leaks under control
"""
inFile = open(inFileName,'r')
outFile = open(outFileName,'w+')
problemFile = None
props = {}
lines = []
nextLine = inFile.readline()
skip = 0
nDone = 0
t1 = time.time()
while nextLine != '':
if nextLine.find('M END') != -1:
lines.append(nextLine)
molBlock = string.join(lines,'')
try:
newMolBlock = Add3DCoordsToMol(molBlock,'chemical/mdl-molfile',props=props)
except Exception:
badBlock = molBlock
skip = 1
lines = []
else:
skip = 0
lines = [newMolBlock]
elif nextLine.find('$$$$') != -1:
t2 = time.time()
nDone += 1
print('finished molecule %d in %f seconds'%(nDone,time.time()-t1))
t1 = time.time()
if nDone%restartEvery == 0:
CloseChem3D()
StartChem3D()
outFile.close()
outFile = open(outFileName,'a')
if not skip:
for prop in props.keys():
lines.append('> <%s>\n%f\n\n'%(prop,props[prop]))
lines.append(nextLine)
outFile.write(string.join(lines,''))
lines = []
else:
skip = 0
lines.append(nextLine)
if problemFile is None:
problemFile = open(problemFileName,'w+')
problemFile.write(badBlock)
problemFile.write(string.join(lines,''))
lines = []
else:
lines.append(nextLine)
nextLine = inFile.readline()
outFile.close()
if problemFile is not None:
problemFile.close()
if __name__=='__main__':
inStr = 'CCC(C=O)CCC'
img = SmilesToPilImage(inStr)
img.save('foo.jpg')
convStr = CDXClean(inStr,'chemical/x-daylight-smiles','chemical/x-daylight-smiles')
print('in:',inStr)
print('out:',convStr)
convStr = CDXConvert(inStr,'chemical/x-daylight-smiles','chemical/x-mdl-molfile')
print('in:',inStr)
print('out:',convStr)
convStr2 = CDXClean(convStr,'chemical/x-mdl-molfile','chemical/x-mdl-molfile')
print('out2:',convStr2)
inStr = 'COc1ccc(c2onc(c2C(=O)NCCc3ccc(F)cc3)c4ccc(F)cc4)c(OC)c1'
convStr = CDXConvert(inStr,'chemical/x-daylight-smiles','chemical/x-mdl-molfile')
out = open('test.mol','w+')
out.write(convStr)
out.close()
| {
"repo_name": "adalke/rdkit",
"path": "rdkit/utils/chemdraw.py",
"copies": "1",
"size": "11711",
"license": "bsd-3-clause",
"hash": 1579553171053144300,
"line_mean": 26.3621495327,
"line_max": 102,
"alpha_frac": 0.6540859021,
"autogenerated": false,
"ratio": 3.278555431131019,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.9279102036682836,
"avg_score": 0.030707859309636817,
"num_lines": 428
} |
""" tools for interacting with chemdraw
"""
from __future__ import print_function
import string, tempfile, os, time
try:
import pythoncom
from win32com.client import gencache, Dispatch, constants
import win32com.client.gencache
cdxModule = win32com.client.gencache.EnsureModule("{5F646AAB-3B56-48D2-904C-A68D7989C251}", 0, 7,
0)
except Exception:
cdxModule = None
_cdxVersion = 0
raise ImportError("ChemDraw version (at least version 7) not found.")
else:
_cdxVersion = 7
if cdxModule:
from win32com.client import Dispatch
import win32gui
import re
cdApp = None
theDoc = None
theObjs = None
selectItem = None
cleanItem = None
centerItem = None
def StartChemDraw(visible=True, openDoc=False, showDoc=False):
""" launches chemdraw """
global cdApp, theDoc, theObjs, selectItem, cleanItem, centerItem
if cdApp is not None:
# if called more than once, do a restart
holder = None
selectItem = None
cleanItem = None
centerItem = None
theObjs = None
theDoc = None
cdApp = None
cdApp = Dispatch('ChemDraw.Application')
if openDoc:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
else:
theDoc = None
selectItem = cdApp.MenuBars(1).Menus(2).MenuItems(8)
cleanItem = cdApp.MenuBars(1).Menus(5).MenuItems(6)
if _cdxVersion == 6:
centerItem = cdApp.MenuBars(1).Menus(4).MenuItems(1)
else:
centerItem = cdApp.MenuBars(1).Menus(4).MenuItems(7)
if visible:
cdApp.Visible = 1
if theDoc and showDoc:
theDoc.Activate()
def ReactivateChemDraw(openDoc=True, showDoc=True):
global cdApp, theDoc, theObjs
cdApp.Visible = 1
if openDoc:
theDoc = cdApp.Documents.Add()
if theDoc and showDoc:
theDoc.Activate()
theObjs = theDoc.Objects
# ------------------------------------------------------------------
# interactions with Chemdraw
# ------------------------------------------------------------------
def CDXConvert(inData, inFormat, outFormat):
"""converts the data passed in from one format to another
inFormat should be one of the following:
chemical/x-cdx chemical/cdx
chemical/x-daylight-smiles chemical/daylight-smiles
chemical/x-mdl-isis chemical/mdl-isis
chemical/x-mdl-molfile chemical/mdl-molfile
chemical/x-mdl-rxn chemical/mdl-rxn
chemical/x-mdl-tgf chemical/mdl-tgf
chemical/x-questel-F1
chemical/x-questel-F1-query
outFormat should be one of the preceding or:
image/x-png image/png
image/x-wmf image/wmf
image/tiff
application/postscript
image/gif
"""
global theObjs, theDoc
if cdApp is None:
StartChemDraw()
if theObjs is None:
if theDoc is None:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
theObjs.SetData(inFormat, inData, pythoncom.Missing)
outD = theObjs.GetData(outFormat)
theObjs.Clear()
return outD
def CDXClean(inData, inFormat, outFormat):
"""calls the CDXLib Clean function on the data passed in.
CDXLib_Clean attempts to clean (prettify) the data before
doing an output conversion. It can be thought of as CDXConvert++.
CDXClean supports the same input and output specifiers as CDXConvert
(see above)
"""
global cdApp, theDoc, theObjs, selectItem, cleanItem
if cdApp is None:
StartChemDraw()
if theObjs is None:
if theDoc is None:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
theObjs.SetData(inFormat, inData, pythoncom.Missing)
theObjs.Select()
cleanItem.Execute()
outD = theObjs.GetData(outFormat)
theObjs.Clear()
return outD
def CDXDisplay(inData, inFormat='chemical/cdx', clear=1):
""" displays the data in Chemdraw """
global cdApp, theDoc, theObjs, selectItem, cleanItem, centerItem
if cdApp is None:
StartChemDraw()
try:
theDoc.Activate()
except Exception:
ReactivateChemDraw()
theObjs = theDoc.Objects
if clear:
theObjs.Clear()
theObjs.SetData(inFormat, inData, pythoncom.Missing)
return
def CDXGrab(outFormat='chemical/x-mdl-molfile'):
""" returns the contents of the active chemdraw document
"""
global cdApp, theDoc
if cdApp is None:
res = ""
else:
cdApp.Visible = 1
if not cdApp.ActiveDocument:
ReactivateChemDraw()
try:
res = cdApp.ActiveDocument.Objects.GetData(outFormat)
except Exception:
res = ""
return res
def CloseChemdraw():
""" shuts down chemdraw
"""
global cdApp
try:
cdApp.Quit()
except Exception:
pass
Exit()
def Exit():
""" destroys our link to Chemdraw
"""
global cdApp
cdApp = None
def SaveChemDrawDoc(fileName='save.cdx'):
"""force chemdraw to save the active document
NOTE: the extension of the filename will determine the format
used to save the file.
"""
d = cdApp.ActiveDocument
d.SaveAs(fileName)
def CloseChemDrawDoc():
"""force chemdraw to save the active document
NOTE: the extension of the filename will determine the format
used to save the file.
"""
d = cdApp.ActiveDocument
d.Close()
def RaiseWindowNamed(nameRe):
# start by getting a list of all the windows:
cb = lambda x, y: y.append(x)
wins = []
win32gui.EnumWindows(cb, wins)
# now check to see if any match our regexp:
tgtWin = -1
for win in wins:
txt = win32gui.GetWindowText(win)
if nameRe.match(txt):
tgtWin = win
break
if tgtWin >= 0:
win32gui.ShowWindow(tgtWin, 1)
win32gui.BringWindowToTop(tgtWin)
def RaiseChemDraw():
e = re.compile('^ChemDraw')
RaiseWindowNamed(e)
try:
from PIL import Image
from io import StringIO
def SmilesToPilImage(smilesStr):
"""takes a SMILES string and returns a PIL image using chemdraw
"""
return MolToPilImage(smilesStr, inFormat='chemical/daylight-smiles', outFormat='image/gif')
def MolToPilImage(dataStr, inFormat='chemical/daylight-smiles', outFormat='image/gif'):
"""takes a molecule string and returns a PIL image using chemdraw
"""
# do the conversion...
res = CDXConvert(dataStr, inFormat, outFormat)
dataFile = StringIO(str(res))
img = Image.open(dataFile).convert('RGB')
return img
except ImportError:
def SmilesToPilImage(smilesStr):
print('You need to have PIL installed to use this functionality')
return None
def MolToPilImage(dataStr, inFormat='chemical/daylight-smiles', outFormat='image/gif'):
print('You need to have PIL installed to use this functionality')
return None
# ------------------------------------------------------------------
# interactions with Chem3D
# ------------------------------------------------------------------
c3dApp = None
def StartChem3D(visible=0):
""" launches Chem3D """
global c3dApp
c3dApp = Dispatch('Chem3D.Application')
if not c3dApp.Visible:
c3dApp.Visible = visible
def CloseChem3D():
""" shuts down Chem3D """
global c3dApp
c3dApp.Quit()
c3dApp = None
availChem3DProps = ('DipoleMoment', 'BendEnergy', 'Non14VDWEnergy', 'StericEnergy',
'StretchBendEnergy', 'StretchEnergy', 'TorsionEnergy', 'VDW14Energy')
def Add3DCoordsToMol(data, format, props={}):
""" adds 3D coordinates to the data passed in using Chem3D
**Arguments**
- data: the molecular data
- format: the format of _data_. Should be something accepted by
_CDXConvert_
- props: (optional) a dictionary used to return calculated properties
"""
global c3dApp
if c3dApp is None:
StartChem3D()
if format != 'chemical/mdl-molfile':
molData = CDXClean(data, format, 'chemical/mdl-molfile')
else:
molData = data
molFName = tempfile.mktemp('.mol')
open(molFName, 'wb+').write(molData)
doc = c3dApp.Documents.Open(molFName)
if not doc:
print('cannot open molecule')
raise ValueError('No Molecule')
# set up the MM2 job
job = Dispatch('Chem3D.MM2Job')
job.Type = 1
job.DisplayEveryIteration = 0
job.RecordEveryIteration = 0
# start the calculation...
doc.MM2Compute(job)
# and wait for it to finish
while doc.ComputeStatus in [0x434f4d50, 0x50454e44]:
pass
#outFName = tempfile.mktemp('.mol')
# this is horrible, but apparently Chem3D gets pissy with tempfiles:
outFName = os.getcwd() + '/to3d.mol'
doc.SaveAs(outFName)
# generate the properties
for prop in availChem3DProps:
props[prop] = eval('doc.%s' % prop)
doc.Close(0)
os.unlink(molFName)
c3dData = open(outFName, 'r').read()
gone = 0
while not gone:
try:
os.unlink(outFName)
except Exception:
time.sleep(.5)
else:
gone = 1
return c3dData
def OptimizeSDFile(inFileName, outFileName, problemFileName='problems.sdf', restartEvery=20):
""" optimizes the structure of every molecule in the input SD file
**Arguments**
- inFileName: name of the input SD file
- outFileName: name of the output SD file
- problemFileName: (optional) name of the SD file used to store molecules which
fail during the optimization process
- restartEvery: (optional) Chem3D will be shut down and restarted
every _restartEvery_ molecules to try and keep core leaks under control
"""
inFile = open(inFileName, 'r')
outFile = open(outFileName, 'w+')
problemFile = None
props = {}
lines = []
nextLine = inFile.readline()
skip = 0
nDone = 0
t1 = time.time()
while nextLine != '':
if nextLine.find('M END') != -1:
lines.append(nextLine)
molBlock = string.join(lines, '')
try:
newMolBlock = Add3DCoordsToMol(molBlock, 'chemical/mdl-molfile', props=props)
except Exception:
badBlock = molBlock
skip = 1
lines = []
else:
skip = 0
lines = [newMolBlock]
elif nextLine.find('$$$$') != -1:
t2 = time.time()
nDone += 1
print('finished molecule %d in %f seconds' % (nDone, time.time() - t1))
t1 = time.time()
if nDone % restartEvery == 0:
CloseChem3D()
StartChem3D()
outFile.close()
outFile = open(outFileName, 'a')
if not skip:
for prop in props.keys():
lines.append('> <%s>\n%f\n\n' % (prop, props[prop]))
lines.append(nextLine)
outFile.write(string.join(lines, ''))
lines = []
else:
skip = 0
lines.append(nextLine)
if problemFile is None:
problemFile = open(problemFileName, 'w+')
problemFile.write(badBlock)
problemFile.write(string.join(lines, ''))
lines = []
else:
lines.append(nextLine)
nextLine = inFile.readline()
outFile.close()
if problemFile is not None:
problemFile.close()
if __name__ == '__main__':
inStr = 'CCC(C=O)CCC'
img = SmilesToPilImage(inStr)
img.save('foo.jpg')
convStr = CDXClean(inStr, 'chemical/x-daylight-smiles', 'chemical/x-daylight-smiles')
print('in:', inStr)
print('out:', convStr)
convStr = CDXConvert(inStr, 'chemical/x-daylight-smiles', 'chemical/x-mdl-molfile')
print('in:', inStr)
print('out:', convStr)
convStr2 = CDXClean(convStr, 'chemical/x-mdl-molfile', 'chemical/x-mdl-molfile')
print('out2:', convStr2)
inStr = 'COc1ccc(c2onc(c2C(=O)NCCc3ccc(F)cc3)c4ccc(F)cc4)c(OC)c1'
convStr = CDXConvert(inStr, 'chemical/x-daylight-smiles', 'chemical/x-mdl-molfile')
out = open('test.mol', 'w+')
out.write(convStr)
out.close()
| {
"repo_name": "jandom/rdkit",
"path": "rdkit/utils/chemdraw.py",
"copies": "1",
"size": "11869",
"license": "bsd-3-clause",
"hash": 7721305097626846000,
"line_mean": 25.4933035714,
"line_max": 99,
"alpha_frac": 0.6453787177,
"autogenerated": false,
"ratio": 3.2969444444444442,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.93413107287757,
"avg_score": 0.020202486673748802,
"num_lines": 448
} |
""" tools for interacting with chemdraw
"""
from __future__ import print_function
import tempfile, os, time
try:
import pythoncom
from win32com.client import gencache, Dispatch, constants
import win32com.client.gencache
cdxModule = win32com.client.gencache.EnsureModule("{5F646AAB-3B56-48D2-904C-A68D7989C251}", 0, 7,
0)
except Exception:
cdxModule = None
_cdxVersion = 0
raise ImportError("ChemDraw version (at least version 7) not found.")
else:
_cdxVersion = 7
if cdxModule:
from win32com.client import Dispatch
import win32gui
import re
cdApp = None
theDoc = None
theObjs = None
selectItem = None
cleanItem = None
centerItem = None
def StartChemDraw(visible=True, openDoc=False, showDoc=False):
""" launches chemdraw """
global cdApp, theDoc, theObjs, selectItem, cleanItem, centerItem
if cdApp is not None:
# if called more than once, do a restart
holder = None
selectItem = None
cleanItem = None
centerItem = None
theObjs = None
theDoc = None
cdApp = None
cdApp = Dispatch('ChemDraw.Application')
if openDoc:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
else:
theDoc = None
selectItem = cdApp.MenuBars(1).Menus(2).MenuItems(8)
cleanItem = cdApp.MenuBars(1).Menus(5).MenuItems(6)
if _cdxVersion == 6:
centerItem = cdApp.MenuBars(1).Menus(4).MenuItems(1)
else:
centerItem = cdApp.MenuBars(1).Menus(4).MenuItems(7)
if visible:
cdApp.Visible = 1
if theDoc and showDoc:
theDoc.Activate()
def ReactivateChemDraw(openDoc=True, showDoc=True):
global cdApp, theDoc, theObjs
cdApp.Visible = 1
if openDoc:
theDoc = cdApp.Documents.Add()
if theDoc and showDoc:
theDoc.Activate()
theObjs = theDoc.Objects
# ------------------------------------------------------------------
# interactions with Chemdraw
# ------------------------------------------------------------------
def CDXConvert(inData, inFormat, outFormat):
"""converts the data passed in from one format to another
inFormat should be one of the following:
chemical/x-cdx chemical/cdx
chemical/x-daylight-smiles chemical/daylight-smiles
chemical/x-mdl-isis chemical/mdl-isis
chemical/x-mdl-molfile chemical/mdl-molfile
chemical/x-mdl-rxn chemical/mdl-rxn
chemical/x-mdl-tgf chemical/mdl-tgf
chemical/x-questel-F1
chemical/x-questel-F1-query
outFormat should be one of the preceding or:
image/x-png image/png
image/x-wmf image/wmf
image/tiff
application/postscript
image/gif
"""
global theObjs, theDoc
if cdApp is None:
StartChemDraw()
if theObjs is None:
if theDoc is None:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
theObjs.SetData(inFormat, inData, pythoncom.Missing)
outD = theObjs.GetData(outFormat)
theObjs.Clear()
return outD
def CDXClean(inData, inFormat, outFormat):
"""calls the CDXLib Clean function on the data passed in.
CDXLib_Clean attempts to clean (prettify) the data before
doing an output conversion. It can be thought of as CDXConvert++.
CDXClean supports the same input and output specifiers as CDXConvert
(see above)
"""
global cdApp, theDoc, theObjs, selectItem, cleanItem
if cdApp is None:
StartChemDraw()
if theObjs is None:
if theDoc is None:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
theObjs.SetData(inFormat, inData, pythoncom.Missing)
theObjs.Select()
cleanItem.Execute()
outD = theObjs.GetData(outFormat)
theObjs.Clear()
return outD
def CDXDisplay(inData, inFormat='chemical/cdx', clear=1):
""" displays the data in Chemdraw """
global cdApp, theDoc, theObjs, selectItem, cleanItem, centerItem
if cdApp is None:
StartChemDraw()
try:
theDoc.Activate()
except Exception:
ReactivateChemDraw()
theObjs = theDoc.Objects
if clear:
theObjs.Clear()
theObjs.SetData(inFormat, inData, pythoncom.Missing)
return
def CDXGrab(outFormat='chemical/x-mdl-molfile'):
""" returns the contents of the active chemdraw document
"""
global cdApp, theDoc
if cdApp is None:
res = ""
else:
cdApp.Visible = 1
if not cdApp.ActiveDocument:
ReactivateChemDraw()
try:
res = cdApp.ActiveDocument.Objects.GetData(outFormat)
except Exception:
res = ""
return res
def CloseChemdraw():
""" shuts down chemdraw
"""
global cdApp
try:
cdApp.Quit()
except Exception:
pass
Exit()
def Exit():
""" destroys our link to Chemdraw
"""
global cdApp
cdApp = None
def SaveChemDrawDoc(fileName='save.cdx'):
"""force chemdraw to save the active document
NOTE: the extension of the filename will determine the format
used to save the file.
"""
d = cdApp.ActiveDocument
d.SaveAs(fileName)
def CloseChemDrawDoc():
"""force chemdraw to save the active document
NOTE: the extension of the filename will determine the format
used to save the file.
"""
d = cdApp.ActiveDocument
d.Close()
def RaiseWindowNamed(nameRe):
# start by getting a list of all the windows:
cb = lambda x, y: y.append(x)
wins = []
win32gui.EnumWindows(cb, wins)
# now check to see if any match our regexp:
tgtWin = -1
for win in wins:
txt = win32gui.GetWindowText(win)
if nameRe.match(txt):
tgtWin = win
break
if tgtWin >= 0:
win32gui.ShowWindow(tgtWin, 1)
win32gui.BringWindowToTop(tgtWin)
def RaiseChemDraw():
e = re.compile('^ChemDraw')
RaiseWindowNamed(e)
try:
from PIL import Image
from io import StringIO
def SmilesToPilImage(smilesStr):
"""takes a SMILES string and returns a PIL image using chemdraw
"""
return MolToPilImage(smilesStr, inFormat='chemical/daylight-smiles', outFormat='image/gif')
def MolToPilImage(dataStr, inFormat='chemical/daylight-smiles', outFormat='image/gif'):
"""takes a molecule string and returns a PIL image using chemdraw
"""
# do the conversion...
res = CDXConvert(dataStr, inFormat, outFormat)
dataFile = StringIO(str(res))
img = Image.open(dataFile).convert('RGB')
return img
except ImportError:
def SmilesToPilImage(smilesStr):
print('You need to have PIL installed to use this functionality')
return None
def MolToPilImage(dataStr, inFormat='chemical/daylight-smiles', outFormat='image/gif'):
print('You need to have PIL installed to use this functionality')
return None
# ------------------------------------------------------------------
# interactions with Chem3D
# ------------------------------------------------------------------
c3dApp = None
def StartChem3D(visible=0):
""" launches Chem3D """
global c3dApp
c3dApp = Dispatch('Chem3D.Application')
if not c3dApp.Visible:
c3dApp.Visible = visible
def CloseChem3D():
""" shuts down Chem3D """
global c3dApp
c3dApp.Quit()
c3dApp = None
availChem3DProps = ('DipoleMoment', 'BendEnergy', 'Non14VDWEnergy', 'StericEnergy',
'StretchBendEnergy', 'StretchEnergy', 'TorsionEnergy', 'VDW14Energy')
def Add3DCoordsToMol(data, format, props={}):
""" adds 3D coordinates to the data passed in using Chem3D
**Arguments**
- data: the molecular data
- format: the format of _data_. Should be something accepted by
_CDXConvert_
- props: (optional) a dictionary used to return calculated properties
"""
global c3dApp
if c3dApp is None:
StartChem3D()
if format != 'chemical/mdl-molfile':
molData = CDXClean(data, format, 'chemical/mdl-molfile')
else:
molData = data
molFName = tempfile.mktemp('.mol')
open(molFName, 'wb+').write(molData)
doc = c3dApp.Documents.Open(molFName)
if not doc:
print('cannot open molecule')
raise ValueError('No Molecule')
# set up the MM2 job
job = Dispatch('Chem3D.MM2Job')
job.Type = 1
job.DisplayEveryIteration = 0
job.RecordEveryIteration = 0
# start the calculation...
doc.MM2Compute(job)
# and wait for it to finish
while doc.ComputeStatus in [0x434f4d50, 0x50454e44]:
pass
#outFName = tempfile.mktemp('.mol')
# this is horrible, but apparently Chem3D gets pissy with tempfiles:
outFName = os.getcwd() + '/to3d.mol'
doc.SaveAs(outFName)
# generate the properties
for prop in availChem3DProps:
props[prop] = eval('doc.%s' % prop)
doc.Close(0)
os.unlink(molFName)
c3dData = open(outFName, 'r').read()
gone = 0
while not gone:
try:
os.unlink(outFName)
except Exception:
time.sleep(.5)
else:
gone = 1
return c3dData
def OptimizeSDFile(inFileName, outFileName, problemFileName='problems.sdf', restartEvery=20):
""" optimizes the structure of every molecule in the input SD file
**Arguments**
- inFileName: name of the input SD file
- outFileName: name of the output SD file
- problemFileName: (optional) name of the SD file used to store molecules which
fail during the optimization process
- restartEvery: (optional) Chem3D will be shut down and restarted
every _restartEvery_ molecules to try and keep core leaks under control
"""
inFile = open(inFileName, 'r')
outFile = open(outFileName, 'w+')
problemFile = None
props = {}
lines = []
nextLine = inFile.readline()
skip = 0
nDone = 0
t1 = time.time()
while nextLine != '':
if nextLine.find('M END') != -1:
lines.append(nextLine)
molBlock = ''.join(lines)
try:
newMolBlock = Add3DCoordsToMol(molBlock, 'chemical/mdl-molfile', props=props)
except Exception:
badBlock = molBlock
skip = 1
lines = []
else:
skip = 0
lines = [newMolBlock]
elif nextLine.find('$$$$') != -1:
t2 = time.time()
nDone += 1
print('finished molecule %d in %f seconds' % (nDone, time.time() - t1))
t1 = time.time()
if nDone % restartEvery == 0:
CloseChem3D()
StartChem3D()
outFile.close()
outFile = open(outFileName, 'a')
if not skip:
for prop in props.keys():
lines.append('> <%s>\n%f\n\n' % (prop, props[prop]))
lines.append(nextLine)
outFile.write(''.join(lines))
lines = []
else:
skip = 0
lines.append(nextLine)
if problemFile is None:
problemFile = open(problemFileName, 'w+')
problemFile.write(badBlock)
problemFile.write(''.join(lines))
lines = []
else:
lines.append(nextLine)
nextLine = inFile.readline()
outFile.close()
if problemFile is not None:
problemFile.close()
if __name__ == '__main__':
inStr = 'CCC(C=O)CCC'
img = SmilesToPilImage(inStr)
img.save('foo.jpg')
convStr = CDXClean(inStr, 'chemical/x-daylight-smiles', 'chemical/x-daylight-smiles')
print('in:', inStr)
print('out:', convStr)
convStr = CDXConvert(inStr, 'chemical/x-daylight-smiles', 'chemical/x-mdl-molfile')
print('in:', inStr)
print('out:', convStr)
convStr2 = CDXClean(convStr, 'chemical/x-mdl-molfile', 'chemical/x-mdl-molfile')
print('out2:', convStr2)
inStr = 'COc1ccc(c2onc(c2C(=O)NCCc3ccc(F)cc3)c4ccc(F)cc4)c(OC)c1'
convStr = CDXConvert(inStr, 'chemical/x-daylight-smiles', 'chemical/x-mdl-molfile')
out = open('test.mol', 'w+')
out.write(convStr)
out.close()
| {
"repo_name": "rvianello/rdkit",
"path": "rdkit/utils/chemdraw.py",
"copies": "4",
"size": "11837",
"license": "bsd-3-clause",
"hash": 4634962496583773000,
"line_mean": 25.421875,
"line_max": 99,
"alpha_frac": 0.6450958858,
"autogenerated": false,
"ratio": 3.2972144846796656,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 1,
"avg_score": 0.02023663795445339,
"num_lines": 448
} |
""" tools for interacting with chemdraw
"""
import string,tempfile,os,time
try:
import pythoncom
from win32com.client import gencache,Dispatch,constants
import win32com.client.gencache
cdxModule = win32com.client.gencache.EnsureModule("{5F646AAB-3B56-48D2-904C-A68D7989C251}", 0, 7, 0)
except:
cdxModule = None
_cdxVersion=0
raise ImportError,"ChemDraw version (at least version 7) not found."
else:
_cdxVersion=7
if cdxModule:
from win32com.client import Dispatch
import win32gui
import re
cdApp = None
theDoc = None
theObjs = None
selectItem = None
cleanItem = None
centerItem = None
def StartChemDraw(visible=True,openDoc=False,showDoc=False):
""" launches chemdraw """
global cdApp,theDoc,theObjs,selectItem,cleanItem,centerItem
if cdApp is not None:
# if called more than once, do a restart
holder = None
selectItem = None
cleanItem = None
centerItem = None
theObjs = None
theDoc = None
cdApp = None
cdApp = Dispatch('ChemDraw.Application')
if openDoc:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
else:
theDoc = None
selectItem = cdApp.MenuBars(1).Menus(2).MenuItems(8)
cleanItem = cdApp.MenuBars(1).Menus(5).MenuItems(6)
if _cdxVersion == 6:
centerItem = cdApp.MenuBars(1).Menus(4).MenuItems(1)
else:
centerItem = cdApp.MenuBars(1).Menus(4).MenuItems(7)
if visible:
cdApp.Visible=1
if theDoc and showDoc:
theDoc.Activate()
def ReactivateChemDraw(openDoc=True,showDoc=True):
global cdApp,theDoc,theObjs
cdApp.Visible=1
if openDoc:
theDoc = cdApp.Documents.Add()
if theDoc and showDoc:
theDoc.Activate()
theObjs = theDoc.Objects
# ------------------------------------------------------------------
# interactions with Chemdraw
# ------------------------------------------------------------------
def CDXConvert(inData,inFormat,outFormat):
"""converts the data passed in from one format to another
inFormat should be one of the following:
chemical/x-cdx chemical/cdx
chemical/x-daylight-smiles chemical/daylight-smiles
chemical/x-mdl-isis chemical/mdl-isis
chemical/x-mdl-molfile chemical/mdl-molfile
chemical/x-mdl-rxn chemical/mdl-rxn
chemical/x-mdl-tgf chemical/mdl-tgf
chemical/x-questel-F1
chemical/x-questel-F1-query
outFormat should be one of the preceding or:
image/x-png image/png
image/x-wmf image/wmf
image/tiff
application/postscript
image/gif
"""
global theObjs,theDoc
if cdApp is None:
StartChemDraw()
if theObjs is None:
if theDoc is None:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
theObjs.SetData(inFormat,inData,pythoncom.Missing)
outD = theObjs.GetData(outFormat)
theObjs.Clear()
return outD
def CDXClean(inData,inFormat,outFormat):
"""calls the CDXLib Clean function on the data passed in.
CDXLib_Clean attempts to clean (prettify) the data before
doing an output conversion. It can be thought of as CDXConvert++.
CDXClean supports the same input and output specifiers as CDXConvert
(see above)
"""
global cdApp,theDoc,theObjs,selectItem,cleanItem
if cdApp is None:
StartChemDraw()
if theObjs is None:
if theDoc is None:
theDoc = cdApp.Documents.Add()
theObjs = theDoc.Objects
theObjs.SetData(inFormat,inData,pythoncom.Missing)
theObjs.Select()
cleanItem.Execute()
outD = theObjs.GetData(outFormat)
theObjs.Clear()
return outD
def CDXDisplay(inData,inFormat='chemical/cdx',clear=1):
""" displays the data in Chemdraw """
global cdApp,theDoc,theObjs,selectItem,cleanItem,centerItem
if cdApp is None:
StartChemDraw()
try:
theDoc.Activate()
except:
ReactivateChemDraw()
theObjs = theDoc.Objects
if clear:
theObjs.Clear()
theObjs.SetData(inFormat,inData,pythoncom.Missing)
return
def CDXGrab(outFormat='chemical/x-mdl-molfile'):
""" returns the contents of the active chemdraw document
"""
global cdApp,theDoc
if cdApp is None:
res = ""
else:
cdApp.Visible=1
if not cdApp.ActiveDocument:
ReactivateChemDraw()
try:
res = cdApp.ActiveDocument.Objects.GetData(outFormat)
except:
res = ""
return res
def CloseChemdraw():
""" shuts down chemdraw
"""
global cdApp
try:
cdApp.Quit()
except:
pass
Exit()
def Exit():
""" destroys our link to Chemdraw
"""
global cdApp
cdApp = None
def SaveChemDrawDoc(fileName='save.cdx'):
"""force chemdraw to save the active document
NOTE: the extension of the filename will determine the format
used to save the file.
"""
d = cdApp.ActiveDocument
d.SaveAs(fileName)
def CloseChemDrawDoc():
"""force chemdraw to save the active document
NOTE: the extension of the filename will determine the format
used to save the file.
"""
d = cdApp.ActiveDocument
d.Close()
def RaiseWindowNamed(nameRe):
# start by getting a list of all the windows:
cb = lambda x,y: y.append(x)
wins = []
win32gui.EnumWindows(cb,wins)
# now check to see if any match our regexp:
tgtWin = -1
for win in wins:
txt = win32gui.GetWindowText(win)
if nameRe.match(txt):
tgtWin=win
break
if tgtWin>=0:
win32gui.ShowWindow(tgtWin,1)
win32gui.BringWindowToTop(tgtWin)
def RaiseChemDraw():
e = re.compile('^ChemDraw')
RaiseWindowNamed(e)
try:
from PIL import Image
import cStringIO
def SmilesToPilImage(smilesStr):
"""takes a SMILES string and returns a PIL image using chemdraw
"""
return MolToPilImage(smilesStr,inFormat='chemical/daylight-smiles',outFormat='image/gif')
def MolToPilImage(dataStr,inFormat='chemical/daylight-smiles',outFormat='image/gif'):
"""takes a molecule string and returns a PIL image using chemdraw
"""
# do the conversion...
res = CDXConvert(dataStr,inFormat,outFormat)
dataFile = cStringIO.StringIO(str(res))
img = Image.open(dataFile).convert('RGB')
return img
except ImportError:
def SmilesToPilImage(smilesStr):
print 'You need to have PIL installed to use this functionality'
return None
def MolToPilImage(dataStr,inFormat='chemical/daylight-smiles',outFormat='image/gif'):
print 'You need to have PIL installed to use this functionality'
return None
# ------------------------------------------------------------------
# interactions with Chem3D
# ------------------------------------------------------------------
c3dApp = None
def StartChem3D(visible=0):
""" launches Chem3D """
global c3dApp
c3dApp = Dispatch('Chem3D.Application')
if not c3dApp.Visible:
c3dApp.Visible = visible
def CloseChem3D():
""" shuts down Chem3D """
global c3dApp
c3dApp.Quit()
c3dApp = None
availChem3DProps = ('DipoleMoment','BendEnergy','Non14VDWEnergy','StericEnergy',
'StretchBendEnergy','StretchEnergy','TorsionEnergy','VDW14Energy')
def Add3DCoordsToMol(data,format,props={}):
""" adds 3D coordinates to the data passed in using Chem3D
**Arguments**
- data: the molecular data
- format: the format of _data_. Should be something accepted by
_CDXConvert_
- props: (optional) a dictionary used to return calculated properties
"""
global c3dApp
if c3dApp is None:
StartChem3D()
if format != 'chemical/mdl-molfile':
molData = CDXClean(data,format,'chemical/mdl-molfile')
else:
molData = data
molFName = tempfile.mktemp('.mol')
open(molFName,'wb+').write(molData)
doc = c3dApp.Documents.Open(molFName)
if not doc:
print 'cannot open molecule'
raise ValueError,'No Molecule'
# set up the MM2 job
job = Dispatch('Chem3D.MM2Job')
job.Type=1
job.DisplayEveryIteration=0
job.RecordEveryIteration=0
# start the calculation...
doc.MM2Compute(job)
# and wait for it to finish
while doc.ComputeStatus in [0x434f4d50,0x50454e44]:
pass
#outFName = tempfile.mktemp('.mol')
# this is horrible, but apparently Chem3D gets pissy with tempfiles:
outFName = os.getcwd()+'/to3d.mol'
doc.SaveAs(outFName)
# generate the properties
for prop in availChem3DProps:
props[prop] = eval('doc.%s'%prop)
doc.Close(0)
os.unlink(molFName)
c3dData = open(outFName,'r').read()
gone = 0
while not gone:
try:
os.unlink(outFName)
except:
time.sleep(.5)
else:
gone = 1
return c3dData
def OptimizeSDFile(inFileName,outFileName,problemFileName='problems.sdf',
restartEvery=20):
""" optimizes the structure of every molecule in the input SD file
**Arguments**
- inFileName: name of the input SD file
- outFileName: name of the output SD file
- problemFileName: (optional) name of the SD file used to store molecules which
fail during the optimization process
- restartEvery: (optional) Chem3D will be shut down and restarted
every _restartEvery_ molecules to try and keep core leaks under control
"""
inFile = open(inFileName,'r')
outFile = open(outFileName,'w+')
problemFile = None
props = {}
lines = []
nextLine = inFile.readline()
skip = 0
nDone = 0
t1 = time.time()
while nextLine != '':
if nextLine.find('M END') != -1:
lines.append(nextLine)
molBlock = string.join(lines,'')
try:
newMolBlock = Add3DCoordsToMol(molBlock,'chemical/mdl-molfile',props=props)
except:
badBlock = molBlock
skip = 1
lines = []
else:
skip = 0
lines = [newMolBlock]
elif nextLine.find('$$$$') != -1:
t2 = time.time()
nDone += 1
print 'finished molecule %d in %f seconds'%(nDone,time.time()-t1)
t1 = time.time()
if nDone%restartEvery == 0:
CloseChem3D()
StartChem3D()
outFile.close()
outFile = open(outFileName,'a')
if not skip:
for prop in props.keys():
lines.append('> <%s>\n%f\n\n'%(prop,props[prop]))
lines.append(nextLine)
outFile.write(string.join(lines,''))
lines = []
else:
skip = 0
lines.append(nextLine)
if problemFile is None:
problemFile = open(problemFileName,'w+')
problemFile.write(badBlock)
problemFile.write(string.join(lines,''))
lines = []
else:
lines.append(nextLine)
nextLine = inFile.readline()
outFile.close()
if problemFile is not None:
problemFile.close()
if __name__=='__main__':
inStr = 'CCC(C=O)CCC'
img = SmilesToPilImage(inStr)
img.save('foo.jpg')
convStr = CDXClean(inStr,'chemical/x-daylight-smiles','chemical/x-daylight-smiles')
print 'in:',inStr
print 'out:',convStr
convStr = CDXConvert(inStr,'chemical/x-daylight-smiles','chemical/x-mdl-molfile')
print 'in:',inStr
print 'out:',convStr
convStr2 = CDXClean(convStr,'chemical/x-mdl-molfile','chemical/x-mdl-molfile')
print 'out2:',convStr2
inStr = 'COc1ccc(c2onc(c2C(=O)NCCc3ccc(F)cc3)c4ccc(F)cc4)c(OC)c1'
convStr = CDXConvert(inStr,'chemical/x-daylight-smiles','chemical/x-mdl-molfile')
out = open('test.mol','w+')
out.write(convStr)
out.close()
| {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/utils/chemdraw.py",
"copies": "2",
"size": "11604",
"license": "bsd-3-clause",
"hash": -1931042545943586300,
"line_mean": 26.2394366197,
"line_max": 102,
"alpha_frac": 0.6533092037,
"autogenerated": false,
"ratio": 3.2678118839763446,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.49211210876763445,
"avg_score": null,
"num_lines": null
} |
""" unit testing code for surface calculations
FIX: add tests for LabuteASA
"""
from __future__ import print_function
from rdkit import RDConfig
import unittest, os
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import MolSurf
import os.path
def feq(n1, n2, tol=1e-4):
return abs(n1 - n2) <= tol
class TestCase(unittest.TestCase):
def setUp(self):
if doLong:
print('\n%s: ' % self.shortDescription(), end='')
def testTPSAShort(self):
" Short TPSA test "
inName = RDConfig.RDDataDir + '/NCI/first_200.tpsa.csv'
with open(inName, 'r') as inF:
lines = inF.readlines()
for line in lines:
if line[0] != '#':
line.strip()
smi, ans = line.split(',')
ans = float(ans)
mol = Chem.MolFromSmiles(smi)
calc = MolSurf.TPSA(mol)
assert feq(calc, ans), 'bad TPSA for SMILES %s (%.2f != %.2f)' % (smi, calc, ans)
def _testTPSALong(self):
" Longer TPSA test "
#inName = RDConfig.RDDataDir+'/NCI/first_5k.tpsa.csv'
inName = os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', 'NCI_5K_TPSA.csv')
with open(inName, 'r') as inF:
lines = inF.readlines()
lineNo = 0
for line in lines:
lineNo += 1
if line[0] != '#':
line.strip()
smi, ans = line.split(',')
ans = float(ans)
mol = Chem.MolFromSmiles(smi)
if not mol:
raise AssertionError('molecule construction failed on line %d' % lineNo)
else:
ok = 1
try:
calc = MolSurf.TPSA(mol)
except Exception:
ok = 0
assert ok, 'Line %d: TPSA Calculation failed for SMILES %s' % (lineNo, smi)
assert feq(calc, ans), 'Line %d: bad TPSA for SMILES %s (%.2f != %.2f)' % (lineNo, smi,
calc, ans)
def testHsAndTPSA(self):
"""
testing the impact of Hs in the graph on PSA calculations
This was sf.net issue 1969745
"""
mol = Chem.MolFromSmiles('c1c[nH]cc1')
molH = Chem.AddHs(mol)
psa = MolSurf.TPSA(mol)
psaH = MolSurf.TPSA(molH)
if (psa != psaH):
psac = MolSurf.rdMolDescriptors._CalcTPSAContribs(mol)
psaHc = MolSurf.rdMolDescriptors._CalcTPSAContribs(molH)
for i, v in enumerate(psac):
print('\t', i, '\t', v, '\t', psaHc[i])
while i < len(psaHc):
print('\t\t\t', psaHc[i])
i += 1
self.assertEqual(psa, psaH)
inName = RDConfig.RDDataDir + '/NCI/first_200.tpsa.csv'
with open(inName, 'r') as inF:
lines = inF.readlines()
for line in lines:
if line[0] != '#':
line.strip()
smi, ans = line.split(',')
ans = float(ans)
mol = Chem.MolFromSmiles(smi)
mol = Chem.AddHs(mol)
calc = MolSurf.TPSA(mol)
self.assertTrue(feq(calc, ans), 'bad TPSA for SMILES %s (%.2f != %.2f)' % (smi, calc, ans))
if doLong:
inName = os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', 'NCI_5K_TPSA.csv')
with open(inName, 'r') as inF:
lines = inF.readlines()
for line in lines:
if line[0] != '#':
line.strip()
smi, ans = line.split(',')
ans = float(ans)
mol = Chem.MolFromSmiles(smi)
mol = Chem.AddHs(mol)
calc = MolSurf.TPSA(mol)
self.assertTrue(
feq(calc, ans), 'bad TPSA for SMILES %s (%.2f != %.2f)' % (smi, calc, ans))
if __name__ == '__main__':
import sys, getopt, re
doLong = 0
if len(sys.argv) > 1:
args, extras = getopt.getopt(sys.argv[1:], 'l')
for arg, val in args:
if arg == '-l':
doLong = 1
sys.argv.remove('-l')
if doLong:
for methName in dir(TestCase):
if re.match('_test', methName):
newName = re.sub('_test', 'test', methName)
exec('TestCase.%s = TestCase.%s' % (newName, methName))
unittest.main()
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"""unit testing code for the Crippen clogp and MR calculators
"""
from __future__ import print_function
from rdkit import RDConfig
import unittest,sys,os
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Crippen
def feq(n1,n2,tol=1e-5):
return abs(n1-n2)<=tol
class TestCase(unittest.TestCase):
def setUp(self):
self.fName = os.path.join(RDConfig.RDCodeDir,'Chem/test_data','aromat_regress.txt')
self.fName2 = os.path.join(RDConfig.RDCodeDir,'Chem/test_data','NCI_aromat_regress.txt')
def _readData(self,fName):
d = []
lineNo=0
for line in open(fName,'r').xreadlines():
lineNo+=1
if len(line) and line[0] != '#':
splitL = line.split('\t')
if len(splitL)==4:
smi1,smi2,count,ats = splitL
d.append((lineNo,smi1,smi2,int(count),eval(ats)))
self.data = d
def test1(self,maxFailures=50):
self._readData(self.fName)
nMols = len(self.data)
nFailed = 0
for i in range(nMols):
lineNo,smi,smi2,tgtCount,tgtAts = self.data[i]
try:
mol = Chem.MolFromSmiles(smi)
if not mol: raise ValueError
except:
mol = None
print('failure(%d): '%lineNo,smi)
print('-----------------------------')
else:
count = 0
aroms = []
for at in mol.GetAtoms():
if at.GetIsAromatic():
aroms.append(at.GetIdx())
count+=1
if count != tgtCount:
print('Fail(%d): %s, %s'%(lineNo,smi,Chem.MolToSmiles(mol)))
print('\t %d != %d'%(count,tgtCount))
print('\t ',repr(aroms))
print('\t ',repr(tgtAts))
print('-----------------------------')
nFailed += 1
if nFailed >= maxFailures:
assert 0
def test2(self,maxFailures=50):
self._readData(self.fName2)
nMols = len(self.data)
nFailed = 0
for i in range(nMols):
lineNo,smi,smi2,tgtCount,tgtAts = self.data[i]
try:
mol = Chem.MolFromSmiles(smi)
if not mol: raise ValueError
except:
mol = None
print('failure(%d): '%lineNo,smi)
print('-----------------------------')
else:
count = 0
aroms = []
for at in mol.GetAtoms():
if at.GetIsAromatic():
aroms.append(at.GetIdx())
count+=1
if count != tgtCount:
print('Fail(%d): %s, %s'%(lineNo,smi,Chem.MolToSmiles(mol)))
print('\t %d != %d'%(count,tgtCount))
print('\t ',repr(aroms))
print('\t ',repr(tgtAts))
print('-----------------------------')
nFailed += 1
if nFailed >= maxFailures:
assert 0
if __name__ == '__main__':
unittest.main()
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"""unit testing code for the Crippen clogp and MR calculators
"""
from __future__ import print_function
from rdkit import RDConfig
import unittest, sys, os
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Crippen
def feq(n1, n2, tol=1e-5):
return abs(n1 - n2) <= tol
class TestCase(unittest.TestCase):
def setUp(self):
self.fName = os.path.join(RDConfig.RDCodeDir, 'Chem/test_data', 'aromat_regress.txt')
self.fName2 = os.path.join(RDConfig.RDCodeDir, 'Chem/test_data', 'NCI_aromat_regress.txt')
def _readData(self, fName):
d = []
lineNo = 0
for line in open(fName, 'r').xreadlines():
lineNo += 1
if len(line) and line[0] != '#':
splitL = line.split('\t')
if len(splitL) == 4:
smi1, smi2, count, ats = splitL
d.append((lineNo, smi1, smi2, int(count), eval(ats)))
self.data = d
def test1(self, maxFailures=50):
self._readData(self.fName)
nMols = len(self.data)
nFailed = 0
for i in range(nMols):
lineNo, smi, smi2, tgtCount, tgtAts = self.data[i]
mol = Chem.MolFromSmiles(smi)
if mol is None:
print('failure(%d): ' % lineNo, smi)
print('-----------------------------')
else:
count = 0
aroms = []
for at in mol.GetAtoms():
if at.GetIsAromatic():
aroms.append(at.GetIdx())
count += 1
if count != tgtCount:
print('Fail(%d): %s, %s' % (lineNo, smi, Chem.MolToSmiles(mol)))
print('\t %d != %d' % (count, tgtCount))
print('\t ', repr(aroms))
print('\t ', repr(tgtAts))
print('-----------------------------')
nFailed += 1
if nFailed >= maxFailures:
assert 0
def test2(self, maxFailures=50):
self._readData(self.fName2)
nMols = len(self.data)
nFailed = 0
for i in range(nMols):
lineNo, smi, smi2, tgtCount, tgtAts = self.data[i]
mol = Chem.MolFromSmiles(smi)
if mol is None:
print('failure(%d): ' % lineNo, smi)
print('-----------------------------')
else:
count = 0
aroms = []
for at in mol.GetAtoms():
if at.GetIsAromatic():
aroms.append(at.GetIdx())
count += 1
if count != tgtCount:
print('Fail(%d): %s, %s' % (lineNo, smi, Chem.MolToSmiles(mol)))
print('\t %d != %d' % (count, tgtCount))
print('\t ', repr(aroms))
print('\t ', repr(tgtAts))
print('-----------------------------')
nFailed += 1
if nFailed >= maxFailures:
assert 0
if __name__ == '__main__':
unittest.main()
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"""unit testing code for the database utilities
"""
from rdkit import RDConfig
import unittest, os, tempfile
from rdkit.Dbase import DbUtils
from rdkit.Dbase.DbConnection import DbConnect
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
self.baseDir = os.path.join(RDConfig.RDCodeDir, 'Dbase', 'test_data')
self.dbName = RDConfig.RDTestDatabase
if RDConfig.useSqlLite:
tmpf, tempName = tempfile.mkstemp(suffix='sqlt')
self.tempDbName = tempName
else:
self.tempDbName = '::RDTests'
self.colHeads = ('int_col', 'floatCol', 'strCol')
self.colTypes = ('integer', 'float', 'string')
def tearDown(self):
if RDConfig.useSqlLite and os.path.exists(self.tempDbName):
try:
os.unlink(self.tempDbName)
except:
import traceback
traceback.print_exc()
def _confirm(self, tblName, dbName=None):
if dbName is None:
dbName = self.dbName
conn = DbConnect(dbName, tblName)
res = conn.GetColumnNamesAndTypes()
assert len(res) == len(self.colHeads), 'bad number of columns'
names = [x[0] for x in res]
for i in range(len(names)):
assert names[i].upper() == self.colHeads[i].upper(), 'bad column head'
if RDConfig.useSqlLite:
# doesn't seem to be any column type info available
return
types = [x[1] for x in res]
for i in range(len(types)):
assert types[i] == self.colTypes[i], 'bad column type'
def test1Txt(self):
""" test reading from a text file """
with open(os.path.join(self.baseDir, 'dbtest.csv'), 'r') as inF:
tblName = 'fromtext'
DbUtils.TextFileToDatabase(self.tempDbName, tblName, inF)
self._confirm(tblName, dbName=self.tempDbName)
def test3Txt(self):
""" test reading from a text file including null markers"""
with open(os.path.join(self.baseDir, 'dbtest.nulls.csv'), 'r') as inF:
tblName = 'fromtext2'
DbUtils.TextFileToDatabase(self.tempDbName, tblName, inF, nullMarker='NA')
self._confirm(tblName, dbName=self.tempDbName)
def testGetData1(self):
""" basic functionality
"""
d = DbUtils.GetData(self.dbName, 'ten_elements', forceList=1)
assert len(d) == 10
assert tuple(d[0]) == (0, 11)
assert tuple(d[2]) == (4, 31)
with self.assertRaisesRegexp(IndexError, ""):
d[11]
def testGetData2(self):
""" using a RandomAccessDbResultSet
"""
d = DbUtils.GetData(self.dbName, 'ten_elements', forceList=0, randomAccess=1)
assert tuple(d[0]) == (0, 11)
assert tuple(d[2]) == (4, 31)
assert len(d) == 10
with self.assertRaisesRegexp(IndexError, ""):
d[11]
def testGetData3(self):
""" using a DbResultSet
"""
d = DbUtils.GetData(self.dbName, 'ten_elements', forceList=0, randomAccess=0)
with self.assertRaisesRegexp(TypeError, ""):
len(d)
rs = []
for thing in d:
rs.append(thing)
assert len(rs) == 10
assert tuple(rs[0]) == (0, 11)
assert tuple(rs[2]) == (4, 31)
def testGetData4(self):
""" using a RandomAccessDbResultSet with a Transform
"""
fn = lambda x: (x[0], x[1] * 2)
d = DbUtils.GetData(self.dbName, 'ten_elements', forceList=0, randomAccess=1, transform=fn)
assert tuple(d[0]) == (0, 22)
assert tuple(d[2]) == (4, 62)
assert len(d) == 10
with self.assertRaisesRegexp(IndexError, ""):
d[11]
def testGetData5(self):
""" using a DbResultSet with a Transform
"""
fn = lambda x: (x[0], x[1] * 2)
d = DbUtils.GetData(self.dbName, 'ten_elements', forceList=0, randomAccess=0, transform=fn)
with self.assertRaisesRegexp(TypeError, ""):
len(d)
rs = []
for thing in d:
rs.append(thing)
assert len(rs) == 10
assert tuple(rs[0]) == (0, 22)
assert tuple(rs[2]) == (4, 62)
if __name__ == '__main__':
unittest.main()
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"""unit testing code for the database utilities
"""
import os
import tempfile
import unittest
from six import StringIO
from rdkit import RDConfig
from rdkit.Dbase import DbUtils
from rdkit.Dbase.DbConnection import DbConnect
try:
from contextlib import redirect_stdout
except:
from rdkit.TestRunner import redirect_stdout
class TestCase(unittest.TestCase):
def setUp(self):
self.baseDir = os.path.join(RDConfig.RDCodeDir, 'Dbase', 'test_data')
self.dbName = RDConfig.RDTestDatabase
if RDConfig.useSqlLite:
_, tempName = tempfile.mkstemp(suffix='sqlt')
self.tempDbName = tempName
else:
self.tempDbName = '::RDTests'
self.colHeads = ('int_col', 'floatCol', 'strCol')
self.colTypes = ('integer', 'float', 'string')
def tearDown(self):
if RDConfig.useSqlLite and os.path.exists(self.tempDbName):
try:
os.unlink(self.tempDbName)
except:
import traceback
traceback.print_exc()
def _confirm(self, tblName, dbName=None, colHeads=None, colTypes=None):
dbName = dbName or self.dbName
colHeads = colHeads or self.colHeads
colTypes = colTypes or self.colTypes
conn = DbConnect(dbName, tblName)
res = conn.GetColumnNamesAndTypes()
assert len(res) == len(colHeads), 'bad number of columns'
names = [x[0] for x in res]
for i in range(len(names)):
assert names[i].upper() == colHeads[i].upper(), 'bad column head'
if RDConfig.useSqlLite:
# doesn't seem to be any column type info available
return
types = [x[1] for x in res]
for i in range(len(types)):
assert types[i] == colTypes[i], 'bad column type'
def test1Txt(self):
""" test reading from a text file """
with open(os.path.join(self.baseDir, 'dbtest.csv'), 'r') as inF:
tblName = 'fromtext'
f = StringIO()
with redirect_stdout(f):
DbUtils.TextFileToDatabase(self.tempDbName, tblName, inF)
self._confirm(tblName, dbName=self.tempDbName)
def test3Txt(self):
""" test reading from a text file including null markers"""
with open(os.path.join(self.baseDir, 'dbtest.nulls.csv'), 'r') as inF:
tblName = 'fromtext2'
f = StringIO()
with redirect_stdout(f):
DbUtils.TextFileToDatabase(self.tempDbName, tblName, inF, nullMarker='NA')
self._confirm(tblName, dbName=self.tempDbName)
def testGetData1(self):
""" basic functionality
"""
d = DbUtils.GetData(self.dbName, 'ten_elements', forceList=1)
assert len(d) == 10
assert tuple(d[0]) == (0, 11)
assert tuple(d[2]) == (4, 31)
with self.assertRaisesRegexp(IndexError, ""):
d[11]
def testGetData2(self):
""" using a RandomAccessDbResultSet
"""
d = DbUtils.GetData(self.dbName, 'ten_elements', forceList=0, randomAccess=1)
assert tuple(d[0]) == (0, 11)
assert tuple(d[2]) == (4, 31)
assert len(d) == 10
with self.assertRaisesRegexp(IndexError, ""):
d[11]
def testGetData3(self):
""" using a DbResultSet
"""
d = DbUtils.GetData(self.dbName, 'ten_elements', forceList=0, randomAccess=0)
with self.assertRaisesRegexp(TypeError, ""):
len(d)
rs = []
for thing in d:
rs.append(thing)
assert len(rs) == 10
assert tuple(rs[0]) == (0, 11)
assert tuple(rs[2]) == (4, 31)
def testGetData4(self):
""" using a RandomAccessDbResultSet with a Transform
"""
def fn(x):
return (x[0], x[1] * 2)
d = DbUtils.GetData(self.dbName, 'ten_elements', forceList=0, randomAccess=1, transform=fn)
assert tuple(d[0]) == (0, 22)
assert tuple(d[2]) == (4, 62)
assert len(d) == 10
with self.assertRaisesRegexp(IndexError, ""):
d[11]
def testGetData5(self):
""" using a DbResultSet with a Transform
"""
def fn(x):
return (x[0], x[1] * 2)
d = DbUtils.GetData(self.dbName, 'ten_elements', forceList=0, randomAccess=0, transform=fn)
with self.assertRaisesRegexp(TypeError, ""):
len(d)
rs = []
for thing in d:
rs.append(thing)
assert len(rs) == 10
assert tuple(rs[0]) == (0, 22)
assert tuple(rs[2]) == (4, 62)
def test_take(self):
self.assertEqual(list(DbUtils._take([1, 2, 3, 4], [2, 3])), [3, 4])
self.assertEqual(list(DbUtils._take([1, 2, 3, 4], [0, 3])), [1, 4])
def test_GetColumns(self):
d = DbUtils.GetColumns(self.dbName, 'ten_elements', 'val')
self.assertEqual(len(d), 10)
def test_GetData_where(self):
d = DbUtils.GetData(self.dbName, 'ten_elements_dups', forceList=0, randomAccess=0,
whereString='id<4')
self.assertEqual(len(list(d)), 4)
self.assertTrue(all(x[0] < 4 for x in d))
d = DbUtils.GetData(self.dbName, 'ten_elements_dups', forceList=0, randomAccess=0,
whereString='id<10')
self.assertEqual(len(list(d)), 10)
self.assertTrue(all(x[0] < 10 for x in d))
d = DbUtils.GetData(self.dbName, 'ten_elements_dups', removeDups=1, forceList=True)
self.assertEqual(len(list(d)), 10)
def test_DatabaseToText(self):
txt = DbUtils.DatabaseToText(self.dbName, 'ten_elements')
self.assertIn('id,val', txt)
self.assertIn('0,11', txt)
self.assertIn('18,101', txt)
self.assertEqual(len(txt.split('\n')), 11)
txt = DbUtils.DatabaseToText(self.dbName, 'ten_elements', fields='val')
self.assertNotIn('id', txt)
self.assertNotIn(',', txt)
txt = DbUtils.DatabaseToText(self.dbName, 'ten_elements', where='id<4')
self.assertIn('id,val', txt)
self.assertEqual(len(txt.split('\n')), 3)
def test_TypeFinder(self):
data = [('-', 1.45, 'abc', None), (20, 3, 'defgh', None)]
self.assertEqual(
DbUtils.TypeFinder(data, 2, 4, nullMarker='-'), [[int, 2], [float, 4], [str, 5], [-1, 1]])
def test_AdjustColHeadings(self):
headers = ['abc def', ' abc def', 'abc-def ', 'abc.def']
self.assertEqual(DbUtils._AdjustColHeadings(headers, 7), ['abc_def'] * 4)
f = StringIO()
with redirect_stdout(f):
headers = ['abc def', ' abc def', 'abc-def ', 'abc.def']
self.assertEqual(DbUtils._AdjustColHeadings(headers, 3), ['abc'] * 4)
self.assertIn('Heading', f.getvalue())
def test_GetTypeStrings(self):
headers = ['pk', 'a', 'b', 'c']
colTypes = [(int, 2), (int, 3), (float, 5), (str, 10)]
self.assertEqual(
DbUtils.GetTypeStrings(headers, colTypes),
['pk integer', 'a integer', 'b double precision', 'c varchar(10)'])
self.assertEqual(
DbUtils.GetTypeStrings(headers, colTypes, keyCol='pk'),
['pk integer not null primary key', 'a integer', 'b double precision', 'c varchar(10)'])
def test_DatabaseToDatabase(self):
tblName = 'db2db'
f = StringIO()
with redirect_stdout(f):
DbUtils.DatabaseToDatabase(self.dbName, 'ten_elements', self.tempDbName, tblName)
self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val'])
if __name__ == '__main__': # pragma: nocover
unittest.main()
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"""unit testing code for the EState fingerprinting
validation values are from the paper (JCICS _35_ 1039-1045 (1995))
"""
from __future__ import print_function
import unittest
import numpy
from rdkit import Chem
from rdkit.Chem import EState
from rdkit.Chem.EState import Fingerprinter
class TestCase(unittest.TestCase):
def setUp(self):
pass
def _validate(self,vals,tol=1e-2,show=0):
for smi,c,v in vals:
mol = Chem.MolFromSmiles(smi)
counts,vals = Fingerprinter.FingerprintMol(mol)
counts = counts[numpy.nonzero(counts)]
vals = vals[numpy.nonzero(vals)]
if show:
print(counts)
print(vals)
assert len(c)==len(counts),'bad count len for smiles: %s'%(smi)
assert len(v)==len(vals),'bad val len for smiles: %s'%(smi)
c = numpy.array(c)
assert max(abs(c-counts))<tol,'bad count for SMILES: %s'%(smi)
v = numpy.array(v)
assert max(abs(v-vals))<tol,'bad val for SMILES: %s'%(smi)
def test1(self):
""" molecules
"""
data = [
('c1[nH]cnc1CC(N)C(O)=O',[1,2,1,1,1,1,1,1,1,1],
[0.26,3.12,-0.86,-1.01,0.67,5.25,2.71,3.84,8.42,10.26]),
('NCCc1ccc(O)c(O)c1',[2,3,3,1,2],
[1.26,4.71,0.75,5.30,17.97]),
]
self._validate(data,show=0)
if __name__ == '__main__':
unittest.main()
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"""unit testing code for the EState indices
validation values are from the paper (JCICS _31_ 76-81 (1991))
"""
from __future__ import print_function
import unittest
import numpy
from rdkit import Chem
from rdkit.Chem import EState
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
pass
def _validate(self,vals,tol=1e-2,show=0):
for smi,ans in vals:
mol = Chem.MolFromSmiles(smi)
ans = numpy.array(ans)
inds = EState.EStateIndices(mol)
maxV = max(abs(ans-inds))
if show: print(inds)
assert maxV<tol,'bad EStates for smiles: %s'%(smi)
def test1(self):
""" simple molecules
"""
data = [
('CCCC',[2.18,1.32,1.32,2.18]),
('CCCCC',[2.21,1.34,1.39,1.34,2.21]),
('CCCCCCC',[2.24,1.36,1.42,1.44,1.42,1.36,2.24]),
('CCCCCCCCCC',[2.27,1.37,1.44,1.46,1.47,1.47,1.46,1.44,1.37,2.27]),
]
self._validate(data)
def test2(self):
""" isomers
"""
data = [
('CCCCCC',[2.23,1.36,1.41,1.41,1.36,2.23]),
('CCC(C)CC',[2.23,1.33,0.94,2.28,1.33,2.23]),
('CC(C)CCC',[2.25,0.90,2.25,1.38,1.33,2.22]),
('CC(C)(C)CC',[2.24,0.54,2.24,2.24,1.27,2.20]),
]
self._validate(data)
def test3(self):
""" heteroatoms
"""
data = [
('CCCCOCCCC',[2.18,1.24,1.21,0.95,5.31,0.95,1.21,1.24,2.18]),
('CCC(C)OC(C)CC',[2.15,1.12,0.43,2.12,5.54,0.43,2.12,1.12,2.15]),
('CC(C)(C)OC(C)(C)C',[2.07,-0.02,2.07,2.07,5.63,-0.02,2.07,2.07,2.07]),
('CC(C)CC',[2.22,0.88,2.22,1.31,2.20]),
('CC(C)CN',[2.10,0.66,2.10,0.81,5.17]),
('CC(C)CO',[1.97,0.44,1.97,0.31,8.14]),
('CC(C)CF',[1.85,0.22,1.85,-0.19,11.11]),
('CC(C)CCl',[2.09,0.65,2.09,0.78,5.34]),
('CC(C)CBr',[2.17,0.80,2.17,1.11,3.31]),
('CC(C)CI',[2.21,0.87,2.21,1.28,2.38]),
]
self._validate(data,show=0)
def test4(self):
""" more heteroatoms
"""
data = [
('CC(N)C(=O)O',[1.42,-0.73,4.84,-0.96,9.57,7.86]),
('CCOCC',[1.99,0.84,4.83,0.84,1.99]),
('CCSCC',[2.17,1.26,1.96,1.26,2.17]), #NOTE: this does not match the values in the paper
('CC(=O)OC',[1.36,-0.24,9.59,4.11,1.35]),
('CC(=S)OC',[1.73,0.59,4.47,4.48,1.56]),
]
self._validate(data,show=0)
def test5(self):
""" aromatics with heteroatoms
"""
data = [
('Fc1ccc(C)cc1',[12.09,-0.17,1.45,1.75,1.09,1.93,1.75,1.45]),
('Clc1ccc(C)cc1',[5.61,0.80,1.89,1.99,1.24,2.04,1.99,1.89]),
('Brc1ccc(C)cc1',[3.35,1.14,2.04,2.07,1.30,2.08,2.07,2.04]),
('Ic1ccc(C)cc1',[2.30,1.30,2.10,2.11,1.32,2.09,2.11,2.10]),
]
self._validate(data,show=0)
if __name__ == '__main__':
unittest.main()
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"""unit testing code for the EState indices
validation values are from the paper (JCICS _31_ 76-81 (1991))
"""
from __future__ import print_function
import unittest
from six import StringIO
import numpy as np
from rdkit import Chem
from rdkit.Chem import EState
class TestCase(unittest.TestCase):
def _compareEstates(self, val1, val2, msg, tol=1e-2):
maxV = max(abs(val1 - val2))
self.assertLess(maxV, tol, msg)
def _validate(self, vals, places=2, tol=1e-2, debug=False):
for smi, ans in vals:
ans = np.array(ans)
mol = Chem.MolFromSmiles(smi)
inds = EState.EStateIndices(mol)
if debug: # pragma: nocover
print(inds)
self._compareEstates(ans, inds, 'bad EStates for smiles: {0}'.format(smi), tol=tol)
self.assertLess(abs(EState.MaxEStateIndex(mol) - max(ans)), tol)
self.assertLess(abs(EState.MinEStateIndex(mol) - min(ans)), tol)
self.assertLess(abs(EState.MaxAbsEStateIndex(mol) - max(abs(ans))), tol)
self.assertLess(abs(EState.MinAbsEStateIndex(mol) - min(abs(ans))), tol)
def test_simpleMolecules(self):
data = [
('CCCC', [2.18, 1.32, 1.32, 2.18]),
('CCCCC', [2.21, 1.34, 1.39, 1.34, 2.21]),
('CCCCCCC', [2.24, 1.36, 1.42, 1.44, 1.42, 1.36, 2.24]),
('CCCCCCCCCC', [2.27, 1.37, 1.44, 1.46, 1.47, 1.47, 1.46, 1.44, 1.37, 2.27]),
]
self._validate(data)
def test_isomers(self):
data = [
('CCCCCC', [2.23, 1.36, 1.41, 1.41, 1.36, 2.23]),
('CCC(C)CC', [2.23, 1.33, 0.94, 2.28, 1.33, 2.23]),
('CC(C)CCC', [2.25, 0.90, 2.25, 1.38, 1.33, 2.22]),
('CC(C)(C)CC', [2.24, 0.54, 2.24, 2.24, 1.27, 2.20]),
]
self._validate(data)
def test_heteroatoms1(self):
data = [
('CCCCOCCCC', [2.18, 1.24, 1.21, 0.95, 5.31, 0.95, 1.21, 1.24, 2.18]),
('CCC(C)OC(C)CC', [2.15, 1.12, 0.43, 2.12, 5.54, 0.43, 2.12, 1.12, 2.15]),
('CC(C)(C)OC(C)(C)C', [2.07, -0.02, 2.07, 2.07, 5.63, -0.02, 2.07, 2.07, 2.07]),
('CC(C)CC', [2.22, 0.88, 2.22, 1.31, 2.20]),
('CC(C)CN', [2.10, 0.66, 2.10, 0.81, 5.17]),
('CC(C)CO', [1.97, 0.44, 1.97, 0.31, 8.14]),
('CC(C)CF', [1.85, 0.22, 1.85, -0.19, 11.11]),
('CC(C)CCl', [2.09, 0.65, 2.09, 0.78, 5.34]),
('CC(C)CBr', [2.17, 0.80, 2.17, 1.11, 3.31]),
('CC(C)CI', [2.21, 0.87, 2.21, 1.28, 2.38]),
]
self._validate(data, debug=False)
def test_heteroatoms2(self):
data = [
('CC(N)C(=O)O', [1.42, -0.73, 4.84, -0.96, 9.57, 7.86]),
('CCOCC', [1.99, 0.84, 4.83, 0.84, 1.99]),
('CCSCC', [2.17, 1.26, 1.96, 1.26, 2.17]), # NOTE: this doesn't match the values in the paper
('CC(=O)OC', [1.36, -0.24, 9.59, 4.11, 1.35]),
('CC(=S)OC', [1.73, 0.59, 4.47, 4.48, 1.56]),
]
self._validate(data, debug=False)
def test_aromatics(self):
# aromatics with heteroatoms
data = [
('Fc1ccc(C)cc1', [12.09, -0.17, 1.45, 1.75, 1.09, 1.93, 1.75, 1.45]),
('Clc1ccc(C)cc1', [5.61, 0.80, 1.89, 1.99, 1.24, 2.04, 1.99, 1.89]),
('Brc1ccc(C)cc1', [3.35, 1.14, 2.04, 2.07, 1.30, 2.08, 2.07, 2.04]),
('Ic1ccc(C)cc1', [2.30, 1.30, 2.10, 2.11, 1.32, 2.09, 2.11, 2.10]),
]
self._validate(data, debug=False)
def test_GetPrincipleQuantumNumber(self):
for principalQN, (nmin, nmax) in enumerate(
[(1, 2), (3, 10), (11, 18), (19, 36), (37, 54), (55, 86), (87, 120)], 1):
for n in range(nmin, nmax + 1):
self.assertEqual(EState.GetPrincipleQuantumNumber(n), principalQN)
def test_cacheEstate(self):
mol = Chem.MolFromSmiles('CCCC')
expected = [2.18, 1.32, 1.32, 2.18]
# The mol object has no information about E-states
self.assertFalse(hasattr(mol, '_eStateIndices'))
inds = EState.EStateIndices(mol)
self._compareEstates(inds, expected, 'cacheTest')
# We now have E-states stored with the molecule
self.assertTrue(hasattr(mol, '_eStateIndices'))
# Let's make sure that we skip the calculation next time if force is False
mol._eStateIndices = 'cached'
self.assertTrue(hasattr(mol, '_eStateIndices'))
inds = EState.EStateIndices(mol, force=False)
self.assertEqual(inds, 'cached')
# But with force (default) we calculate again
inds = EState.EStateIndices(mol)
self._compareEstates(inds, expected, 'cacheTest')
self._compareEstates(mol._eStateIndices, expected, 'cacheTest')
def test_exampleCode(self):
# We make sure that the example code runs
from rdkit.TestRunner import redirect_stdout
f = StringIO()
with redirect_stdout(f):
EState.EState._exampleCode()
s = f.getvalue()
self.assertIn('CC(N)C(=O)O', s)
if __name__ == '__main__': # pragma: nocover
unittest.main()
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"""unit testing code for the signatures
"""
from __future__ import print_function
import unittest
import os
from rdkit.six import next
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem.Pharm2D import Gobbi_Pharm2D,Generate
class TestCase(unittest.TestCase):
def setUp(self):
self.factory = Gobbi_Pharm2D.factory
def test1Sigs(self):
probes = [
('OCCC=O',{'HA':(1,((0,),(4,))),
'HD':(1,((0,),)),
'LH':(0,None),
'AR':(0,None),
'RR':(0,None),
'X':(0,None),
'BG':(0,None),
'AG':(0,None),
}
),
('OCCC(=O)O',{'HA':(1,((0,),(4,))),
'HD':(1,((0,),(5,))),
'LH':(0,None),
'AR':(0,None),
'RR':(0,None),
'X':(0,None),
'BG':(0,None),
'AG':(1,((3,),)),
}
),
('CCCN',{'HA':(1,((3,),)),
'HD':(1,((3,),)),
'LH':(0,None),
'AR':(0,None),
'RR':(0,None),
'X':(0,None),
'BG':(1,((3,),)),
'AG':(0,None),
}
),
('CCCCC',{'HA':(0,None),
'HD':(0,None),
'LH':(1,((1,),(3,))),
'AR':(0,None),
'RR':(0,None),
'X':(0,None),
'BG':(0,None),
'AG':(0,None),
}
),
('CC1CCC1',{'HA':(0,None),
'HD':(0,None),
'LH':(1,((1,),(3,))),
'AR':(0,None),
'RR':(1,((1,),)),
'X':(0,None),
'BG':(0,None),
'AG':(0,None),
}
),
('[SiH3]C1CCC1',{'HA':(0,None),
'HD':(0,None),
'LH':(1,((1,),)),
'AR':(0,None),
'RR':(1,((1,),)),
'X':(1,((0,),)),
'BG':(0,None),
'AG':(0,None),
}
),
('[SiH3]c1ccccc1',{'HA':(0,None),
'HD':(0,None),
'LH':(0,None),
'AR':(1,((1,),)),
'RR':(0,None),
'X':(1,((0,),)),
'BG':(0,None),
'AG':(0,None),
}
),
]
for smi,d in probes:
mol = Chem.MolFromSmiles(smi)
feats=self.factory.featFactory.GetFeaturesForMol(mol)
for k in d.keys():
shouldMatch,mapList=d[k]
feats=self.factory.featFactory.GetFeaturesForMol(mol,includeOnly=k)
if shouldMatch:
self.assertTrue(feats)
self.assertEqual(len(feats),len(mapList))
aids = [(x.GetAtomIds()[0],) for x in feats]
aids.sort()
self.assertEqual(tuple(aids),mapList)
def test2Sigs(self):
probes = [('O=CCC=O',(149,)),
('OCCC=O',(149,156)),
('OCCC(=O)O',(22, 29, 149, 154, 156, 184, 28822, 30134)),
]
for smi,tgt in probes:
sig = Generate.Gen2DFingerprint(Chem.MolFromSmiles(smi),self.factory)
self.assertEqual(len(sig),39972)
bs = tuple(sig.GetOnBits())
self.assertEqual(len(bs),len(tgt))
self.assertEqual(bs,tgt)
def testOrderBug(self):
sdFile = os.path.join(RDConfig.RDCodeDir,'Chem','Pharm2D','test_data','orderBug.sdf')
suppl = Chem.SDMolSupplier(sdFile)
m1 = next(suppl)
m2 = next(suppl)
sig1 = Generate.Gen2DFingerprint(m1,self.factory)
sig2 = Generate.Gen2DFingerprint(m2,self.factory)
ob1 = set(sig1.GetOnBits())
ob2 = set(sig2.GetOnBits())
self.assertEqual(sig1,sig2)
def testOrderBug2(self):
from rdkit.Chem import Randomize
from rdkit import DataStructs
probes = ['Oc1nc(Oc2ncccc2)ccc1']
for smi in probes:
m1 = Chem.MolFromSmiles(smi)
#m1.Debug()
sig1 = Generate.Gen2DFingerprint(m1,self.factory)
csmi = Chem.MolToSmiles(m1)
m2 = Chem.MolFromSmiles(csmi)
#m2.Debug()
sig2 = Generate.Gen2DFingerprint(m2,self.factory)
self.assertTrue(list(sig1.GetOnBits())==list(sig2.GetOnBits()),'%s %s'%(smi,csmi))
self.assertEqual(DataStructs.DiceSimilarity(sig1,sig2),1.0)
self.assertEqual(sig1,sig2)
for i in range(10):
m2 = Randomize.RandomizeMol(m1)
sig2 = Generate.Gen2DFingerprint(m2,self.factory)
if sig2!=sig1:
Generate._verbose=True
print('----------------')
sig1 = Generate.Gen2DFingerprint(m1,self.factory)
print('----------------')
sig2 = Generate.Gen2DFingerprint(m2,self.factory)
print('----------------')
print(Chem.MolToMolBlock(m1))
print('----------------')
print(Chem.MolToMolBlock(m2))
print('----------------')
s1 = set(sig1.GetOnBits())
s2= set(sig2.GetOnBits())
print(s1.difference(s2))
self.assertEqual(sig1,sig2)
def testBitInfo(self):
m = Chem.MolFromSmiles('OCC=CC(=O)O')
bi = {}
sig = Generate.Gen2DFingerprint(m,Gobbi_Pharm2D.factory,bitInfo=bi)
self.assertEqual(sig.GetNumOnBits(),len(bi))
self.assertEqual(list(sig.GetOnBits()),sorted(bi.keys()))
self.assertEqual(sorted(bi.keys()),[23, 30, 150, 154, 157, 185, 28878, 30184])
self.assertEqual(sorted(bi[28878]),[[(0,), (5,), (6,)]])
self.assertEqual(sorted(bi[157]),[[(0,), (6,)], [(5,), (0,)]])
if __name__ == '__main__':
unittest.main()
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"""unit testing code for the signatures
"""
import unittest
import os
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem.Pharm2D import Gobbi_Pharm2D,Generate
class TestCase(unittest.TestCase):
def setUp(self):
self.factory = Gobbi_Pharm2D.factory
def test1Sigs(self):
probes = [
('OCCC=O',{'HA':(1,((0,),(4,))),
'HD':(1,((0,),)),
'LH':(0,None),
'AR':(0,None),
'RR':(0,None),
'X':(0,None),
'BG':(0,None),
'AG':(0,None),
}
),
('OCCC(=O)O',{'HA':(1,((0,),(4,))),
'HD':(1,((0,),(5,))),
'LH':(0,None),
'AR':(0,None),
'RR':(0,None),
'X':(0,None),
'BG':(0,None),
'AG':(1,((3,),)),
}
),
('CCCN',{'HA':(1,((3,),)),
'HD':(1,((3,),)),
'LH':(0,None),
'AR':(0,None),
'RR':(0,None),
'X':(0,None),
'BG':(1,((3,),)),
'AG':(0,None),
}
),
('CCCCC',{'HA':(0,None),
'HD':(0,None),
'LH':(1,((1,),(3,))),
'AR':(0,None),
'RR':(0,None),
'X':(0,None),
'BG':(0,None),
'AG':(0,None),
}
),
('CC1CCC1',{'HA':(0,None),
'HD':(0,None),
'LH':(1,((1,),(3,))),
'AR':(0,None),
'RR':(1,((1,),)),
'X':(0,None),
'BG':(0,None),
'AG':(0,None),
}
),
('[SiH3]C1CCC1',{'HA':(0,None),
'HD':(0,None),
'LH':(1,((1,),)),
'AR':(0,None),
'RR':(1,((1,),)),
'X':(1,((0,),)),
'BG':(0,None),
'AG':(0,None),
}
),
('[SiH3]c1ccccc1',{'HA':(0,None),
'HD':(0,None),
'LH':(0,None),
'AR':(1,((1,),)),
'RR':(0,None),
'X':(1,((0,),)),
'BG':(0,None),
'AG':(0,None),
}
),
]
for smi,d in probes:
mol = Chem.MolFromSmiles(smi)
feats=self.factory.featFactory.GetFeaturesForMol(mol)
for k in d.keys():
shouldMatch,mapList=d[k]
feats=self.factory.featFactory.GetFeaturesForMol(mol,includeOnly=k)
if shouldMatch:
self.failUnless(feats)
self.failUnlessEqual(len(feats),len(mapList))
aids = [(x.GetAtomIds()[0],) for x in feats]
aids.sort()
self.failUnlessEqual(tuple(aids),mapList)
def test2Sigs(self):
probes = [('O=CCC=O',(149,)),
('OCCC=O',(149,156)),
('OCCC(=O)O',(22, 29, 149, 154, 156, 184, 28822, 30134)),
]
for smi,tgt in probes:
sig = Generate.Gen2DFingerprint(Chem.MolFromSmiles(smi),self.factory)
self.failUnlessEqual(len(sig),39972)
bs = tuple(sig.GetOnBits())
self.failUnlessEqual(len(bs),len(tgt))
self.failUnlessEqual(bs,tgt)
def testOrderBug(self):
sdFile = os.path.join(RDConfig.RDCodeDir,'Chem','Pharm2D','test_data','orderBug.sdf')
suppl = Chem.SDMolSupplier(sdFile)
m1 =suppl.next()
m2 = suppl.next()
sig1 = Generate.Gen2DFingerprint(m1,self.factory)
sig2 = Generate.Gen2DFingerprint(m2,self.factory)
ob1 = set(sig1.GetOnBits())
ob2 = set(sig2.GetOnBits())
self.failUnlessEqual(sig1,sig2)
def testOrderBug2(self):
from rdkit.Chem import Randomize
from rdkit import DataStructs
probes = ['Oc1nc(Oc2ncccc2)ccc1']
for smi in probes:
m1 = Chem.MolFromSmiles(smi)
#m1.Debug()
sig1 = Generate.Gen2DFingerprint(m1,self.factory)
csmi = Chem.MolToSmiles(m1)
m2 = Chem.MolFromSmiles(csmi)
#m2.Debug()
sig2 = Generate.Gen2DFingerprint(m2,self.factory)
self.failUnless(list(sig1.GetOnBits())==list(sig2.GetOnBits()),'%s %s'%(smi,csmi))
self.failUnlessEqual(DataStructs.DiceSimilarity(sig1,sig2),1.0)
self.failUnlessEqual(sig1,sig2)
for i in range(10):
m2 = Randomize.RandomizeMol(m1)
sig2 = Generate.Gen2DFingerprint(m2,self.factory)
if sig2!=sig1:
Generate._verbose=True
print '----------------'
sig1 = Generate.Gen2DFingerprint(m1,self.factory)
print '----------------'
sig2 = Generate.Gen2DFingerprint(m2,self.factory)
print '----------------'
print Chem.MolToMolBlock(m1)
print '----------------'
print Chem.MolToMolBlock(m2)
print '----------------'
s1 = set(sig1.GetOnBits())
s2= set(sig2.GetOnBits())
print s1.difference(s2)
self.failUnlessEqual(sig1,sig2)
if __name__ == '__main__':
unittest.main()
| {
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""" utility functionality for the 2D pharmacophores code
See Docs/Chem/Pharm2D.triangles.jpg for an illustration of the way
pharmacophores are broken into triangles and labelled.
See Docs/Chem/Pharm2D.signatures.jpg for an illustration of bit
numbering
"""
import numpy
#
# number of points in a scaffold -> sequence of distances (p1,p2) in
# the scaffold
#
nPointDistDict = {
2: ((0,1),),
3: ((0,1),(0,2),
(1,2)),
4: ((0,1),(0,2),(0,3),
(1,2),(2,3)),
5: ((0,1),(0,2),(0,3),(0,4),
(1,2),(2,3),(3,4)),
6: ((0,1),(0,2),(0,3),(0,4),(0,5),
(1,2),(2,3),(3,4),(4,5)),
7: ((0,1),(0,2),(0,3),(0,4),(0,5),(0,6),
(1,2),(2,3),(3,4),(4,5),(5,6)),
8: ((0,1),(0,2),(0,3),(0,4),(0,5),(0,6),(0,7),
(1,2),(2,3),(3,4),(4,5),(5,6),(6,7)),
9: ((0,1),(0,2),(0,3),(0,4),(0,5),(0,6),(0,7),(0,8),
(1,2),(2,3),(3,4),(4,5),(5,6),(6,7),(7,8)),
10: ((0,1),(0,2),(0,3),(0,4),(0,5),(0,6),(0,7),(0,8),(0,9),
(1,2),(2,3),(3,4),(4,5),(5,6),(6,7),(7,8),(8,9)),
}
#
# number of distances in a scaffold -> number of points in the scaffold
#
nDistPointDict = {
1:2,
3:3,
5:4,
7:5,
9:6,
11:7,
13:8,
15:9,
17:10,
}
_trianglesInPharmacophore = {}
def GetTriangles(nPts):
""" returns a tuple with the distance indices for
triangles composing an nPts-pharmacophore
"""
global _trianglesInPharmacophore
if nPts < 3: return []
res = _trianglesInPharmacophore.get(nPts,[])
if not res:
idx1,idx2,idx3=(0,1,nPts-1)
while idx1<nPts-2:
res.append((idx1,idx2,idx3))
idx1 += 1
idx2 += 1
idx3 += 1
res = tuple(res)
_trianglesInPharmacophore[nPts] = res
return res
def _fact(x):
if x <= 1:
return 1
accum = 1
for i in range(x):
accum *= i+1
return accum
def BinsTriangleInequality(d1,d2,d3):
""" checks the triangle inequality for combinations
of distance bins.
the general triangle inequality is:
d1 + d2 >= d3
the conservative binned form of this is:
d1(upper) + d2(upper) >= d3(lower)
"""
if d1[1]+d2[1]<d3[0]: return False
if d2[1]+d3[1]<d1[0]: return False
if d3[1]+d1[1]<d2[0]: return False
return True
def ScaffoldPasses(combo,bins=None):
""" checks the scaffold passed in to see if all
contributing triangles can satisfy the triangle inequality
the scaffold itself (encoded in combo) is a list of binned distances
"""
# this is the number of points in the pharmacophore
nPts = nDistPointDict[len(combo)]
tris = GetTriangles(nPts)
for tri in tris:
ds = [bins[combo[x]] for x in tri]
if not BinsTriangleInequality(ds[0],ds[1],ds[2]):
return False
return True
_numCombDict = {}
def NumCombinations(nItems,nSlots):
""" returns the number of ways to fit nItems into nSlots
We assume that (x,y) and (y,x) are equivalent, and
(x,x) is allowed.
General formula is, for N items and S slots:
res = (N+S-1)! / ( (N-1)! * S! )
"""
global _numCombDict
res = _numCombDict.get((nItems,nSlots),-1)
if res == -1:
res = _fact(nItems+nSlots-1) / (_fact(nItems-1)*_fact(nSlots))
_numCombDict[(nItems,nSlots)] = res
return res
_verbose = 0
_countCache={}
def CountUpTo(nItems,nSlots,vs,idx=0,startAt=0):
""" Figures out where a given combination of indices would
occur in the combinatorial explosion generated by _GetIndexCombinations_
**Arguments**
- nItems: the number of items to distribute
- nSlots: the number of slots in which to distribute them
- vs: a sequence containing the values to find
- idx: used in the recursion
- startAt: used in the recursion
**Returns**
an integer
"""
global _countCache
if _verbose:
print ' '*idx,'CountUpTo(%d)'%idx,vs[idx],startAt
if idx==0 and _countCache.has_key((nItems,nSlots,tuple(vs))):
return _countCache[(nItems,nSlots,tuple(vs))]
elif idx >= nSlots:
accum = 0
elif idx == nSlots-1:
accum = vs[idx]-startAt
else:
accum = 0
# get the digit at idx correct
for i in range(startAt,vs[idx]):
nLevsUnder = nSlots-idx-1
nValsOver = nItems-i
if _verbose:
print ' '*idx,' ',i,nValsOver,nLevsUnder,\
NumCombinations(nValsOver,nLevsUnder)
accum += NumCombinations(nValsOver,nLevsUnder)
accum += CountUpTo(nItems,nSlots,vs,idx+1,vs[idx])
if _verbose: print ' '*idx,'>',accum
if idx == 0:
_countCache[(nItems,nSlots,tuple(vs))] = accum
return accum
_indexCombinations={}
def GetIndexCombinations(nItems,nSlots,slot=0,lastItemVal=0):
""" Generates all combinations of nItems in nSlots without including
duplicates
**Arguments**
- nItems: the number of items to distribute
- nSlots: the number of slots in which to distribute them
- slot: used in recursion
- lastItemVal: used in recursion
**Returns**
a list of lists
"""
global _indexCombinations
if not slot and _indexCombinations.has_key((nItems,nSlots)):
res = _indexCombinations[(nItems,nSlots)]
elif slot >= nSlots:
res = []
elif slot == nSlots-1:
res = [[x] for x in range(lastItemVal,nItems)]
else:
res = []
for x in range(lastItemVal,nItems):
tmp = GetIndexCombinations(nItems,nSlots,slot+1,x)
for entry in tmp:
res.append([x]+entry)
if not slot:
_indexCombinations[(nItems,nSlots)] = res
return res
def GetAllCombinations(choices,noDups=1,which=0):
""" Does the combinatorial explosion of the possible combinations
of the elements of _choices_.
**Arguments**
- choices: sequence of sequences with the elements to be enumerated
- noDups: (optional) if this is nonzero, results with duplicates,
e.g. (1,1,0), will not be generated
- which: used in recursion
**Returns**
a list of lists
>>> GetAllCombinations([(0,),(1,),(2,)])
[[0, 1, 2]]
>>> GetAllCombinations([(0,),(1,3),(2,)])
[[0, 1, 2], [0, 3, 2]]
>>> GetAllCombinations([(0,1),(1,3),(2,)])
[[0, 1, 2], [0, 3, 2], [1, 3, 2]]
"""
if which >= len(choices):
res = []
elif which == len(choices)-1:
res = [[x] for x in choices[which]]
else:
res = []
tmp = GetAllCombinations(choices,noDups=noDups,
which=which+1)
for thing in choices[which]:
for other in tmp:
if not noDups or thing not in other:
res.append([thing]+other)
return res
def GetUniqueCombinations(choices,classes,which=0):
""" Does the combinatorial explosion of the possible combinations
of the elements of _choices_.
"""
assert len(choices)==len(classes)
if which >= len(choices):
res = []
elif which == len(choices)-1:
res = [[(classes[which],x)] for x in choices[which]]
else:
res = []
tmp = GetUniqueCombinations(choices,classes,
which=which+1)
for thing in choices[which]:
for other in tmp:
idxThere=0
for x in other:
if x[1]==thing:idxThere+=1
if not idxThere:
newL = [(classes[which],thing)]+other
newL.sort()
if newL not in res:
res.append(newL)
return res
def UniquifyCombinations(combos):
""" uniquifies the combinations in the argument
**Arguments**:
- combos: a sequence of sequences
**Returns**
- a list of tuples containing the unique combos
"""
print '>>> u:',combos
resD = {}
for combo in combos:
k = combo[:]
k.sort()
resD[tuple(k)] = tuple(combo)
print ' >>> u:',resD.values()
return resD.values()
def GetPossibleScaffolds(nPts,bins,useTriangleInequality=True):
""" gets all realizable scaffolds (passing the triangle inequality) with the
given number of points and returns them as a list of tuples
"""
if nPts < 2:
res = 0
elif nPts == 2:
res = [(x,) for x in range(len(bins))]
else:
nDists = len(nPointDistDict[nPts])
combos = GetAllCombinations([range(len(bins))]*nDists,noDups=0)
res = []
for combo in combos:
if not useTriangleInequality or ScaffoldPasses(combo,bins):
res.append(tuple(combo))
return res
def OrderTriangle(featIndices,dists):
"""
put the distances for a triangle into canonical order
It's easy if the features are all different:
>>> OrderTriangle([0,2,4],[1,2,3])
([0, 2, 4], [1, 2, 3])
It's trickiest if they are all the same:
>>> OrderTriangle([0,0,0],[1,2,3])
([0, 0, 0], [3, 2, 1])
>>> OrderTriangle([0,0,0],[2,1,3])
([0, 0, 0], [3, 2, 1])
>>> OrderTriangle([0,0,0],[1,3,2])
([0, 0, 0], [3, 2, 1])
>>> OrderTriangle([0,0,0],[3,1,2])
([0, 0, 0], [3, 2, 1])
>>> OrderTriangle([0,0,0],[3,2,1])
([0, 0, 0], [3, 2, 1])
>>> OrderTriangle([0,0,1],[3,2,1])
([0, 0, 1], [3, 2, 1])
>>> OrderTriangle([0,0,1],[1,3,2])
([0, 0, 1], [1, 3, 2])
>>> OrderTriangle([0,0,1],[1,2,3])
([0, 0, 1], [1, 3, 2])
>>> OrderTriangle([0,0,1],[1,3,2])
([0, 0, 1], [1, 3, 2])
"""
if len(featIndices)!=3: raise ValueError,'bad indices'
if len(dists)!=3: raise ValueError,'bad dists'
fs = set(featIndices)
if len(fs)==3:
return featIndices,dists
dSums=[0]*3
dSums[0] = dists[0]+dists[1]
dSums[1] = dists[0]+dists[2]
dSums[2] = dists[1]+dists[2]
mD = max(dSums)
if len(fs)==1:
if dSums[0]==mD:
if dists[0]>dists[1]:
ireorder=(0,1,2)
dreorder=(0,1,2)
else:
ireorder=(0,2,1)
dreorder=(1,0,2)
elif dSums[1]==mD:
if dists[0]>dists[2]:
ireorder=(1,0,2)
dreorder=(0,2,1)
else:
ireorder=(1,2,0)
dreorder=(2,0,1)
else:
if dists[1]>dists[2]:
ireorder = (2,0,1)
dreorder=(1,2,0)
else:
ireorder = (2,1,0)
dreorder=(2,1,0)
else:
# two classes
if featIndices[0]==featIndices[1]:
if dists[1]>dists[2]:
ireorder=(0,1,2)
dreorder=(0,1,2)
else:
ireorder=(1,0,2)
dreorder=(0,2,1)
elif featIndices[0]==featIndices[2]:
if dists[0]>dists[2]:
ireorder=(0,1,2)
dreorder=(0,1,2)
else:
ireorder=(2,1,0)
dreorder=(2,1,0)
else: #featIndices[1]==featIndices[2]:
if dists[0]>dists[1]:
ireorder=(0,1,2)
dreorder=(0,1,2)
else:
ireorder=(0,2,1)
dreorder=(1,0,2)
dists = [dists[x] for x in dreorder]
featIndices = [featIndices[x] for x in ireorder]
return featIndices,dists
#------------------------------------
#
# doctest boilerplate
#
def _test():
import doctest,sys
return doctest.testmod(sys.modules["__main__"])
if __name__ == '__main__':
import sys
failed,tried = _test()
sys.exit(failed)
| {
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"path": "rdkit/Chem/Pharm2D/Utils.py",
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""" Atom-based calculation of LogP and MR using Crippen's approach
Reference:
S. A. Wildman and G. M. Crippen *JCICS* _39_ 868-873 (1999)
"""
from __future__ import print_function
import os
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
import numpy
_smartsPatterns = {}
_patternOrder = []
# this is the file containing the atom contributions
defaultPatternFileName = os.path.join(RDConfig.RDDataDir,'Crippen.txt')
def _ReadPatts(fileName):
""" *Internal Use Only*
parses the pattern list from the data file
"""
patts = {}
order = []
with open(fileName,'r') as f:
lines = f.readlines()
for line in lines:
if line[0] != '#':
splitLine = line.split('\t')
if len(splitLine)>=4 and splitLine[0] != '':
sma = splitLine[1]
if sma!='SMARTS':
sma.replace('"','')
p = Chem.MolFromSmarts(sma)
if p:
if len(splitLine[0])>1 and splitLine[0][1] not in 'S0123456789':
cha = splitLine[0][:2]
else:
cha = splitLine[0][0]
logP = float(splitLine[2])
if splitLine[3] != '':
mr = float(splitLine[3])
else:
mr = 0.0
if cha not in order:
order.append(cha)
l = patts.get(cha,[])
l.append((sma,p,logP,mr))
patts[cha] = l
else:
print('Problems parsing smarts: %s'%(sma))
return order,patts
_GetAtomContribs=rdMolDescriptors._CalcCrippenContribs
def _pyGetAtomContribs(mol,patts=None,order=None,verbose=0,force=0):
""" *Internal Use Only*
calculates atomic contributions to the LogP and MR values
if the argument *force* is not set, we'll use the molecules stored
_crippenContribs value when possible instead of re-calculating.
**Note:** Changes here affect the version numbers of MolLogP and MolMR
as well as the VSA descriptors in Chem.MolSurf
"""
if not force and hasattr(mol,'_crippenContribs'):
return mol._crippenContribs
if patts is None:
patts = _smartsPatterns
order = _patternOrder
nAtoms = mol.GetNumAtoms()
atomContribs = [(0.,0.)]*nAtoms
doneAtoms=[0]*nAtoms
nAtomsFound=0
done = False
for cha in order:
pattVect = patts[cha]
for sma,patt,logp,mr in pattVect:
#print('try:',entry[0])
for match in mol.GetSubstructMatches(patt,False,False):
firstIdx = match[0]
if not doneAtoms[firstIdx]:
doneAtoms[firstIdx]=1
atomContribs[firstIdx] = (logp,mr)
if verbose:
print('\tAtom %d: %s %4.4f %4.4f'%(match[0],sma,logp,mr))
nAtomsFound+=1
if nAtomsFound>=nAtoms:
done=True
break
if done: break
mol._crippenContribs = atomContribs
return atomContribs
def _Init():
global _smartsPatterns,_patternOrder
if _smartsPatterns == {}:
_patternOrder,_smartsPatterns = _ReadPatts(defaultPatternFileName)
def _pyMolLogP(inMol,patts=None,order=None,verbose=0,addHs=1):
""" DEPRECATED
"""
if addHs < 0:
mol = Chem.AddHs(inMol,1)
elif addHs > 0:
mol = Chem.AddHs(inMol,0)
else:
mol = inMol
if patts is None:
global _smartsPatterns,_patternOrder
if _smartsPatterns == {}:
_patternOrder,_smartsPatterns = _ReadPatts(defaultPatternFileName)
patts = _smartsPatterns
order = _patternOrder
atomContribs = _pyGetAtomContribs(mol,patts,order,verbose=verbose)
return numpy.sum(atomContribs,0)[0]
_pyMolLogP.version="1.1.0"
def _pyMolMR(inMol,patts=None,order=None,verbose=0,addHs=1):
""" DEPRECATED
"""
if addHs < 0:
mol = Chem.AddHs(inMol,1)
elif addHs > 0:
mol = Chem.AddHs(inMol,0)
else:
mol = inMol
if patts is None:
global _smartsPatterns,_patternOrder
if _smartsPatterns == {}:
_patternOrder,_smartsPatterns = _ReadPatts(defaultPatternFileName)
patts = _smartsPatterns
order = _patternOrder
atomContribs = _pyGetAtomContribs(mol,patts,order,verbose=verbose)
return numpy.sum(atomContribs,0)[1]
_pyMolMR.version="1.1.0"
MolLogP=lambda *x,**y:rdMolDescriptors.CalcCrippenDescriptors(*x,**y)[0]
MolLogP.version=rdMolDescriptors._CalcCrippenDescriptors_version
MolLogP.__doc__=""" Wildman-Crippen LogP value
Uses an atom-based scheme based on the values in the paper:
S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999)
**Arguments**
- inMol: a molecule
- addHs: (optional) toggles adding of Hs to the molecule for the calculation.
If true, hydrogens will be added to the molecule and used in the calculation.
"""
MolMR=lambda *x,**y:rdMolDescriptors.CalcCrippenDescriptors(*x,**y)[1]
MolMR.version=rdMolDescriptors._CalcCrippenDescriptors_version
MolMR.__doc__=""" Wildman-Crippen MR value
Uses an atom-based scheme based on the values in the paper:
S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999)
**Arguments**
- inMol: a molecule
- addHs: (optional) toggles adding of Hs to the molecule for the calculation.
If true, hydrogens will be added to the molecule and used in the calculation.
"""
if __name__=='__main__':
import sys
if len(sys.argv):
ms = []
verbose=0
if '-v' in sys.argv:
verbose=1
sys.argv.remove('-v')
for smi in sys.argv[1:]:
ms.append((smi,Chem.MolFromSmiles(smi)))
for smi,m in ms:
print('Mol: %s'%(smi))
logp = MolLogP(m,verbose=verbose)
print('----')
mr = MolMR(m,verbose=verbose)
print('Res:',logp,mr)
newM = Chem.AddHs(m)
logp = MolLogP(newM,addHs=0)
mr = MolMR(newM,addHs=0)
print('\t',logp,mr)
print('-*-*-*-*-*-*-*-*')
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""" Atom-based calculation of LogP and MR using Crippen's approach
Reference:
S. A. Wildman and G. M. Crippen *JCICS* _39_ 868-873 (1999)
"""
import os
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
import numpy
_smartsPatterns = {}
_patternOrder = []
# this is the file containing the atom contributions
defaultPatternFileName = os.path.join(RDConfig.RDDataDir,'Crippen.txt')
def _ReadPatts(fileName):
""" *Internal Use Only*
parses the pattern list from the data file
"""
patts = {}
order = []
for line in open(fileName,'r').xreadlines():
if line[0] != '#':
splitLine = line.split('\t')
if len(splitLine)>=4 and splitLine[0] != '':
sma = splitLine[1]
if sma!='SMARTS':
sma.replace('"','')
try:
p = Chem.MolFromSmarts(sma)
except:
pass
else:
if p:
if len(splitLine[0])>1 and splitLine[0][1] not in 'S0123456789':
cha = splitLine[0][:2]
else:
cha = splitLine[0][0]
logP = float(splitLine[2])
if splitLine[3] != '':
mr = float(splitLine[3])
else:
mr = 0.0
if cha not in order:
order.append(cha)
l = patts.get(cha,[])
l.append((sma,p,logP,mr))
patts[cha] = l
else:
print 'Problems parsing smarts: %s'%(sma)
return order,patts
_GetAtomContribs=rdMolDescriptors._CalcCrippenContribs
def _pyGetAtomContribs(mol,patts=None,order=None,verbose=0,force=0):
""" *Internal Use Only*
calculates atomic contributions to the LogP and MR values
if the argument *force* is not set, we'll use the molecules stored
_crippenContribs value when possible instead of re-calculating.
**Note:** Changes here affect the version numbers of MolLogP and MolMR
as well as the VSA descriptors in Chem.MolSurf
"""
if not force and hasattr(mol,'_crippenContribs'):
return mol._crippenContribs
if patts is None:
patts = _smartsPatterns
order = _patternOrder
nAtoms = mol.GetNumAtoms()
atomContribs = [(0.,0.)]*nAtoms
doneAtoms=[0]*nAtoms
nAtomsFound=0
done = False
for cha in order:
pattVect = patts[cha]
for sma,patt,logp,mr in pattVect:
#print 'try:',entry[0]
for match in mol.GetSubstructMatches(patt,False,False):
firstIdx = match[0]
if not doneAtoms[firstIdx]:
doneAtoms[firstIdx]=1
atomContribs[firstIdx] = (logp,mr)
if verbose:
print '\tAtom %d: %s %4.4f %4.4f'%(match[0],sma,logp,mr)
nAtomsFound+=1
if nAtomsFound>=nAtoms:
done=True
break
if done: break
mol._crippenContribs = atomContribs
return atomContribs
def _Init():
global _smartsPatterns,_patternOrder
if _smartsPatterns == {}:
_patternOrder,_smartsPatterns = _ReadPatts(defaultPatternFileName)
def _pyMolLogP(inMol,patts=None,order=None,verbose=0,addHs=1):
""" DEPRECATED
"""
if addHs < 0:
mol = Chem.AddHs(inMol,1)
elif addHs > 0:
mol = Chem.AddHs(inMol,0)
else:
mol = inMol
if patts is None:
global _smartsPatterns,_patternOrder
if _smartsPatterns == {}:
_patternOrder,_smartsPatterns = _ReadPatts(defaultPatternFileName)
patts = _smartsPatterns
order = _patternOrder
atomContribs = _pyGetAtomContribs(mol,patts,order,verbose=verbose)
return numpy.sum(atomContribs,0)[0]
_pyMolLogP.version="1.1.0"
def _pyMolMR(inMol,patts=None,order=None,verbose=0,addHs=1):
""" DEPRECATED
"""
if addHs < 0:
mol = Chem.AddHs(inMol,1)
elif addHs > 0:
mol = Chem.AddHs(inMol,0)
else:
mol = inMol
if patts is None:
global _smartsPatterns,_patternOrder
if _smartsPatterns == {}:
_patternOrder,_smartsPatterns = _ReadPatts(defaultPatternFileName)
patts = _smartsPatterns
order = _patternOrder
atomContribs = _pyGetAtomContribs(mol,patts,order,verbose=verbose)
return numpy.sum(atomContribs,0)[1]
_pyMolMR.version="1.1.0"
MolLogP=lambda *x,**y:rdMolDescriptors.CalcCrippenDescriptors(*x,**y)[0]
MolLogP.version=rdMolDescriptors._CalcCrippenDescriptors_version
MolLogP.__doc__=""" Wildman-Crippen LogP value
Uses an atom-based scheme based on the values in the paper:
S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999)
**Arguments**
- inMol: a molecule
- addHs: (optional) toggles adding of Hs to the molecule for the calculation.
If true, hydrogens will be added to the molecule and used in the calculation.
"""
MolMR=lambda *x,**y:rdMolDescriptors.CalcCrippenDescriptors(*x,**y)[1]
MolMR.version=rdMolDescriptors._CalcCrippenDescriptors_version
MolMR.__doc__=""" Wildman-Crippen MR value
Uses an atom-based scheme based on the values in the paper:
S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999)
**Arguments**
- inMol: a molecule
- addHs: (optional) toggles adding of Hs to the molecule for the calculation.
If true, hydrogens will be added to the molecule and used in the calculation.
"""
if __name__=='__main__':
import sys
if len(sys.argv):
ms = []
verbose=0
if '-v' in sys.argv:
verbose=1
sys.argv.remove('-v')
for smi in sys.argv[1:]:
ms.append((smi,Chem.MolFromSmiles(smi)))
for smi,m in ms:
print 'Mol: %s'%(smi)
logp = MolLogP(m,verbose=verbose)
print '----'
mr = MolMR(m,verbose=verbose)
print 'Res:',logp,mr
newM = Chem.AddHs(m)
logp = MolLogP(newM,addHs=0)
mr = MolMR(newM,addHs=0)
print '\t',logp,mr
print '-*-*-*-*-*-*-*-*'
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""" command line utility to report on the contributions of descriptors to
tree-based composite models
Usage: AnalyzeComposite [optional args] <models>
<models>: file name(s) of pickled composite model(s)
(this is the name of the db table if using a database)
Optional Arguments:
-n number: the number of levels of each model to consider
-d dbname: the database from which to read the models
-N Note: the note string to search for to pull models from the database
-v: be verbose whilst screening
"""
from __future__ import print_function
import numpy
import sys
from rdkit.six.moves import cPickle
from rdkit.ML.DecTree import TreeUtils,Tree
from rdkit.ML.Data import Stats
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.ML import ScreenComposite
__VERSION_STRING="2.2.0"
def ProcessIt(composites,nToConsider=3,verbose=0):
composite=composites[0]
nComposites =len(composites)
ns = composite.GetDescriptorNames()
#nDesc = len(ns)-2
if len(ns)>2:
globalRes = {}
nDone = 1
descNames = {}
for composite in composites:
if verbose > 0:
print('#------------------------------------')
print('Doing: ',nDone)
nModels = len(composite)
nDone += 1
res = {}
for i in range(len(composite)):
model = composite.GetModel(i)
if isinstance(model,Tree.TreeNode):
levels = TreeUtils.CollectLabelLevels(model,{},0,nToConsider)
TreeUtils.CollectDescriptorNames(model,descNames,0,nToConsider)
for descId in levels.keys():
v = res.get(descId,numpy.zeros(nToConsider,numpy.float))
v[levels[descId]] += 1./nModels
res[descId] = v
for k in res:
v = globalRes.get(k,numpy.zeros(nToConsider,numpy.float))
v += res[k]/nComposites
globalRes[k] = v
if verbose > 0:
for k in res.keys():
name = descNames[k]
strRes = ', '.join(['%4.2f'%x for x in res[k]])
print('%s,%s,%5.4f'%(name,strRes,sum(res[k])))
print()
if verbose >= 0:
print('# Average Descriptor Positions')
retVal = []
for k in globalRes.keys():
name = descNames[k]
if verbose >= 0:
strRes = ', '.join(['%4.2f'%x for x in globalRes[k]])
print('%s,%s,%5.4f'%(name,strRes,sum(globalRes[k])))
tmp = [name]
tmp.extend(globalRes[k])
tmp.append(sum(globalRes[k]))
retVal.append(tmp)
if verbose >= 0:
print()
else:
retVal = []
return retVal
def ErrorStats(conn,where,enrich=1):
fields = 'overall_error,holdout_error,overall_result_matrix,holdout_result_matrix,overall_correct_conf,overall_incorrect_conf,holdout_correct_conf,holdout_incorrect_conf'
try:
data = conn.GetData(fields=fields,where=where)
except:
import traceback
traceback.print_exc()
return None
nPts = len(data)
if not nPts:
sys.stderr.write('no runs found\n')
return None
overall = numpy.zeros(nPts,numpy.float)
overallEnrich = numpy.zeros(nPts,numpy.float)
oCorConf = 0.0
oInCorConf = 0.0
holdout = numpy.zeros(nPts,numpy.float)
holdoutEnrich = numpy.zeros(nPts,numpy.float)
hCorConf = 0.0
hInCorConf = 0.0
overallMatrix = None
holdoutMatrix = None
for i in range(nPts):
if data[i][0] is not None:
overall[i] = data[i][0]
oCorConf += data[i][4]
oInCorConf += data[i][5]
if data[i][1] is not None:
holdout[i] = data[i][1]
haveHoldout=1
else:
haveHoldout=0
tmpOverall = 1.*eval(data[i][2])
if enrich >=0:
overallEnrich[i] = ScreenComposite.CalcEnrichment(tmpOverall,tgt=enrich)
if haveHoldout:
tmpHoldout = 1.*eval(data[i][3])
if enrich >=0:
holdoutEnrich[i] = ScreenComposite.CalcEnrichment(tmpHoldout,tgt=enrich)
if overallMatrix is None:
if data[i][2] is not None:
overallMatrix = tmpOverall
if haveHoldout and data[i][3] is not None:
holdoutMatrix = tmpHoldout
else:
overallMatrix += tmpOverall
if haveHoldout:
holdoutMatrix += tmpHoldout
if haveHoldout:
hCorConf += data[i][6]
hInCorConf += data[i][7]
avgOverall = sum(overall)/nPts
oCorConf /= nPts
oInCorConf /= nPts
overallMatrix /= nPts
oSort = numpy.argsort(overall)
oMin = overall[oSort[0]]
overall -= avgOverall
devOverall = sqrt(sum(overall**2)/(nPts-1))
res = {}
res['oAvg'] = 100*avgOverall
res['oDev'] = 100*devOverall
res['oCorrectConf'] = 100*oCorConf
res['oIncorrectConf'] = 100*oInCorConf
res['oResultMat']=overallMatrix
res['oBestIdx']=oSort[0]
res['oBestErr']=100*oMin
if enrich>=0:
mean,dev = Stats.MeanAndDev(overallEnrich)
res['oAvgEnrich'] = mean
res['oDevEnrich'] = dev
if haveHoldout:
avgHoldout = sum(holdout)/nPts
hCorConf /= nPts
hInCorConf /= nPts
holdoutMatrix /= nPts
hSort = numpy.argsort(holdout)
hMin = holdout[hSort[0]]
holdout -= avgHoldout
devHoldout = sqrt(sum(holdout**2)/(nPts-1))
res['hAvg'] = 100*avgHoldout
res['hDev'] = 100*devHoldout
res['hCorrectConf'] = 100*hCorConf
res['hIncorrectConf'] = 100*hInCorConf
res['hResultMat']=holdoutMatrix
res['hBestIdx']=hSort[0]
res['hBestErr']=100*hMin
if enrich>=0:
mean,dev = Stats.MeanAndDev(holdoutEnrich)
res['hAvgEnrich'] = mean
res['hDevEnrich'] = dev
return res
def ShowStats(statD,enrich=1):
statD = statD.copy()
statD['oBestIdx'] = statD['oBestIdx']+1
txt="""
# Error Statistics:
\tOverall: %(oAvg)6.3f%% (%(oDev)6.3f) %(oCorrectConf)4.1f/%(oIncorrectConf)4.1f
\t\tBest: %(oBestIdx)d %(oBestErr)6.3f%%"""%(statD)
if 'hAvg' in statD:
statD['hBestIdx'] = statD['hBestIdx']+1
txt += """
\tHoldout: %(hAvg)6.3f%% (%(hDev)6.3f) %(hCorrectConf)4.1f/%(hIncorrectConf)4.1f
\t\tBest: %(hBestIdx)d %(hBestErr)6.3f%%
"""%(statD)
print(txt)
print()
print('# Results matrices:')
print('\tOverall:')
tmp = transpose(statD['oResultMat'])
colCounts = sum(tmp)
rowCounts = sum(tmp,1)
for i in range(len(tmp)):
if rowCounts[i]==0: rowCounts[i]=1
row = tmp[i]
print('\t\t', end='')
for j in range(len(row)):
print('% 6.2f'%row[j], end='')
print('\t| % 4.2f'%(100.*tmp[i,i]/rowCounts[i]))
print('\t\t', end='')
for i in range(len(tmp)):
print('------',end='')
print()
print('\t\t',end='')
for i in range(len(tmp)):
if colCounts[i]==0: colCounts[i]=1
print('% 6.2f'%(100.*tmp[i,i]/colCounts[i]), end='')
print()
if enrich>-1 and 'oAvgEnrich' in statD:
print('\t\tEnrich(%d): %.3f (%.3f)'%(enrich,statD['oAvgEnrich'],statD['oDevEnrich']))
if 'hResultMat' in statD:
print('\tHoldout:')
tmp = transpose(statD['hResultMat'])
colCounts = sum(tmp)
rowCounts = sum(tmp,1)
for i in range(len(tmp)):
if rowCounts[i]==0: rowCounts[i]=1
row = tmp[i]
print('\t\t', end='')
for j in range(len(row)):
print('% 6.2f'%row[j], end='')
print('\t| % 4.2f'%(100.*tmp[i,i]/rowCounts[i]))
print('\t\t',end='')
for i in range(len(tmp)):
print('------',end='')
print()
print('\t\t',end='')
for i in range(len(tmp)):
if colCounts[i]==0: colCounts[i]=1
print('% 6.2f'%(100.*tmp[i,i]/colCounts[i]),end='')
print()
if enrich>-1 and 'hAvgEnrich' in statD:
print('\t\tEnrich(%d): %.3f (%.3f)'%(enrich,statD['hAvgEnrich'],statD['hDevEnrich']))
return
def Usage():
print(__doc__)
sys.exit(-1)
if __name__ == "__main__":
import getopt
try:
args,extras = getopt.getopt(sys.argv[1:],'n:d:N:vX',('skip',
'enrich=',
))
except:
Usage()
count = 3
db = None
note = ''
verbose = 0
skip = 0
enrich = 1
for arg,val in args:
if arg == '-n':
count = int(val)+1
elif arg == '-d':
db = val
elif arg == '-N':
note = val
elif arg == '-v':
verbose = 1
elif arg == '--skip':
skip = 1
elif arg == '--enrich':
enrich = int(val)
composites = []
if db is None:
for arg in extras:
composite = cPickle.load(open(arg,'rb'))
composites.append(composite)
else:
tbl = extras[0]
conn = DbConnect(db,tbl)
if note:
where="where note='%s'"%(note)
else:
where = ''
if not skip:
pkls = conn.GetData(fields='model',where=where)
composites = []
for pkl in pkls:
pkl = str(pkl[0])
comp = cPickle.loads(pkl)
composites.append(comp)
if len(composites):
ProcessIt(composites,count,verbose=verbose)
elif not skip:
print('ERROR: no composite models found')
sys.exit(-1)
if db:
res = ErrorStats(conn,where,enrich=enrich)
if res:
ShowStats(res)
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""" generation of 2D pharmacophores
**Notes**
- The terminology for this gets a bit rocky, so here's a glossary of what
terms used here mean:
1) *N-point pharmacophore* a combination of N features along with
distances betwen them.
2) *N-point proto-pharmacophore*: a combination of N feature
definitions without distances. Each N-point
proto-pharmacophore defines a manifold of potential N-point
pharmacophores.
3) *N-point scaffold*: a collection of the distances defining
an N-point pharmacophore without feature identities.
See Docs/Chem/Pharm2D.triangles.jpg for an illustration of the way
pharmacophores are broken into triangles and labelled.
See Docs/Chem/Pharm2D.signatures.jpg for an illustration of bit
numbering
"""
from __future__ import print_function
from rdkit.Chem.Pharm2D import Utils, SigFactory
from rdkit.RDLogger import logger
logger = logger()
_verbose = 0
def _ShortestPathsMatch(match, featureSet, sig, dMat, sigFactory):
""" Internal use only
"""
if _verbose:
print('match:', match)
nPts = len(match)
distsToCheck = Utils.nPointDistDict[nPts]
nDists = len(distsToCheck)
dist = [0] * nDists
bins = sigFactory.GetBins()
minD, maxD = bins[0][0], bins[-1][1]
for i in range(nDists):
pt0, pt1 = distsToCheck[i]
minSeen = maxD
for idx1 in match[pt0]:
for idx2 in match[pt1]:
minSeen = min(minSeen, dMat[idx1, idx2])
if minSeen == 0 or minSeen < minD:
return
# FIX: this won't be an int if we're using the bond order.
d = int(minSeen)
# do a quick distance filter
if d == 0 or d < minD or d >= maxD:
return
dist[i] = d
idx = sigFactory.GetBitIdx(featureSet, dist, sortIndices=False)
if _verbose:
print('\t', dist, minD, maxD, idx)
if sigFactory.useCounts:
sig[idx] = sig[idx] + 1
else:
sig.SetBit(idx)
return idx
def Gen2DFingerprint(mol, sigFactory, perms=None, dMat=None, bitInfo=None):
""" generates a 2D fingerprint for a molecule using the
parameters in _sig_
**Arguments**
- mol: the molecule for which the signature should be generated
- sigFactory : the SigFactory object with signature parameters
NOTE: no preprocessing is carried out for _sigFactory_.
It *must* be pre-initialized.
- perms: (optional) a sequence of permutation indices limiting which
pharmacophore combinations are allowed
- dMat: (optional) the distance matrix to be used
- bitInfo: (optional) used to return the atoms involved in the bits
"""
if not isinstance(sigFactory, SigFactory.SigFactory):
raise ValueError('bad factory')
featFamilies = sigFactory.GetFeatFamilies()
if _verbose:
print('* feat famillies:', featFamilies)
nFeats = len(featFamilies)
minCount = sigFactory.minPointCount
maxCount = sigFactory.maxPointCount
if maxCount > 3:
logger.warning(
' Pharmacophores with more than 3 points are not currently supported.\nSetting maxCount to 3.')
maxCount = 3
# generate the molecule's distance matrix, if required
if dMat is None:
from rdkit import Chem
useBO = sigFactory.includeBondOrder
dMat = Chem.GetDistanceMatrix(mol, useBO)
# generate the permutations, if required
if perms is None:
perms = []
for count in range(minCount, maxCount + 1):
perms += Utils.GetIndexCombinations(nFeats, count)
# generate the matches:
featMatches = sigFactory.GetMolFeats(mol)
if _verbose:
print(' featMatches:', featMatches)
sig = sigFactory.GetSignature()
for perm in perms:
# the permutation is a combination of feature indices
# defining the feature set for a proto-pharmacophore
featClasses = [0]
for i in range(1, len(perm)):
if perm[i] == perm[i - 1]:
featClasses.append(featClasses[-1])
else:
featClasses.append(featClasses[-1] + 1)
# Get a set of matches at each index of
# the proto-pharmacophore.
matchPerms = [featMatches[x] for x in perm]
if _verbose:
print('\n->Perm: %s' % (str(perm)))
print(' matchPerms: %s' % (str(matchPerms)))
# Get all unique combinations of those possible matches:
matchesToMap = Utils.GetUniqueCombinations(matchPerms, featClasses)
for i, entry in enumerate(matchesToMap):
entry = [x[1] for x in entry]
matchesToMap[i] = entry
if _verbose:
print(' mtM:', matchesToMap)
for match in matchesToMap:
if sigFactory.shortestPathsOnly:
idx = _ShortestPathsMatch(match, perm, sig, dMat, sigFactory)
if idx is not None and bitInfo is not None:
l = bitInfo.get(idx, [])
l.append(match)
bitInfo[idx] = l
return sig
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"""unit testing code for the Crippen clogp and MR calculators
"""
from __future__ import print_function
import unittest,sys,os
import io
import numpy
from rdkit import RDConfig
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Crippen
def feq(n1,n2,tol=1e-5):
return abs(n1-n2)<=tol
class TestCase(unittest.TestCase):
def setUp(self):
self.fName = os.path.join(RDConfig.RDCodeDir,'Chem/test_data','Crippen.csv')
self.detailName = os.path.join(RDConfig.RDCodeDir,'Chem/test_data','Crippen_contribs_regress.pkl')
self.detailName2 = os.path.join(RDConfig.RDCodeDir,'Chem/test_data','Crippen_contribs_regress.2.pkl')
def _readData(self):
smis=[]
clogs=[]
mrs=[]
with open(self.fName,'r') as f:
lines = f.readlines()
for line in lines:
if len(line) and line[0] != '#':
splitL = line.split(',')
if len(splitL)==3:
smi,clog,mr=splitL
smis.append(smi)
clogs.append(float(clog))
mrs.append(float(mr))
self.smis = smis
self.clogs = clogs
self.mrs = mrs
def testLogP(self):
self._readData()
nMols = len(self.smis)
#outF = file(self.fName,'w')
for i in range(nMols):
smi = self.smis[i]
mol = Chem.MolFromSmiles(smi)
if 1:
clog = self.clogs[i]
tmp = Crippen.MolLogP(mol)
self.assertTrue(feq(clog,tmp),'bad logp for %s: %4.4f != %4.4f'%(smi,clog,tmp))
mr = self.mrs[i]
tmp = Crippen.MolMR(mol)
self.assertTrue(feq(mr,tmp),'bad MR for %s: %4.4f != %4.4f'%(smi,mr,tmp))
else:
clog = Crippen.MolLogP(mol)
mr = Crippen.MolMR(mol)
print('%s,%.4f,%.4f'%(smi,clog,mr), file=outF)
def testRepeat(self):
self._readData()
nMols = len(self.smis)
for i in range(nMols):
smi = self.smis[i]
mol = Chem.MolFromSmiles(smi)
clog = self.clogs[i]
tmp = Crippen.MolLogP(mol)
tmp = Crippen.MolLogP(mol)
self.assertTrue(feq(clog,tmp),'bad logp fooutF,r %s: %4.4f != %4.4f'%(smi,clog,tmp))
mr = self.mrs[i]
tmp = Crippen.MolMR(mol)
tmp = Crippen.MolMR(mol)
self.assertTrue(feq(mr,tmp),'bad MR for %s: %4.4f != %4.4f'%(smi,mr,tmp))
def _writeDetailFile(self,inF,outF):
while 1:
try:
smi,refContribs = cPickle.load(inF)
except EOFError:
break
else:
mol = Chem.MolFromSmiles(smi)
if mol:
mol=Chem.AddHs(mol,1)
smi2 = Chem.MolToSmiles(mol)
contribs = Crippen._GetAtomContribs(mol)
cPickle.dump((smi,contribs),outF)
else:
print('Problems with SMILES:',smi)
def _doDetailFile(self,inF,nFailsAllowed=1):
done = 0
verbose=0
nFails=0
while not done:
if verbose: print('---------------')
try:
smi,refContribs = cPickle.load(inF)
except EOFError:
done = 1
else:
refContribs = [x[0] for x in refContribs]
refOrder= numpy.argsort(refContribs)
mol = Chem.MolFromSmiles(smi)
if mol:
mol=Chem.AddHs(mol,1)
smi2 = Chem.MolToSmiles(mol)
contribs = Crippen._GetAtomContribs(mol)
contribs = [x[0] for x in contribs]
#
# we're comparing to the old results using the oelib code.
# Since we have some disagreements with them as to what is
# aromatic and what isn't, we may have different numbers of
# Hs. For the sake of comparison, just pop those off our
# new results.
#
while len(contribs)>len(refContribs):
del contribs[-1]
order = numpy.argsort(contribs)
for i in range(len(refContribs)):
refL = refContribs[refOrder[i]]
l = contribs[order[i]]
if not feq(refL,l):
print('%s (%s): %d %6.5f != %6.5f'%(smi,smi2,order[i],refL,l))
Crippen._GetAtomContribs(mol,force=1)
print('-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*')
nFails +=1
break;
else:
print('Problems with SMILES:',smi)
self.assertTrue(nFails<nFailsAllowed)
def testDetails(self):
Crippen._Init()
with open(self.detailName,'r') as inTF:
buf = inTF.read().replace('\r\n', '\n').encode('utf-8')
inTF.close()
with io.BytesIO(buf) as inF:
if 0:
outF = open('tmp.pkl','wb+')
self._writeDetailFile(inF,outF)
self._doDetailFile(inF)
def testDetails2(self):
Crippen._Init()
with open(self.detailName2,'r') as inTF:
buf = inTF.read().replace('\r\n', '\n').encode('utf-8')
inTF.close()
with io.BytesIO(buf) as inF:
if 0:
outF = open('tmp.pkl','wb+')
self._writeDetailFile(inF,outF)
self._doDetailFile(inF)
def testIssue80(self):
from rdkit.Chem import Lipinski
m = Chem.MolFromSmiles('CCOC')
ref = Crippen.MolLogP(m)
Lipinski.NHOHCount(m)
probe = Crippen.MolLogP(m)
self.assertTrue(probe==ref)
def testIssue1749494(self):
m1 = Chem.MolFromSmiles('[*]CC')
v = Crippen.MolLogP(m1)
self.assertTrue(feq(v,0.9739))
if __name__ == '__main__':
unittest.main()
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"""unit testing code for the Crippen clogp and MR calculators
"""
from __future__ import print_function
import unittest,sys,os
import numpy
from rdkit import RDConfig
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Crippen
def feq(n1,n2,tol=1e-5):
return abs(n1-n2)<=tol
class TestCase(unittest.TestCase):
def setUp(self):
self.fName = os.path.join(RDConfig.RDCodeDir,'Chem/test_data','Crippen.csv')
self.detailName = os.path.join(RDConfig.RDCodeDir,'Chem/test_data','Crippen_contribs_regress.pkl')
self.detailName2 = os.path.join(RDConfig.RDCodeDir,'Chem/test_data','Crippen_contribs_regress.2.pkl')
def _readData(self):
smis=[]
clogs=[]
mrs=[]
with open(self.fName,'r') as f:
lines = f.readlines()
for line in lines:
if len(line) and line[0] != '#':
splitL = line.split(',')
if len(splitL)==3:
smi,clog,mr=splitL
smis.append(smi)
clogs.append(float(clog))
mrs.append(float(mr))
self.smis = smis
self.clogs = clogs
self.mrs = mrs
def testLogP(self):
self._readData()
nMols = len(self.smis)
#outF = file(self.fName,'w')
for i in range(nMols):
smi = self.smis[i]
mol = Chem.MolFromSmiles(smi)
if 1:
clog = self.clogs[i]
tmp = Crippen.MolLogP(mol)
self.assertTrue(feq(clog,tmp),'bad logp for %s: %4.4f != %4.4f'%(smi,clog,tmp))
mr = self.mrs[i]
tmp = Crippen.MolMR(mol)
self.assertTrue(feq(mr,tmp),'bad MR for %s: %4.4f != %4.4f'%(smi,mr,tmp))
else:
clog = Crippen.MolLogP(mol)
mr = Crippen.MolMR(mol)
print('%s,%.4f,%.4f'%(smi,clog,mr), file=outF)
def testRepeat(self):
self._readData()
nMols = len(self.smis)
for i in range(nMols):
smi = self.smis[i]
mol = Chem.MolFromSmiles(smi)
clog = self.clogs[i]
tmp = Crippen.MolLogP(mol)
tmp = Crippen.MolLogP(mol)
self.assertTrue(feq(clog,tmp),'bad logp fooutF,r %s: %4.4f != %4.4f'%(smi,clog,tmp))
mr = self.mrs[i]
tmp = Crippen.MolMR(mol)
tmp = Crippen.MolMR(mol)
self.assertTrue(feq(mr,tmp),'bad MR for %s: %4.4f != %4.4f'%(smi,mr,tmp))
def _writeDetailFile(self,inF,outF):
while 1:
try:
smi,refContribs = cPickle.load(inF)
except EOFError:
break
else:
try:
mol = Chem.MolFromSmiles(smi)
except:
import traceback
traceback.print_exc()
mol = None
if mol:
mol=Chem.AddHs(mol,1)
smi2 = Chem.MolToSmiles(mol)
contribs = Crippen._GetAtomContribs(mol)
cPickle.dump((smi,contribs),outF)
else:
print('Problems with SMILES:',smi)
def _doDetailFile(self,inF,nFailsAllowed=1):
done = 0
verbose=0
nFails=0
while not done:
if verbose: print('---------------')
try:
smi,refContribs = cPickle.load(inF)
except EOFError:
done = 1
else:
refContribs = [x[0] for x in refContribs]
refOrder= numpy.argsort(refContribs)
try:
mol = Chem.MolFromSmiles(smi)
except:
import traceback
traceback.print_exc()
mol = None
if mol:
mol=Chem.AddHs(mol,1)
smi2 = Chem.MolToSmiles(mol)
contribs = Crippen._GetAtomContribs(mol)
contribs = [x[0] for x in contribs]
#
# we're comparing to the old results using the oelib code.
# Since we have some disagreements with them as to what is
# aromatic and what isn't, we may have different numbers of
# Hs. For the sake of comparison, just pop those off our
# new results.
#
while len(contribs)>len(refContribs):
del contribs[-1]
order = numpy.argsort(contribs)
for i in range(len(refContribs)):
refL = refContribs[refOrder[i]]
l = contribs[order[i]]
if not feq(refL,l):
print('%s (%s): %d %6.5f != %6.5f'%(smi,smi2,order[i],refL,l))
Crippen._GetAtomContribs(mol,force=1)
print('-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*')
nFails +=1
break;
else:
print('Problems with SMILES:',smi)
self.assertTrue(nFails<nFailsAllowed)
def testDetails(self):
Crippen._Init()
with open(self.detailName,'rb') as inF:
if 0:
outF = open('tmp.pkl','wb+')
self._writeDetailFile(inF,outF)
self._doDetailFile(inF)
def testDetails2(self):
Crippen._Init()
with open(self.detailName2,'rb') as inF:
if 0:
outF = open('tmp.pkl','wb+')
self._writeDetailFile(inF,outF)
self._doDetailFile(inF)
def testIssue80(self):
from rdkit.Chem import Lipinski
m = Chem.MolFromSmiles('CCOC')
ref = Crippen.MolLogP(m)
Lipinski.NHOHCount(m)
probe = Crippen.MolLogP(m)
self.assertTrue(probe==ref)
def testIssue1749494(self):
m1 = Chem.MolFromSmiles('[*]CC')
v = Crippen.MolLogP(m1)
self.assertTrue(feq(v,0.9739))
if __name__ == '__main__':
unittest.main()
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"""unit testing code for the Crippen clogp and MR calculators
"""
from rdkit import RDConfig
import unittest,sys,os,cPickle
from rdkit import Chem
from rdkit.Chem import Crippen
import numpy
def feq(n1,n2,tol=1e-5):
return abs(n1-n2)<=tol
class TestCase(unittest.TestCase):
def setUp(self):
self.fName = os.path.join(RDConfig.RDCodeDir,'Chem/tests','Crippen.csv')
self.detailName = os.path.join(RDConfig.RDCodeDir,'Chem/tests','Crippen_contribs_regress.pkl')
self.detailName2 = os.path.join(RDConfig.RDCodeDir,'Chem/tests','Crippen_contribs_regress.2.pkl')
def _readData(self):
smis=[]
clogs=[]
mrs=[]
for line in file(self.fName,'r').xreadlines():
if len(line) and line[0] != '#':
splitL = line.split(',')
if len(splitL)==3:
smi,clog,mr=splitL
smis.append(smi)
clogs.append(float(clog))
mrs.append(float(mr))
self.smis = smis
self.clogs = clogs
self.mrs = mrs
def testLogP(self):
self._readData()
nMols = len(self.smis)
#outF = file(self.fName,'w')
for i in range(nMols):
smi = self.smis[i]
mol = Chem.MolFromSmiles(smi)
if 1:
clog = self.clogs[i]
tmp = Crippen.MolLogP(mol)
self.failUnless(feq(clog,tmp),'bad logp for %s: %4.4f != %4.4f'%(smi,clog,tmp))
mr = self.mrs[i]
tmp = Crippen.MolMR(mol)
self.failUnless(feq(mr,tmp),'bad MR for %s: %4.4f != %4.4f'%(smi,mr,tmp))
else:
clog = Crippen.MolLogP(mol)
mr = Crippen.MolMR(mol)
print >>outF,'%s,%.4f,%.4f'%(smi,clog,mr)
def testRepeat(self):
self._readData()
nMols = len(self.smis)
for i in range(nMols):
smi = self.smis[i]
mol = Chem.MolFromSmiles(smi)
clog = self.clogs[i]
tmp = Crippen.MolLogP(mol)
tmp = Crippen.MolLogP(mol)
self.failUnless(feq(clog,tmp),'bad logp fooutF,r %s: %4.4f != %4.4f'%(smi,clog,tmp))
mr = self.mrs[i]
tmp = Crippen.MolMR(mol)
tmp = Crippen.MolMR(mol)
self.failUnless(feq(mr,tmp),'bad MR for %s: %4.4f != %4.4f'%(smi,mr,tmp))
def _writeDetailFile(self,inF,outF):
while 1:
try:
smi,refContribs = cPickle.load(inF)
except EOFError:
break
else:
try:
mol = Chem.MolFromSmiles(smi)
except:
import traceback
traceback.print_exc()
mol = None
if mol:
mol=Chem.AddHs(mol,1)
smi2 = Chem.MolToSmiles(mol)
contribs = Crippen._GetAtomContribs(mol)
cPickle.dump((smi,contribs),outF)
else:
print 'Problems with SMILES:',smi
def _doDetailFile(self,inF,nFailsAllowed=1):
done = 0
verbose=0
nFails=0
while not done:
if verbose: print '---------------'
try:
smi,refContribs = cPickle.load(inF)
except EOFError:
done = 1
else:
refContribs = [x[0] for x in refContribs]
refOrder= numpy.argsort(refContribs)
try:
mol = Chem.MolFromSmiles(smi)
except:
import traceback
traceback.print_exc()
mol = None
if mol:
mol=Chem.AddHs(mol,1)
smi2 = Chem.MolToSmiles(mol)
contribs = Crippen._GetAtomContribs(mol)
contribs = [x[0] for x in contribs]
#
# we're comparing to the old results using the oelib code.
# Since we have some disagreements with them as to what is
# aromatic and what isn't, we may have different numbers of
# Hs. For the sake of comparison, just pop those off our
# new results.
#
while len(contribs)>len(refContribs):
del contribs[-1]
order = numpy.argsort(contribs)
for i in range(len(refContribs)):
refL = refContribs[refOrder[i]]
l = contribs[order[i]]
if not feq(refL,l):
print '%s (%s): %d %6.5f != %6.5f'%(smi,smi2,order[i],refL,l)
Crippen._GetAtomContribs(mol,force=1)
print '-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*'
nFails +=1
break;
self.failUnless(nFails<nFailsAllowed)
else:
print 'Problems with SMILES:',smi
def testDetails(self):
Crippen._Init()
inF = open(self.detailName,'rb')
if 0:
outF = open('tmp.pkl','wb+')
self._writeDetailFile(inF,outF)
self._doDetailFile(inF)
def testDetails2(self):
Crippen._Init()
inF = open(self.detailName2,'rb')
if 0:
outF = open('tmp.pkl','wb+')
self._writeDetailFile(inF,outF)
self._doDetailFile(inF)
def testIssue80(self):
from rdkit.Chem import Lipinski
m = Chem.MolFromSmiles('CCOC')
ref = Crippen.MolLogP(m)
Lipinski.NHOHCount(m)
probe = Crippen.MolLogP(m)
self.failUnless(probe==ref)
def testIssue1749494(self):
m1 = Chem.MolFromSmiles('[*]CC')
v = Crippen.MolLogP(m1)
self.failUnless(feq(v,0.9739))
if __name__ == '__main__':
unittest.main()
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""" Various bits and pieces for calculating Molecular descriptors
"""
from rdkit import RDConfig
from rdkit.ML.Descriptors import Descriptors
from rdkit.Chem import Descriptors as DescriptorsMod
from rdkit.RDLogger import logger
logger = logger()
import re
class MolecularDescriptorCalculator(Descriptors.DescriptorCalculator):
""" used for calculating descriptors for molecules
"""
def __init__(self,simpleList,*args,**kwargs):
""" Constructor
**Arguments**
- simpleList: list of simple descriptors to be calculated
(see below for format)
**Note**
- format of simpleList:
a list of strings which are functions in the rdkit.Chem.Descriptors module
"""
self.simpleList = tuple(simpleList)
self.descriptorNames = tuple(self.simpleList)
self.compoundList = None
self._findVersions()
def _findVersions(self):
""" returns a tuple of the versions of the descriptor calculators
"""
self.descriptorVersions=[]
for nm in self.simpleList:
vers='N/A'
if hasattr(DescriptorsMod,nm):
fn = getattr(DescriptorsMod,nm)
if hasattr(fn,'version'):
vers = fn.version
self.descriptorVersions.append(vers)
def SaveState(self,fileName):
""" Writes this calculator off to a file so that it can be easily loaded later
**Arguments**
- fileName: the name of the file to be written
"""
from rdkit.six.moves import cPickle
try:
f = open(fileName,'wb+')
except Exception:
logger.error('cannot open output file %s for writing'%(fileName))
return
cPickle.dump(self,f)
f.close()
def CalcDescriptors(self,mol,*args,**kwargs):
""" calculates all descriptors for a given molecule
**Arguments**
- mol: the molecule to be used
**Returns**
a tuple of all descriptor values
"""
res = [-666]*len(self.simpleList)
for i,nm in enumerate(self.simpleList):
fn = getattr(DescriptorsMod,nm,lambda x:777)
try:
res[i] = fn(mol)
except Exception:
import traceback
traceback.print_exc()
return tuple(res)
def GetDescriptorNames(self):
""" returns a tuple of the names of the descriptors this calculator generates
"""
return self.descriptorNames
def GetDescriptorSummaries(self):
""" returns a tuple of summaries for the descriptors this calculator generates
"""
res = []
for nm in self.simpleList:
fn = getattr(DescriptorsMod,nm,lambda x:777)
if hasattr(fn,'__doc__') and fn.__doc__:
doc = fn.__doc__.split('\n\n')[0].strip()
doc = re.sub('\ *\n\ *',' ',doc)
else:
doc = 'N/A'
res.append(doc)
return res
def GetDescriptorFuncs(self):
""" returns a tuple of the functions used to generate this calculator's descriptors
"""
res = []
for nm in self.simpleList:
fn = getattr(DescriptorsMod,nm,lambda x:777)
res.append(fn)
return tuple(res)
def GetDescriptorVersions(self):
""" returns a tuple of the versions of the descriptor calculators
"""
return tuple(self.descriptorVersions)
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""" Various bits and pieces for calculating Molecular descriptors
"""
import re
from rdkit.Chem import Descriptors as DescriptorsMod
from rdkit.ML.Descriptors import Descriptors
from rdkit.RDLogger import logger
from rdkit.six.moves import cPickle
logger = logger()
class MolecularDescriptorCalculator(Descriptors.DescriptorCalculator):
""" used for calculating descriptors for molecules
"""
def __init__(self, simpleList, *args, **kwargs):
""" Constructor
**Arguments**
- simpleList: list of simple descriptors to be calculated
(see below for format)
**Note**
- format of simpleList:
a list of strings which are functions in the rdkit.Chem.Descriptors module
"""
self.simpleList = tuple(simpleList)
self.descriptorNames = tuple(self.simpleList)
self.compoundList = None
self._findVersions()
def _findVersions(self):
""" returns a tuple of the versions of the descriptor calculators
"""
self.descriptorVersions = []
for nm in self.simpleList:
vers = 'N/A'
if hasattr(DescriptorsMod, nm):
fn = getattr(DescriptorsMod, nm)
if hasattr(fn, 'version'):
vers = fn.version
self.descriptorVersions.append(vers)
def SaveState(self, fileName):
""" Writes this calculator off to a file so that it can be easily loaded later
**Arguments**
- fileName: the name of the file to be written
"""
try:
f = open(fileName, 'wb+')
except Exception:
logger.error('cannot open output file %s for writing' % (fileName))
return
cPickle.dump(self, f)
f.close()
def CalcDescriptors(self, mol, *args, **kwargs):
""" calculates all descriptors for a given molecule
**Arguments**
- mol: the molecule to be used
**Returns**
a tuple of all descriptor values
"""
res = [-666] * len(self.simpleList)
for i, nm in enumerate(self.simpleList):
fn = getattr(DescriptorsMod, nm, lambda x: 777)
try:
res[i] = fn(mol)
except Exception:
import traceback
traceback.print_exc()
return tuple(res)
def GetDescriptorNames(self):
""" returns a tuple of the names of the descriptors this calculator generates
"""
return self.descriptorNames
def GetDescriptorSummaries(self):
""" returns a tuple of summaries for the descriptors this calculator generates
"""
res = []
for nm in self.simpleList:
fn = getattr(DescriptorsMod, nm, lambda x: 777)
if hasattr(fn, '__doc__') and fn.__doc__:
doc = fn.__doc__.split('\n\n')[0].strip()
doc = re.sub('\ *\n\ *', ' ', doc)
else:
doc = 'N/A'
res.append(doc)
return res
def GetDescriptorFuncs(self):
""" returns a tuple of the functions used to generate this calculator's descriptors
"""
res = []
for nm in self.simpleList:
fn = getattr(DescriptorsMod, nm, lambda x: 777)
res.append(fn)
return tuple(res)
def GetDescriptorVersions(self):
""" returns a tuple of the versions of the descriptor calculators
"""
return tuple(self.descriptorVersions)
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""" functions to match a bunch of fragment descriptors from a file
No user-servicable parts inside. ;-)
"""
import os
from rdkit import RDConfig
from rdkit import Chem
defaultPatternFileName = os.path.join(RDConfig.RDDataDir, 'FragmentDescriptors.csv')
def _CountMatches(mol, patt, unique=True):
return len(mol.GetSubstructMatches(patt, uniquify=unique))
fns = []
def _LoadPatterns(fileName=None):
if fileName is None:
fileName = defaultPatternFileName
try:
with open(fileName, 'r') as inF:
for line in inF.readlines():
if len(line) and line[0] != '#':
splitL = line.split('\t')
if len(splitL) >= 3:
name = splitL[0]
descr = splitL[1]
sma = splitL[2]
descr = descr.replace('"', '')
patt = Chem.MolFromSmarts(sma)
if not patt or patt.GetNumAtoms() == 0:
raise ImportError('Smarts %s could not be parsed' % (repr(sma)))
fn = lambda mol, countUnique=True, pattern=patt: _CountMatches(mol, pattern, unique=countUnique)
fn.__doc__ = descr
name = name.replace('=', '_')
name = name.replace('-', '_')
fns.append((name, fn))
except IOError:
pass
_LoadPatterns()
for name, fn in fns:
exec('%s=fn' % (name))
fn = None
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""" functions to match a bunch of fragment descriptors from a file
No user-servicable parts inside. ;-)
"""
import os
from rdkit import RDConfig
from rdkit import Chem
defaultPatternFileName = os.path.join(RDConfig.RDDataDir,'FragmentDescriptors.csv')
def _CountMatches(mol,patt,unique=True):
return len(mol.GetSubstructMatches(patt,uniquify=unique))
fns = []
def _LoadPatterns(fileName=None):
if fileName is None:
fileName = defaultPatternFileName
try:
inF = open(fileName,'r')
except IOError:
pass
else:
for line in inF.readlines():
if len(line) and line[0] != '#':
splitL = line.split('\t')
if len(splitL)>=3:
name = splitL[0]
descr = splitL[1]
sma = splitL[2]
descr=descr.replace('"','')
ok=1
try:
patt = Chem.MolFromSmarts(sma)
except:
ok=0
else:
if not patt or patt.GetNumAtoms()==0: ok=0
if not ok: raise ImportError,'Smarts %s could not be parsed'%(repr(sma))
fn = lambda mol,countUnique=True,pattern=patt:_CountMatches(mol,pattern,unique=countUnique)
fn.__doc__ = descr
name = name.replace('=','_')
name = name.replace('-','_')
fns.append((name,fn))
_LoadPatterns()
for name,fn in fns:
exec('%s=fn'%(name))
fn=None
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""" This is a rough coverage test of the python wrapper
it's intended to be shallow, but broad
"""
import unittest,os
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit.RDLogger import logger
logger=logger()
from rdkit import Chem
from rdkit.Chem import FragmentCatalog
from rdkit import DataStructs
class TestCase(unittest.TestCase):
def setUp(self) :
self.fName=os.path.join(RDConfig.RDBaseDir,'Code','GraphMol',
'FragCatalog','test_data','funcGroups.txt')
self.smiName=os.path.join(RDConfig.RDBaseDir,'Code','GraphMol',
'FragCatalog','test_data','mols.smi')
def test0Params(self) :
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
ctype = fparams.GetTypeString()
assert(ctype == "Fragment Catalog Parameters")
assert(fparams.GetLowerFragLength() == 1)
assert(fparams.GetUpperFragLength() == 6)
ngps = fparams.GetNumFuncGroups()
assert ngps==15
for i in range(ngps) :
mol = fparams.GetFuncGroup(i)
def test1Catalog(self) :
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
fcat = FragmentCatalog.FragCatalog(fparams)
assert(fcat.GetNumEntries() == 0)
assert( fcat.GetFPLength() == 0)
nparams = fcat.GetCatalogParams()
assert(nparams.GetLowerFragLength() == 1)
assert(nparams.GetUpperFragLength() == 6)
def test2Generator(self) :
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName," ",0,1,0)
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
assert fcat.GetNumEntries()==21
assert fcat.GetFPLength()==21
for id in range(fcat.GetNumEntries()):
assert fcat.GetEntryBitId(id)==id
assert fcat.GetEntryOrder(id)==fcat.GetBitOrder(id)
assert fcat.GetEntryDescription(id)==fcat.GetBitDescription(id)
assert tuple(fcat.GetEntryFuncGroupIds(id))==tuple(fcat.GetBitFuncGroupIds(id))
def test3FPgenerator(self) :
with open(self.smiName,'r') as smiF:
smiLines = smiF.readlines()
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName," ",0,1,0)
smiles = []
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
smiles.append(Chem.MolToSmiles(mol))
assert fcat.GetNumEntries()==21
assert fcat.GetFPLength()==21,fcat.GetFPLength()
fpgen = FragmentCatalog.FragFPGenerator()
obits = [3,2,3,3,2,3,5,5,5,4,5,6]
obls = [(0,1,2),(1,3),(1,4,5),(1,6,7),(0,8),(0,6,9),(0,1,2,3,10),
(0,1,2,8,11),(1,3,4,5,12),(1,4,5,13),(1,3,6,7,14),(0,1,6,7,9,15)]
for i in range(len(smiles)):
smi = smiles[i]
mol = Chem.MolFromSmiles(smi)
fp = fpgen.GetFPForMol(mol, fcat)
if i < len(obits):
assert fp.GetNumOnBits()==obits[i],'%s: %s'%(smi,str(fp.GetOnBits()))
obl = fp.GetOnBits()
if i < len(obls):
assert tuple(obl)==obls[i],'%s: %s'%(smi,obl)
def test4Serialize(self) :
with open(self.smiName,'r') as smiF:
smiLines = smiF.readlines()
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName," ",0,1,0)
smiles = []
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
smiles.append(Chem.MolToSmiles(mol))
assert fcat.GetNumEntries()==21
assert fcat.GetFPLength()==21,fcat.GetFPLength()
pkl = cPickle.dumps(fcat)
fcat2 = cPickle.loads(pkl)
assert fcat2.GetNumEntries()==21
assert fcat2.GetFPLength()==21,fcat2.GetFPLength()
fpgen = FragmentCatalog.FragFPGenerator()
for i in range(len(smiles)):
smi = smiles[i]
mol = Chem.MolFromSmiles(smi)
fp1 = fpgen.GetFPForMol(mol, fcat)
fp2 = fpgen.GetFPForMol(mol, fcat2)
assert fp1.GetNumOnBits()==fp2.GetNumOnBits()
obl1 = fp1.GetOnBits()
obl2 = fp2.GetOnBits()
assert tuple(obl1)==tuple(obl2)
def test5FPsize(self) :
with open(self.smiName,'r') as smiF:
smiLines = smiF.readlines()
fparams = FragmentCatalog.FragCatParams(6, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = [Chem.MolFromSmiles('C1CCCOC1O')]
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
assert fcat.GetFPLength()==1
for i in range(fcat.GetFPLength()):
assert fcat.GetBitOrder(i)==6
assert fcat.GetBitDescription(i)=="C1CCOC<-O>C1",fcat.GetBitDescription(i)
assert tuple(fcat.GetBitFuncGroupIds(i))==(1,)
def test6DownEntries(self) :
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName," ",0,1,0)
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
assert fcat.GetNumEntries()==21
assert fcat.GetFPLength()==21
assert tuple(fcat.GetEntryDownIds(0))==(2,8,9,16)
assert tuple(fcat.GetEntryDownIds(1))==(2,3,5,7)
def test7Issue116(self):
smiList = ['Cc1ccccc1']
suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList),
',',0,-1,0)
fparams = FragmentCatalog.FragCatParams(2, 2, self.fName, 1.0e-8)
cat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, cat)
assert cat.GetFPLength()==2
assert cat.GetBitDescription(0)=='ccC'
fpgen = FragmentCatalog.FragFPGenerator()
mol = Chem.MolFromSmiles('Cc1ccccc1')
fp = fpgen.GetFPForMol(mol,cat)
assert fp[0]
assert fp[1]
mol = Chem.MolFromSmiles('c1ccccc1-c1ccccc1')
fp = fpgen.GetFPForMol(mol,cat)
assert not fp[0]
assert fp[1]
def test8Issue118(self):
smiList = ['CCN(C(N)=O)N=O']
fName=os.path.join(RDConfig.RDDataDir,'FunctionalGroups.txt')
suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList),
',',0,-1,0)
fparams = FragmentCatalog.FragCatParams(2, 4, fName, 1.0e-8)
cat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, cat)
assert cat.GetFPLength()==1
assert cat.GetBitDescription(0)=='CCN(<-C(=O)N>)<-N=O>'
if __name__ == '__main__':
unittest.main()
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""" Calculation of topological/topochemical descriptors.
"""
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import Graphs
from rdkit.Chem import rdchem
from rdkit.Chem import rdMolDescriptors
# FIX: remove this dependency here and below
from rdkit.Chem import pyPeriodicTable as PeriodicTable
import numpy
import math
from rdkit.ML.InfoTheory import entropy
periodicTable = rdchem.GetPeriodicTable()
_log2val = math.log(2)
def _log2(x):
return math.log(x) / _log2val
def _VertexDegrees(mat, onlyOnes=0):
""" *Internal Use Only*
this is just a row sum of the matrix... simple, neh?
"""
if not onlyOnes:
res = sum(mat)
else:
res = sum(numpy.equal(mat, 1))
return res
def _NumAdjacencies(mol, dMat):
""" *Internal Use Only*
"""
res = mol.GetNumBonds()
return res
def _GetCountDict(arr):
""" *Internal Use Only*
"""
res = {}
for v in arr:
res[v] = res.get(v, 0) + 1
return res
def _pyHallKierAlpha(m):
""" calculate the Hall-Kier alpha value for a molecule
From equations (58) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
alphaSum = 0.0
rC = PeriodicTable.nameTable['C'][5]
for atom in m.GetAtoms():
atNum = atom.GetAtomicNum()
if not atNum:
continue
symb = atom.GetSymbol()
alphaV = PeriodicTable.hallKierAlphas.get(symb, None)
if alphaV is not None:
hyb = atom.GetHybridization() - 2
if (hyb < len(alphaV)):
alpha = alphaV[hyb]
if alpha is None:
alpha = alphaV[-1]
else:
alpha = alphaV[-1]
else:
rA = PeriodicTable.nameTable[symb][5]
alpha = rA / rC - 1
print(atom.GetIdx(), atom.GetSymbol(), alpha)
alphaSum += alpha
return alphaSum
#HallKierAlpha.version="1.0.2"
def Ipc(mol, avg=0, dMat=None, forceDMat=0):
"""This returns the information content of the coefficients of the characteristic
polynomial of the adjacency matrix of a hydrogen-suppressed graph of a molecule.
'avg = 1' returns the information content divided by the total population.
From D. Bonchev & N. Trinajstic, J. Chem. Phys. vol 67, 4517-4533 (1977)
"""
if forceDMat or dMat is None:
if forceDMat:
dMat = Chem.GetDistanceMatrix(mol, 0)
mol._adjMat = dMat
else:
try:
dMat = mol._adjMat
except AttributeError:
dMat = Chem.GetDistanceMatrix(mol, 0)
mol._adjMat = dMat
adjMat = numpy.equal(dMat, 1)
cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat))
if avg:
return entropy.InfoEntropy(cPoly)
else:
return sum(cPoly) * entropy.InfoEntropy(cPoly)
Ipc.version = "1.0.0"
def _pyKappa1(mol):
""" Hall-Kier Kappa1 value
From equations (58) and (59) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
P1 = mol.GetNumBonds(1)
A = mol.GetNumHeavyAtoms()
alpha = HallKierAlpha(mol)
denom = P1 + alpha
if denom:
kappa = (A + alpha) * (A + alpha - 1)**2 / denom**2
else:
kappa = 0.0
return kappa
#Kappa1.version="1.0.0"
def _pyKappa2(mol):
""" Hall-Kier Kappa2 value
From equations (58) and (60) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
P2 = len(Chem.FindAllPathsOfLengthN(mol, 2))
A = mol.GetNumHeavyAtoms()
alpha = HallKierAlpha(mol)
denom = (P2 + alpha)**2
if denom:
kappa = (A + alpha - 1) * (A + alpha - 2)**2 / denom
else:
kappa = 0
return kappa
#Kappa2.version="1.0.0"
def _pyKappa3(mol):
""" Hall-Kier Kappa3 value
From equations (58), (61) and (62) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
P3 = len(Chem.FindAllPathsOfLengthN(mol, 3))
A = mol.GetNumHeavyAtoms()
alpha = HallKierAlpha(mol)
denom = (P3 + alpha)**2
if denom:
if A % 2 == 1:
kappa = (A + alpha - 1) * (A + alpha - 3)**2 / denom
else:
kappa = (A + alpha - 2) * (A + alpha - 3)**2 / denom
else:
kappa = 0
return kappa
#Kappa3.version="1.0.0"
HallKierAlpha = lambda x: rdMolDescriptors.CalcHallKierAlpha(x)
HallKierAlpha.version = rdMolDescriptors._CalcHallKierAlpha_version
Kappa1 = lambda x: rdMolDescriptors.CalcKappa1(x)
Kappa1.version = rdMolDescriptors._CalcKappa1_version
Kappa2 = lambda x: rdMolDescriptors.CalcKappa2(x)
Kappa2.version = rdMolDescriptors._CalcKappa2_version
Kappa3 = lambda x: rdMolDescriptors.CalcKappa3(x)
Kappa3.version = rdMolDescriptors._CalcKappa3_version
def Chi0(mol):
""" From equations (1),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
deltas = [x.GetDegree() for x in mol.GetAtoms()]
while 0 in deltas:
deltas.remove(0)
deltas = numpy.array(deltas, 'd')
res = sum(numpy.sqrt(1. / deltas))
return res
Chi0.version = "1.0.0"
def Chi1(mol):
""" From equations (1),(11) and (12) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
c1s = [x.GetBeginAtom().GetDegree() * x.GetEndAtom().GetDegree() for x in mol.GetBonds()]
while 0 in c1s:
c1s.remove(0)
c1s = numpy.array(c1s, 'd')
res = sum(numpy.sqrt(1. / c1s))
return res
Chi1.version = "1.0.0"
def _nVal(atom):
return periodicTable.GetNOuterElecs(atom.GetAtomicNum()) - atom.GetTotalNumHs()
def _hkDeltas(mol, skipHs=1):
global periodicTable
res = []
if hasattr(mol, '_hkDeltas') and mol._hkDeltas is not None:
return mol._hkDeltas
for atom in mol.GetAtoms():
n = atom.GetAtomicNum()
if n > 1:
nV = periodicTable.GetNOuterElecs(n)
nHs = atom.GetTotalNumHs()
if n <= 10:
# first row
res.append(float(nV - nHs))
else:
# second row and up
res.append(float(nV - nHs) / float(n - nV - 1))
elif n == 1:
if not skipHs:
res.append(0.0)
else:
res.append(0.0)
mol._hkDeltas = res
return res
def _pyChi0v(mol):
""" From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
deltas = _hkDeltas(mol)
while 0 in deltas:
deltas.remove(0)
mol._hkDeltas = None
res = sum(numpy.sqrt(1. / numpy.array(deltas)))
return res
def _pyChi1v(mol):
""" From equations (5),(11) and (12) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
deltas = numpy.array(_hkDeltas(mol, skipHs=0))
res = 0.0
for bond in mol.GetBonds():
v = deltas[bond.GetBeginAtomIdx()] * deltas[bond.GetEndAtomIdx()]
if v != 0.0:
res += numpy.sqrt(1. / v)
return res
def _pyChiNv_(mol, order=2):
""" From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
**NOTE**: because the current path finding code does, by design,
detect rings as paths (e.g. in C1CC1 there is *1* atom path of
length 3), values of ChiNv with N >= 3 may give results that differ
from those provided by the old code in molecules that have rings of
size 3.
"""
deltas = numpy.array(
[(1. / numpy.sqrt(hkd) if hkd != 0.0 else 0.0) for hkd in _hkDeltas(mol, skipHs=0)])
accum = 0.0
for path in Chem.FindAllPathsOfLengthN(mol, order + 1, useBonds=0):
accum += numpy.prod(deltas[numpy.array(path)])
return accum
def _pyChi2v(mol):
""" From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
return _pyChiNv_(mol, 2)
def _pyChi3v(mol):
""" From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
return _pyChiNv_(mol, 3)
def _pyChi4v(mol):
""" From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
**NOTE**: because the current path finding code does, by design,
detect rings as paths (e.g. in C1CC1 there is *1* atom path of
length 3), values of Chi4v may give results that differ from those
provided by the old code in molecules that have 3 rings.
"""
return _pyChiNv_(mol, 4)
def _pyChi0n(mol):
""" Similar to Hall Kier Chi0v, but uses nVal instead of valence
This makes a big difference after we get out of the first row.
"""
deltas = [_nVal(x) for x in mol.GetAtoms()]
while deltas.count(0):
deltas.remove(0)
deltas = numpy.array(deltas, 'd')
res = sum(numpy.sqrt(1. / deltas))
return res
def _pyChi1n(mol):
""" Similar to Hall Kier Chi1v, but uses nVal instead of valence
"""
delts = numpy.array([_nVal(x) for x in mol.GetAtoms()], 'd')
res = 0.0
for bond in mol.GetBonds():
v = delts[bond.GetBeginAtomIdx()] * delts[bond.GetEndAtomIdx()]
if v != 0.0:
res += numpy.sqrt(1. / v)
return res
def _pyChiNn_(mol, order=2):
""" Similar to Hall Kier ChiNv, but uses nVal instead of valence
This makes a big difference after we get out of the first row.
**NOTE**: because the current path finding code does, by design,
detect rings as paths (e.g. in C1CC1 there is *1* atom path of
length 3), values of ChiNn with N >= 3 may give results that differ
from those provided by the old code in molecules that have rings of
size 3.
"""
nval = [_nVal(x) for x in mol.GetAtoms()]
deltas = numpy.array([(1. / numpy.sqrt(x) if x else 0.0) for x in nval])
accum = 0.0
for path in Chem.FindAllPathsOfLengthN(mol, order + 1, useBonds=0):
accum += numpy.prod(deltas[numpy.array(path)])
return accum
def _pyChi2n(mol):
""" Similar to Hall Kier Chi2v, but uses nVal instead of valence
This makes a big difference after we get out of the first row.
"""
return _pyChiNn_(mol, 2)
def _pyChi3n(mol):
""" Similar to Hall Kier Chi3v, but uses nVal instead of valence
This makes a big difference after we get out of the first row.
"""
return _pyChiNn_(mol, 3)
def _pyChi4n(mol):
""" Similar to Hall Kier Chi4v, but uses nVal instead of valence
This makes a big difference after we get out of the first row.
**NOTE**: because the current path finding code does, by design,
detect rings as paths (e.g. in C1CC1 there is *1* atom path of
length 3), values of Chi4n may give results that differ from those
provided by the old code in molecules that have 3 rings.
"""
return _pyChiNn_(mol, 4)
Chi0v = lambda x: rdMolDescriptors.CalcChi0v(x)
Chi0v.version = rdMolDescriptors._CalcChi0v_version
Chi1v = lambda x: rdMolDescriptors.CalcChi1v(x)
Chi1v.version = rdMolDescriptors._CalcChi1v_version
Chi2v = lambda x: rdMolDescriptors.CalcChi2v(x)
Chi2v.version = rdMolDescriptors._CalcChi2v_version
Chi3v = lambda x: rdMolDescriptors.CalcChi3v(x)
Chi3v.version = rdMolDescriptors._CalcChi3v_version
Chi4v = lambda x: rdMolDescriptors.CalcChi4v(x)
Chi4v.version = rdMolDescriptors._CalcChi4v_version
ChiNv_ = lambda x, y: rdMolDescriptors.CalcChiNv(x, y)
ChiNv_.version = rdMolDescriptors._CalcChiNv_version
Chi0n = lambda x: rdMolDescriptors.CalcChi0n(x)
Chi0n.version = rdMolDescriptors._CalcChi0n_version
Chi1n = lambda x: rdMolDescriptors.CalcChi1n(x)
Chi1n.version = rdMolDescriptors._CalcChi1n_version
Chi2n = lambda x: rdMolDescriptors.CalcChi2n(x)
Chi2n.version = rdMolDescriptors._CalcChi2n_version
Chi3n = lambda x: rdMolDescriptors.CalcChi3n(x)
Chi3n.version = rdMolDescriptors._CalcChi3n_version
Chi4n = lambda x: rdMolDescriptors.CalcChi4n(x)
Chi4n.version = rdMolDescriptors._CalcChi4n_version
ChiNn_ = lambda x, y: rdMolDescriptors.CalcChiNn(x, y)
ChiNn_.version = rdMolDescriptors._CalcChiNn_version
def BalabanJ(mol, dMat=None, forceDMat=0):
""" Calculate Balaban's J value for a molecule
**Arguments**
- mol: a molecule
- dMat: (optional) a distance/adjacency matrix for the molecule, if this
is not provide, one will be calculated
- forceDMat: (optional) if this is set, the distance/adjacency matrix
will be recalculated regardless of whether or not _dMat_ is provided
or the molecule already has one
**Returns**
- a float containing the J value
We follow the notation of Balaban's paper:
Chem. Phys. Lett. vol 89, 399-404, (1982)
"""
# if no dMat is passed in, calculate one ourselves
if forceDMat or dMat is None:
if forceDMat:
# FIX: should we be using atom weights here or not?
dMat = Chem.GetDistanceMatrix(mol, useBO=1, useAtomWts=0, force=1)
mol._balabanMat = dMat
adjMat = Chem.GetAdjacencyMatrix(mol, useBO=0, emptyVal=0, force=0, prefix="NoBO")
mol._adjMat = adjMat
else:
try:
# first check if the molecule already has one
dMat = mol._balabanMat
except AttributeError:
# nope, gotta calculate one
dMat = Chem.GetDistanceMatrix(mol, useBO=1, useAtomWts=0, force=0, prefix="Balaban")
# now store it
mol._balabanMat = dMat
try:
adjMat = mol._adjMat
except AttributeError:
adjMat = Chem.GetAdjacencyMatrix(mol, useBO=0, emptyVal=0, force=0, prefix="NoBO")
mol._adjMat = adjMat
else:
adjMat = Chem.GetAdjacencyMatrix(mol, useBO=0, emptyVal=0, force=0, prefix="NoBO")
s = _VertexDegrees(dMat)
q = _NumAdjacencies(mol, dMat)
n = mol.GetNumAtoms()
mu = q - n + 1
sum = 0.
nS = len(s)
for i in range(nS):
si = s[i]
for j in range(i, nS):
if adjMat[i, j] == 1:
sum += 1. / numpy.sqrt(si * s[j])
if mu + 1 != 0:
J = float(q) / float(mu + 1) * sum
else:
J = 0
return J
BalabanJ.version = "1.0.0"
#------------------------------------------------------------------------
#
# Start block of BertzCT stuff.
#
def _AssignSymmetryClasses(mol, vdList, bdMat, forceBDMat, numAtoms, cutoff):
"""
Used by BertzCT
vdList: the number of neighbors each atom has
bdMat: "balaban" distance matrix
"""
if forceBDMat:
bdMat = Chem.GetDistanceMatrix(mol, useBO=1, useAtomWts=0, force=1, prefix="Balaban")
mol._balabanMat = bdMat
atomIdx = 0
keysSeen = []
symList = [0] * numAtoms
for i in range(numAtoms):
tmpList = bdMat[i].tolist()
tmpList.sort()
theKey = tuple(['%.4f' % x for x in tmpList[:cutoff]])
try:
idx = keysSeen.index(theKey)
except ValueError:
idx = len(keysSeen)
keysSeen.append(theKey)
symList[i] = idx + 1
return tuple(symList)
def _LookUpBondOrder(atom1Id, atom2Id, bondDic):
"""
Used by BertzCT
"""
if atom1Id < atom2Id:
theKey = (atom1Id, atom2Id)
else:
theKey = (atom2Id, atom1Id)
tmp = bondDic[theKey]
if tmp == Chem.BondType.AROMATIC:
tmp = 1.5
else:
tmp = float(tmp)
#tmp = int(tmp)
return tmp
def _CalculateEntropies(connectionDict, atomTypeDict, numAtoms):
"""
Used by BertzCT
"""
connectionList = list(connectionDict.values())
totConnections = sum(connectionList)
connectionIE = totConnections * (
entropy.InfoEntropy(numpy.array(connectionList)) + math.log(totConnections) / _log2val)
atomTypeList = list(atomTypeDict.values())
atomTypeIE = numAtoms * entropy.InfoEntropy(numpy.array(atomTypeList))
return atomTypeIE + connectionIE
def _CreateBondDictEtc(mol, numAtoms):
""" _Internal Use Only_
Used by BertzCT
"""
bondDict = {}
nList = [None] * numAtoms
vdList = [0] * numAtoms
for aBond in mol.GetBonds():
atom1 = aBond.GetBeginAtomIdx()
atom2 = aBond.GetEndAtomIdx()
if atom1 > atom2:
atom2, atom1 = atom1, atom2
if not aBond.GetIsAromatic():
bondDict[(atom1, atom2)] = aBond.GetBondType()
else:
# mark Kekulized systems as aromatic
bondDict[(atom1, atom2)] = Chem.BondType.AROMATIC
if nList[atom1] is None:
nList[atom1] = [atom2]
elif atom2 not in nList[atom1]:
nList[atom1].append(atom2)
if nList[atom2] is None:
nList[atom2] = [atom1]
elif atom1 not in nList[atom2]:
nList[atom2].append(atom1)
for i, element in enumerate(nList):
try:
element.sort()
vdList[i] = len(element)
except Exception:
vdList[i] = 0
return bondDict, nList, vdList
def BertzCT(mol, cutoff=100, dMat=None, forceDMat=1):
""" A topological index meant to quantify "complexity" of molecules.
Consists of a sum of two terms, one representing the complexity
of the bonding, the other representing the complexity of the
distribution of heteroatoms.
From S. H. Bertz, J. Am. Chem. Soc., vol 103, 3599-3601 (1981)
"cutoff" is an integer value used to limit the computational
expense. A cutoff value tells the program to consider vertices
topologically identical if their distance vectors (sets of
distances to all other vertices) are equal out to the "cutoff"th
nearest-neighbor.
**NOTE** The original implementation had the following comment:
> this implementation treats aromatic rings as the
> corresponding Kekule structure with alternating bonds,
> for purposes of counting "connections".
Upon further thought, this is the WRONG thing to do. It
results in the possibility of a molecule giving two different
CT values depending on the kekulization. For example, in the
old implementation, these two SMILES:
CC2=CN=C1C3=C(C(C)=C(C=N3)C)C=CC1=C2C
CC3=CN=C2C1=NC=C(C)C(C)=C1C=CC2=C3C
which correspond to differentk kekule forms, yield different
values.
The new implementation uses consistent (aromatic) bond orders
for aromatic bonds.
THIS MEANS THAT THIS IMPLEMENTATION IS NOT BACKWARDS COMPATIBLE.
Any molecule containing aromatic rings will yield different
values with this implementation. The new behavior is the correct
one, so we're going to live with the breakage.
**NOTE** this barfs if the molecule contains a second (or
nth) fragment that is one atom.
"""
atomTypeDict = {}
connectionDict = {}
numAtoms = mol.GetNumAtoms()
if forceDMat or dMat is None:
if forceDMat:
# nope, gotta calculate one
dMat = Chem.GetDistanceMatrix(mol, useBO=0, useAtomWts=0, force=1)
mol._adjMat = dMat
else:
try:
dMat = mol._adjMat
except AttributeError:
dMat = Chem.GetDistanceMatrix(mol, useBO=0, useAtomWts=0, force=1)
mol._adjMat = dMat
if numAtoms < 2:
return 0
bondDict, neighborList, vdList = _CreateBondDictEtc(mol, numAtoms)
symmetryClasses = _AssignSymmetryClasses(mol, vdList, dMat, forceDMat, numAtoms, cutoff)
#print('Symmm Classes:',symmetryClasses)
for atomIdx in range(numAtoms):
hingeAtomNumber = mol.GetAtomWithIdx(atomIdx).GetAtomicNum()
atomTypeDict[hingeAtomNumber] = atomTypeDict.get(hingeAtomNumber, 0) + 1
hingeAtomClass = symmetryClasses[atomIdx]
numNeighbors = vdList[atomIdx]
for i in range(numNeighbors):
neighbor_iIdx = neighborList[atomIdx][i]
NiClass = symmetryClasses[neighbor_iIdx]
bond_i_order = _LookUpBondOrder(atomIdx, neighbor_iIdx, bondDict)
#print('\t',atomIdx,i,hingeAtomClass,NiClass,bond_i_order)
if (bond_i_order > 1) and (neighbor_iIdx > atomIdx):
numConnections = bond_i_order * (bond_i_order - 1) / 2
connectionKey = (min(hingeAtomClass, NiClass), max(hingeAtomClass, NiClass))
connectionDict[connectionKey] = connectionDict.get(connectionKey, 0) + numConnections
for j in range(i + 1, numNeighbors):
neighbor_jIdx = neighborList[atomIdx][j]
NjClass = symmetryClasses[neighbor_jIdx]
bond_j_order = _LookUpBondOrder(atomIdx, neighbor_jIdx, bondDict)
numConnections = bond_i_order * bond_j_order
connectionKey = (min(NiClass, NjClass), hingeAtomClass, max(NiClass, NjClass))
connectionDict[connectionKey] = connectionDict.get(connectionKey, 0) + numConnections
if not connectionDict:
connectionDict = {'a': 1}
return _CalculateEntropies(connectionDict, atomTypeDict, numAtoms)
BertzCT.version = "2.0.0"
# Recent Revisions:
# 1.0.0 -> 2.0.0:
# - force distance matrix updates properly (Fixed as part of Issue 125)
# - handle single-atom fragments (Issue 136)
#
# End block of BertzCT stuff.
#
#------------------------------------------------------------------------
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""" Calculation of topological/topochemical descriptors.
"""
from rdkit import Chem
from rdkit.Chem import Graphs
from rdkit.Chem import rdchem
from rdkit.Chem import rdMolDescriptors
# FIX: remove this dependency here and below
from rdkit.Chem import pyPeriodicTable as PeriodicTable
import numpy
import math
from rdkit.ML.InfoTheory import entropy
periodicTable = rdchem.GetPeriodicTable()
_log2val = math.log(2)
def _log2(x):
return math.log(x) / _log2val
def _VertexDegrees(mat,onlyOnes=0):
""" *Internal Use Only*
this is just a row sum of the matrix... simple, neh?
"""
if not onlyOnes:
res = sum(mat)
else:
res = sum(numpy.equal(mat,1))
return res
def _NumAdjacencies(mol,dMat):
""" *Internal Use Only*
"""
res = mol.GetNumBonds()
return res
def _GetCountDict(arr):
""" *Internal Use Only*
"""
res = {}
for v in arr:
res[v] = res.get(v,0)+1
return res
def _pyHallKierAlpha(m):
""" calculate the Hall-Kier alpha value for a molecule
From equations (58) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
alphaSum = 0.0
rC = PeriodicTable.nameTable['C'][5]
for atom in m.GetAtoms():
atNum=atom.GetAtomicNum()
if not atNum: continue
symb = atom.GetSymbol()
alphaV = PeriodicTable.hallKierAlphas.get(symb,None)
if alphaV is not None:
hyb = atom.GetHybridization()-2
if(hyb<len(alphaV)):
alpha = alphaV[hyb]
if alpha is None:
alpha = alphaV[-1]
else:
alpha = alphaV[-1]
else:
rA = PeriodicTable.nameTable[symb][5]
alpha = rA/rC - 1
print atom.GetIdx(),atom.GetSymbol(),alpha
alphaSum += alpha
return alphaSum
#HallKierAlpha.version="1.0.2"
def Ipc(mol, avg = 0, dMat = None, forceDMat = 0):
"""This returns the information content of the coefficients of the characteristic
polynomial of the adjacency matrix of a hydrogen-suppressed graph of a molecule.
'avg = 1' returns the information content divided by the total population.
From D. Bonchev & N. Trinajstic, J. Chem. Phys. vol 67, 4517-4533 (1977)
"""
if forceDMat or dMat is None:
if forceDMat:
dMat = Chem.GetDistanceMatrix(mol,0)
mol._adjMat = dMat
else:
try:
dMat = mol._adjMat
except AttributeError:
dMat = Chem.GetDistanceMatrix(mol,0)
mol._adjMat = dMat
adjMat = numpy.equal(dMat,1)
cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat))
if avg:
return entropy.InfoEntropy(cPoly)
else:
return sum(cPoly)*entropy.InfoEntropy(cPoly)
Ipc.version="1.0.0"
def _pyKappa1(mol):
""" Hall-Kier Kappa1 value
From equations (58) and (59) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
P1 = mol.GetNumBonds(1)
A = mol.GetNumHeavyAtoms()
alpha = HallKierAlpha(mol)
denom = P1 + alpha
if denom:
kappa = (A + alpha)*(A + alpha - 1)**2 / denom**2
else:
kappa = 0.0
return kappa
#Kappa1.version="1.0.0"
def _pyKappa2(mol):
""" Hall-Kier Kappa2 value
From equations (58) and (60) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
P2 = len(Chem.FindAllPathsOfLengthN(mol,2))
A = mol.GetNumHeavyAtoms()
alpha = HallKierAlpha(mol)
denom = (P2 + alpha)**2
if denom:
kappa = (A + alpha - 1)*(A + alpha - 2)**2 / denom
else:
kappa = 0
return kappa
#Kappa2.version="1.0.0"
def _pyKappa3(mol):
""" Hall-Kier Kappa3 value
From equations (58), (61) and (62) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
P3 = len(Chem.FindAllPathsOfLengthN(mol,3))
A = mol.GetNumHeavyAtoms()
alpha = HallKierAlpha(mol)
denom = (P3 + alpha)**2
if denom:
if A % 2 == 1:
kappa = (A + alpha - 1)*(A + alpha - 3)**2 / denom
else:
kappa = (A + alpha - 2)*(A + alpha - 3)**2 / denom
else:
kappa = 0
return kappa
#Kappa3.version="1.0.0"
HallKierAlpha = lambda x:rdMolDescriptors.CalcHallKierAlpha(x)
HallKierAlpha.version=rdMolDescriptors._CalcHallKierAlpha_version
Kappa1 = lambda x:rdMolDescriptors.CalcKappa1(x)
Kappa1.version=rdMolDescriptors._CalcKappa1_version
Kappa2 = lambda x:rdMolDescriptors.CalcKappa2(x)
Kappa2.version=rdMolDescriptors._CalcKappa2_version
Kappa3 = lambda x:rdMolDescriptors.CalcKappa3(x)
Kappa3.version=rdMolDescriptors._CalcKappa3_version
def Chi0(mol):
""" From equations (1),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
deltas = [x.GetDegree() for x in mol.GetAtoms()]
while 0 in deltas:
deltas.remove(0)
deltas = numpy.array(deltas,'d')
res = sum(numpy.sqrt(1./deltas))
return res
Chi0.version="1.0.0"
def Chi1(mol):
""" From equations (1),(11) and (12) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
c1s = [x.GetBeginAtom().GetDegree()*x.GetEndAtom().GetDegree() for x in mol.GetBonds()]
while 0 in c1s:
c1s.remove(0)
c1s = numpy.array(c1s,'d')
res = sum(numpy.sqrt(1./c1s))
return res
Chi1.version="1.0.0"
def _nVal(atom):
return periodicTable.GetNOuterElecs(atom.GetAtomicNum())-atom.GetTotalNumHs()
def _hkDeltas(mol,skipHs=1):
global periodicTable
res = []
if hasattr(mol,'_hkDeltas') and mol._hkDeltas is not None:
return mol._hkDeltas
for atom in mol.GetAtoms():
n = atom.GetAtomicNum()
if n>1:
nV = periodicTable.GetNOuterElecs(n)
nHs = atom.GetTotalNumHs()
if n <= 10:
# first row
res.append(float(nV-nHs))
else:
# second row and up
res.append(float(nV-nHs)/float(n-nV-1))
elif n==1:
if not skipHs:
res.append(0.0)
else:
res.append(0.0)
mol._hkDeltas = res
return res
def _pyChi0v(mol):
""" From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
deltas = _hkDeltas(mol)
while 0 in deltas:
deltas.remove(0)
mol._hkDeltas=None
res = sum(numpy.sqrt(1./numpy.array(deltas)))
return res
def _pyChi1v(mol):
""" From equations (5),(11) and (12) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
deltas = numpy.array(_hkDeltas(mol,skipHs=0))
res = 0.0
for bond in mol.GetBonds():
v = deltas[bond.GetBeginAtomIdx()]*deltas[bond.GetEndAtomIdx()]
if v != 0.0:
res += numpy.sqrt(1./v)
return res
def _pyChiNv_(mol,order=2):
""" From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
**NOTE**: because the current path finding code does, by design,
detect rings as paths (e.g. in C1CC1 there is *1* atom path of
length 3), values of ChiNv with N >= 3 may give results that differ
from those provided by the old code in molecules that have rings of
size 3.
"""
deltas = numpy.array([(1. / numpy.sqrt(hkd) if hkd!=0.0 else 0.0) for hkd in _hkDeltas(mol, skipHs=0)])
accum = 0.0
for path in Chem.FindAllPathsOfLengthN(mol, order + 1, useBonds=0):
accum += numpy.prod(deltas[numpy.array(path)])
return accum
def _pyChi2v(mol):
""" From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
return _pyChiNv_(mol,2)
def _pyChi3v(mol):
""" From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
return _pyChiNv_(mol,3)
def _pyChi4v(mol):
""" From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
**NOTE**: because the current path finding code does, by design,
detect rings as paths (e.g. in C1CC1 there is *1* atom path of
length 3), values of Chi4v may give results that differ from those
provided by the old code in molecules that have 3 rings.
"""
return _pyChiNv_(mol,4)
def _pyChi0n(mol):
""" Similar to Hall Kier Chi0v, but uses nVal instead of valence
This makes a big difference after we get out of the first row.
"""
deltas = [_nVal(x) for x in mol.GetAtoms()]
while deltas.count(0):
deltas.remove(0)
deltas = numpy.array(deltas,'d')
res = sum(numpy.sqrt(1./deltas))
return res
def _pyChi1n(mol):
""" Similar to Hall Kier Chi1v, but uses nVal instead of valence
"""
delts = numpy.array([_nVal(x) for x in mol.GetAtoms()],'d')
res = 0.0
for bond in mol.GetBonds():
v = delts[bond.GetBeginAtomIdx()]*delts[bond.GetEndAtomIdx()]
if v != 0.0:
res += numpy.sqrt(1./v)
return res
def _pyChiNn_(mol,order=2):
""" Similar to Hall Kier ChiNv, but uses nVal instead of valence
This makes a big difference after we get out of the first row.
**NOTE**: because the current path finding code does, by design,
detect rings as paths (e.g. in C1CC1 there is *1* atom path of
length 3), values of ChiNn with N >= 3 may give results that differ
from those provided by the old code in molecules that have rings of
size 3.
"""
nval = [_nVal(x) for x in mol.GetAtoms()]
deltas = numpy.array([(1. / numpy.sqrt(x) if x else 0.0) for x in nval])
accum = 0.0
for path in Chem.FindAllPathsOfLengthN(mol,order+1,useBonds=0):
accum += numpy.prod(deltas[numpy.array(path)])
return accum
def _pyChi2n(mol):
""" Similar to Hall Kier Chi2v, but uses nVal instead of valence
This makes a big difference after we get out of the first row.
"""
return _pyChiNn_(mol,2)
def _pyChi3n(mol):
""" Similar to Hall Kier Chi3v, but uses nVal instead of valence
This makes a big difference after we get out of the first row.
"""
return _pyChiNn_(mol,3)
def _pyChi4n(mol):
""" Similar to Hall Kier Chi4v, but uses nVal instead of valence
This makes a big difference after we get out of the first row.
**NOTE**: because the current path finding code does, by design,
detect rings as paths (e.g. in C1CC1 there is *1* atom path of
length 3), values of Chi4n may give results that differ from those
provided by the old code in molecules that have 3 rings.
"""
return _pyChiNn_(mol,4)
Chi0v = lambda x:rdMolDescriptors.CalcChi0v(x)
Chi0v.version=rdMolDescriptors._CalcChi0v_version
Chi1v = lambda x:rdMolDescriptors.CalcChi1v(x)
Chi1v.version=rdMolDescriptors._CalcChi1v_version
Chi2v = lambda x:rdMolDescriptors.CalcChi2v(x)
Chi2v.version=rdMolDescriptors._CalcChi2v_version
Chi3v = lambda x:rdMolDescriptors.CalcChi3v(x)
Chi3v.version=rdMolDescriptors._CalcChi3v_version
Chi4v = lambda x:rdMolDescriptors.CalcChi4v(x)
Chi4v.version=rdMolDescriptors._CalcChi4v_version
ChiNv_ = lambda x,y:rdMolDescriptors.CalcChiNv(x,y)
ChiNv_.version=rdMolDescriptors._CalcChiNv_version
Chi0n = lambda x:rdMolDescriptors.CalcChi0n(x)
Chi0n.version=rdMolDescriptors._CalcChi0n_version
Chi1n = lambda x:rdMolDescriptors.CalcChi1n(x)
Chi1n.version=rdMolDescriptors._CalcChi1n_version
Chi2n = lambda x:rdMolDescriptors.CalcChi2n(x)
Chi2n.version=rdMolDescriptors._CalcChi2n_version
Chi3n = lambda x:rdMolDescriptors.CalcChi3n(x)
Chi3n.version=rdMolDescriptors._CalcChi3n_version
Chi4n = lambda x:rdMolDescriptors.CalcChi4n(x)
Chi4n.version=rdMolDescriptors._CalcChi4n_version
ChiNn_ = lambda x,y:rdMolDescriptors.CalcChiNn(x,y)
ChiNn_.version=rdMolDescriptors._CalcChiNn_version
def BalabanJ(mol,dMat=None,forceDMat=0):
""" Calculate Balaban's J value for a molecule
**Arguments**
- mol: a molecule
- dMat: (optional) a distance/adjacency matrix for the molecule, if this
is not provide, one will be calculated
- forceDMat: (optional) if this is set, the distance/adjacency matrix
will be recalculated regardless of whether or not _dMat_ is provided
or the molecule already has one
**Returns**
- a float containing the J value
We follow the notation of Balaban's paper:
Chem. Phys. Lett. vol 89, 399-404, (1982)
"""
# if no dMat is passed in, calculate one ourselves
if forceDMat or dMat is None:
if forceDMat:
# FIX: should we be using atom weights here or not?
dMat = Chem.GetDistanceMatrix(mol,useBO=1,useAtomWts=0,force=1)
mol._balabanMat = dMat
adjMat = Chem.GetAdjacencyMatrix(mol,useBO=0,emptyVal=0,force=0,prefix="NoBO")
mol._adjMat = adjMat
else:
try:
# first check if the molecule already has one
dMat = mol._balabanMat
except AttributeError:
# nope, gotta calculate one
dMat = Chem.GetDistanceMatrix(mol,useBO=1,useAtomWts=0,force=0,prefix="Balaban")
# now store it
mol._balabanMat = dMat
try:
adjMat = mol._adjMat
except AttributeError:
adjMat = Chem.GetAdjacencyMatrix(mol,useBO=0,emptyVal=0,force=0,prefix="NoBO")
mol._adjMat = adjMat
else:
adjMat = Chem.GetAdjacencyMatrix(mol,useBO=0,emptyVal=0,force=0,prefix="NoBO")
s = _VertexDegrees(dMat)
q = _NumAdjacencies(mol,dMat)
n = mol.GetNumAtoms()
mu = q - n + 1
sum = 0.
nS = len(s)
for i in range(nS):
si = s[i]
for j in range(i,nS):
if adjMat[i,j] == 1:
sum += 1./numpy.sqrt(si*s[j])
if mu+1 != 0:
J = float(q) / float(mu + 1) * sum
else:
J = 0
return J
BalabanJ.version="1.0.0"
#------------------------------------------------------------------------
#
# Start block of BertzCT stuff.
#
def _AssignSymmetryClasses(mol, vdList, bdMat, forceBDMat, numAtoms, cutoff):
"""
Used by BertzCT
vdList: the number of neighbors each atom has
bdMat: "balaban" distance matrix
"""
if forceBDMat:
bdMat = Chem.GetDistanceMatrix(mol,useBO=1,useAtomWts=0,force=1,
prefix="Balaban")
mol._balabanMat = bdMat
atomIdx = 0
keysSeen = []
symList = [0]*numAtoms
for i in range(numAtoms):
tmpList = bdMat[i].tolist()
tmpList.sort()
theKey = tuple(['%.4f'%x for x in tmpList[:cutoff]])
try:
idx = keysSeen.index(theKey)
except ValueError:
idx = len(keysSeen)
keysSeen.append(theKey)
symList[i] = idx+1
return tuple(symList)
def _LookUpBondOrder(atom1Id, atom2Id, bondDic):
"""
Used by BertzCT
"""
if atom1Id < atom2Id:
theKey = (atom1Id,atom2Id)
else:
theKey = (atom2Id,atom1Id)
tmp = bondDic[theKey]
if tmp == Chem.BondType.AROMATIC:
tmp = 1.5
else:
tmp = float(tmp)
#tmp = int(tmp)
return tmp
def _CalculateEntropies(connectionDict, atomTypeDict, numAtoms):
"""
Used by BertzCT
"""
connectionList = connectionDict.values()
totConnections = sum(connectionList)
connectionIE = totConnections*(entropy.InfoEntropy(numpy.array(connectionList)) +
math.log(totConnections)/_log2val)
atomTypeList = atomTypeDict.values()
atomTypeIE = numAtoms*entropy.InfoEntropy(numpy.array(atomTypeList))
return atomTypeIE + connectionIE
def _CreateBondDictEtc(mol, numAtoms):
""" _Internal Use Only_
Used by BertzCT
"""
bondDict = {}
nList = [None]*numAtoms
vdList = [0]*numAtoms
for aBond in mol.GetBonds():
atom1=aBond.GetBeginAtomIdx()
atom2=aBond.GetEndAtomIdx()
if atom1>atom2: atom2,atom1=atom1,atom2
if not aBond.GetIsAromatic():
bondDict[(atom1,atom2)] = aBond.GetBondType()
else:
# mark Kekulized systems as aromatic
bondDict[(atom1,atom2)] = Chem.BondType.AROMATIC
if nList[atom1] is None:
nList[atom1] = [atom2]
elif atom2 not in nList[atom1]:
nList[atom1].append(atom2)
if nList[atom2] is None:
nList[atom2] = [atom1]
elif atom1 not in nList[atom2]:
nList[atom2].append(atom1)
for i,element in enumerate(nList):
try:
element.sort()
vdList[i] = len(element)
except:
vdList[i] = 0
return bondDict, nList, vdList
def BertzCT(mol, cutoff = 100, dMat = None, forceDMat = 1):
""" A topological index meant to quantify "complexity" of molecules.
Consists of a sum of two terms, one representing the complexity
of the bonding, the other representing the complexity of the
distribution of heteroatoms.
From S. H. Bertz, J. Am. Chem. Soc., vol 103, 3599-3601 (1981)
"cutoff" is an integer value used to limit the computational
expense. A cutoff value tells the program to consider vertices
topologically identical if their distance vectors (sets of
distances to all other vertices) are equal out to the "cutoff"th
nearest-neighbor.
**NOTE** The original implementation had the following comment:
> this implementation treats aromatic rings as the
> corresponding Kekule structure with alternating bonds,
> for purposes of counting "connections".
Upon further thought, this is the WRONG thing to do. It
results in the possibility of a molecule giving two different
CT values depending on the kekulization. For example, in the
old implementation, these two SMILES:
CC2=CN=C1C3=C(C(C)=C(C=N3)C)C=CC1=C2C
CC3=CN=C2C1=NC=C(C)C(C)=C1C=CC2=C3C
which correspond to differentk kekule forms, yield different
values.
The new implementation uses consistent (aromatic) bond orders
for aromatic bonds.
THIS MEANS THAT THIS IMPLEMENTATION IS NOT BACKWARDS COMPATIBLE.
Any molecule containing aromatic rings will yield different
values with this implementation. The new behavior is the correct
one, so we're going to live with the breakage.
**NOTE** this barfs if the molecule contains a second (or
nth) fragment that is one atom.
"""
atomTypeDict = {}
connectionDict = {}
numAtoms = mol.GetNumAtoms()
if forceDMat or dMat is None:
if forceDMat:
# nope, gotta calculate one
dMat = Chem.GetDistanceMatrix(mol,useBO=0,useAtomWts=0,force=1)
mol._adjMat = dMat
else:
try:
dMat = mol._adjMat
except AttributeError:
dMat = Chem.GetDistanceMatrix(mol,useBO=0,useAtomWts=0,force=1)
mol._adjMat = dMat
if numAtoms < 2:
return 0
bondDict, neighborList, vdList = _CreateBondDictEtc(mol, numAtoms)
symmetryClasses = _AssignSymmetryClasses(mol, vdList, dMat, forceDMat, numAtoms, cutoff)
#print 'Symmm Classes:',symmetryClasses
for atomIdx in range(numAtoms):
hingeAtomNumber = mol.GetAtomWithIdx(atomIdx).GetAtomicNum()
atomTypeDict[hingeAtomNumber] = atomTypeDict.get(hingeAtomNumber,0)+1
hingeAtomClass = symmetryClasses[atomIdx]
numNeighbors = vdList[atomIdx]
for i in range(numNeighbors):
neighbor_iIdx = neighborList[atomIdx][i]
NiClass = symmetryClasses[neighbor_iIdx]
bond_i_order = _LookUpBondOrder(atomIdx, neighbor_iIdx, bondDict)
#print '\t',atomIdx,i,hingeAtomClass,NiClass,bond_i_order
if (bond_i_order > 1) and (neighbor_iIdx > atomIdx):
numConnections = bond_i_order*(bond_i_order - 1)/2
connectionKey = (min(hingeAtomClass, NiClass), max(hingeAtomClass, NiClass))
connectionDict[connectionKey] = connectionDict.get(connectionKey,0)+numConnections
for j in range(i+1, numNeighbors):
neighbor_jIdx = neighborList[atomIdx][j]
NjClass = symmetryClasses[neighbor_jIdx]
bond_j_order = _LookUpBondOrder(atomIdx, neighbor_jIdx, bondDict)
numConnections = bond_i_order*bond_j_order
connectionKey = (min(NiClass, NjClass), hingeAtomClass, max(NiClass, NjClass))
connectionDict[connectionKey] = connectionDict.get(connectionKey,0)+numConnections
if not connectionDict:
connectionDict = {'a':1}
ks = connectionDict.keys()
ks.sort()
return _CalculateEntropies(connectionDict, atomTypeDict, numAtoms)
BertzCT.version="2.0.0"
# Recent Revisions:
# 1.0.0 -> 2.0.0:
# - force distance matrix updates properly (Fixed as part of Issue 125)
# - handle single-atom fragments (Issue 136)
#
# End block of BertzCT stuff.
#
#------------------------------------------------------------------------
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""" class definitions for similarity screening
See _SimilarityScreener_ for overview of required API
"""
from rdkit import DataStructs
from rdkit.DataStructs import TopNContainer
from rdkit import RDConfig
from rdkit import six
class SimilarityScreener(object):
""" base class
important attributes:
probe: the probe fingerprint against which we screen.
metric: a function that takes two arguments and returns a similarity
measure between them
dataSource: the source pool from which to draw, needs to support
a next() method
fingerprinter: a function that takes a molecule and returns a
fingerprint of the appropriate format
**Notes**
subclasses must support either an iterator interface
or __len__ and __getitem__
"""
def __init__(self,probe=None,metric=None,dataSource=None,fingerprinter=None):
self.metric = metric
self.dataSource = dataSource
self.fingerprinter = fingerprinter
self.probe = probe
def Reset(self):
""" used to reset screeners that behave as iterators
"""
pass
# FIX: add setters/getters for attributes
def SetProbe(self,probeFingerprint):
""" sets our probe fingerprint """
self.probe = probeFingerprint
def GetSingleFingerprint(self,probe):
""" returns a fingerprint for a single probe object
This is potentially useful in initializing our internal
probe object.
"""
return self.fingerprinter(probe)
class ThresholdScreener(SimilarityScreener):
""" Used to return all compounds that have a similarity
to the probe beyond a threshold value
**Notes**:
- This is as lazy as possible, so the data source isn't
queried until the client asks for a hit.
- In addition to being lazy, this class is as thin as possible.
(Who'd have thought it was possible!)
Hits are *not* stored locally, so if a client resets
the iteration and starts over, the same amount of work must
be done to retrieve the hits.
- The thinness and laziness forces us to support only forward
iteration (not random access)
"""
def __init__(self,threshold,**kwargs):
SimilarityScreener.__init__(self,**kwargs)
self.threshold = threshold
self.dataIter = iter(self.dataSource)
# FIX: add setters/getters for attributes
def _nextMatch(self):
""" *Internal use only* """
done = 0
res = None
sim = 0
while not done:
# this is going to crap out when the data source iterator finishes,
# that's how we stop when no match is found
obj = six.next(self.dataIter)
fp = self.fingerprinter(obj)
sim = DataStructs.FingerprintSimilarity(fp,self.probe,self.metric)
if sim >= self.threshold:
res = obj
done = 1
return sim,res
def Reset(self):
""" used to reset our internal state so that iteration
starts again from the beginning
"""
self.dataSource.reset()
self.dataIter = iter(self.dataSource)
def __iter__(self):
""" returns an iterator for this screener
"""
self.Reset()
return self
def next(self):
""" required part of iterator interface """
return self._nextMatch()
__next__ = next
class TopNScreener(SimilarityScreener):
""" A screener that only returns the top N hits found
**Notes**
- supports forward iteration and getitem
"""
def __init__(self,num,**kwargs):
SimilarityScreener.__init__(self,**kwargs)
self.numToGet = num
self.topN = None
self._pos = 0
def Reset(self):
self._pos = 0
def __iter__(self):
if self.topN is None:
self._initTopN()
self.Reset()
return self
def next(self):
if self._pos >= self.numToGet:
raise StopIteration
else:
res = self.topN[self._pos]
self._pos += 1
return res
__next__ = next
def _initTopN(self):
self.topN = TopNContainer.TopNContainer(self.numToGet)
for obj in self.dataSource:
fp = self.fingerprinter(obj)
sim = DataStructs.FingerprintSimilarity(fp,self.probe,self.metric)
self.topN.Insert(sim,obj)
def __len__(self):
if self.topN is None:
self._initTopN()
return self.numToGet
def __getitem__(self,idx):
if self.topN is None:
self._initTopN()
return self.topN[idx]
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""" class definitions for similarity screening
See _SimilarityScreener_ for overview of required API
"""
from rdkit import DataStructs
from rdkit import six
from rdkit.DataStructs import TopNContainer
class SimilarityScreener(object):
""" base class
important attributes:
probe: the probe fingerprint against which we screen.
metric: a function that takes two arguments and returns a similarity
measure between them
dataSource: the source pool from which to draw, needs to support
a next() method
fingerprinter: a function that takes a molecule and returns a
fingerprint of the appropriate format
**Notes**
subclasses must support either an iterator interface
or __len__ and __getitem__
"""
def __init__(self, probe=None, metric=None, dataSource=None, fingerprinter=None):
self.metric = metric
self.dataSource = dataSource
self.fingerprinter = fingerprinter
self.probe = probe
def Reset(self):
""" used to reset screeners that behave as iterators """
pass
# FIX: add setters/getters for attributes
def SetProbe(self, probeFingerprint):
""" sets our probe fingerprint """
self.probe = probeFingerprint
def GetSingleFingerprint(self, probe):
""" returns a fingerprint for a single probe object
This is potentially useful in initializing our internal
probe object.
"""
return self.fingerprinter(probe)
class ThresholdScreener(SimilarityScreener):
""" Used to return all compounds that have a similarity
to the probe beyond a threshold value
**Notes**:
- This is as lazy as possible, so the data source isn't
queried until the client asks for a hit.
- In addition to being lazy, this class is as thin as possible.
(Who'd have thought it was possible!)
Hits are *not* stored locally, so if a client resets
the iteration and starts over, the same amount of work must
be done to retrieve the hits.
- The thinness and laziness forces us to support only forward
iteration (not random access)
"""
def __init__(self, threshold, **kwargs):
SimilarityScreener.__init__(self, **kwargs)
self.threshold = threshold
self.dataIter = iter(self.dataSource)
# FIX: add setters/getters for attributes
def _nextMatch(self):
""" *Internal use only* """
done = 0
res = None
sim = 0
while not done:
# this is going to crap out when the data source iterator finishes,
# that's how we stop when no match is found
obj = six.next(self.dataIter)
fp = self.fingerprinter(obj)
sim = DataStructs.FingerprintSimilarity(fp, self.probe, self.metric)
if sim >= self.threshold:
res = obj
done = 1
return sim, res
def Reset(self):
""" used to reset our internal state so that iteration
starts again from the beginning
"""
self.dataSource.reset()
self.dataIter = iter(self.dataSource)
def __iter__(self):
""" returns an iterator for this screener
"""
self.Reset()
return self
def next(self):
""" required part of iterator interface """
return self._nextMatch()
__next__ = next
class TopNScreener(SimilarityScreener):
""" A screener that only returns the top N hits found
**Notes**
- supports forward iteration and getitem
"""
def __init__(self, num, **kwargs):
SimilarityScreener.__init__(self, **kwargs)
self.numToGet = num
self.topN = None
self._pos = 0
def Reset(self):
self._pos = 0
def __iter__(self):
if self.topN is None:
self._initTopN()
self.Reset()
return self
def next(self):
if self._pos >= self.numToGet:
raise StopIteration
else:
res = self.topN[self._pos]
self._pos += 1
return res
__next__ = next
def _initTopN(self):
self.topN = TopNContainer.TopNContainer(self.numToGet)
for obj in self.dataSource:
fp = self.fingerprinter(obj)
sim = DataStructs.FingerprintSimilarity(fp, self.probe, self.metric)
self.topN.Insert(sim, obj)
def __len__(self):
if self.topN is None:
self._initTopN()
return self.numToGet
def __getitem__(self, idx):
if self.topN is None:
self._initTopN()
return self.topN[idx]
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""" #DOC
"""
class BitEnsemble(object):
""" used to store a collection of bits and score
BitVects (or signatures) against them.
"""
def __init__(self, bits=None):
if bits is not None:
self._bits = list(bits)
else:
self._bits = []
def SetBits(self, bits):
self._bits = list(bits)
def AddBit(self, bit):
self._bits.append(bit)
def GetBits(self):
return tuple(self._bits)
def GetNumBits(self):
return len(self._bits)
def ScoreWithOnBits(self, other):
""" other must support GetOnBits() """
obl = other.GetOnBits()
cnt = 0
for bit in self.GetBits():
if bit in obl:
cnt += 1
return cnt
def ScoreWithIndex(self, other):
""" other must support __getitem__() """
cnt = 0
for bit in self.GetBits():
if other[bit]:
cnt += 1
return cnt
if __name__ == '__main__':
pass
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from __future__ import print_function
import sys
from rdkit import RDConfig
from rdkit.Dbase import DbModule
from rdkit import six
sqlTextTypes = DbModule.sqlTextTypes
sqlIntTypes = DbModule.sqlIntTypes
sqlFloatTypes = DbModule.sqlFloatTypes
sqlBinTypes = DbModule.sqlBinTypes
def GetDbNames(user='sysdba', password='masterkey', dirName='.', dBase='::template1', cn=None):
""" returns a list of databases that are available
**Arguments**
- user: the username for DB access
- password: the password to be used for DB access
**Returns**
- a list of db names (strings)
"""
if DbModule.getDbSql:
if not cn:
try:
cn = DbModule.connect(dBase, user, password)
except Exception:
print('Problems opening database: %s' % (dBase))
return []
c = cn.cursor()
c.execute(DbModule.getDbSql)
if RDConfig.usePgSQL:
names = ['::' + str(x[0]) for x in c.fetchall()]
else:
names = ['::' + str(x[0]) for x in c.fetchall()]
names.remove(dBase)
elif DbModule.fileWildcard:
import os.path
import glob
names = glob.glob(os.path.join(dirName, DbModule.fileWildcard))
else:
names = []
return names
def GetTableNames(dBase, user='sysdba', password='masterkey', includeViews=0, cn=None):
""" returns a list of tables available in a database
**Arguments**
- dBase: the name of the DB file to be used
- user: the username for DB access
- password: the password to be used for DB access
- includeViews: if this is non-null, the views in the db will
also be returned
**Returns**
- a list of table names (strings)
"""
if not cn:
try:
cn = DbModule.connect(dBase, user, password)
except Exception:
print('Problems opening database: %s' % (dBase))
return []
c = cn.cursor()
if not includeViews:
comm = DbModule.getTablesSql
else:
comm = DbModule.getTablesAndViewsSql
c.execute(comm)
names = [str(x[0]).upper() for x in c.fetchall()]
if RDConfig.usePgSQL and 'PG_LOGDIR_LS' in names:
names.remove('PG_LOGDIR_LS')
return names
def GetColumnInfoFromCursor(cursor):
if cursor is None or cursor.description is None:
return []
results = []
if not RDConfig.useSqlLite:
for item in cursor.description:
cName = item[0]
cType = item[1]
if cType in sqlTextTypes:
typeStr = 'string'
elif cType in sqlIntTypes:
typeStr = 'integer'
elif cType in sqlFloatTypes:
typeStr = 'float'
elif cType in sqlBinTypes:
typeStr = 'binary'
else:
sys.stderr.write('odd type in col %s: %s\n' % (cName, str(cType)))
results.append((cName, typeStr))
else:
r = cursor.fetchone()
if not r:
return results
for i, v in enumerate(r):
cName = cursor.description[i][0]
typ = type(v)
if isinstance(v, six.string_types):
typeStr = 'string'
elif typ == int:
typeStr = 'integer'
elif typ == float:
typeStr = 'float'
elif (six.PY2 and typ == buffer) or (six.PY3 and typ in (memoryview, bytes)):
typeStr = 'binary'
else:
sys.stderr.write('odd type in col %s: %s\n' % (cName, typ))
results.append((cName, typeStr))
return results
def GetColumnNamesAndTypes(dBase, table, user='sysdba', password='masterkey', join='', what='*',
cn=None):
""" gets a list of columns available in a DB table along with their types
**Arguments**
- dBase: the name of the DB file to be used
- table: the name of the table to query
- user: the username for DB access
- password: the password to be used for DB access
- join: an optional join clause (omit the verb 'join')
- what: an optional clause indicating what to select
**Returns**
- a list of 2-tuples containing:
1) column name
2) column type
"""
if not cn:
cn = DbModule.connect(dBase, user, password)
c = cn.cursor()
cmd = 'select %s from %s' % (what, table)
if join:
cmd += ' join %s' % (join)
c.execute(cmd)
return GetColumnInfoFromCursor(c)
def GetColumnNames(dBase, table, user='sysdba', password='masterkey', join='', what='*', cn=None):
""" gets a list of columns available in a DB table
**Arguments**
- dBase: the name of the DB file to be used
- table: the name of the table to query
- user: the username for DB access
- password: the password to be used for DB access
- join: an optional join clause (omit the verb 'join')
- what: an optional clause indicating what to select
**Returns**
- a list of column names
"""
if not cn:
cn = DbModule.connect(dBase, user, password)
c = cn.cursor()
cmd = 'select %s from %s' % (what, table)
if join:
if join.strip().find('join') != 0:
join = 'join %s' % (join)
cmd += ' ' + join
c.execute(cmd)
c.fetchone()
desc = c.description
res = [str(x[0]) for x in desc]
return res
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"quality_score": 0.6147101791834426,
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from __future__ import print_function
import sys
from rdkit import RDConfig
from rdkit.Dbase import DbModule
sqlTextTypes = DbModule.sqlTextTypes
sqlIntTypes = DbModule.sqlIntTypes
sqlFloatTypes = DbModule.sqlFloatTypes
sqlBinTypes = DbModule.sqlBinTypes
def GetDbNames(user='sysdba',password='masterkey',dirName='.',dBase='::template1',cn=None):
""" returns a list of databases that are available
**Arguments**
- user: the username for DB access
- password: the password to be used for DB access
**Returns**
- a list of db names (strings)
"""
if DbModule.getDbSql:
if not cn:
try:
cn = DbModule.connect(dBase,user,password)
except Exception:
print('Problems opening database: %s'%(dBase))
return []
c = cn.cursor()
c.execute(DbModule.getDbSql)
if RDConfig.usePgSQL:
names = ['::'+str(x[0]) for x in c.fetchall()]
else:
names = ['::'+str(x[0]) for x in c.fetchall()]
names.remove(dBase)
elif DbModule.fileWildcard:
import os.path,glob
names = glob.glob(os.path.join(dirName,DbModule.fileWildcard))
else:
names = []
return names
def GetTableNames(dBase,user='sysdba',password='masterkey',
includeViews=0,cn=None):
""" returns a list of tables available in a database
**Arguments**
- dBase: the name of the DB file to be used
- user: the username for DB access
- password: the password to be used for DB access
- includeViews: if this is non-null, the views in the db will
also be returned
**Returns**
- a list of table names (strings)
"""
if not cn:
try:
cn = DbModule.connect(dBase,user,password)
except Exception:
print('Problems opening database: %s'%(dBase))
return []
c = cn.cursor()
if not includeViews:
comm = DbModule.getTablesSql
else:
comm = DbModule.getTablesAndViewsSql
c.execute(comm)
names = [str(x[0]).upper() for x in c.fetchall()]
if RDConfig.usePgSQL and 'PG_LOGDIR_LS' in names:
names.remove('PG_LOGDIR_LS')
return names
def GetColumnInfoFromCursor(cursor):
if cursor is None or cursor.description is None: return []
results = []
if not RDConfig.useSqlLite:
for item in cursor.description:
cName = item[0]
cType = item[1]
if cType in sqlTextTypes:
typeStr='string'
elif cType in sqlIntTypes:
typeStr='integer'
elif cType in sqlFloatTypes:
typeStr='float'
elif cType in sqlBinTypes:
typeStr='binary'
else:
sys.stderr.write('odd type in col %s: %s\n'%(cName,str(cType)))
results.append((cName,typeStr))
else:
from rdkit.six import PY2, PY3
r = cursor.fetchone()
if not r: return results
for i,v in enumerate(r):
cName = cursor.description[i][0]
typ = type(v)
if typ == str or (PY2 and typ == unicode):
typeStr='string'
elif typ == int:
typeStr='integer'
elif typ == float:
typeStr='float'
elif (PY2 and typ == buffer) or (PY3 and typ in (memoryview, bytes)):
typeStr='binary'
else:
sys.stderr.write('odd type in col %s: %s\n'%(cName,typ))
results.append((cName,typeStr))
return results
def GetColumnNamesAndTypes(dBase,table,
user='sysdba',password='masterkey',
join='',what='*',cn=None):
""" gets a list of columns available in a DB table along with their types
**Arguments**
- dBase: the name of the DB file to be used
- table: the name of the table to query
- user: the username for DB access
- password: the password to be used for DB access
- join: an optional join clause (omit the verb 'join')
- what: an optional clause indicating what to select
**Returns**
- a list of 2-tuples containing:
1) column name
2) column type
"""
if not cn:
cn = DbModule.connect(dBase,user,password)
c = cn.cursor()
cmd = 'select %s from %s'%(what,table)
if join:
cmd += ' join %s'%(join)
c.execute(cmd)
return GetColumnInfoFromCursor(c)
def GetColumnNames(dBase,table,user='sysdba',password='masterkey',
join='',what='*',cn=None):
""" gets a list of columns available in a DB table
**Arguments**
- dBase: the name of the DB file to be used
- table: the name of the table to query
- user: the username for DB access
- password: the password to be used for DB access
- join: an optional join clause (omit the verb 'join')
- what: an optional clause indicating what to select
**Returns**
- a list of column names
"""
if not cn:
cn = DbModule.connect(dBase,user,password)
c = cn.cursor()
cmd = 'select %s from %s'%(what,table)
if join:
if join.strip().find('join') != 0:
join = 'join %s'%(join)
cmd +=' ' + join
c.execute(cmd)
c.fetchone()
desc = c.description
res = [str(x[0]) for x in desc]
return res
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from __future__ import print_function
raise NotImplementedError('not finished yet')
""" lazy generator of 2D pharmacophore signature data
"""
import rdkit.Chem
from rdkit.Chem.Pharm2D import SigFactory, Matcher, Utils
class Generator(object):
"""
Important attributes:
- mol: the molecules whose signature is being worked with
- sigFactory : the SigFactory object with signature parameters
NOTE: no preprocessing is carried out for _sigFactory_.
It *must* be pre-initialized.
**Notes**
-
"""
def __init__(self, sigFactory, mol, dMat=None, bitCache=True):
""" constructor
**Arguments**
- sigFactory: a signature factory, see class docs
- mol: a molecule, see class docs
- dMat: (optional) a distance matrix for the molecule. If this
is not provided, one will be calculated
- bitCache: (optional) if nonzero, a local cache of which bits
have been queried will be maintained. Otherwise things must
be recalculate each time a bit is queried.
"""
if not isinstance(sigFactory, SigFactory.SigFactory):
raise ValueError('bad factory')
self.sigFactory = sigFactory
self.mol = mol
if dMat is None:
useBO = sigFactory.includeBondOrder
dMat = Chem.GetDistanceMatrix(mol, useBO)
self.dMat = dMat
if bitCache:
self.bits = {}
else:
self.bits = None
featFamilies = [fam for fam in sigFactory.featFactory.GetFeatureFamilies()
if fam not in sigFactory.skipFeats]
nFeats = len(featFamilies)
featMatches = {}
for fam in featFamilies:
featMatches[fam] = []
feats = sigFactory.featFactory.GetFeaturesForMol(mol)
for feat in feats:
if feat.GetFamily() not in sigFactory.skipFeats:
featMatches[feat.GetFamily()].append(feat.GetAtomIds())
featMatches = [None] * nFeats
for i in range(nFeats):
featMatches[i] = sigFactory.featFactory.GetMolFeature()
self.pattMatches = pattMatches
def GetBit(self, idx):
""" returns a bool indicating whether or not the bit is set
"""
if idx < 0 or idx >= self.sig.GetSize():
raise IndexError('Index %d invalid' % (idx))
if self.bits is not None and self.bits.has_key(idx):
return self.bits[idx]
tmp = Matcher.GetAtomsMatchingBit(self.sig, idx, self.mol, dMat=self.dMat, justOne=1,
matchingAtoms=self.pattMatches)
if not tmp or len(tmp) == 0:
res = 0
else:
res = 1
if self.bits is not None:
self.bits[idx] = res
return res
def __len__(self):
""" allows class to support len()
"""
return self.sig.GetSize()
def __getitem__(self, itm):
""" allows class to support random access.
Calls self.GetBit()
"""
return self.GetBit(itm)
if __name__ == '__main__':
import time
from rdkit import RDConfig, Chem
from rdkit.Chem.Pharm2D import Gobbi_Pharm2D, Generate
import random
factory = Gobbi_Pharm2D.factory
nToDo = 100
inD = open(RDConfig.RDDataDir + "/NCI/first_5K.smi", 'r').readlines()[:nToDo]
mols = [None] * len(inD)
for i in range(len(inD)):
smi = inD[i].split('\t')[0]
smi.strip()
mols[i] = Chem.MolFromSmiles(smi)
sig = factory.GetSignature()
nBits = 300
random.seed(23)
bits = [random.randint(0, sig.GetSize() - 1) for x in range(nBits)]
print('Using the Lazy Generator')
t1 = time.time()
for i in range(len(mols)):
if not i % 10:
print('done mol %d of %d' % (i, len(mols)))
gen = Generator(factory, mols[i])
for bit in bits:
v = gen[bit]
t2 = time.time()
print('\tthat took %4.2f seconds' % (t2 - t1))
print('Generating and checking signatures')
t1 = time.time()
for i in range(len(mols)):
if not i % 10:
print('done mol %d of %d' % (i, len(mols)))
sig = Generate.Gen2DFingerprint(mols[i], factory)
for bit in bits:
v = sig[bit]
t2 = time.time()
print('\tthat took %4.2f seconds' % (t2 - t1))
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from rdkit import RDConfig
import DbModule
import sys
sqlTextTypes = DbModule.sqlTextTypes
sqlIntTypes = DbModule.sqlIntTypes
sqlFloatTypes = DbModule.sqlFloatTypes
sqlBinTypes = DbModule.sqlBinTypes
def GetDbNames(user='sysdba',password='masterkey',dirName='.',dBase='::template1',cn=None):
""" returns a list of databases that are available
**Arguments**
- user: the username for DB access
- password: the password to be used for DB access
**Returns**
- a list of db names (strings)
"""
if DbModule.getDbSql:
if not cn:
try:
cn = DbModule.connect(dBase,user,password)
except:
print 'Problems opening database: %s'%(dBase)
return []
c = cn.cursor()
c.execute(DbModule.getDbSql)
if RDConfig.usePgSQL:
names = ['::'+str(x[0]) for x in c.fetchall()]
else:
names = ['::'+str(x[0]) for x in c.fetchall()]
names.remove(dBase)
elif DbModule.fileWildcard:
import os.path,glob
names = glob.glob(os.path.join(dirName,DbModule.fileWildcard))
else:
names = []
return names
def GetTableNames(dBase,user='sysdba',password='masterkey',
includeViews=0,cn=None):
""" returns a list of tables available in a database
**Arguments**
- dBase: the name of the DB file to be used
- user: the username for DB access
- password: the password to be used for DB access
- includeViews: if this is non-null, the views in the db will
also be returned
**Returns**
- a list of table names (strings)
"""
if not cn:
try:
cn = DbModule.connect(dBase,user,password)
except:
print 'Problems opening database: %s'%(dBase)
return []
c = cn.cursor()
if not includeViews:
comm = DbModule.getTablesSql
else:
comm = DbModule.getTablesAndViewsSql
c.execute(comm)
names = [str(x[0]).upper() for x in c.fetchall()]
if RDConfig.usePgSQL and 'PG_LOGDIR_LS' in names:
names.remove('PG_LOGDIR_LS')
return names
def GetColumnInfoFromCursor(cursor):
if cursor is None or cursor.description is None: return []
results = []
if not RDConfig.useSqlLite:
for item in cursor.description:
cName = item[0]
cType = item[1]
if cType in sqlTextTypes:
typeStr='string'
elif cType in sqlIntTypes:
typeStr='integer'
elif cType in sqlFloatTypes:
typeStr='float'
elif cType in sqlBinTypes:
typeStr='binary'
else:
sys.stderr.write('odd type in col %s: %s\n'%(cName,str(cType)))
results.append((cName,typeStr))
else:
import types
r = cursor.fetchone()
if not r: return results
for i,v in enumerate(r):
cName = cursor.description[i][0]
typ = type(v)
if typ in types.StringTypes:
typeStr='string'
elif typ == types.IntType:
typeStr='integer'
elif typ == types.FloatType:
typeStr='float'
elif typ == types.BufferType:
typeStr='binary'
else:
sys.stderr.write('odd type in col %s: %s\n'%(cName,typ))
results.append((cName,typeStr))
return results
def GetColumnNamesAndTypes(dBase,table,
user='sysdba',password='masterkey',
join='',what='*',cn=None):
""" gets a list of columns available in a DB table along with their types
**Arguments**
- dBase: the name of the DB file to be used
- table: the name of the table to query
- user: the username for DB access
- password: the password to be used for DB access
- join: an optional join clause (omit the verb 'join')
- what: an optional clause indicating what to select
**Returns**
- a list of 2-tuples containing:
1) column name
2) column type
"""
if not cn:
cn = DbModule.connect(dBase,user,password)
c = cn.cursor()
cmd = 'select %s from %s'%(what,table)
if join:
cmd += ' join %s'%(join)
c.execute(cmd)
return GetColumnInfoFromCursor(c)
def GetColumnNames(dBase,table,user='sysdba',password='masterkey',
join='',what='*',cn=None):
""" gets a list of columns available in a DB table
**Arguments**
- dBase: the name of the DB file to be used
- table: the name of the table to query
- user: the username for DB access
- password: the password to be used for DB access
- join: an optional join clause (omit the verb 'join')
- what: an optional clause indicating what to select
**Returns**
- a list of column names
"""
if not cn:
cn = DbModule.connect(dBase,user,password)
c = cn.cursor()
cmd = 'select %s from %s'%(what,table)
if join:
if join.strip().find('join') != 0:
join = 'join %s'%(join)
cmd +=' ' + join
c.execute(cmd)
c.fetchone()
desc = c.description
res = map(lambda x:str(x[0]),desc)
return res
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""" command line utility for growing composite models
**Usage**
_GrowComposite [optional args] filename_
**Command Line Arguments**
- -n *count*: number of new models to build
- -C *pickle file name*: name of file containing composite upon which to build.
- --inNote *note*: note to be used in loading composite models from the database
for growing
- --balTable *table name*: table from which to take the original data set
(for balancing)
- --balWeight *weight*: (between 0 and 1) weighting factor for the new data
(for balancing). OR, *weight* can be a list of weights
- --balCnt *count*: number of individual models in the balanced composite
(for balancing)
- --balH: use only the holdout set from the original data set in the balancing
(for balancing)
- --balT: use only the training set from the original data set in the balancing
(for balancing)
- -S: shuffle the original data set
(for balancing)
- -r: randomize the activities of the original data set
(for balancing)
- -N *note*: note to be attached to the grown composite when it's saved in the
database
- --outNote *note*: equivalent to -N
- -o *filename*: name of an output file to hold the pickled composite after
it has been grown.
If multiple balance weights are used, the weights will be added to
the filenames.
- -L *limit*: provide an (integer) limit on individual model complexity
- -d *database name*: instead of reading the data from a QDAT file,
pull it from a database. In this case, the _filename_ argument
provides the name of the database table containing the data set.
- -p *tablename*: store persistence data in the database
in table *tablename*
- -l: locks the random number generator to give consistent sets
of training and hold-out data. This is primarily intended
for testing purposes.
- -g: be less greedy when training the models.
- -G *number*: force trees to be rooted at descriptor *number*.
- -D: show a detailed breakdown of the composite model performance
across the training and, when appropriate, hold-out sets.
- -t *threshold value*: use high-confidence predictions for the final
analysis of the hold-out data.
- -q *list string*: Add QuantTrees to the composite and use the list
specified in *list string* as the number of target quantization
bounds for each descriptor. Don't forget to include 0's at the
beginning and end of *list string* for the name and value fields.
For example, if there are 4 descriptors and you want 2 quant bounds
apiece, you would use _-q "[0,2,2,2,2,0]"_.
Two special cases:
1) If you would like to ignore a descriptor in the model building,
use '-1' for its number of quant bounds.
2) If you have integer valued data that should not be quantized
further, enter 0 for that descriptor.
- -V: print the version number and exit
"""
from rdkit import RDConfig
import numpy
from rdkit.ML.Data import DataUtils,SplitData
from rdkit.ML import ScreenComposite,BuildComposite
from rdkit.ML.Composite import AdjustComposite
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.ML import CompositeRun
import sys,cPickle,time,types
_runDetails = CompositeRun.CompositeRun()
__VERSION_STRING="0.5.0"
_verbose = 1
def message(msg):
""" emits messages to _sys.stdout_
override this in modules which import this one to redirect output
**Arguments**
- msg: the string to be displayed
"""
if _verbose: sys.stdout.write('%s\n'%(msg))
def GrowIt(details,composite,progressCallback=None,
saveIt=1,setDescNames=0,data=None):
""" does the actual work of building a composite model
**Arguments**
- details: a _CompositeRun.CompositeRun_ object containing details
(options, parameters, etc.) about the run
- composite: the composite model to grow
- progressCallback: (optional) a function which is called with a single
argument (the number of models built so far) after each model is built.
- saveIt: (optional) if this is nonzero, the resulting model will be pickled
and dumped to the filename specified in _details.outName_
- setDescNames: (optional) if nonzero, the composite's _SetInputOrder()_ method
will be called using the results of the data set's _GetVarNames()_ method;
it is assumed that the details object has a _descNames attribute which
is passed to the composites _SetDescriptorNames()_ method. Otherwise
(the default), _SetDescriptorNames()_ gets the results of _GetVarNames()_.
- data: (optional) the data set to be used. If this is not provided, the
data set described in details will be used.
**Returns**
the enlarged composite model
"""
details.rundate = time.asctime()
if data is None:
fName = details.tableName.strip()
if details.outName == '':
details.outName = fName + '.pkl'
if details.dbName == '':
data = DataUtils.BuildQuantDataSet(fName)
elif details.qBounds != []:
details.tableName = fName
data = details.GetDataSet()
else:
data = DataUtils.DBToQuantData(details.dbName,fName,quantName=details.qTableName,
user=details.dbUser,password=details.dbPassword)
nExamples = data.GetNPts()
seed = composite._randomSeed
DataUtils.InitRandomNumbers(seed)
testExamples = []
if details.shuffleActivities == 1:
DataUtils.RandomizeActivities(data,shuffle=1,runDetails=details)
elif details.randomActivities == 1:
DataUtils.RandomizeActivities(data,shuffle=0,runDetails=details)
namedExamples = data.GetNamedData()
trainExamples = namedExamples
nExamples = len(trainExamples)
message('Training with %d examples'%(nExamples))
message('\t%d descriptors'%(len(trainExamples[0])-2))
nVars = data.GetNVars()
nPossibleVals = composite.nPossibleVals
attrs = range(1,nVars+1)
if details.useTrees:
from rdkit.ML.DecTree import CrossValidate,PruneTree
if details.qBounds != []:
from rdkit.ML.DecTree import BuildQuantTree
builder = BuildQuantTree.QuantTreeBoot
else:
from rdkit.ML.DecTree import ID3
builder = ID3.ID3Boot
driver = CrossValidate.CrossValidationDriver
pruner = PruneTree.PruneTree
if setDescNames:
composite.SetInputOrder(data.GetVarNames())
composite.Grow(trainExamples,attrs,[0]+nPossibleVals,
buildDriver=driver,
pruner=pruner,
nTries=details.nModels,pruneIt=details.pruneIt,
lessGreedy=details.lessGreedy,needsQuantization=0,
treeBuilder=builder,nQuantBounds=details.qBounds,
startAt=details.startAt,
maxDepth=details.limitDepth,
progressCallback=progressCallback,
silent=not _verbose)
else:
from rdkit.ML.Neural import CrossValidate
driver = CrossValidate.CrossValidationDriver
composite.Grow(trainExamples,attrs,[0]+nPossibleVals,nTries=details.nModels,
buildDriver=driver,needsQuantization=0)
composite.AverageErrors()
composite.SortModels()
modelList,counts,avgErrs = composite.GetAllData()
counts = numpy.array(counts)
avgErrs = numpy.array(avgErrs)
composite._varNames = data.GetVarNames()
for i in xrange(len(modelList)):
modelList[i].NameModel(composite._varNames)
# do final statistics
weightedErrs = counts*avgErrs
averageErr = sum(weightedErrs)/sum(counts)
devs = (avgErrs - averageErr)
devs = devs * counts
devs = numpy.sqrt(devs*devs)
avgDev = sum(devs)/sum(counts)
if _verbose:
message('# Overall Average Error: %%% 5.2f, Average Deviation: %%% 6.2f'%(100.*averageErr,100.*avgDev))
if details.bayesModel:
composite.Train(trainExamples,verbose=0)
badExamples = []
if not details.detailedRes:
if _verbose:
message('Testing all examples')
wrong = BuildComposite.testall(composite,namedExamples,badExamples)
if _verbose:
message('%d examples (%% %5.2f) were misclassified'%(len(wrong),100.*float(len(wrong))/float(len(namedExamples))))
_runDetails.overall_error = float(len(wrong))/len(namedExamples)
if details.detailedRes:
if _verbose:
message('\nEntire data set:')
resTup = ScreenComposite.ShowVoteResults(range(data.GetNPts()),data,composite,
nPossibleVals[-1],details.threshold)
nGood,nBad,nSkip,avgGood,avgBad,avgSkip,voteTab = resTup
nPts = len(namedExamples)
nClass = nGood+nBad
_runDetails.overall_error = float(nBad) / nClass
_runDetails.overall_correct_conf = avgGood
_runDetails.overall_incorrect_conf = avgBad
_runDetails.overall_result_matrix = repr(voteTab)
nRej = nClass-nPts
if nRej > 0:
_runDetails.overall_fraction_dropped = float(nRej)/nPts
return composite
def GetComposites(details):
res = []
if details.persistTblName and details.inNote:
conn = DbConnect(details.dbName,details.persistTblName)
mdls = conn.GetData(fields='MODEL',where="where note='%s'"%(details.inNote))
for row in mdls:
rawD = row[0]
res.append(cPickle.loads(str(rawD)))
elif details.composFileName:
res.append(cPickle.load(open(details.composFileName,'rb')))
return res
def BalanceComposite(details,composite,data1=None,data2=None):
""" balances the composite using the parameters provided in details
**Arguments**
- details a _CompositeRun.RunDetails_ object
- composite: the composite model to be balanced
- data1: (optional) if provided, this should be the
data set used to construct the original models
- data2: (optional) if provided, this should be the
data set used to construct the new individual models
"""
if not details.balCnt or details.balCnt > len(composite):
return composite
message("Balancing Composite")
#
# start by getting data set 1: which is the data set used to build the
# original models
#
if data1 is None:
message("\tReading First Data Set")
fName = details.balTable.strip()
tmp = details.tableName
details.tableName = fName
dbName = details.dbName
details.dbName = details.balDb
data1 = details.GetDataSet()
details.tableName = tmp
details.dbName = dbName
if data1 is None:
return composite
details.splitFrac = composite._splitFrac
details.randomSeed = composite._randomSeed
DataUtils.InitRandomNumbers(details.randomSeed)
if details.shuffleActivities == 1:
DataUtils.RandomizeActivities(data1,shuffle=1,runDetails=details)
elif details.randomActivities == 1:
DataUtils.RandomizeActivities(data1,shuffle=0,runDetails=details)
namedExamples = data1.GetNamedData()
if details.balDoHoldout or details.balDoTrain:
trainIdx,testIdx = SplitData.SplitIndices(len(namedExamples),details.splitFrac,
silent=1)
trainExamples = [namedExamples[x] for x in trainIdx]
testExamples = [namedExamples[x] for x in testIdx]
if details.filterFrac != 0.0:
trainIdx,temp = DataUtils.FilterData(trainExamples,details.filterVal,
details.filterFrac,-1,
indicesOnly=1)
tmp = [trainExamples[x] for x in trainIdx]
testExamples += [trainExamples[x] for x in temp]
trainExamples = tmp
if details.balDoHoldout:
testExamples,trainExamples = trainExamples,testExamples
else:
trainExamples = namedExamples
dataSet1 = trainExamples
cols1 = [x.upper() for x in data1.GetVarNames()]
data1 = None
#
# now grab data set 2: the data used to build the new individual models
#
if data2 is None:
message("\tReading Second Data Set")
data2 = details.GetDataSet()
if data2 is None:
return composite
details.splitFrac = composite._splitFrac
details.randomSeed = composite._randomSeed
DataUtils.InitRandomNumbers(details.randomSeed)
if details.shuffleActivities == 1:
DataUtils.RandomizeActivities(data2,shuffle=1,runDetails=details)
elif details.randomActivities == 1:
DataUtils.RandomizeActivities(data2,shuffle=0,runDetails=details)
dataSet2 = data2.GetNamedData()
cols2 = [x.upper() for x in data2.GetVarNames()]
data2 = None
# and balance it:
res = []
weights = details.balWeight
if type(weights) not in (types.TupleType,types.ListType):
weights = (weights,)
for weight in weights:
message("\tBalancing with Weight: %.4f"%(weight))
res.append(AdjustComposite.BalanceComposite(composite,dataSet1,dataSet2,
weight,
details.balCnt,
names1=cols1,names2=cols2))
return res
def ShowVersion(includeArgs=0):
""" prints the version number
"""
print 'This is GrowComposite.py version %s'%(__VERSION_STRING)
if includeArgs:
import sys
print 'command line was:'
print ' '.join(sys.argv)
def Usage():
""" provides a list of arguments for when this is used from the command line
"""
import sys
print __doc__
sys.exit(-1)
def SetDefaults(runDetails=None):
""" initializes a details object with default values
**Arguments**
- details: (optional) a _CompositeRun.CompositeRun_ object.
If this is not provided, the global _runDetails will be used.
**Returns**
the initialized _CompositeRun_ object.
"""
if runDetails is None: runDetails = _runDetails
return CompositeRun.SetDefaults(runDetails)
def ParseArgs(runDetails):
""" parses command line arguments and updates _runDetails_
**Arguments**
- runDetails: a _CompositeRun.CompositeRun_ object.
"""
import getopt
args,extra = getopt.getopt(sys.argv[1:],'P:o:n:p:b:sf:F:v:hlgd:rSTt:Q:q:DVG:L:C:N:',
['inNote=','outNote=','balTable=','balWeight=','balCnt=',
'balH','balT','balDb=',])
runDetails.inNote=''
runDetails.composFileName=''
runDetails.balTable=''
runDetails.balWeight=(0.5,)
runDetails.balCnt=0
runDetails.balDoHoldout=0
runDetails.balDoTrain=0
runDetails.balDb=''
for arg,val in args:
if arg == '-n':
runDetails.nModels = int(val)
elif arg == '-C':
runDetails.composFileName=val
elif arg=='--balTable':
runDetails.balTable=val
elif arg=='--balWeight':
runDetails.balWeight=eval(val)
if type(runDetails.balWeight) not in (types.TupleType,types.ListType):
runDetails.balWeight=(runDetails.balWeight,)
elif arg=='--balCnt':
runDetails.balCnt=int(val)
elif arg=='--balH':
runDetails.balDoHoldout=1
elif arg=='--balT':
runDetails.balDoTrain=1
elif arg=='--balDb':
runDetails.balDb=val
elif arg == '--inNote':
runDetails.inNote=val
elif arg == '-N' or arg=='--outNote':
runDetails.note=val
elif arg == '-o':
runDetails.outName = val
elif arg == '-p':
runDetails.persistTblName=val
elif arg == '-r':
runDetails.randomActivities = 1
elif arg == '-S':
runDetails.shuffleActivities = 1
elif arg == '-h':
Usage()
elif arg == '-l':
runDetails.lockRandom = 1
elif arg == '-g':
runDetails.lessGreedy=1
elif arg == '-G':
runDetails.startAt = int(val)
elif arg == '-d':
runDetails.dbName=val
elif arg == '-T':
runDetails.useTrees = 0
elif arg == '-t':
runDetails.threshold=float(val)
elif arg == '-D':
runDetails.detailedRes = 1
elif arg == '-L':
runDetails.limitDepth = int(val)
elif arg == '-q':
qBounds = eval(val)
assert type(qBounds) in (types.TupleType,types.ListType),'bad argument type for -q, specify a list as a string'
runDetails.qBoundCount=val
runDetails.qBounds = qBounds
elif arg == '-Q':
qBounds = eval(val)
assert type(qBounds) in [type([]),type(())],'bad argument type for -Q, specify a list as a string'
runDetails.activityBounds=qBounds
runDetails.activityBoundsVals=val
elif arg == '-V':
ShowVersion()
sys.exit(0)
else:
print >>sys.stderr,'bad argument:',arg
Usage()
runDetails.tableName=extra[0]
if not runDetails.balDb:
runDetails.balDb=runDetails.dbName
if __name__ == '__main__':
if len(sys.argv) < 2:
Usage()
_runDetails.cmd = ' '.join(sys.argv)
SetDefaults(_runDetails)
ParseArgs(_runDetails)
ShowVersion(includeArgs=1)
initModels = GetComposites(_runDetails)
nModels = len(initModels)
if nModels>1:
for i in range(nModels):
sys.stderr.write('---------------------------------\n\tDoing %d of %d\n---------------------------------\n'%(i+1,nModels))
composite = GrowIt(_runDetails,initModels[i],setDescNames=1)
if _runDetails.balTable and _runDetails.balCnt:
composites = BalanceComposite(_runDetails,composite)
else:
composites=[composite]
for mdl in composites:
mdl.ClearModelExamples()
if _runDetails.outName:
nWeights = len(_runDetails.balWeight)
if nWeights==1:
outName = _runDetails.outName
composites[0].Pickle(outName)
else:
for i in range(nWeights):
weight = int(100*_runDetails.balWeight[i])
model = composites[i]
outName = '%s.%d.pkl'%(_runDetails.outName.split('.pkl')[0],weight)
model.Pickle(outName)
if _runDetails.persistTblName and _runDetails.dbName:
message('Updating results table %s:%s'%(_runDetails.dbName,_runDetails.persistTblName))
if(len(_runDetails.balWeight))>1:
message('WARNING: updating results table with models having different weights')
# save the composite
for i in range(len(composites)):
_runDetails.model = cPickle.dumps(composites[i])
_runDetails.Store(db=_runDetails.dbName,table=_runDetails.persistTblName)
elif nModels==1:
composite = GrowIt(_runDetails,initModels[0],setDescNames=1)
if _runDetails.balTable and _runDetails.balCnt:
composites = BalanceComposite(_runDetails,composite)
else:
composites=[composite]
for mdl in composites:
mdl.ClearModelExamples()
if _runDetails.outName:
nWeights = len(_runDetails.balWeight)
if nWeights==1:
outName = _runDetails.outName
composites[0].Pickle(outName)
else:
for i in range(nWeights):
weight = int(100*_runDetails.balWeight[i])
model = composites[i]
outName = '%s.%d.pkl'%(_runDetails.outName.split('.pkl')[0],weight)
model.Pickle(outName)
if _runDetails.persistTblName and _runDetails.dbName:
message('Updating results table %s:%s'%(_runDetails.dbName,_runDetails.persistTblName))
if(len(composites))>1:
message('WARNING: updating results table with models having different weights')
for i in range(len(composites)):
_runDetails.model = cPickle.dumps(composites[i])
_runDetails.Store(db=_runDetails.dbName,table=_runDetails.persistTblName)
else:
message("No models found")
| {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/ML/GrowComposite.py",
"copies": "2",
"size": "19705",
"license": "bsd-3-clause",
"hash": -7406231364026530000,
"line_mean": 33.8144876325,
"line_max": 128,
"alpha_frac": 0.6660746004,
"autogenerated": false,
"ratio": 3.759778668193093,
"config_test": true,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.5425853268593093,
"avg_score": null,
"num_lines": null
} |
"""
unit testing code for the Smiles file handling stuff
"""
import unittest
from rdkit import Chem
from rdkit.six import next
from rdkit import RDLogger
class TestCase(unittest.TestCase):
def setUp(self):
self.smis = ['CC', 'CCC', 'CCCCC', 'CCCCCC', 'CCCCCCC', 'CC', 'CCCCOC']
self.nMolecules = len(self.smis)
def tearDown(self):
RDLogger.EnableLog('rdApp.error')
def assertMolecule(self, mol, i, msg=''):
""" Assert that we have a valid molecule """
self.assertIsNotNone(mol, '{0}read {1} failed'.format(msg, i))
self.assertGreater(mol.GetNumAtoms(), 0, '{0}no atoms in mol {1}'.format(msg, i))
def test_SmilesReaderIndex(self):
# tests lazy reads
supp = Chem.SmilesMolSupplierFromText('\n'.join(self.smis), ',', 0, -1, 0)
for i in range(4):
self.assertMolecule(next(supp), i)
i = len(supp) - 1
self.assertMolecule(supp[i], i)
# Use in a list comprehension
ms = [Chem.MolToSmiles(mol) for mol in supp]
self.assertEqual(ms, self.smis)
self.assertEqual(len(supp), self.nMolecules, 'bad supplier length')
# Despite iterating through the whole supplier, we can still access by index
i = self.nMolecules - 3
self.assertMolecule(supp[i - 1], i, msg='back index: ')
with self.assertRaises(IndexError):
_ = supp[self.nMolecules] # out of bound read must fail
# and we can access with negative numbers
mol1 = supp[len(supp) - 1]
mol2 = supp[-1]
self.assertEqual(Chem.MolToSmiles(mol1), Chem.MolToSmiles(mol2))
def test_SmilesReaderIterator(self):
# tests lazy reads using the iterator interface "
supp = Chem.SmilesMolSupplierFromText('\n'.join(self.smis), ',', 0, -1, 0)
nDone = 0
for mol in supp:
self.assertMolecule(mol, nDone)
nDone += 1
self.assertEqual(nDone, self.nMolecules, 'bad number of molecules')
self.assertEqual(len(supp), self.nMolecules, 'bad supplier length')
# Despite iterating through the whole supplier, we can still access by index
i = self.nMolecules - 3
self.assertMolecule(supp[i - 1], i, msg='back index: ')
with self.assertRaises(IndexError):
_ = supp[self.nMolecules] # out of bound read must not fail
def test_SmilesReaderBoundaryConditions(self):
# Suppress the error message due to the incorrect smiles
RDLogger.DisableLog('rdApp.error')
smis = ['CC', 'CCOC', 'fail', 'CCO']
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis), ',', 0, -1, 0)
self.assertEqual(len(supp), 4)
self.assertIsNone(supp[2])
self.assertIsNotNone(supp[3])
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis), ',', 0, -1, 0)
self.assertIsNone(supp[2])
self.assertIsNotNone(supp[3])
self.assertEqual(len(supp), 4)
with self.assertRaises(IndexError):
supp[4]
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis), ',', 0, -1, 0)
self.assertEqual(len(supp), 4)
self.assertIsNotNone(supp[3])
with self.assertRaises(IndexError):
supp[4]
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis), ',', 0, -1, 0)
with self.assertRaises(IndexError):
supp[4]
self.assertEqual(len(supp), 4)
self.assertIsNotNone(supp[3])
if __name__ == '__main__': # pragma: nocover
unittest.main()
| {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/Suppliers/UnitTestSmilesMolSupplier.py",
"copies": "4",
"size": "3573",
"license": "bsd-3-clause",
"hash": -4142047755766020600,
"line_mean": 30.6194690265,
"line_max": 85,
"alpha_frac": 0.6644276518,
"autogenerated": false,
"ratio": 3.213129496402878,
"config_test": true,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.5877557148202878,
"avg_score": null,
"num_lines": null
} |
raise NotImplementedError,'not finished yet'
""" lazy generator of 2D pharmacophore signature data
"""
import rdkit.Chem
from rdkit.Chem.Pharm2D import SigFactory,Matcher,Utils
class Generator(object):
"""
Important attributes:
- mol: the molecules whose signature is being worked with
- sigFactory : the SigFactory object with signature parameters
NOTE: no preprocessing is carried out for _sigFactory_.
It *must* be pre-initialized.
**Notes**
-
"""
def __init__(self,sigFactory,mol,dMat=None,bitCache=True):
""" constructor
**Arguments**
- sigFactory: a signature factory, see class docs
- mol: a molecule, see class docs
- dMat: (optional) a distance matrix for the molecule. If this
is not provided, one will be calculated
- bitCache: (optional) if nonzero, a local cache of which bits
have been queried will be maintained. Otherwise things must
be recalculate each time a bit is queried.
"""
if not isinstance(sigFactory,SigFactory.SigFactory):
raise ValueError,'bad factory'
self.sigFactory = sigFactory
self.mol = mol
if dMat is None:
useBO = sigFactory.includeBondOrder
dMat = Chem.GetDistanceMatrix(mol,useBO)
self.dMat = dMat
if bitCache:
self.bits = {}
else:
self.bits = None
featFamilies=[fam for fam in sigFactory.featFactory.GetFeatureFamilies() if fam not in sigFactory.skipFeats]
nFeats = len(featFamilies)
featMatches={}
for fam in featFamilies:
featMatches[fam] = []
feats = sigFactory.featFactory.GetFeaturesForMol(mol)
for feat in feats:
if feat.GetFamily() not in sigFactory.skipFeats:
featMatches[feat.GetFamily()].append(feat.GetAtomIds())
featMatches = [None]*nFeats
for i in range(nFeats):
featMatches[i]=sigFactory.featFactory.GetMolFeature()
self.pattMatches = pattMatches
def GetBit(self,idx):
""" returns a bool indicating whether or not the bit is set
"""
if idx < 0 or idx >= self.sig.GetSize():
raise IndexError,'Index %d invalid'%(idx)
if self.bits is not None and self.bits.has_key(idx):
return self.bits[idx]
tmp = Matcher.GetAtomsMatchingBit(self.sig,idx,self.mol,
dMat=self.dMat,justOne=1,
matchingAtoms=self.pattMatches)
if not tmp or len(tmp)==0: res = 0
else: res = 1
if self.bits is not None:
self.bits[idx] = res
return res
def __len__(self):
""" allows class to support len()
"""
return self.sig.GetSize()
def __getitem__(self,itm):
""" allows class to support random access.
Calls self.GetBit()
"""
return self.GetBit(itm)
if __name__ == '__main__':
import time
from rdkit import RDConfig,Chem
from rdkit.Chem.Pharm2D import Gobbi_Pharm2D,Generate
import random
factory = Gobbi_Pharm2D.factory
nToDo=100
inD = open(RDConfig.RDDataDir+"/NCI/first_5K.smi",'r').readlines()[:nToDo]
mols = [None]*len(inD)
for i in range(len(inD)):
smi = inD[i].split('\t')[0]
smi.strip()
mols[i] = Chem.MolFromSmiles(smi)
sig = factory.GetSignature()
nBits = 300
random.seed(23)
bits = [random.randint(0,sig.GetSize()-1) for x in range(nBits)]
print 'Using the Lazy Generator'
t1 = time.time()
for i in range(len(mols)):
if not i % 10: print 'done mol %d of %d'%(i,len(mols))
gen = Generator(factory,mols[i])
for bit in bits:
v = gen[bit]
t2 = time.time()
print '\tthat took %4.2f seconds'%(t2-t1)
print 'Generating and checking signatures'
t1 = time.time()
for i in range(len(mols)):
if not i % 10: print 'done mol %d of %d'%(i,len(mols))
sig = Generate.Gen2DFingerprint(mols[i],factory)
for bit in bits:
v = sig[bit]
t2 = time.time()
print '\tthat took %4.2f seconds'%(t2-t1)
| {
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"path": "rdkit/Chem/Pharm2D/LazyGenerator.py",
"copies": "2",
"size": "4289",
"license": "bsd-3-clause",
"hash": 6513829194663768000,
"line_mean": 26.4935897436,
"line_max": 112,
"alpha_frac": 0.6348799254,
"autogenerated": false,
"ratio": 3.4120922832140015,
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"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.5046972208614002,
"avg_score": null,
"num_lines": null
} |
""" Supplies a class for working with fingerprints from databases
#DOC
"""
from rdkit import RDConfig
from rdkit.VLib.Node import VLibNode
from rdkit import DataStructs
import cPickle
import sys
def warning(msg,dest=sys.stderr):
dest.write(msg)
class DbFpSupplier(VLibNode):
"""
new fps come back with all additional fields from the
database set in a "_fieldsFromDb" data member
"""
def __init__(self,dbResults,fpColName='AutoFragmentFp',usePickles=True):
"""
DbResults should be a subclass of Dbase.DbResultSet.DbResultBase
"""
VLibNode.__init__(self)
self._usePickles = usePickles
self._data = dbResults
self._fpColName = fpColName.upper()
self._colNames = [x.upper() for x in self._data.GetColumnNames()]
if self._fpColName not in self._colNames:
raise ValueError,'fp column name "%s" not found in result set: %s'%(self._fpColName,str(self._colNames))
self.fpCol = self._colNames.index(self._fpColName)
del self._colNames[self.fpCol]
self._colNames = tuple(self._colNames)
self._numProcessed=0
def GetColumnNames(self):
return self._colNames
def _BuildFp(self,data):
data = list(data)
pkl = str(data[self.fpCol])
del data[self.fpCol]
self._numProcessed+=1;
try:
if self._usePickles:
newFp = cPickle.loads(pkl)
else:
newFp = DataStructs.ExplicitBitVect(pkl)
except:
import traceback
traceback.print_exc()
newFp = None
if newFp:
newFp._fieldsFromDb = data
return newFp
def next(self):
itm = self.NextItem()
if itm is None:
raise StopIteration
return itm
class ForwardDbFpSupplier(DbFpSupplier):
""" DbFp supplier supporting only forward iteration
>>> import os.path
>>> from rdkit.Dbase.DbConnection import DbConnect
>>> fName = RDConfig.RDTestDatabase
>>> conn = DbConnect(fName,'simple_combined')
>>> suppl = ForwardDbFpSupplier(conn.GetData())
we can loop over the supplied fingerprints:
>>> fps = []
>>> for fp in suppl:
... fps.append(fp)
>>> len(fps)
12
"""
def __init__(self,*args,**kwargs):
DbFpSupplier.__init__(self,*args,**kwargs)
self.reset()
def reset(self):
DbFpSupplier.reset(self)
self._dataIter = iter(self._data)
def NextItem(self):
"""
NOTE: this has side effects
"""
try:
d = self._dataIter.next()
except StopIteration:
d = None
if d is not None:
newFp = self._BuildFp(d)
else:
newFp = None
return newFp
class RandomAccessDbFpSupplier(DbFpSupplier):
""" DbFp supplier supporting random access:
>>> import os.path
>>> from rdkit.Dbase.DbConnection import DbConnect
>>> fName = RDConfig.RDTestDatabase
>>> conn = DbConnect(fName,'simple_combined')
>>> suppl = RandomAccessDbFpSupplier(conn.GetData())
>>> len(suppl)
12
we can pull individual fingerprints:
>>> fp = suppl[5]
>>> fp.GetNumBits()
128
>>> fp.GetNumOnBits()
54
a standard loop over the fingerprints:
>>> fps = []
>>> for fp in suppl:
... fps.append(fp)
>>> len(fps)
12
or we can use an indexed loop:
>>> fps = [None]*len(suppl)
>>> for i in range(len(suppl)):
... fps[i] = suppl[i]
>>> len(fps)
12
"""
def __init__(self,*args,**kwargs):
DbFpSupplier.__init__(self,*args,**kwargs)
self.reset()
def __len__(self):
return len(self._data)
def __getitem__(self,idx):
newD = self._data[idx]
return self._BuildFp(newD)
def reset(self):
self._pos = -1
def NextItem(self):
self._pos += 1
res = None
if self._pos < len(self):
res = self[self._pos]
return res
#------------------------------------
#
# doctest boilerplate
#
def _test():
import doctest,sys
return doctest.testmod(sys.modules["__main__"])
if __name__ == '__main__':
import sys
failed,tried = _test()
sys.exit(failed)
| {
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"path": "rdkit/Chem/Fingerprints/DbFpSupplier.py",
"copies": "2",
"size": "4222",
"license": "bsd-3-clause",
"hash": 1819110671782756900,
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"ratio": 3.3217938630999213,
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"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.4952537586499921,
"avg_score": null,
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} |
""" Supplies a class for working with molecules from databases
#DOC
"""
from rdkit import Chem
from rdkit.Chem.Suppliers.MolSupplier import MolSupplier
import sys
def warning(msg,dest=sys.stderr):
dest.write(msg)
class DbMolSupplier(MolSupplier):
"""
new molecules come back with all additional fields from the
database set in a "_fieldsFromDb" data member
"""
def __init__(self,dbResults,
molColumnFormats={'SMILES':'SMI',
'SMI':'SMI',
'MOLPKL':'PKL'},
nameCol='',
transformFunc=None,
**kwargs):
"""
DbResults should be a subclass of Dbase.DbResultSet.DbResultBase
"""
self._data = dbResults
self._colNames = [x.upper() for x in self._data.GetColumnNames()]
nameCol = nameCol.upper()
self.molCol = -1
self.transformFunc=transformFunc
try:
self.nameCol = self._colNames.index(nameCol)
except ValueError:
self.nameCol = -1
for name in molColumnFormats.keys():
name = name.upper()
try:
idx = self._colNames.index(name)
except ValueError:
pass
else:
self.molCol = idx
self.molFmt = molColumnFormats[name]
break
if self.molCol < 0:
raise ValueError('DbResultSet has no recognizable molecule column')
del self._colNames[self.molCol]
self._colNames = tuple(self._colNames)
self._numProcessed=0
def GetColumnNames(self):
return self._colNames
def _BuildMol(self,data):
data = list(data)
molD = data[self.molCol]
del data[self.molCol]
self._numProcessed+=1;
try:
if self.molFmt =='SMI':
newM = Chem.MolFromSmiles(str(molD))
if not newM:
warning('Problems processing mol %d, smiles: %s\n'%(self._numProcessed,molD))
elif self.molFmt =='PKL':
newM = Chem.Mol(str(molD))
except Exception:
import traceback
traceback.print_exc()
newM = None
else:
if newM and self.transformFunc:
try:
newM = self.transformFunc(newM,data)
except Exception:
import traceback
traceback.print_exc()
newM = None
if newM:
newM._fieldsFromDb = data
nFields = len(data)
for i in range(nFields):
newM.SetProp(self._colNames[i],str(data[i]))
if self.nameCol >=0 :
newM.SetProp('_Name',str(data[self.nameCol]))
return newM
class ForwardDbMolSupplier(DbMolSupplier):
""" DbMol supplier supporting only forward iteration
new molecules come back with all additional fields from the
database set in a "_fieldsFromDb" data member
"""
def __init__(self,dbResults,**kwargs):
"""
DbResults should be an iterator for Dbase.DbResultSet.DbResultBase
"""
DbMolSupplier.__init__(self,dbResults,**kwargs)
self.Reset()
def Reset(self):
self._dataIter = iter(self._data)
def NextMol(self):
"""
NOTE: this has side effects
"""
try:
d = self._dataIter.next()
except StopIteration:
d = None
if d is not None:
newM = self._BuildMol(d)
else:
newM = None
return newM
class RandomAccessDbMolSupplier(DbMolSupplier):
def __init__(self,dbResults,**kwargs):
"""
DbResults should be a Dbase.DbResultSet.RandomAccessDbResultSet
"""
DbMolSupplier.__init__(self,dbResults,**kwargs)
self._pos = -1
def __len__(self):
return len(self._data)
def __getitem__(self,idx):
newD = self._data[idx]
return self._BuildMol(newD)
def Reset(self):
self._pos = -1
def NextMol(self):
self._pos += 1
res = None
if self._pos < len(self):
res = self[self._pos]
return res
| {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/Suppliers/DbMolSupplier.py",
"copies": "1",
"size": "4108",
"license": "bsd-3-clause",
"hash": 6291392567617086000,
"line_mean": 24.675,
"line_max": 87,
"alpha_frac": 0.6085686465,
"autogenerated": false,
"ratio": 3.594050743657043,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.9546244839223041,
"avg_score": 0.031274910186800245,
"num_lines": 160
} |
""" Supplies a class for working with molecules from databases
#DOC
"""
from rdkit import Chem
from rdkit.Chem.Suppliers.MolSupplier import MolSupplier
import sys
def warning(msg, dest=sys.stderr):
dest.write(msg)
class DbMolSupplier(MolSupplier):
"""
new molecules come back with all additional fields from the
database set in a "_fieldsFromDb" data member
"""
def __init__(self, dbResults, molColumnFormats={'SMILES': 'SMI',
'SMI': 'SMI',
'MOLPKL': 'PKL'}, nameCol='', transformFunc=None,
**kwargs):
"""
DbResults should be a subclass of Dbase.DbResultSet.DbResultBase
"""
self._data = dbResults
self._colNames = [x.upper() for x in self._data.GetColumnNames()]
nameCol = nameCol.upper()
self.molCol = -1
self.transformFunc = transformFunc
try:
self.nameCol = self._colNames.index(nameCol)
except ValueError:
self.nameCol = -1
for name in molColumnFormats.keys():
name = name.upper()
try:
idx = self._colNames.index(name)
except ValueError:
pass
else:
self.molCol = idx
self.molFmt = molColumnFormats[name]
break
if self.molCol < 0:
raise ValueError('DbResultSet has no recognizable molecule column')
del self._colNames[self.molCol]
self._colNames = tuple(self._colNames)
self._numProcessed = 0
def GetColumnNames(self):
return self._colNames
def _BuildMol(self, data):
data = list(data)
molD = data[self.molCol]
del data[self.molCol]
self._numProcessed += 1
try:
if self.molFmt == 'SMI':
newM = Chem.MolFromSmiles(str(molD))
if not newM:
warning('Problems processing mol %d, smiles: %s\n' % (self._numProcessed, molD))
elif self.molFmt == 'PKL':
newM = Chem.Mol(str(molD))
except Exception:
import traceback
traceback.print_exc()
newM = None
else:
if newM and self.transformFunc:
try:
newM = self.transformFunc(newM, data)
except Exception:
import traceback
traceback.print_exc()
newM = None
if newM:
newM._fieldsFromDb = data
nFields = len(data)
for i in range(nFields):
newM.SetProp(self._colNames[i], str(data[i]))
if self.nameCol >= 0:
newM.SetProp('_Name', str(data[self.nameCol]))
return newM
class ForwardDbMolSupplier(DbMolSupplier):
""" DbMol supplier supporting only forward iteration
new molecules come back with all additional fields from the
database set in a "_fieldsFromDb" data member
"""
def __init__(self, dbResults, **kwargs):
"""
DbResults should be an iterator for Dbase.DbResultSet.DbResultBase
"""
DbMolSupplier.__init__(self, dbResults, **kwargs)
self.Reset()
def Reset(self):
self._dataIter = iter(self._data)
def NextMol(self):
"""
NOTE: this has side effects
"""
try:
d = self._dataIter.next()
except StopIteration:
d = None
if d is not None:
newM = self._BuildMol(d)
else:
newM = None
return newM
class RandomAccessDbMolSupplier(DbMolSupplier):
def __init__(self, dbResults, **kwargs):
"""
DbResults should be a Dbase.DbResultSet.RandomAccessDbResultSet
"""
DbMolSupplier.__init__(self, dbResults, **kwargs)
self._pos = -1
def __len__(self):
return len(self._data)
def __getitem__(self, idx):
newD = self._data[idx]
return self._BuildMol(newD)
def Reset(self):
self._pos = -1
def NextMol(self):
self._pos += 1
res = None
if self._pos < len(self):
res = self[self._pos]
return res
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""" This functionality gets mixed into the BitEnsemble class
"""
from rdkit.DataStructs.BitEnsemble import BitEnsemble
def _InitScoreTable(self,dbConn,tableName,idInfo='',actInfo=''):
""" inializes a db table to store our scores
idInfo and actInfo should be strings with the definitions of the id and
activity columns of the table (when desired)
"""
if idInfo:
cols = [idInfo]
else:
cols = []
for bit in self.GetBits():
cols.append('Bit_%d smallint'%(bit))
if actInfo :
cols.append(actInfo)
dbConn.AddTable(tableName,','.join(cols))
self._dbTableName=tableName
def _ScoreToDb(self,sig,dbConn,tableName=None,id=None,act=None):
""" scores the "signature" that is passed in and puts the
results in the db table
"""
if tableName is None:
try:
tableName = self._dbTableName
except AttributeError:
raise ValueError,'table name not set in BitEnsemble pre call to ScoreToDb()'
if id is not None:
cols = [id]
else:
cols = []
score = 0
for bit in self.GetBits():
b = sig[bit]
cols.append(b)
score += b
if act is not None:
cols.append(act)
dbConn.InsertData(tableName,cols)
BitEnsemble.InitScoreTable = _InitScoreTable
BitEnsemble.ScoreToDb = _ScoreToDb
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""" This functionality gets mixed into the BitEnsemble class
"""
from rdkit.DataStructs.BitEnsemble import BitEnsemble
def _InitScoreTable(self, dbConn, tableName, idInfo='', actInfo=''):
""" inializes a db table to store our scores
idInfo and actInfo should be strings with the definitions of the id and
activity columns of the table (when desired)
"""
if idInfo:
cols = [idInfo]
else:
cols = []
for bit in self.GetBits():
cols.append('Bit_%d smallint' % (bit))
if actInfo:
cols.append(actInfo)
dbConn.AddTable(tableName, ','.join(cols))
self._dbTableName = tableName
def _ScoreToDb(self, sig, dbConn, tableName=None, id=None, act=None):
""" scores the "signature" that is passed in and puts the
results in the db table
"""
if tableName is None:
try:
tableName = self._dbTableName
except AttributeError:
raise ValueError('table name not set in BitEnsemble pre call to ScoreToDb()')
if id is not None:
cols = [id]
else:
cols = []
score = 0
for bit in self.GetBits():
b = sig[bit]
cols.append(b)
score += b
if act is not None:
cols.append(act)
dbConn.InsertData(tableName, cols)
BitEnsemble.InitScoreTable = _InitScoreTable
BitEnsemble.ScoreToDb = _ScoreToDb
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""" unit testing code for BitEnsembles
"""
from rdkit import RDConfig
import os
import unittest
from rdkit.DataStructs.BitEnsemble import BitEnsemble
from rdkit.DataStructs import BitEnsembleDb
from rdkit.DataStructs import SparseBitVect
class TestCase(unittest.TestCase):
def test1(self):
ensemble = BitEnsemble()
ensemble.SetBits([1,11,21,31])
bv = SparseBitVect(100)
bv.SetBit(1)
bv.SetBit(11)
bv.SetBit(13)
score = ensemble.ScoreWithOnBits(bv)
assert score==2,'bad score: %d'%(score)
score = ensemble.ScoreWithIndex(bv)
assert score==2,'bad score: %d'%(score)
def test2(self):
ensemble = BitEnsemble([1,11,21,31])
bv = SparseBitVect(100)
bv.SetBit(1)
bv.SetBit(11)
bv.SetBit(13)
score = ensemble.ScoreWithOnBits(bv)
assert score==2,'bad score: %d'%(score)
score = ensemble.ScoreWithIndex(bv)
assert score==2,'bad score: %d'%(score)
def test3(self):
ensemble = BitEnsemble()
for bit in [1,11,21,31]:
ensemble.AddBit(bit)
bv = SparseBitVect(100)
bv.SetBit(1)
bv.SetBit(11)
bv.SetBit(13)
score = ensemble.ScoreWithOnBits(bv)
assert score==2,'bad score: %d'%(score)
score = ensemble.ScoreWithIndex(bv)
assert score==2,'bad score: %d'%(score)
def _setupDb(self):
from rdkit.Dbase.DbConnection import DbConnect
fName = RDConfig.RDTestDatabase
self.conn = DbConnect(fName)
self.dbTblName = 'bit_ensemble_test'
return self.conn
def testdb1(self):
""" test the sig - db functionality """
conn = self._setupDb()
ensemble = BitEnsemble()
for bit in [1,3,4]:
ensemble.AddBit(bit)
sigBs = [([0,0,0,0,0,0],(0,0,0)),
([0,1,0,1,0,0],(1,1,0)),
([0,1,0,0,1,0],(1,0,1)),
([0,1,0,0,1,1],(1,0,1)),
]
ensemble.InitScoreTable(conn,self.dbTblName)
for bs,tgt in sigBs:
ensemble.ScoreToDb(bs,conn)
conn.Commit()
d = conn.GetData(table=self.dbTblName)
assert len(d) == len(sigBs),'bad number of results returned'
for i in range(len(sigBs)):
bs,tgt = tuple(sigBs[i])
dbRes = tuple(d[i])
assert dbRes==tgt,'bad bits returned: %s != %s'%(str(dbRes),str(tgt))
d = None
self.conn = None
def testdb2(self):
""" test the sig - db functionality """
conn = self._setupDb()
ensemble = BitEnsemble()
for bit in [1,3,4]:
ensemble.AddBit(bit)
sigBs = [([0,0,0,0,0,0],(0,0,0)),
([0,1,0,1,0,0],(1,1,0)),
([0,1,0,0,1,0],(1,0,1)),
([0,1,0,0,1,1],(1,0,1)),
]
ensemble.InitScoreTable(conn,self.dbTblName,idInfo='id varchar(10)',actInfo='act int')
for bs,tgt in sigBs:
ensemble.ScoreToDb(bs,conn,id='foo',act=1)
conn.Commit()
d = conn.GetData(table=self.dbTblName)
assert len(d) == len(sigBs),'bad number of results returned'
for i in range(len(sigBs)):
bs,tgt = tuple(sigBs[i])
dbRes = tuple(d[i])
assert dbRes[1:-1]==tgt,'bad bits returned: %s != %s'%(str(dbRes[1:-1]),str(tgt))
d = None
self.conn = None
if __name__ == '__main__':
unittest.main()
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""" unit testing code for BitEnsembles
"""
import os
import shutil
import tempfile
import unittest
from rdkit import RDConfig
from rdkit.DataStructs import SparseBitVect
# This import is important to initialize the BitEnsemble module
from rdkit.DataStructs import BitEnsembleDb
from rdkit.DataStructs.BitEnsemble import BitEnsemble
class TestCase(unittest.TestCase):
def test1(self):
ensemble = BitEnsemble()
ensemble.SetBits([1, 11, 21, 31])
self.assertEqual(ensemble.GetNumBits(), 4)
bv = SparseBitVect(100)
bv.SetBit(1)
bv.SetBit(11)
bv.SetBit(13)
score = ensemble.ScoreWithOnBits(bv)
assert score == 2, 'bad score: %d' % (score)
score = ensemble.ScoreWithIndex(bv)
assert score == 2, 'bad score: %d' % (score)
def test2(self):
ensemble = BitEnsemble([1, 11, 21, 31])
bv = SparseBitVect(100)
bv.SetBit(1)
bv.SetBit(11)
bv.SetBit(13)
score = ensemble.ScoreWithOnBits(bv)
assert score == 2, 'bad score: %d' % (score)
score = ensemble.ScoreWithIndex(bv)
assert score == 2, 'bad score: %d' % (score)
def test3(self):
ensemble = BitEnsemble()
for bit in [1, 11, 21, 31]:
ensemble.AddBit(bit)
bv = SparseBitVect(100)
bv.SetBit(1)
bv.SetBit(11)
bv.SetBit(13)
score = ensemble.ScoreWithOnBits(bv)
assert score == 2, 'bad score: %d' % (score)
score = ensemble.ScoreWithIndex(bv)
assert score == 2, 'bad score: %d' % (score)
def _setupDb(self):
from rdkit.Dbase.DbConnection import DbConnect
fName = RDConfig.RDTestDatabase
if RDConfig.useSqlLite:
_, tempName = tempfile.mkstemp(suffix='sqlt')
self.tempDbName = tempName
shutil.copyfile(fName, tempName)
else: # pragma: nocover
tempName = '::RDTests'
self.conn = DbConnect(tempName)
self.dbTblName = 'bit_ensemble_test'
return self.conn
def tearDown(self):
if hasattr(self, 'tempDbName') and RDConfig.useSqlLite and os.path.exists(self.tempDbName):
try:
os.unlink(self.tempDbName)
except: # pragma: nocover
import traceback
traceback.print_exc()
def testdb1(self):
""" test the sig - db functionality """
conn = self._setupDb()
ensemble = BitEnsemble()
for bit in [1, 3, 4]:
ensemble.AddBit(bit)
sigBs = [([0, 0, 0, 0, 0, 0], (0, 0, 0)),
([0, 1, 0, 1, 0, 0], (1, 1, 0)),
([0, 1, 0, 0, 1, 0], (1, 0, 1)),
([0, 1, 0, 0, 1, 1], (1, 0, 1)), ]
ensemble.InitScoreTable(conn, self.dbTblName)
for bs, tgt in sigBs:
ensemble.ScoreToDb(bs, conn)
conn.Commit()
d = conn.GetData(table=self.dbTblName)
assert len(d) == len(sigBs), 'bad number of results returned'
for i in range(len(sigBs)):
bs, tgt = tuple(sigBs[i])
dbRes = tuple(d[i])
assert dbRes == tgt, 'bad bits returned: %s != %s' % (str(dbRes), str(tgt))
d = None
self.conn = None
def testdb2(self):
""" test the sig - db functionality """
conn = self._setupDb()
ensemble = BitEnsemble()
for bit in [1, 3, 4]:
ensemble.AddBit(bit)
sigBs = [([0, 0, 0, 0, 0, 0], (0, 0, 0)),
([0, 1, 0, 1, 0, 0], (1, 1, 0)),
([0, 1, 0, 0, 1, 0], (1, 0, 1)),
([0, 1, 0, 0, 1, 1], (1, 0, 1)), ]
ensemble.InitScoreTable(conn, self.dbTblName, idInfo='id varchar(10)', actInfo='act int')
for bs, tgt in sigBs:
ensemble.ScoreToDb(bs, conn, id='foo', act=1)
conn.Commit()
d = conn.GetData(table=self.dbTblName)
assert len(d) == len(sigBs), 'bad number of results returned'
for i in range(len(sigBs)):
bs, tgt = tuple(sigBs[i])
dbRes = tuple(d[i])
assert dbRes[1:-1] == tgt, 'bad bits returned: %s != %s' % (str(dbRes[1:-1]), str(tgt))
d = None
self.conn = None
if __name__ == '__main__': # pragma: nocover
unittest.main()
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"""unit testing code for fingerprinting
"""
import unittest
from rdkit import Chem
from rdkit import DataStructs
def feq(v1,v2,tol=1e-4):
return abs(v1-v2)<=tol
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
pass
def test1(self):
# FIX: test HashAtom
pass
def test2(self):
# FIX: test HashBond
pass
def test3(self):
# FIX: test HashPath
pass
def test4(self):
""" check containing mols, no Hs, no valence
"""
tgts = [ ('CCC(O)C(=O)O',
('CCC','OCC','OCC=O','OCCO','CCCC','OC=O','CC(O)C')),
]
for smi,matches in tgts:
m = Chem.MolFromSmiles(smi)
fp1 = Chem.RDKFingerprint(m,2,7,9192,4,0)
obs = fp1.GetOnBits()
for match in matches:
m2 = Chem.MolFromSmiles(match)
fp2 = Chem.RDKFingerprint(m2,2,7,9192,4,0)
v1,v2 = DataStructs.OnBitProjSimilarity(fp2,fp1)
assert feq(v1,1.0000),'substruct %s not properly contained in %s'%(match,smi)
def test5(self):
""" check containing mols, use Hs, no valence
"""
tgts = [ ('CCC(O)C(=O)O',
('O[CH-][CH2-]','O[CH-][C-]=O')),
]
for smi,matches in tgts:
m = Chem.MolFromSmiles(smi)
fp1 = Chem.RDKFingerprint(m,2,7,9192,4,1)
obs = fp1.GetOnBits()
for match in matches:
m2 = Chem.MolFromSmiles(match)
fp2 = Chem.RDKFingerprint(m2,2,7,9192,4,1)
v1,v2 = DataStructs.OnBitProjSimilarity(fp2,fp1)
assert feq(v1,1.0000),'substruct %s not properly contained in %s'%(match,smi)
def test6(self):
""" check that the bits in a signature of size N which has been folded in half
are the same as those in a signature of size N/2
"""
smis = [ 'CCC(O)C(=O)O','c1ccccc1','C1CCCCC1','C1NCCCC1','CNCNCNC']
for smi in smis:
m = Chem.MolFromSmiles(smi)
fp1 = Chem.RDKFingerprint(m,2,7,4096)
fp2 = DataStructs.FoldFingerprint(fp1,2)
fp3 = Chem.RDKFingerprint(m,2,7,2048)
assert tuple(fp2.GetOnBits())==tuple(fp3.GetOnBits())
fp2 = DataStructs.FoldFingerprint(fp2,2)
fp3 = Chem.RDKFingerprint(m,2,7,1024)
assert tuple(fp2.GetOnBits())==tuple(fp3.GetOnBits())
fp2 = DataStructs.FoldFingerprint(fp1,4)
assert tuple(fp2.GetOnBits())==tuple(fp3.GetOnBits())
if __name__ == '__main__':
unittest.main()
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"""unit testing code for fingerprinting
"""
import unittest
from rdkit import Chem
from rdkit import DataStructs
class TestCase(unittest.TestCase):
def test1(self):
# FIX: test HashAtom
pass
def test2(self):
# FIX: test HashBond
pass
def test3(self):
# FIX: test HashPath
pass
def test4(self):
""" check containing mols, no Hs, no valence """
tgts = [('CCC(O)C(=O)O', ('CCC', 'OCC', 'OCC=O', 'OCCO', 'CCCC', 'OC=O', 'CC(O)C')), ]
for smi, matches in tgts:
m = Chem.MolFromSmiles(smi)
fp1 = Chem.RDKFingerprint(m, 2, 7, 9192, 4, 0)
_ = fp1.GetOnBits()
for match in matches:
m2 = Chem.MolFromSmiles(match)
fp2 = Chem.RDKFingerprint(m2, 2, 7, 9192, 4, 0)
v1, _ = DataStructs.OnBitProjSimilarity(fp2, fp1)
self.assertAlmostEqual(v1, 1, 'substruct %s not properly contained in %s' % (match, smi))
def test5(self):
""" check containing mols, use Hs, no valence """
tgts = [('CCC(O)C(=O)O', ('O[CH-][CH2-]', 'O[CH-][C-]=O')), ]
for smi, matches in tgts:
m = Chem.MolFromSmiles(smi)
fp1 = Chem.RDKFingerprint(m, 2, 7, 9192, 4, 1)
_ = fp1.GetOnBits()
for match in matches:
m2 = Chem.MolFromSmiles(match)
fp2 = Chem.RDKFingerprint(m2, 2, 7, 9192, 4, 1)
v1, _ = DataStructs.OnBitProjSimilarity(fp2, fp1)
self.assertAlmostEqual(v1, 1, 'substruct %s not properly contained in %s' % (match, smi))
def test6(self):
""" check that the bits in a signature of size N which has been folded in half
are the same as those in a signature of size N/2 """
smis = ['CCC(O)C(=O)O', 'c1ccccc1', 'C1CCCCC1', 'C1NCCCC1', 'CNCNCNC']
for smi in smis:
m = Chem.MolFromSmiles(smi)
fp1 = Chem.RDKFingerprint(m, 2, 7, 4096)
fp2 = DataStructs.FoldFingerprint(fp1, 2)
fp3 = Chem.RDKFingerprint(m, 2, 7, 2048)
self.assertEqual(tuple(fp2.GetOnBits()), tuple(fp3.GetOnBits()))
fp2 = DataStructs.FoldFingerprint(fp2, 2)
fp3 = Chem.RDKFingerprint(m, 2, 7, 1024)
self.assertEqual(tuple(fp2.GetOnBits()), tuple(fp3.GetOnBits()))
fp2 = DataStructs.FoldFingerprint(fp1, 4)
self.assertEqual(tuple(fp2.GetOnBits()), tuple(fp3.GetOnBits()))
if __name__ == '__main__': # pragma: nocover
unittest.main()
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"""unit testing code for the DbResultSet object
"""
from rdkit import RDConfig
import unittest,os
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase.DbResultSet import DbResultSet,RandomAccessDbResultSet
class TestCase(unittest.TestCase):
def setUp(self):
self.dbName = RDConfig.RDTestDatabase
self.conn = DbConnect(self.dbName)
self.curs = self.conn.GetCursor()
def test1(self):
""" test indexing in, ensure acceptable error conditions
"""
cmd = 'select * from ten_elements'
set = RandomAccessDbResultSet(self.curs,self.conn,cmd)
for i in range(12):
try:
val = set[i]
except IndexError:
assert i >= 10
def test2(self):
"""
"""
cmd = 'select * from ten_elements'
set = RandomAccessDbResultSet(self.curs,self.conn,cmd)
assert len(set)==10
for i in range(len(set)):
val = set[i]
def test3(self):
"""
"""
cmd = 'select * from ten_elements'
set = DbResultSet(self.curs,self.conn,cmd)
r = []
for thing in set:
r.append(thing)
assert len(r)==10
def test4(self):
"""
"""
cmd = 'select * from ten_elements_dups'
set = DbResultSet(self.curs,self.conn,cmd,removeDups=0)
r = []
for thing in set:
r.append(thing)
assert len(r)==10
def test5(self):
"""
"""
cmd='select * from ten_elements_dups'
set = RandomAccessDbResultSet(self.curs,self.conn,cmd,removeDups=0)
assert len(set)==10
for i in range(len(set)):
val = set[i]
def test6(self):
"""
"""
cmd = 'select * from ten_elements_dups'
set = DbResultSet(self.curs,self.conn,cmd,removeDups=0)
r = []
for thing in set:
r.append(thing)
assert len(r)==10
if __name__ == '__main__':
unittest.main()
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"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.44377420574435733,
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"""unit testing code for the lazy signature generator
"""
import unittest
from rdkit import Chem
from rdkit.Chem.Pharm2D import SigFactory,LazyGenerator
class TestCase(unittest.TestCase):
def setUp(self):
self.factory = SigFactory.SigFactory()
self.factory.SetPatternsFromSmarts(['O','N'])
self.factory.SetBins([(0,2),(2,5),(5,8)])
self.factory.SetMinCount(2)
self.factory.SetMaxCount(3)
def test1(self):
""" simple tests
"""
mol = Chem.MolFromSmiles('OCC(=O)CCCN')
sig = self.factory.GetSignature()
assert sig.GetSize()==105,'bad signature size: %d'%(sig.GetSize())
sig.SetIncludeBondOrder(0)
gen = LazyGenerator.Generator(sig,mol)
assert len(gen) == sig.GetSize(),'length mismatch %d!=%d'%(len(gen),sig.GetSize())
tgt = (1,5,48)
for bit in tgt:
assert gen[bit],'bit %d not properly set'%(bit)
assert gen.GetBit(bit),'bit %d not properly set'%(bit)
assert not gen[bit+50],'bit %d improperly set'%(bit+100)
sig = self.factory.GetSignature()
assert sig.GetSize()==105,'bad signature size: %d'%(sig.GetSize())
sig.SetIncludeBondOrder(1)
gen = LazyGenerator.Generator(sig,mol)
assert len(gen) == sig.GetSize(),'length mismatch %d!=%d'%(len(gen),sig.GetSize())
tgt = (1,4,5,45)
for bit in tgt:
assert gen[bit],'bit %d not properly set'%(bit)
assert gen.GetBit(bit),'bit %d not properly set'%(bit)
assert not gen[bit+50],'bit %d improperly set'%(bit+100)
try:
gen[sig.GetSize()+1]
except IndexError:
ok = 1
else:
ok = 0
assert ok,'accessing bogus bit did not fail'
try:
gen[-1]
except IndexError:
ok = 1
else:
ok = 0
assert ok,'accessing bogus bit did not fail'
if __name__ == '__main__':
unittest.main()
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"""unit testing code for the Smiles file handling stuff
"""
import unittest,sys,os
from rdkit import RDConfig
from rdkit import Chem
from rdkit.six import next
class TestCase(unittest.TestCase):
def setUp(self):
self.smis = ['CC','CCC','CCCCC','CCCCCC','CCCCCCC','CC','CCCCOC']
def test1LazyReader(self):
" tests lazy reads """
supp = Chem.SmilesMolSupplierFromText('\n'.join(self.smis),',',0,-1,0)
for i in range(4):
m = next(supp)
assert m,'read %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
i = len(supp)-1
m = supp[i]
assert m,'read %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
ms = [x for x in supp]
for i in range(len(supp)):
m = ms[i]
if m:
ms[i] = Chem.MolToSmiles(m)
l = len(supp)
assert l == len(self.smis),'bad supplier length: %d'%(l)
i = len(self.smis)-3
m = supp[i-1]
assert m,'back index %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
with self.assertRaisesRegexp(Exception, ""):
m = supp[len(self.smis)] # out of bound read must fail
def test2LazyIter(self):
" tests lazy reads using the iterator interface "
supp = Chem.SmilesMolSupplierFromText('\n'.join(self.smis),',',0,-1,0)
nDone = 0
for mol in supp:
assert mol,'read %d failed'%nDone
assert mol.GetNumAtoms(),'no atoms in mol %d'%nDone
nDone += 1
assert nDone==len(self.smis),'bad number of molecules'
l = len(supp)
assert l == len(self.smis),'bad supplier length: %d'%(l)
i = len(self.smis)-3
m = supp[i-1]
assert m,'back index %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
with self.assertRaisesRegexp(Exception, ""):
m = supp[len(self.smis)] # out of bound read must not fail
def test3BoundaryConditions(self):
smis = ['CC','CCOC','fail','CCO']
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis),',',0,-1,0)
self.assertEqual(len(supp), 4)
self.assertIs(supp[2], None)
self.assertTrue(supp[3])
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis),',',0,-1,0)
self.assertIs(supp[2], None)
self.assertTrue(supp[3])
self.assertEqual(len(supp), 4)
with self.assertRaisesRegexp(Exception, ""):
supp[4]
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis),',',0,-1,0)
self.assertEqual(len(supp), 4)
self.assertTrue(supp[3])
with self.assertRaisesRegexp(Exception, ""):
supp[4]
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis),',',0,-1,0)
with self.assertRaisesRegexp(Exception, ""):
supp[4]
self.assertEqual(len(supp), 4)
self.assertTrue(supp[3])
if __name__ == '__main__':
unittest.main()
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"""unit testing code for the Smiles file handling stuff
"""
import unittest, sys, os
from rdkit import RDConfig
from rdkit import Chem
from rdkit.six import next
class TestCase(unittest.TestCase):
def setUp(self):
self.smis = ['CC', 'CCC', 'CCCCC', 'CCCCCC', 'CCCCCCC', 'CC', 'CCCCOC']
def test1LazyReader(self):
" tests lazy reads " ""
supp = Chem.SmilesMolSupplierFromText('\n'.join(self.smis), ',', 0, -1, 0)
for i in range(4):
m = next(supp)
assert m, 'read %d failed' % i
assert m.GetNumAtoms(), 'no atoms in mol %d' % i
i = len(supp) - 1
m = supp[i]
assert m, 'read %d failed' % i
assert m.GetNumAtoms(), 'no atoms in mol %d' % i
ms = [x for x in supp]
for i in range(len(supp)):
m = ms[i]
if m:
ms[i] = Chem.MolToSmiles(m)
l = len(supp)
assert l == len(self.smis), 'bad supplier length: %d' % (l)
i = len(self.smis) - 3
m = supp[i - 1]
assert m, 'back index %d failed' % i
assert m.GetNumAtoms(), 'no atoms in mol %d' % i
with self.assertRaisesRegexp(Exception, ""):
m = supp[len(self.smis)] # out of bound read must fail
def test2LazyIter(self):
" tests lazy reads using the iterator interface "
supp = Chem.SmilesMolSupplierFromText('\n'.join(self.smis), ',', 0, -1, 0)
nDone = 0
for mol in supp:
assert mol, 'read %d failed' % nDone
assert mol.GetNumAtoms(), 'no atoms in mol %d' % nDone
nDone += 1
assert nDone == len(self.smis), 'bad number of molecules'
l = len(supp)
assert l == len(self.smis), 'bad supplier length: %d' % (l)
i = len(self.smis) - 3
m = supp[i - 1]
assert m, 'back index %d failed' % i
assert m.GetNumAtoms(), 'no atoms in mol %d' % i
with self.assertRaisesRegexp(Exception, ""):
m = supp[len(self.smis)] # out of bound read must not fail
def test3BoundaryConditions(self):
smis = ['CC', 'CCOC', 'fail', 'CCO']
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis), ',', 0, -1, 0)
self.assertEqual(len(supp), 4)
self.assertIs(supp[2], None)
self.assertTrue(supp[3])
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis), ',', 0, -1, 0)
self.assertIs(supp[2], None)
self.assertTrue(supp[3])
self.assertEqual(len(supp), 4)
with self.assertRaisesRegexp(Exception, ""):
supp[4]
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis), ',', 0, -1, 0)
self.assertEqual(len(supp), 4)
self.assertTrue(supp[3])
with self.assertRaisesRegexp(Exception, ""):
supp[4]
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis), ',', 0, -1, 0)
with self.assertRaisesRegexp(Exception, ""):
supp[4]
self.assertEqual(len(supp), 4)
self.assertTrue(supp[3])
if __name__ == '__main__':
unittest.main()
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"""unit testing code for the Smiles file handling stuff
"""
import unittest,sys,os
from rdkit import RDConfig
from rdkit import Chem
class TestCase(unittest.TestCase):
def setUp(self):
self.smis = ['CC','CCC','CCCCC','CCCCCC','CCCCCCC','CC','CCCCOC']
def test1LazyReader(self):
" tests lazy reads """
supp = Chem.SmilesMolSupplierFromText('\n'.join(self.smis),',',0,-1,0)
for i in range(4):
m = supp.next()
assert m,'read %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
i = len(supp)-1
m = supp[i]
assert m,'read %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
ms = [x for x in supp]
for i in range(len(supp)):
m = ms[i]
if m:
ms[i] = Chem.MolToSmiles(m)
l = len(supp)
assert l == len(self.smis),'bad supplier length: %d'%(l)
i = len(self.smis)-3
m = supp[i-1]
assert m,'back index %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
try:
m = supp[len(self.smis)]
except:
fail = 1
else:
fail = 0
assert fail,'out of bound read did not fail'
def test2LazyIter(self):
" tests lazy reads using the iterator interface "
supp = Chem.SmilesMolSupplierFromText('\n'.join(self.smis),',',0,-1,0)
nDone = 0
for mol in supp:
assert mol,'read %d failed'%i
assert mol.GetNumAtoms(),'no atoms in mol %d'%i
nDone += 1
assert nDone==len(self.smis),'bad number of molecules'
l = len(supp)
assert l == len(self.smis),'bad supplier length: %d'%(l)
i = len(self.smis)-3
m = supp[i-1]
assert m,'back index %d failed'%i
assert m.GetNumAtoms(),'no atoms in mol %d'%i
try:
m = supp[len(self.smis)]
except:
fail = 1
else:
fail = 0
assert fail,'out of bound read did not fail'
def test3BoundaryConditions(self):
smis = ['CC','CCOC','fail','CCO']
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis),',',0,-1,0)
assert len(supp)==4
assert supp[2] is None
assert supp[3]
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis),',',0,-1,0)
assert supp[2] is None
assert supp[3]
assert len(supp)==4
try:
supp[4]
except:
ok=1
else:
ok=0
assert ok
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis),',',0,-1,0)
assert len(supp)==4
assert supp[3]
try:
supp[4]
except:
ok=1
else:
ok=0
assert ok
supp = Chem.SmilesMolSupplierFromText('\n'.join(smis),',',0,-1,0)
try:
supp[4]
except:
ok=1
else:
ok=0
assert ok
assert len(supp)==4
assert supp[3]
if __name__ == '__main__':
unittest.main()
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"""basic unit testing code for atoms
"""
import unittest
from rdkit import Chem
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
self.m = Chem.MolFromSmiles('CC(=O)CCSC')
def test1Implicit(self):
" testing ImplicitValence "
a = self.m.GetAtoms()[0]
iV = a.GetImplicitValence()
assert iV == 3
assert self.m.GetAtomWithIdx(1).GetImplicitValence() == 0
assert self.m.GetAtomWithIdx(2).GetImplicitValence() == 0
assert self.m.GetAtomWithIdx(3).GetImplicitValence() == 2
def test2BondIter(self):
" testing bond iteration "
a = self.m.GetAtomWithIdx(1)
bs = a.GetBonds()
r = []
for b in bs:
r.append(b)
assert len(r) == 3
def test3GetBond(self):
" testing GetBondBetweenAtoms(idx,idx) "
b = self.m.GetBondBetweenAtoms(1, 2)
assert b.GetBondType() == Chem.BondType.DOUBLE, 'GetBond failed'
def test4Props(self):
" testing atomic props "
a = self.m.GetAtomWithIdx(1)
assert a.GetSymbol() == 'C'
assert a.GetAtomicNum() == 6
assert a.GetFormalCharge() == 0
assert a.GetDegree() == 3
assert a.GetImplicitValence() == 0
assert a.GetExplicitValence() == 4
def test5Setters(self):
" testing setting atomic props "
a = Chem.Atom(6)
assert a.GetSymbol() == 'C'
assert a.GetAtomicNum() == 6
a.SetFormalCharge(1)
assert a.GetFormalCharge() == 1
try:
a.GetImplicitValence()
except RuntimeError:
ok = 1
else:
ok = 0
assert ok
if __name__ == '__main__':
unittest.main()
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"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.967819066518374,
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from __future__ import print_function
try:
from reportlab import platypus
except ImportError:
import sys
sys.stderr.write('ReportLab module could not be imported. Db->PDF functionality not available')
GetReportlabTable = None
QuickReport = None
else:
from rdkit import Chem
try:
from pyRDkit.utils import chemdraw
except ImportError:
hasCDX = 0
else:
hasCDX = 1
from rdkit.utils import cactvs
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import DrawUtils
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbInfo
from rdkit.Reports.PDFReport import PDFReport, ReportUtils
from rdkit.sping.ReportLab.pidReportLab import RLCanvas as Canvas
from rdkit.Chem.Draw.MolDrawing import MolDrawing, DrawingOptions
from reportlab.lib import colors
from reportlab.lib.units import inch
import sys
def GetReportlabTable(self, *args, **kwargs):
""" this becomes a method of DbConnect """
dbRes = self.GetData(*args, **kwargs)
rawD = [dbRes.GetColumnNames()]
colTypes = dbRes.GetColumnTypes()
binCols = []
for i in range(len(colTypes)):
if colTypes[i] in DbInfo.sqlBinTypes or colTypes[i] == 'binary':
binCols.append(i)
nRows = 0
for entry in dbRes:
nRows += 1
for col in binCols:
entry = list(entry)
entry[col] = 'N/A'
rawD.append(entry)
res = platypus.Table(rawD)
return res
class CDXImageTransformer(object):
def __init__(self, smiCol, width=1, verbose=1, tempHandler=None):
self.smiCol = smiCol
if tempHandler is None:
tempHandler = ReportUtils.TempFileHandler()
self.tempHandler = tempHandler
self.width = width * inch
self.verbose = verbose
def __call__(self, arg):
res = list(arg)
if self.verbose:
print('Render:', res[0])
if hasCDX:
smi = res[self.smiCol]
tmpName = self.tempHandler.get('.jpg')
try:
img = chemdraw.SmilesToPilImage(smi)
w, h = img.size
aspect = float(h) / w
img.save(tmpName)
img = platypus.Image(tmpName)
img.drawWidth = self.width
img.drawHeight = aspect * self.width
res[self.smiCol] = img
except Exception:
import traceback
traceback.print_exc()
res[self.smiCol] = 'Failed'
return res
class CactvsImageTransformer(object):
def __init__(self, smiCol, width=1., verbose=1, tempHandler=None):
self.smiCol = smiCol
if tempHandler is None:
tempHandler = ReportUtils.TempFileHandler()
self.tempHandler = tempHandler
self.width = width * inch
self.verbose = verbose
def __call__(self, arg):
res = list(arg)
if self.verbose:
sys.stderr.write('Render(%d): %s\n' % (self.smiCol, str(res[0])))
smi = res[self.smiCol]
tmpName = self.tempHandler.get('.gif')
aspect = 1
width = 300
height = aspect * width
ok = cactvs.SmilesToGif(smi, tmpName, (width, height))
if ok:
try:
img = platypus.Image(tmpName)
img.drawWidth = self.width
img.drawHeight = aspect * self.width
except Exception:
ok = 0
if ok:
res[self.smiCol] = img
else:
# FIX: maybe include smiles here in a Paragraph?
res[self.smiCol] = 'Failed'
return res
class ReportLabImageTransformer(object):
def __init__(self, smiCol, width=1., verbose=1, tempHandler=None):
self.smiCol = smiCol
self.width = width * inch
self.verbose = verbose
def __call__(self, arg):
res = list(arg)
if self.verbose:
sys.stderr.write('Render(%d): %s\n' % (self.smiCol, str(res[0])))
smi = res[self.smiCol]
aspect = 1
width = self.width
height = aspect * width
try:
mol = Chem.MolFromSmiles(smi)
Chem.Kekulize(mol)
canv = Canvas((width, height))
options = DrawingOptions()
options.atomLabelMinFontSize = 3
options.bondLineWidth = 0.5
drawing = MolDrawing(options=options)
if not mol.GetNumConformers():
rdDepictor.Compute2DCoords(mol)
drawing.AddMol(mol, canvas=canv)
ok = True
except Exception:
if self.verbose:
import traceback
traceback.print_exc()
ok = False
if ok:
res[self.smiCol] = canv.drawing
else:
# FIX: maybe include smiles here in a Paragraph?
res[self.smiCol] = 'Failed'
return res
class RDImageTransformer(object):
def __init__(self, smiCol, width=1., verbose=1, tempHandler=None):
self.smiCol = smiCol
if tempHandler is None:
tempHandler = ReportUtils.TempFileHandler()
self.tempHandler = tempHandler
self.width = width * inch
self.verbose = verbose
def __call__(self, arg):
res = list(arg)
if self.verbose:
sys.stderr.write('Render(%d): %s\n' % (self.smiCol, str(res[0])))
smi = res[self.smiCol]
tmpName = self.tempHandler.get('.jpg')
aspect = 1
width = 300
height = aspect * width
ok = DrawUtils.SmilesToJpeg(smi, tmpName, size=(width, height))
if ok:
try:
img = platypus.Image(tmpName)
img.drawWidth = self.width
img.drawHeight = aspect * self.width
except Exception:
ok = 0
if ok:
res[self.smiCol] = img
else:
# FIX: maybe include smiles here in a Paragraph?
res[self.smiCol] = 'Failed'
return res
def QuickReport(conn, fileName, *args, **kwargs):
title = 'Db Report'
if 'title' in kwargs:
title = kwargs['title']
del kwargs['title']
names = [x.upper() for x in conn.GetColumnNames()]
try:
smiCol = names.index('SMILES')
except ValueError:
try:
smiCol = names.index('SMI')
except ValueError:
smiCol = -1
if smiCol > -1:
if hasCDX:
tform = CDXImageTransformer(smiCol)
elif 1:
tform = ReportLabImageTransformer(smiCol)
else:
tform = CactvsImageTransformer(smiCol)
else:
tform = None
kwargs['transform'] = tform
tbl = conn.GetReportlabTable(*args, **kwargs)
tbl.setStyle(
platypus.TableStyle([('GRID', (0, 0), (-1, -1), 1, colors.black),
('FONT', (0, 0), (-1, -1), 'Times-Roman', 8), ]))
if smiCol > -1 and tform:
tbl._argW[smiCol] = tform.width * 1.2
elements = [tbl]
reportTemplate = PDFReport()
reportTemplate.pageHeader = title
doc = platypus.SimpleDocTemplate(fileName)
doc.build(elements, onFirstPage=reportTemplate.onPage, onLaterPages=reportTemplate.onPage)
DbConnect.GetReportlabTable = GetReportlabTable
if __name__ == '__main__':
dbName = sys.argv[1]
tblName = sys.argv[2]
fName = 'report.pdf'
conn = DbConnect(dbName, tblName)
QuickReport(conn, fName, where="where mol_id in ('1','100','104','107')")
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"few_assignments": false,
"quality_score": 1,
"avg_score": 0.021081300847869935,
"num_lines": 246
} |
from __future__ import print_function
try:
from reportlab import platypus
except ImportError:
import sys
sys.stderr.write('ReportLab module could not be imported. Db->PDF functionality not available')
GetReportlabTable = None
QuickReport = None
else:
from rdkit import Chem
try:
from pyRDkit.utils import chemdraw
except ImportError:
hasCDX = 0
else:
hasCDX = 1
from rdkit.utils import cactvs
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import DrawUtils
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbInfo
from rdkit.Reports.PDFReport import PDFReport, ReportUtils
import os, tempfile, sys
def GetReportlabTable(self, *args, **kwargs):
""" this becomes a method of DbConnect """
dbRes = self.GetData(*args, **kwargs)
rawD = [dbRes.GetColumnNames()]
colTypes = dbRes.GetColumnTypes()
binCols = []
for i in range(len(colTypes)):
if colTypes[i] in DbInfo.sqlBinTypes or colTypes[i] == 'binary':
binCols.append(i)
nRows = 0
for entry in dbRes:
nRows += 1
for col in binCols:
entry = list(entry)
entry[col] = 'N/A'
rawD.append(entry)
#if nRows >10: break
res = platypus.Table(rawD)
return res
from reportlab.lib.units import inch
class CDXImageTransformer(object):
def __init__(self, smiCol, width=1, verbose=1, tempHandler=None):
self.smiCol = smiCol
if tempHandler is None:
tempHandler = ReportUtils.TempFileHandler()
self.tempHandler = tempHandler
self.width = width * inch
self.verbose = verbose
def __call__(self, arg):
res = list(arg)
if self.verbose:
print('Render:', res[0])
if hasCDX:
smi = res[self.smiCol]
tmpName = self.tempHandler.get('.jpg')
try:
img = chemdraw.SmilesToPilImage(smi)
w, h = img.size
aspect = float(h) / w
img.save(tmpName)
img = platypus.Image(tmpName)
img.drawWidth = self.width
img.drawHeight = aspect * self.width
res[self.smiCol] = img
except Exception:
import traceback
traceback.print_exc()
res[self.smiCol] = 'Failed'
return res
class CactvsImageTransformer(object):
def __init__(self, smiCol, width=1., verbose=1, tempHandler=None):
self.smiCol = smiCol
if tempHandler is None:
tempHandler = ReportUtils.TempFileHandler()
self.tempHandler = tempHandler
self.width = width * inch
self.verbose = verbose
def __call__(self, arg):
res = list(arg)
if self.verbose:
sys.stderr.write('Render(%d): %s\n' % (self.smiCol, str(res[0])))
smi = res[self.smiCol]
tmpName = self.tempHandler.get('.gif')
aspect = 1
width = 300
height = aspect * width
ok = cactvs.SmilesToGif(smi, tmpName, (width, height))
if ok:
try:
img = platypus.Image(tmpName)
img.drawWidth = self.width
img.drawHeight = aspect * self.width
except Exception:
ok = 0
if ok:
res[self.smiCol] = img
else:
# FIX: maybe include smiles here in a Paragraph?
res[self.smiCol] = 'Failed'
return res
from rdkit.sping.ReportLab.pidReportLab import RLCanvas as Canvas
from rdkit.Chem.Draw.MolDrawing import MolDrawing, DrawingOptions
class ReportLabImageTransformer(object):
def __init__(self, smiCol, width=1., verbose=1, tempHandler=None):
self.smiCol = smiCol
self.width = width * inch
self.verbose = verbose
def __call__(self, arg):
res = list(arg)
if self.verbose:
sys.stderr.write('Render(%d): %s\n' % (self.smiCol, str(res[0])))
smi = res[self.smiCol]
aspect = 1
width = self.width
height = aspect * width
try:
mol = Chem.MolFromSmiles(smi)
Chem.Kekulize(mol)
canv = Canvas((width, height))
options = DrawingOptions()
options.atomLabelMinFontSize = 3
options.bondLineWidth = 0.5
drawing = MolDrawing(options=options)
if not mol.GetNumConformers():
rdDepictor.Compute2DCoords(mol)
drawing.AddMol(mol, canvas=canv)
ok = True
except Exception:
if self.verbose:
import traceback
traceback.print_exc()
ok = False
if ok:
res[self.smiCol] = canv.drawing
else:
# FIX: maybe include smiles here in a Paragraph?
res[self.smiCol] = 'Failed'
return res
class RDImageTransformer(object):
def __init__(self, smiCol, width=1., verbose=1, tempHandler=None):
self.smiCol = smiCol
if tempHandler is None:
tempHandler = ReportUtils.TempFileHandler()
self.tempHandler = tempHandler
self.width = width * inch
self.verbose = verbose
def __call__(self, arg):
res = list(arg)
if self.verbose:
sys.stderr.write('Render(%d): %s\n' % (self.smiCol, str(res[0])))
smi = res[self.smiCol]
tmpName = self.tempHandler.get('.jpg')
aspect = 1
width = 300
height = aspect * width
ok = DrawUtils.SmilesToJpeg(smi, tmpName, size=(width, height))
if ok:
try:
img = platypus.Image(tmpName)
img.drawWidth = self.width
img.drawHeight = aspect * self.width
except Exception:
ok = 0
if ok:
res[self.smiCol] = img
else:
# FIX: maybe include smiles here in a Paragraph?
res[self.smiCol] = 'Failed'
return res
def QuickReport(conn, fileName, *args, **kwargs):
from reportlab.lib import colors
from reportlab.lib.styles import getSampleStyleSheet
from reportlab.lib.units import inch
styles = getSampleStyleSheet()
title = 'Db Report'
if kwargs.has_key('title'):
title = kwargs['title']
del kwargs['title']
names = [x.upper() for x in conn.GetColumnNames()]
try:
smiCol = names.index('SMILES')
except ValueError:
try:
smiCol = names.index('SMI')
except ValueError:
smiCol = -1
if smiCol > -1:
if hasCDX:
tform = CDXImageTransformer(smiCol)
elif 1:
tform = ReportLabImageTransformer(smiCol)
else:
tform = CactvsImageTransformer(smiCol)
else:
tform = None
kwargs['transform'] = tform
tbl = conn.GetReportlabTable(*args, **kwargs)
tbl.setStyle(
platypus.TableStyle([('GRID', (0, 0), (-1, -1), 1, colors.black),
('FONT', (0, 0), (-1, -1), 'Times-Roman', 8), ]))
if smiCol > -1 and tform:
tbl._argW[smiCol] = tform.width * 1.2
elements = [tbl]
reportTemplate = PDFReport()
reportTemplate.pageHeader = title
doc = platypus.SimpleDocTemplate(fileName)
doc.build(elements, onFirstPage=reportTemplate.onPage, onLaterPages=reportTemplate.onPage)
DbConnect.GetReportlabTable = GetReportlabTable
if __name__ == '__main__':
import sys
dbName = sys.argv[1]
tblName = sys.argv[2]
fName = 'report.pdf'
conn = DbConnect(dbName, tblName)
QuickReport(conn, fName, where="where mol_id in ('1','100','104','107')")
| {
"repo_name": "jandom/rdkit",
"path": "rdkit/Dbase/DbReport.py",
"copies": "1",
"size": "7541",
"license": "bsd-3-clause",
"hash": 9116067528467865000,
"line_mean": 28.8063241107,
"line_max": 98,
"alpha_frac": 0.6133138841,
"autogenerated": false,
"ratio": 3.478321033210332,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.9486164033354745,
"avg_score": 0.02109417679111748,
"num_lines": 253
} |
from rdkit import RDConfig
if hasattr(RDConfig,"usePgSQL") and RDConfig.usePgSQL:
from pyPgSQL import PgSQL
# as of this writing (March 2004), this results in a speedup in
# getting results back from the wrapper:
PgSQL.fetchReturnsList=1
from pyPgSQL.PgSQL import *
sqlTextTypes = [PG_CHAR,PG_BPCHAR,PG_TEXT,PG_VARCHAR,PG_NAME]
sqlIntTypes = [PG_INT8,PG_INT2,PG_INT4]
sqlFloatTypes = [PG_FLOAT4,PG_FLOAT8]
sqlBinTypes = [PG_OID,PG_BLOB,PG_BYTEA]
getTablesSql = """select tablename from pg_tables where schemaname='public'"""
getTablesAndViewsSql = """SELECT c.relname as "Name"
FROM pg_catalog.pg_class c
LEFT JOIN pg_catalog.pg_user u ON u.usesysid = c.relowner
LEFT JOIN pg_catalog.pg_namespace n ON n.oid = c.relnamespace
WHERE c.relkind IN ('r','v','S','')
AND n.nspname NOT IN ('pg_catalog', 'pg_toast')
AND pg_catalog.pg_table_is_visible(c.oid)
"""
getDbSql = """ select datname from pg_database where datallowconn """
fileWildcard=None
placeHolder='%s'
binaryTypeName="bytea"
binaryHolder = PgBytea
RDTestDatabase="::RDTests"
elif hasattr(RDConfig,"useSqlLite") and RDConfig.useSqlLite:
try:
import sqlite3 as sqlite
#from sqlite3 import *
except ImportError:
from pysqlite2 import dbapi2 as sqlite
#from pysqlite2 import *
sqlTextTypes = []
sqlIntTypes = []
sqlFloatTypes = []
sqlBinTypes = []
getTablesSql = """select name from SQLite_Master where type='table'"""
getTablesAndViewsSql = """select name from SQLite_Master where type in ('table','view')"""
getDbSql = None
dbFileWildcard='*.sqlt'
placeHolder='?'
binaryTypeName="blob"
binaryHolder = buffer
connect = lambda x,*args:sqlite.connect(x)
else:
raise ImportError,"Neither sqlite nor PgSQL support found."
| {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Dbase/DbModule.py",
"copies": "2",
"size": "2081",
"license": "bsd-3-clause",
"hash": 1634136791542979800,
"line_mean": 33.1147540984,
"line_max": 92,
"alpha_frac": 0.7025468525,
"autogenerated": false,
"ratio": 3.2566510172143976,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.4959197869714398,
"avg_score": null,
"num_lines": null
} |
from rdkit import six
from rdkit import RDConfig
if hasattr(RDConfig,"usePgSQL") and RDConfig.usePgSQL:
from pyPgSQL import PgSQL
# as of this writing (March 2004), this results in a speedup in
# getting results back from the wrapper:
PgSQL.fetchReturnsList=1
from pyPgSQL.PgSQL import *
sqlTextTypes = [PG_CHAR,PG_BPCHAR,PG_TEXT,PG_VARCHAR,PG_NAME]
sqlIntTypes = [PG_INT8,PG_INT2,PG_INT4]
sqlFloatTypes = [PG_FLOAT4,PG_FLOAT8]
sqlBinTypes = [PG_OID,PG_BLOB,PG_BYTEA]
getTablesSql = """select tablename from pg_tables where schemaname='public'"""
getTablesAndViewsSql = """SELECT c.relname as "Name"
FROM pg_catalog.pg_class c
LEFT JOIN pg_catalog.pg_user u ON u.usesysid = c.relowner
LEFT JOIN pg_catalog.pg_namespace n ON n.oid = c.relnamespace
WHERE c.relkind IN ('r','v','S','')
AND n.nspname NOT IN ('pg_catalog', 'pg_toast')
AND pg_catalog.pg_table_is_visible(c.oid)
"""
getDbSql = """ select datname from pg_database where datallowconn """
fileWildcard=None
placeHolder='%s'
binaryTypeName="bytea"
binaryHolder = PgBytea
RDTestDatabase="::RDTests"
elif hasattr(RDConfig,"useSqlLite") and RDConfig.useSqlLite:
try:
import sqlite3 as sqlite
#from sqlite3 import *
except ImportError:
from pysqlite2 import dbapi2 as sqlite
#from pysqlite2 import *
sqlTextTypes = []
sqlIntTypes = []
sqlFloatTypes = []
sqlBinTypes = []
getTablesSql = """select name from SQLite_Master where type='table'"""
getTablesAndViewsSql = """select name from SQLite_Master where type in ('table','view')"""
getDbSql = None
dbFileWildcard='*.sqlt'
placeHolder='?'
binaryTypeName="blob"
binaryHolder = memoryview if six.PY3 else buffer
connect = lambda x,*args:sqlite.connect(x)
else:
raise ImportError("Neither sqlite nor PgSQL support found.")
| {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/Dbase/DbModule.py",
"copies": "4",
"size": "2131",
"license": "bsd-3-clause",
"hash": -681594176932317000,
"line_mean": 33.3709677419,
"line_max": 92,
"alpha_frac": 0.7048334115,
"autogenerated": false,
"ratio": 3.26840490797546,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.597323831947546,
"avg_score": null,
"num_lines": null
} |
from xml.etree import ElementTree
# check the version of ElementTree. We need at least version 1.2
# in order for the XPath-style parsing stuff to work
import re
vers = re.split("[a-zA-Z]",ElementTree.VERSION)[0]
if vers < '1.2':
raise ImportError,'The PubMed record interface requires a version of ElementTree >= 1.2'
class Record(object):
def __init__(self,element):
for field in self._fieldsOfInterest:
setattr(self,field,'')
self._element = element
def toXML(self):
from cStringIO import StringIO
sio = StringIO()
ElementTree.ElementTree(self._element).write(sio)
return sio.getvalue()
class SummaryRecord(Record):
_fieldsOfInterest=['PubMedId','PubDate','Source','Authors',
'Title','Volume','Issue','Pages','Lang',
'HasAbstract','RecordStatus']
def __init__(self,element):
Record.__init__(self,element)
for item in element.getiterator('Item'):
if item.attrib['Name'] in self._fieldsOfInterest:
setattr(self,item.attrib['Name'],item.text)
if self.PubDate:
self.PubYear = str(self.PubDate).split(' ')[0]
class JournalArticleRecord(Record):
_fieldsOfInterest=['PubMedId','PubYear','Source','Authors',
'Title','Volume','Issue','Pages','Lang',
'Abstract']
def __init__(self,element):
Record.__init__(self,element)
cite = self._element.find('MedlineCitation')
self.PubMedId = cite.findtext('PMID')
article = cite.find('Article')
issue = article.find('Journal/JournalIssue')
self.Volume = issue.findtext('Volume')
self.Issue = issue.findtext('Issue')
self.PubYear = issue.findtext('PubDate/Year')
if not self.PubYear:
txt = issue.findtext('PubDate/MedlineDate')
self.PubYear = txt.split(' ')[0]
self.Title = unicode(article.findtext('ArticleTitle'))
self.Pages = article.findtext('Pagination/MedlinePgn')
abs = article.findtext('Abstract/AbstractText')
if abs:
self.Abstract = unicode(abs)
self.authors = []
tmp = []
for author in article.find('AuthorList').getiterator('Author'):
last = unicode(author.findtext('LastName'))
first = unicode(author.findtext('ForeName'))
initials = unicode(author.findtext('Initials'))
self.authors.append((last,first,initials))
tmp.append('%s %s'%(last,initials))
self.Authors=', '.join(tmp)
journal = cite.findtext('MedlineJournalInfo/MedlineTA')
if journal:
self.Source = unicode(journal)
self.ParseKeywords()
self.ParseChemicals()
def ParseKeywords(self):
self.keywords = []
headings = self.find('MedlineCitation/MeshHeadingList')
if headings:
for heading in headings.getiterator('MeshHeading'):
kw = unicode(heading.findtext('DescriptorName'))
for qualifier in heading.getiterator('QualifierName'):
kw += ' / %s'%(unicode(qualifier.text))
self.keywords.append(kw)
def ParseChemicals(self):
self.chemicals = []
chemicals = self.find('MedlineCitation/ChemicalList')
if chemicals:
for chemical in chemicals.getiterator('Chemical'):
name = chemical.findtext('NameOfSubstance').encode('utf-8')
rn = chemical.findtext('RegistryNumber').encode('utf-8')
if rn != '0':
self.chemicals.append('%s <%s>'%(name,rn))
else:
self.chemicals.append('%s'%(name))
# --------------------------------------------
#
# We'll expose these ElementTree methods in case
# client code wants to pull extra info
#
def getiterator(self,key=None):
if key is not None:
return self._element.getiterator(key)
else:
return self._element.getiterator()
def find(self,key):
return self._element.find(key)
def findtext(self,key):
return self._element.findtext(key)
def findall(self,key):
return self._element.findall(key)
class LinkRecord(Record):
_fieldsOfInterest=[]
def __init__(self,element):
Record.__init__(self,element)
self.PubMedId = self._element.text
nbr = self._element.get('HasNeighbor','N')
if nbr == 'Y':
self.HasNeighbor = 1
else:
self.HasNeighbor = 0
| {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Dbase/Pubmed/Records.py",
"copies": "2",
"size": "4495",
"license": "bsd-3-clause",
"hash": 3040483159045184500,
"line_mean": 32.5447761194,
"line_max": 90,
"alpha_frac": 0.6418242492,
"autogenerated": false,
"ratio": 3.598879103282626,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.5240703352482626,
"avg_score": null,
"num_lines": null
} |
""" functionality for drawing hierarchical catalogs on sping
canvases
"""
from sping import pid as piddle
class VisOpts(object):
circRad = 10
minCircRad = 4
maxCircRad = 16
circColor = piddle.Color(0.6, 0.6, 0.9)
terminalEmptyColor = piddle.Color(.8, .8, .2)
terminalOnColor = piddle.Color(0.8, 0.8, 0.8)
terminalOffColor = piddle.Color(0.2, 0.2, 0.2)
outlineColor = piddle.transparent
lineColor = piddle.Color(0, 0, 0)
lineWidth = 1
horizOffset = 5
vertOffset = 75
topMargin = 20
labelFont = piddle.Font(face='helvetica', size=10)
highlightColor = piddle.Color(1., 1., .4)
highlightWidth = 2
visOpts = VisOpts()
def GetMinCanvasSize(adjList, levelList):
maxAcross = -1
for k in levelList.keys():
nHere = len(levelList[k])
maxAcross = max(maxAcross, nHere)
nLevs = len(levelList.keys())
minSize = (maxAcross * (visOpts.minCircRad * 2 + visOpts.horizOffset),
visOpts.topMargin + nLevs * visOpts.vertOffset)
return minSize
def DrawHierarchy(adjList, levelList, canvas, entryColors=None, bitIds=None, minLevel=-1,
maxLevel=1e8):
"""
Arguments:
- adjList: adjacency list representation of the hierarchy to be drawn
- levelList: dictionary mapping level -> list of ids
"""
if bitIds is None:
bitIds = []
if entryColors is None:
entryColors = {}
levelLengths = levelList.keys()
levelLengths.sort()
minLevel = max(minLevel, levelLengths[0])
maxLevel = min(maxLevel, levelLengths[-1])
dims = canvas.size
drawLocs = {}
# start at the bottom of the hierarchy and work up:
for levelLen in range(maxLevel, minLevel - 1, -1):
nLevelsDown = levelLen - minLevel
pos = [0, visOpts.vertOffset * nLevelsDown + visOpts.topMargin]
ids = levelList.get(levelLen, [])
# FIX: we'll eventually want to figure out some kind of sorting here:
nHere = len(ids)
canvas.defaultFont = visOpts.labelFont
if nHere:
# figure the size of each node at this level:
spacePerNode = float(dims[0]) / nHere
spacePerNode -= visOpts.horizOffset
nodeRad = max(spacePerNode / 2, visOpts.minCircRad)
nodeRad = min(nodeRad, visOpts.maxCircRad)
spacePerNode = nodeRad * 2 + visOpts.horizOffset
# start in the midde of the canvas:
pos[0] = dims[0] / 2.
# maybe we need to offset a little:
if nHere % 2:
pos[0] -= spacePerNode / 2
# move to the left by half the number of nodes:
pos[0] -= (nHere // 2 - .5) * spacePerNode
# Find the locations and draw connectors:
for ID in ids:
if not bitIds or ID in bitIds:
# first do lines down to the next level:
if levelLen != maxLevel:
for neighbor in adjList[ID]:
if neighbor in drawLocs:
p2 = drawLocs[neighbor][0]
canvas.drawLine(pos[0], pos[1], p2[0], p2[1], visOpts.lineColor, visOpts.lineWidth)
drawLocs[ID] = tuple(pos), nodeRad
pos[0] += spacePerNode
for ID in drawLocs.keys():
pos, nodeRad = drawLocs[ID]
x1, y1 = pos[0] - nodeRad, pos[1] - nodeRad
x2, y2 = pos[0] + nodeRad, pos[1] + nodeRad
drawColor = entryColors.get(ID, visOpts.circColor)
canvas.drawEllipse(x1, y1, x2, y2, visOpts.outlineColor, 0, drawColor)
label = str(ID)
# txtLoc = ( pos[0]-canvas.stringWidth(label)/2,
# pos[1]+canvas.fontHeight()/4 )
txtLoc = (pos[0] + canvas.fontHeight() / 4, pos[1] + canvas.stringWidth(label) / 2)
canvas.drawString(label, txtLoc[0], txtLoc[1], angle=90)
return drawLocs
| {
"repo_name": "rvianello/rdkit",
"path": "rdkit/DataStructs/HierarchyVis.py",
"copies": "5",
"size": "3875",
"license": "bsd-3-clause",
"hash": 1510835844414436600,
"line_mean": 30.25,
"line_max": 99,
"alpha_frac": 0.6459354839,
"autogenerated": false,
"ratio": 3.1555374592833876,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.6301472943183387,
"avg_score": null,
"num_lines": null
} |
import bisect
class TopNContainer(object):
""" maintains a sorted list of a particular number of data elements.
"""
def __init__(self,size,mostNeg=-1e99):
self._size = size
self.best = [mostNeg]*self._size
self.extras = [None]*self._size
def Insert(self,val,extra=None):
""" only does the insertion if val fits """
if val > self.best[0]:
idx = bisect.bisect(self.best,val)
# insert the new element
if idx == self._size:
self.best.append(val)
self.extras.append(extra)
else:
self.best.insert(idx,val)
self.extras.insert(idx,extra)
# and pop off the head
self.best.pop(0)
self.extras.pop(0)
def GetPts(self):
""" returns our set of points """
return self.best
def GetExtras(self):
""" returns our set of extras """
return self.extras
def __len__(self):
return self._size
def __getitem__(self,which):
return self.best[which],self.extras[which]
def reverse(self):
self.best.reverse()
self.extras.reverse()
if __name__ == '__main__':
import random
pts = [int(100*random.random()) for x in range(10)]
c = TopNContainer(4)
for pt in pts:
c.Insert(pt,extra=str(pt))
print c.GetPts()
print c.GetExtras()
| {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/DataStructs/TopNContainer.py",
"copies": "1",
"size": "1553",
"license": "bsd-3-clause",
"hash": -8394464511504048000,
"line_mean": 24.8833333333,
"line_max": 70,
"alpha_frac": 0.6258853831,
"autogenerated": false,
"ratio": 3.368763557483731,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.9285420157440427,
"avg_score": 0.04184575662866074,
"num_lines": 60
} |
import copy
urlBase="http://eutils.ncbi.nlm.nih.gov/entrez/eutils"
searchBase=urlBase+"/esearch.fcgi"
summaryBase=urlBase+"/esummary.fcgi"
fetchBase=urlBase+"/efetch.fcgi"
linkBase=urlBase+"/elink.fcgi"
# for links to pubmed web pages:
queryBase="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
_details = {
'db':'pubmed',
'retmode':'xml',
'tool':'RDPMTools',
'email':'Info@RationalDiscovery.com',
}
def details():
return copy.copy(_details)
# FIX: Allow PMID searches
searchableFields={
"Author":("AU","Authors' Name "),
"Keyword":("MH","MeSH keyword"),
"Substance":("NM","Substance Name"),
"Title":("TI","Text from the article title"),
"Title/Abstract":("TIAB","Text from the article title and/or abstract"),
"Registry Number":("RN","CAS Registry Number"),
"Subject":("SB","Pubmed Subject Subset (tox,aids,cancer,bioethics,cam,history,space,systematic)"),
"Journal":("TA","Journal Name"),
"Year":("DP","Publication Date"),
"Affiliation":("AD","Authors' affiliation"),
}
searchableFieldsOrder=[
"Author",
"Keyword",
"Title",
"Title/Abstract",
"Substance",
"Registry Number",
"Subject",
"Journal",
"Year",
"Affiliation",
]
| {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "rdkit/Dbase/Pubmed/QueryParams.py",
"copies": "3",
"size": "1462",
"license": "bsd-3-clause",
"hash": -1093318081724212900,
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import os
import io
import unittest
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import FragmentCatalog, BuildFragmentCatalog
from rdkit.six.moves import cPickle
def feq(n1,n2,tol=1e-4):
return abs(n1-n2)<tol
class TestCase(unittest.TestCase):
def setUp(self) :
self.smiList = ["S(SC1=NC2=CC=CC=C2S1)C3=NC4=C(S3)C=CC=C4","CC1=CC(=O)C=CC1=O",
"OC1=C(Cl)C=C(C=C1[N+]([O-])=O)[N+]([O-])=O",
"[O-][N+](=O)C1=CNC(=N)S1", "NC1=CC2=C(C=C1)C(=O)C3=C(C=CC=C3)C2=O",
"OC(=O)C1=C(C=CC=C1)C2=C3C=CC(=O)C(=C3OC4=C2C=CC(=C4Br)O)Br",
"CN(C)C1=C(Cl)C(=O)C2=C(C=CC=C2)C1=O",
"CC1=C(C2=C(C=C1)C(=O)C3=CC=CC=C3C2=O)[N+]([O-])=O",
"CC(=NO)C(C)=NO"]
self.smiList2 = ['OCCC','CCC','C=CC','OC=CC','CC(O)C',
'C=C(O)C','OCCCC','CC(O)CC','C=CCC','CC=CC',
'OC=CCC','CC=C(O)C','OCC=CC','C=C(O)CC',
'C=CC(O)C','C=CCCO',
]
self.list2Acts = [1,0,0,1,1,1,1,1,0,0,1,1,1,1,1,1]
self.list2Obls = [(0,1,2),(1,3),(1,4,5),(1,6,7),(0,8),(0,6,9),(0,1,2,3,10),
(0,1,2,8,11),(1,3,4,5,12),(1,4,5,13),(1,3,6,7,14),(0,1,6,7,9,15)]
ffile = os.path.join(RDConfig.RDDataDir,'FunctionalGroups.txt')
self.catParams = FragmentCatalog.FragCatParams(1,6,ffile)
self.fragCat = FragmentCatalog.FragCatalog(self.catParams)
self.fgen = FragmentCatalog.FragCatGenerator()
def _fillCat(self,smilList):
for smi in self.smiList2:
mol = Chem.MolFromSmiles(smi)
self.fgen.AddFragsFromMol(mol,self.fragCat)
def _testBits(self,fragCat):
fpgen = FragmentCatalog.FragFPGenerator()
obits = [3,2,3,3,2,3,5,5,5,4,5,6]
obls = self.list2Obls
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList2),
',',0,-1,0)
i = 0
for mol in suppl:
fp = fpgen.GetFPForMol(mol, fragCat)
if i < len(obits):
smi = Chem.MolToSmiles(mol)
assert fp.GetNumOnBits()==obits[i],'%s: %s'%(smi,str(fp.GetOnBits()))
obl = fp.GetOnBits()
if i < len(obls):
assert tuple(obl)==obls[i],'%s: %s'%(smi,obl)
i+=1
def test1CatGen(self) :
self._fillCat(self.smiList2)
assert self.fragCat.GetNumEntries()==21
assert self.fragCat.GetFPLength()==21
self._testBits(self.fragCat)
def test2CatStringPickle(self):
self._fillCat(self.smiList2)
# test non-binary pickle:
cat2 = cPickle.loads(cPickle.dumps(self.fragCat))
assert cat2.GetNumEntries()==21
assert cat2.GetFPLength()==21
self._testBits(cat2)
# test binary pickle:
cat2 = cPickle.loads(cPickle.dumps(self.fragCat,1))
assert cat2.GetNumEntries()==21
assert cat2.GetFPLength()==21
self._testBits(cat2)
def test3CatFilePickle(self):
with open(os.path.join(RDConfig.RDCodeDir,'Chem',
'test_data','simple_catalog.pkl'),
'r') as pklTFile:
buf = pklTFile.read().replace('\r\n', '\n').encode('utf-8')
pklTFile.close()
with io.BytesIO(buf) as pklFile:
cat = cPickle.load(pklFile, encoding='bytes')
assert cat.GetNumEntries()==21
assert cat.GetFPLength()==21
self._testBits(cat)
def test4CatGuts(self):
self._fillCat(self.smiList2)
assert self.fragCat.GetNumEntries()==21
assert self.fragCat.GetFPLength()==21
#
# FIX: (Issue 162)
# bits like 11 and 15 are questionable here because the underlying
# fragments are symmetrical, so they can generate one of two
# text representations (i.e. there is nothing to distinguish
# between 'CC<-O>CC' and 'CCC<-O>C').
# This ought to eventually be cleaned up.
descrs = [(0,'C<-O>C',1,(34,)),
(1,'CC',1,()),
(2,'C<-O>CC',2,(34,)),
(3,'CCC',2,()),
(4,'C=C',1,()),
(5,'C=CC',2,()),
(6,'C<-O>=C',1,(34,)),
(7,'C<-O>=CC',2,(34,)),
(8,'CC<-O>C',2,(34,)),
(9,'C=C<-O>C',2,(34,)),
(10,'C<-O>CCC',3,(34,)),
(11,'CC<-O>CC',3,(34,)),
(12,'C=CCC',3,()),
(13,'CC=CC',3,()),
(14,'C<-O>=CCC',3,(34,)),
(15,'CC=C<-O>C',3,(34,)),
(16,'C=CC<-O>',2,(34,)),
]
for i in range(len(descrs)):
id,d,order,ids=descrs[i]
descr = self.fragCat.GetBitDescription(id)
assert descr == d,'%d: %s != %s'%(id,descr,d)
assert self.fragCat.GetBitOrder(id)==order
assert tuple(self.fragCat.GetBitFuncGroupIds(id)) == \
ids,'%d: %s != %s'%(id,
str(self.fragCat.GetBitFuncGroupIds(id)),
str(ids))
def _test5MoreComplex(self):
lastIdx = 0
ranges = {}
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList),
',',0,-1,0)
i = 0
for mol in suppl:
nEnt = self.fgen.AddFragsFromMol(mol,self.fragCat)
ranges[i] = range(lastIdx,lastIdx+nEnt)
lastIdx+=nEnt
i+=1
# now make sure that those bits are contained in the signatures:
fpgen = FragmentCatalog.FragFPGenerator()
i = 0
for mol in suppl:
fp = fpgen.GetFPForMol(mol,self.fragCat)
for bit in ranges[i]:
assert fp[bit],'%s: %s'%(Chem.MolToSmiles(mol),str(bit))
i += 1
def test6Builder(self):
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList2),
',',0,-1,0)
cat = BuildFragmentCatalog.BuildCatalog(suppl,minPath=1,reportFreq=20)
assert cat.GetNumEntries()==21
assert cat.GetFPLength()==21
self._testBits(cat)
def test7ScoreMolecules(self):
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList2),
',',0,-1,0)
cat = BuildFragmentCatalog.BuildCatalog(suppl,minPath=1,reportFreq=20)
assert cat.GetNumEntries()==21
assert cat.GetFPLength()==21
scores,obls = BuildFragmentCatalog.ScoreMolecules(suppl,cat,acts=self.list2Acts,
reportFreq=20)
for i in range(len(self.list2Obls)):
assert tuple(obls[i])==self.list2Obls[i],'%d: %s != %s'%(i,str(obls[i]),
str(self.list2Obls[i]))
scores2 = BuildFragmentCatalog.ScoreFromLists(obls,suppl,cat,acts=self.list2Acts,
reportFreq=20)
for i in range(len(scores)):
assert (scores[i]==scores2[i]).all(),'%d: %s != %s'%(i,str(scores[i]),str(scores2[i]))
def test8MolRanks(self):
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList2),
',',0,-1,0)
cat = BuildFragmentCatalog.BuildCatalog(suppl,minPath=1,reportFreq=20)
assert cat.GetNumEntries()==21
assert cat.GetFPLength()==21
# new InfoGain ranking:
bitInfo,fps = BuildFragmentCatalog.CalcGains(suppl,cat,topN=10,acts=self.list2Acts,
reportFreq=20,biasList=(1,))
entry = bitInfo[0]
assert int(entry[0])==0
assert cat.GetBitDescription(int(entry[0]))=='C<-O>C'
assert feq(entry[1],0.4669)
entry = bitInfo[1]
assert int(entry[0]) in (2,6)
txt = cat.GetBitDescription(int(entry[0]))
self.assertTrue( txt in ('C<-O>CC','C<-O>=C'), txt)
assert feq(entry[1],0.1611)
entry = bitInfo[6]
assert int(entry[0])==16
assert cat.GetBitDescription(int(entry[0]))=='C=CC<-O>'
assert feq(entry[1],0.0560)
# standard InfoGain ranking:
bitInfo,fps = BuildFragmentCatalog.CalcGains(suppl,cat,topN=10,acts=self.list2Acts,
reportFreq=20)
entry = bitInfo[0]
assert int(entry[0])==0
assert cat.GetBitDescription(int(entry[0]))=='C<-O>C'
assert feq(entry[1],0.4669)
entry = bitInfo[1]
assert int(entry[0])==5
assert cat.GetBitDescription(int(entry[0]))=='C=CC'
assert feq(entry[1],0.2057)
def test9Issue116(self):
smiList = ['Cc1ccccc1']
suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList),
',',0,-1,0)
cat = BuildFragmentCatalog.BuildCatalog(suppl,minPath=2,maxPath=2)
assert cat.GetFPLength()==2
assert cat.GetBitDescription(0)=='ccC'
fpgen = FragmentCatalog.FragFPGenerator()
mol = Chem.MolFromSmiles('Cc1ccccc1')
fp = fpgen.GetFPForMol(mol,cat)
assert fp[0]
assert fp[1]
mol = Chem.MolFromSmiles('c1ccccc1-c1ccccc1')
fp = fpgen.GetFPForMol(mol,cat)
assert not fp[0]
assert fp[1]
if __name__ == '__main__':
unittest.main()
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} |
import os
import io
import unittest
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import FragmentCatalog, BuildFragmentCatalog
from rdkit.six.moves import cPickle
def feq(n1, n2, tol=1e-4):
return abs(n1 - n2) < tol
class TestCase(unittest.TestCase):
def setUp(self):
self.smiList = ["S(SC1=NC2=CC=CC=C2S1)C3=NC4=C(S3)C=CC=C4", "CC1=CC(=O)C=CC1=O",
"OC1=C(Cl)C=C(C=C1[N+]([O-])=O)[N+]([O-])=O", "[O-][N+](=O)C1=CNC(=N)S1",
"NC1=CC2=C(C=C1)C(=O)C3=C(C=CC=C3)C2=O",
"OC(=O)C1=C(C=CC=C1)C2=C3C=CC(=O)C(=C3OC4=C2C=CC(=C4Br)O)Br",
"CN(C)C1=C(Cl)C(=O)C2=C(C=CC=C2)C1=O",
"CC1=C(C2=C(C=C1)C(=O)C3=CC=CC=C3C2=O)[N+]([O-])=O", "CC(=NO)C(C)=NO"]
self.smiList2 = ['OCCC',
'CCC',
'C=CC',
'OC=CC',
'CC(O)C',
'C=C(O)C',
'OCCCC',
'CC(O)CC',
'C=CCC',
'CC=CC',
'OC=CCC',
'CC=C(O)C',
'OCC=CC',
'C=C(O)CC',
'C=CC(O)C',
'C=CCCO', ]
self.list2Acts = [1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1]
self.list2Obls = [(0, 1, 2), (1, 3), (1, 4, 5), (1, 6, 7), (0, 8), (0, 6, 9), (0, 1, 2, 3, 10),
(0, 1, 2, 8, 11), (1, 3, 4, 5, 12), (1, 4, 5, 13), (1, 3, 6, 7, 14),
(0, 1, 6, 7, 9, 15)]
ffile = os.path.join(RDConfig.RDDataDir, 'FunctionalGroups.txt')
self.catParams = FragmentCatalog.FragCatParams(1, 6, ffile)
self.fragCat = FragmentCatalog.FragCatalog(self.catParams)
self.fgen = FragmentCatalog.FragCatGenerator()
def _fillCat(self, smilList):
for smi in self.smiList2:
mol = Chem.MolFromSmiles(smi)
self.fgen.AddFragsFromMol(mol, self.fragCat)
def _testBits(self, fragCat):
fpgen = FragmentCatalog.FragFPGenerator()
obits = [3, 2, 3, 3, 2, 3, 5, 5, 5, 4, 5, 6]
obls = self.list2Obls
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList2), ',', 0, -1, 0)
i = 0
for mol in suppl:
fp = fpgen.GetFPForMol(mol, fragCat)
if i < len(obits):
smi = Chem.MolToSmiles(mol)
assert fp.GetNumOnBits() == obits[i], '%s: %s' % (smi, str(fp.GetOnBits()))
obl = fp.GetOnBits()
if i < len(obls):
assert tuple(obl) == obls[i], '%s: %s' % (smi, obl)
i += 1
def test1CatGen(self):
self._fillCat(self.smiList2)
assert self.fragCat.GetNumEntries() == 21
assert self.fragCat.GetFPLength() == 21
self._testBits(self.fragCat)
def test2CatStringPickle(self):
self._fillCat(self.smiList2)
# test non-binary pickle:
cat2 = cPickle.loads(cPickle.dumps(self.fragCat))
assert cat2.GetNumEntries() == 21
assert cat2.GetFPLength() == 21
self._testBits(cat2)
# test binary pickle:
cat2 = cPickle.loads(cPickle.dumps(self.fragCat, 1))
assert cat2.GetNumEntries() == 21
assert cat2.GetFPLength() == 21
self._testBits(cat2)
def test3CatFilePickle(self):
with open(os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', 'simple_catalog.pkl'),
'r') as pklTFile:
buf = pklTFile.read().replace('\r\n', '\n').encode('utf-8')
pklTFile.close()
with io.BytesIO(buf) as pklFile:
cat = cPickle.load(pklFile, encoding='bytes')
assert cat.GetNumEntries() == 21
assert cat.GetFPLength() == 21
self._testBits(cat)
def test4CatGuts(self):
self._fillCat(self.smiList2)
assert self.fragCat.GetNumEntries() == 21
assert self.fragCat.GetFPLength() == 21
#
# FIX: (Issue 162)
# bits like 11 and 15 are questionable here because the underlying
# fragments are symmetrical, so they can generate one of two
# text representations (i.e. there is nothing to distinguish
# between 'CC<-O>CC' and 'CCC<-O>C').
# This ought to eventually be cleaned up.
descrs = [(0, 'C<-O>C', 1, (34, )),
(1, 'CC', 1, ()),
(2, 'C<-O>CC', 2, (34, )),
(3, 'CCC', 2, ()),
(4, 'C=C', 1, ()),
(5, 'C=CC', 2, ()),
(6, 'C<-O>=C', 1, (34, )),
(7, 'C<-O>=CC', 2, (34, )),
(8, 'CC<-O>C', 2, (34, )),
(9, 'C=C<-O>C', 2, (34, )),
(10, 'C<-O>CCC', 3, (34, )),
(11, 'CC<-O>CC', 3, (34, )),
(12, 'C=CCC', 3, ()),
(13, 'CC=CC', 3, ()),
(14, 'C<-O>=CCC', 3, (34, )),
(15, 'CC=C<-O>C', 3, (34, )),
(16, 'C=CC<-O>', 2, (34, )), ]
for i in range(len(descrs)):
id, d, order, ids = descrs[i]
descr = self.fragCat.GetBitDescription(id)
assert descr == d, '%d: %s != %s' % (id, descr, d)
assert self.fragCat.GetBitOrder(id) == order
assert tuple(self.fragCat.GetBitFuncGroupIds(id)) == \
ids,'%d: %s != %s'%(id,
str(self.fragCat.GetBitFuncGroupIds(id)),
str(ids))
def _test5MoreComplex(self):
lastIdx = 0
ranges = {}
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList), ',', 0, -1, 0)
i = 0
for mol in suppl:
nEnt = self.fgen.AddFragsFromMol(mol, self.fragCat)
ranges[i] = range(lastIdx, lastIdx + nEnt)
lastIdx += nEnt
i += 1
# now make sure that those bits are contained in the signatures:
fpgen = FragmentCatalog.FragFPGenerator()
i = 0
for mol in suppl:
fp = fpgen.GetFPForMol(mol, self.fragCat)
for bit in ranges[i]:
assert fp[bit], '%s: %s' % (Chem.MolToSmiles(mol), str(bit))
i += 1
def test6Builder(self):
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList2), ',', 0, -1, 0)
cat = BuildFragmentCatalog.BuildCatalog(suppl, minPath=1, reportFreq=20)
assert cat.GetNumEntries() == 21
assert cat.GetFPLength() == 21
self._testBits(cat)
def test7ScoreMolecules(self):
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList2), ',', 0, -1, 0)
cat = BuildFragmentCatalog.BuildCatalog(suppl, minPath=1, reportFreq=20)
assert cat.GetNumEntries() == 21
assert cat.GetFPLength() == 21
scores, obls = BuildFragmentCatalog.ScoreMolecules(suppl, cat, acts=self.list2Acts,
reportFreq=20)
for i in range(len(self.list2Obls)):
assert tuple(obls[i]) == self.list2Obls[i], '%d: %s != %s' % (i, str(obls[i]),
str(self.list2Obls[i]))
scores2 = BuildFragmentCatalog.ScoreFromLists(obls, suppl, cat, acts=self.list2Acts,
reportFreq=20)
for i in range(len(scores)):
assert (scores[i] == scores2[i]).all(), '%d: %s != %s' % (i, str(scores[i]), str(scores2[i]))
def test8MolRanks(self):
suppl = Chem.SmilesMolSupplierFromText('\n'.join(self.smiList2), ',', 0, -1, 0)
cat = BuildFragmentCatalog.BuildCatalog(suppl, minPath=1, reportFreq=20)
assert cat.GetNumEntries() == 21
assert cat.GetFPLength() == 21
# new InfoGain ranking:
bitInfo, fps = BuildFragmentCatalog.CalcGains(suppl, cat, topN=10, acts=self.list2Acts,
reportFreq=20, biasList=(1, ))
entry = bitInfo[0]
assert int(entry[0]) == 0
assert cat.GetBitDescription(int(entry[0])) == 'C<-O>C'
assert feq(entry[1], 0.4669)
entry = bitInfo[1]
assert int(entry[0]) in (2, 6)
txt = cat.GetBitDescription(int(entry[0]))
self.assertTrue(txt in ('C<-O>CC', 'C<-O>=C'), txt)
assert feq(entry[1], 0.1611)
entry = bitInfo[6]
assert int(entry[0]) == 16
assert cat.GetBitDescription(int(entry[0])) == 'C=CC<-O>'
assert feq(entry[1], 0.0560)
# standard InfoGain ranking:
bitInfo, fps = BuildFragmentCatalog.CalcGains(suppl, cat, topN=10, acts=self.list2Acts,
reportFreq=20)
entry = bitInfo[0]
assert int(entry[0]) == 0
assert cat.GetBitDescription(int(entry[0])) == 'C<-O>C'
assert feq(entry[1], 0.4669)
entry = bitInfo[1]
assert int(entry[0]) == 5
assert cat.GetBitDescription(int(entry[0])) == 'C=CC'
assert feq(entry[1], 0.2057)
def test9Issue116(self):
smiList = ['Cc1ccccc1']
suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList), ',', 0, -1, 0)
cat = BuildFragmentCatalog.BuildCatalog(suppl, minPath=2, maxPath=2)
assert cat.GetFPLength() == 2
assert cat.GetBitDescription(0) == 'ccC'
fpgen = FragmentCatalog.FragFPGenerator()
mol = Chem.MolFromSmiles('Cc1ccccc1')
fp = fpgen.GetFPForMol(mol, cat)
assert fp[0]
assert fp[1]
mol = Chem.MolFromSmiles('c1ccccc1-c1ccccc1')
fp = fpgen.GetFPForMol(mol, cat)
assert not fp[0]
assert fp[1]
if __name__ == '__main__':
unittest.main()
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import random
import unittest
from rdkit.six import StringIO
from rdkit.DataStructs.TopNContainer import TopNContainer, _exampleCode
from rdkit.TestRunner import redirect_stdout
class TestCase(unittest.TestCase):
def test1(self):
# simple test with a known answer
cont = TopNContainer(4)
for foo in range(10):
cont.Insert(foo, str(foo))
assert cont.GetPts() == list(range(6, 10))
assert cont.GetExtras() == [str(x) for x in range(6, 10)]
def test2(self):
# larger scale random test
cont = TopNContainer(50)
for _ in range(1000):
cont.Insert(random.random())
vs = cont.GetPts()
last = vs.pop(0)
while vs:
assert vs[0] >= last
last = vs.pop(0)
def test3(self):
# random test with extras
cont = TopNContainer(10)
for _ in range(100):
v = random.random()
cont.Insert(v, v + 1)
vs = cont.GetExtras()
last = vs.pop(0)
while vs:
assert vs[0] >= last
last = vs.pop(0)
def test4(self):
# random test with extras and getitem
cont = TopNContainer(10)
for i in range(100):
v = random.random()
cont.Insert(v, v + 1)
lastV, lastE = cont[0]
for i in range(1, len(cont)):
v, e = cont[i]
assert v >= lastV
assert e >= lastE
lastV, lastE = v, e
def test5(self):
# random test with extras and getitem, include reverse
cont = TopNContainer(10)
for i in range(100):
v = random.random()
cont.Insert(v, v + 1)
cont.reverse()
lastV, lastE = cont[0]
for i in range(1, len(cont)):
v, e = cont[i]
assert v <= lastV
assert e <= lastE
lastV, lastE = v, e
def test_keepAll(self):
# simple test with a known answer where we keep all
cont = TopNContainer(-1)
for i in range(10):
cont.Insert(9 - i, str(9 - i))
self.assertEqual(len(cont), i + 1)
assert cont.GetPts() == list(range(10))
assert cont.GetExtras() == [str(x) for x in range(10)]
def test_exampleCode(self):
# We make sure that the example code runs
f = StringIO()
with redirect_stdout(f):
_exampleCode()
s = f.getvalue()
self.assertIn('[58, 75, 78, 84]', s)
if __name__ == '__main__': # pragma: nocover
unittest.main()
| {
"repo_name": "rvianello/rdkit",
"path": "rdkit/DataStructs/UnitTestTopNContainer.py",
"copies": "4",
"size": "2548",
"license": "bsd-3-clause",
"hash": -4922052235652594000,
"line_mean": 24.7373737374,
"line_max": 71,
"alpha_frac": 0.6087127159,
"autogenerated": false,
"ratio": 3.2253164556962024,
"config_test": true,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.5834029171596202,
"avg_score": null,
"num_lines": null
} |
import unittest
import random
from rdkit.DataStructs.TopNContainer import TopNContainer
class TestCase(unittest.TestCase):
def test1(self):
""" simple test with a known answer """
cont = TopNContainer(4)
for foo in range(10):
cont.Insert(foo,str(foo))
assert cont.GetPts()==range(6,10)
assert cont.GetExtras()==[str(x) for x in range(6,10)]
def test2(self):
""" larger scale random test """
cont = TopNContainer(50)
for i in range(1000):
cont.Insert(random.random())
vs = cont.GetPts()
last = vs.pop(0)
while vs:
assert vs[0]>=last
last = vs.pop(0)
def test3(self):
""" random test with extras"""
cont = TopNContainer(10)
for i in range(100):
v = random.random()
cont.Insert(v,v+1)
vs = cont.GetExtras()
last = vs.pop(0)
while vs:
assert vs[0]>=last
last = vs.pop(0)
def test4(self):
""" random test with extras and getitem"""
cont = TopNContainer(10)
for i in range(100):
v = random.random()
cont.Insert(v,v+1)
lastV,lastE = cont[0]
for i in range(1,len(cont)):
v,e = cont[i]
assert v>=lastV
assert e>=lastE
lastV,lastE = v,e
def test5(self):
""" random test with extras and getitem, include reverse"""
cont = TopNContainer(10)
for i in range(100):
v = random.random()
cont.Insert(v,v+1)
cont.reverse()
lastV,lastE = cont[0]
for i in range(1,len(cont)):
v,e = cont[i]
assert v<=lastV
assert e<=lastE
lastV,lastE = v,e
if __name__ == '__main__':
unittest.main()
| {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/DataStructs/UnitTestTopNContainer.py",
"copies": "5",
"size": "1888",
"license": "bsd-3-clause",
"hash": -8907564040054778000,
"line_mean": 25.5915492958,
"line_max": 63,
"alpha_frac": 0.6054025424,
"autogenerated": false,
"ratio": 3.1362126245847177,
"config_test": true,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 1,
"avg_score": 0.032759946233565165,
"num_lines": 71
} |
"""basic unit testing code for the Bond wrapper
"""
import unittest
from rdkit import Chem
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
self.m = Chem.MolFromSmiles('CCCC1=CC=C1')
def test1Get(self):
" testing GetBond "
ok = 1
try:
b = self.m.GetBondBetweenAtoms(0,1)
except Exception:
ok = 0
assert ok,'GetBond failed'
def test2Setters(self):
" testing setting bond props "
b = self.m.GetBondBetweenAtoms(0,1)
assert b.GetBondType()==Chem.BondType.SINGLE
b.SetBondDir(Chem.BondDir.BEGINWEDGE)
assert self.m.GetBondBetweenAtoms(0,1).GetBondDir()==Chem.BondDir.BEGINWEDGE
b = self.m.GetBondBetweenAtoms(0,1)
def test3Props(self):
" testing bond props "
b = self.m.GetBondBetweenAtoms(0,1)
assert b.GetBondType()==Chem.BondType.SINGLE
assert b.GetBeginAtom().GetIdx()==self.m.GetAtomWithIdx(0).GetIdx()
assert b.GetBeginAtomIdx()==0
assert b.GetEndAtom().GetIdx()==self.m.GetAtomWithIdx(1).GetIdx()
assert b.GetEndAtomIdx()==1
def test4Props2(self):
" testing more bond props "
b = self.m.GetBondBetweenAtoms(3,4)
assert b.GetBondType()==Chem.BondType.DOUBLE
b2 = self.m.GetBondBetweenAtoms(1,2)
assert b2.GetBondType()==Chem.BondType.SINGLE
assert b.GetIsConjugated()
assert not b2.GetIsConjugated()
if __name__ == '__main__':
unittest.main()
| {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/UnitTestChemBond.py",
"copies": "1",
"size": "1727",
"license": "bsd-3-clause",
"hash": 3068124647451514000,
"line_mean": 25.984375,
"line_max": 80,
"alpha_frac": 0.6763173133,
"autogenerated": false,
"ratio": 2.84983498349835,
"config_test": true,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.402615229679835,
"avg_score": null,
"num_lines": null
} |
""" Tools for doing PubMed searches and processing the results
NOTE: much of the example code in the documentation here uses XML
files from the test_data directory in order to avoid having to call
out to PubMed itself. Actual calls to the functions would not include
the _conn_ argument.
"""
from rdkit import RDConfig
import QueryParams,Records
import urllib,urllib2
from xml.etree import ElementTree
def openURL(url,args):
proxy_support = urllib2.ProxyHandler({})
opener = urllib2.build_opener(proxy_support)
conn = urllib2.urlopen(url,args)
return conn
def GetNumHits(query,url=QueryParams.searchBase):
""" returns a tuple of pubmed ids (strings) for the query provided
To do a search, we need a query object:
>>> query = QueryParams.details()
set up the search parameters:
>>> query['term'] = 'penzotti je AND grootenhuis pd'
>>> query['field'] = 'auth'
now get the search ids:
>>> counts = GetNumHits(query)
>>> counts
2
alternately, we can search using field specifiers:
>>> query = QueryParams.details()
>>> query['term'] = 'penzotti je[au] AND hydrogen bonding[mh]'
>>> counts = GetNumHits(query)
>>> counts
3
"""
query['rettype']='count'
conn = openURL(url,urllib.urlencode(query))
pubmed = ElementTree.parse(conn)
countText = pubmed.findtext('Count')
if countText:
res = int(countText)
else:
res = 0
return res
def GetSearchIds(query,url=QueryParams.searchBase):
""" returns a tuple of pubmed ids (strings) for the query provided
To do a search, we need a query object:
>>> query = QueryParams.details()
set up the search parameters:
>>> query['term'] = 'penzotti je AND grootenhuis pd'
>>> query['field'] = 'auth'
now get the search ids:
>>> ids = GetSearchIds(query)
>>> len(ids)
2
>>> ids[0]
'11960484'
>>> ids[1]
'10893315'
"""
conn = openURL(url,urllib.urlencode(query))
pubmed = ElementTree.parse(conn)
res = [id.text for id in pubmed.getiterator('Id')]
return tuple(res)
def GetSummaries(ids,query=None,url=QueryParams.summaryBase,conn=None):
""" gets a set of document summary records for the ids provided
>>> ids = ['11960484']
>>> summs = GetSummaries(ids,conn=open(os.path.join(testDataDir,'summary.xml'),'r'))
>>> len(summs)
1
>>> rec = summs[0]
>>> isinstance(rec,Records.SummaryRecord)
1
>>> rec.PubMedId
'11960484'
>>> rec.Authors
'Penzotti JE, Lamb ML, Evensen E, Grootenhuis PD'
>>> rec.Title
'A computational ensemble pharmacophore model for identifying substrates of P-glycoprotein.'
>>> rec.Source
'J Med Chem'
>>> rec.Volume
'45'
>>> rec.Pages
'1737-40'
>>> rec.HasAbstract
'1'
"""
if not conn:
try:
iter(ids)
except TypeError:
ids = [ids,]
if not query:
query = QueryParams.details()
ids = map(str,ids)
query['id'] = ','.join(ids)
conn = openURL(url,urllib.urlencode(query))
pubmed = ElementTree.parse(conn)
res = []
for summary in pubmed.getiterator('DocSum'):
rec = Records.SummaryRecord(summary)
if rec.PubMedId in ids:
res.append(rec)
ids.remove(rec.PubMedId)
return tuple(res)
def GetRecords(ids,query=None,url=QueryParams.fetchBase,conn=None):
""" gets a set of document summary records for the ids provided
>>> ids = ['11960484']
>>> recs = GetRecords(ids,conn=open(os.path.join(testDataDir,'records.xml'),'r'))
>>> len(recs)
1
>>> rec = recs[0]
>>> rec.PubMedId
'11960484'
>>> rec.Authors
u'Penzotti JE, Lamb ML, Evensen E, Grootenhuis PD'
>>> rec.Title
u'A computational ensemble pharmacophore model for identifying substrates of P-glycoprotein.'
>>> rec.Source
u'J Med Chem'
>>> rec.Volume
'45'
>>> rec.Pages
'1737-40'
>>> rec.PubYear
'2002'
>>> rec.Abstract[:10]
u'P-glycopro'
We've also got access to keywords:
>>> str(rec.keywords[0])
'Combinatorial Chemistry Techniques'
>>> str(rec.keywords[3])
'Indinavir / chemistry'
and chemicals:
>>> rec.chemicals[0]
'P-Glycoprotein'
>>> rec.chemicals[2]
'Nicardipine <55985-32-5>'
"""
if not conn:
try:
iter(ids)
except TypeError:
ids = [ids,]
if not query:
query = QueryParams.details()
query['id'] = ','.join(map(str,ids))
conn = openURL(url,urllib.urlencode(query))
pubmed = ElementTree.parse(conn)
res = []
for article in pubmed.getiterator('PubmedArticle'):
rec = Records.JournalArticleRecord(article)
if rec.PubMedId in ids:
res.append(rec)
return tuple(res)
def CheckForLinks(ids,query=None,url=QueryParams.linkBase,conn=None):
if not conn:
try:
iter(ids)
except TypeError:
ids = [ids,]
if not query:
query = QueryParams.details()
query['id'] = ','.join(map(str,ids))
conn = openURL(url,urllib.urlencode(query))
query['cmd'] = 'ncheck'
pubmed = ElementTree.parse(conn)
checklist = pubmed.find('LinkSet/IdCheckList')
recs = [Records.LinkRecord(x) for x in checklist.getiterator('Id')]
res = {}
for rec in recs:
id = rec.PubMedId
res[id] = rec.HasNeighbor
return res
def GetLinks(ids,query=None,url=QueryParams.linkBase,conn=None):
if not conn:
try:
iter(ids)
except TypeError:
ids = [ids,]
if not query:
query = QueryParams.details()
query['id'] = ','.join(map(str,ids))
conn = openURL(url,urllib.urlencode(query))
query['cmd'] = 'neighbor'
pubmed = ElementTree.parse(conn)
linkset = pubmed.find('LinkSet/LinkSetDb')
scores = []
scoreNorm = 1.0
for link in linkset.getiterator('Link'):
id = link.findtext('Id')
score = float(link.findtext('Score'))
scores.append([id,score])
# we'll normalize scores by the score for the first of the query ids:
if id == ids[0]:
scoreNorm = score
for i in range(len(scores)):
id,score = scores[i]
scores[i] = id,score/scoreNorm
return tuple(scores)
#------------------------------------
#
# doctest boilerplate
#
def _test():
import doctest,sys
return doctest.testmod(sys.modules["__main__"])
if __name__ == '__main__':
import sys,os.path
testDataDir = os.path.join(RDConfig.RDCodeDir,'Dbase','Pubmed','test_data')
failed,tried = _test()
sys.exit(failed)
#query = QueryParams.details()
#query['term']='landrum ga'
#query['field']='auth'
#ids = GetSearchIds(query)
#print ids
#ids = ids[:2]
ids = ['11666868','11169640']
if 0:
summs = GetSummaries(ids,conn=open('summary.xml','r'))
print 'summs:',summs
for summary in summs:
print summary.Authors
print '\t',summary.Title
print '\t',summary.Source,
print summary.Volume,
print summary.Pages,
print summary.PubDate
if 0:
ids = ['11666868']
res = GetRecords(ids,conn=open('records.xml','r'))
for record in res:
print record.Authors
print '\t',record.Title
print '\t',record.Journal,
print record.Volume,
print record.Pages,
print record.PubYear
print
if 0:
ids = ['11666868','11169640']
res = CheckForLinks(ids,conn=open('haslinks.xml','r'))
print res
if 0:
ids = ['11666868']
res = GetLinks(ids,conn=open('links.xml','r'))
#res = GetLinks(ids)
for id,score in res[:10]:
print id,score
| {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Dbase/Pubmed/Searches.py",
"copies": "2",
"size": "7576",
"license": "bsd-3-clause",
"hash": -8097189635520018000,
"line_mean": 24.3377926421,
"line_max": 95,
"alpha_frac": 0.6446673706,
"autogenerated": false,
"ratio": 3.1765199161425577,
"config_test": true,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.965741477935799,
"avg_score": 0.032754501476913604,
"num_lines": 299
} |
try:
from reportlab import platypus
except ImportError:
import sys
sys.stderr.write('ReportLab module could not be imported. Db->PDF functionality not available')
GetReportlabTable = None
QuickReport = None
else:
from rdkit import Chem
try:
from pyRDkit.utils import chemdraw
except ImportError:
hasCDX=0
else:
hasCDX=1
from rdkit.utils import cactvs
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import DrawUtils
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbInfo
from rdkit.Reports.PDFReport import PDFReport,ReportUtils
import os,tempfile,sys
def GetReportlabTable(self,*args,**kwargs):
""" this becomes a method of DbConnect """
dbRes = self.GetData(*args,**kwargs)
rawD = [dbRes.GetColumnNames()]
colTypes = dbRes.GetColumnTypes()
binCols = []
for i in range(len(colTypes)):
if colTypes[i] in DbInfo.sqlBinTypes or colTypes[i]=='binary':
binCols.append(i)
nRows = 0
for entry in dbRes:
nRows += 1
for col in binCols:
entry = list(entry)
entry[col] = 'N/A'
rawD.append(entry)
#if nRows >10: break
res = platypus.Table(rawD)
return res
from reportlab.lib.units import inch
class CDXImageTransformer(object):
def __init__(self,smiCol,width=1,verbose=1,tempHandler=None):
self.smiCol = smiCol
if tempHandler is None:
tempHandler = ReportUtils.TempFileHandler()
self.tempHandler = tempHandler
self.width = width*inch
self.verbose=verbose
def __call__(self,arg):
res = list(arg)
if self.verbose:
print 'Render:',res[0]
if hasCDX:
smi = res[self.smiCol]
tmpName = self.tempHandler.get('.jpg')
try:
img = chemdraw.SmilesToPilImage(smi)
w,h = img.size
aspect = float(h)/w
img.save(tmpName)
img = platypus.Image(tmpName)
img.drawWidth = self.width
img.drawHeight = aspect*self.width
res[self.smiCol] = img
except:
import traceback
traceback.print_exc()
res[self.smiCol] = 'Failed'
return res
class CactvsImageTransformer(object):
def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None):
self.smiCol = smiCol
if tempHandler is None:
tempHandler = ReportUtils.TempFileHandler()
self.tempHandler = tempHandler
self.width = width*inch
self.verbose=verbose
def __call__(self,arg):
res = list(arg)
if self.verbose:
sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0])))
smi = res[self.smiCol]
tmpName = self.tempHandler.get('.gif')
aspect = 1
width = 300
height = aspect*width
ok = cactvs.SmilesToGif(smi,tmpName,(width,height))
if ok:
try:
img = platypus.Image(tmpName)
img.drawWidth = self.width
img.drawHeight = aspect*self.width
except:
ok = 0
if ok:
res[self.smiCol] = img
else:
# FIX: maybe include smiles here in a Paragraph?
res[self.smiCol] = 'Failed'
return res
from rdkit.sping.ReportLab.pidReportLab import RLCanvas as Canvas
from rdkit.Chem.Draw.MolDrawing import MolDrawing
class ReportLabImageTransformer(object):
def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None):
self.smiCol = smiCol
self.width = width*inch
self.verbose=verbose
def __call__(self,arg):
res = list(arg)
if self.verbose:
sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0])))
smi = res[self.smiCol]
aspect = 1
width = self.width
height = aspect*width
try:
mol = Chem.MolFromSmiles(smi)
Chem.Kekulize(mol)
canv = Canvas((width,height))
drawing = MolDrawing()
drawing.atomLabelMinFontSize=3
drawing.minLabelPadding=(.5,.5)
drawing.bondLineWidth=0.5
if not mol.GetNumConformers():
rdDepictor.Compute2DCoords(mol)
drawing.AddMol(mol,canvas=canv)
ok = True
except:
if self.verbose:
import traceback
traceback.print_exc()
ok = False
if ok:
res[self.smiCol] = canv.drawing
else:
# FIX: maybe include smiles here in a Paragraph?
res[self.smiCol] = 'Failed'
return res
class RDImageTransformer(object):
def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None):
self.smiCol = smiCol
if tempHandler is None:
tempHandler = ReportUtils.TempFileHandler()
self.tempHandler = tempHandler
self.width = width*inch
self.verbose=verbose
def __call__(self,arg):
res = list(arg)
if self.verbose:
sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0])))
smi = res[self.smiCol]
tmpName = self.tempHandler.get('.jpg')
aspect = 1
width = 300
height = aspect*width
ok = DrawUtils.SmilesToJpeg(smi,tmpName,size=(width,height))
if ok:
try:
img = platypus.Image(tmpName)
img.drawWidth = self.width
img.drawHeight = aspect*self.width
except:
ok = 0
if ok:
res[self.smiCol] = img
else:
# FIX: maybe include smiles here in a Paragraph?
res[self.smiCol] = 'Failed'
return res
def QuickReport(conn,fileName,*args,**kwargs):
from reportlab.lib import colors
from reportlab.lib.styles import getSampleStyleSheet
from reportlab.lib.units import inch
styles = getSampleStyleSheet()
title = 'Db Report'
if kwargs.has_key('title'):
title = kwargs['title']
del kwargs['title']
names = [x.upper() for x in conn.GetColumnNames()]
try:
smiCol = names.index('SMILES')
except ValueError:
try:
smiCol = names.index('SMI')
except ValueError:
smiCol = -1
if smiCol >-1:
if hasCDX:
tform = CDXImageTransformer(smiCol)
elif 1:
tform = ReportLabImageTransformer(smiCol)
else:
tform = CactvsImageTransformer(smiCol)
else:
tform = None
kwargs['transform'] = tform
tbl = conn.GetReportlabTable(*args,**kwargs)
tbl.setStyle(platypus.TableStyle([('GRID',(0,0),(-1,-1),1,colors.black),
('FONT',(0,0),(-1,-1),'Times-Roman',8),
]))
if smiCol >-1 and tform:
tbl._argW[smiCol] = tform.width*1.2
elements = [tbl]
reportTemplate = PDFReport()
reportTemplate.pageHeader = title
doc = platypus.SimpleDocTemplate(fileName)
doc.build(elements,onFirstPage=reportTemplate.onPage,
onLaterPages=reportTemplate.onPage)
DbConnect.GetReportlabTable = GetReportlabTable
if __name__=='__main__':
import sys
dbName = sys.argv[1]
tblName = sys.argv[2]
fName = 'report.pdf'
conn = DbConnect(dbName,tblName)
QuickReport(conn,fName,where="where mol_id in ('1','100','104','107')")
| {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Dbase/DbReport.py",
"copies": "1",
"size": "7416",
"license": "bsd-3-clause",
"hash": 6540975674846323000,
"line_mean": 29.024291498,
"line_max": 98,
"alpha_frac": 0.6115156419,
"autogenerated": false,
"ratio": 3.4719101123595504,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.9394748031190312,
"avg_score": 0.03773554461384775,
"num_lines": 247
} |
""" Unit Test code for Fragment Descriptors
"""
import unittest
from rdkit import Chem
from rdkit.Chem import Fragments
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def _runTest(self,data,fn):
for smi,tgtVal in data:
mol = Chem.MolFromSmiles(smi)
assert mol,"Smiles parsing failed for %s"%(smi)
count = fn(mol)
assert count==tgtVal,"bad value (%d != %d) for smiles %s"%(count,tgtVal,smi)
def test1(self):
data = [('C=O',1),
('O=CC=O',2),
('O=CC(=O)O',2),
('O=C(O)C(=O)O',2),
]
self._runTest(data,Fragments.fr_C_O)
def test2(self):
data = [('C=O',1),
('O=CC=O',2),
('O=CC(=O)O',1),
('O=C(O)C(=O)O',0),
]
self._runTest(data,Fragments.fr_C_O_noCOO)
def test3(self):
data = [('[O-][N+](C1=C([N+]([O-])=O)C=C([N+]([O-])=O)C=C1)=O',3),
('[O-][N+](C1=CC=CC=C1)=O', 1),
('[N+]([O-])(=O)C1OC(=CC=1)/C=N/NC(N)=O', 0),
('O=C(O)C(=O)O',0),
]
self._runTest(data,Fragments.fr_nitro_arom)
def test4(self):
data = [('[O-][N+](C1=C([N+]([O-])=O)C=C([N+]([O-])=O)C=C1)=O',1),
('[O-][N+](C1=CC=CC=C1)=O', 1),
('[N+]([O-])(=O)C1OC(=CC=1)/C=N/NC(N)=O', 0),
('O=C(O)C(=O)O',0),
]
self._runTest(data,Fragments.fr_nitro_arom_nonortho)
def test5(self):
data = [('C1(N=[N+]=[N-])=C(C(=C(C(=C1F)F)F)F)F',1),
]
self._runTest(data,Fragments.fr_azide)
def test6(self):
data = [('C1C=CNC=C1',1),
('C1=CCNC=C1',1),
('C1=CCN=CC1',1),
('C1=CC=NCC1',1),
('C1C=CC(=CC=1[N+]([O-])=O)C2C(=C(NC(=C2C(OC)=O)C)C)C(OCCNCC3=CC=CC=C3)=O',1),
('O=C(O)C(=O)O',0),
]
self._runTest(data,Fragments.fr_dihydropyridine)
def test7(self):
data = [('OC1=C(C(O)=O)C=CC=C1',0),
('OC1=CC=CC=C1',1),
('OC1=C(O)C=CC=C1',2),
('O=C(O)C1=CC(O)=CC=C1',1),
('OC1=C(O)C(C(O)=O)=CC=C1',1),
('OC1=C(C(N)=O)C=CC=C1',0),
('OC1=C(CO)C=CC=C1',0),
('OC1=C(C(OC)=O)C=CC=C1',1),
('C1=CC=NCC1',0),
('C1C=CC(=CC=1[N+]([O-])=O)C2C(=C(NC(=C2C(OC)=O)C)C)C(OCCNCC3=CC=CC=C3)=O',0),
('O=C(O)C(=O)O',0),
]
self._runTest(data,Fragments.fr_phenol_noOrthoHbond)
def test8(self):
data = [('OC1=C(C(O)=O)C=CC=C1',0),
('CC(C)(O)C',0),
('CC(O)C',1),
('C=C(O)C',1), # includes enols
('OC1=C(O)C=CC=C1',0),
('OC1=C(CO)C=CC=C1',1),
('C1C=CC(=CC=1[N+]([O-])=O)C2C(=C(NC(=C2C(OC)=O)C)C)C(OCCNCC3=CC=CC=C3)=O',0)
]
self._runTest(data,Fragments.fr_Al_OH_noTert)
def test9(self):
data = [('OC1=C(C(O)=O)C=CC=C1',0),
('C12=CC=CC=C1NCCN=C2',1),
('C1=C(C=C2C(=C1)NC(CN=C2C3=C(C=CC=C3)Cl)=O)[N+]([O-])=O',1), # clonazepam
('C12=C(C(=NCC(N1C)=O)C3=CC=CC=C3)C=C(C=C2)Cl',1), # valium
('CCC1=CC2C(=NCC(=O)N(C)C=2S1)C3=CC=CC=C3Cl',0), # clotiazepam has a 5-mb ring
('CN(C)CCN1C(=O)C2=CC=CC=C2NC3C=C(Cl)C=CC1=3',0), #clobenzepam has a third fused ring
('C1C=CC(=CC=1[N+]([O-])=O)C2C(=C(NC(=C2C(OC)=O)C)C)C(OCCNCC3=CC=CC=C3)=O',0)
]
self._runTest(data,Fragments.fr_benzodiazepine)
def test10(self):
data = [('OC1=C(C(O)=O)C=CC=C1',1),
('c1ccccc1Oc2ccccc2',2), # diphenyl ether has 2 sites
('COC1=CC=CC=C1',1),
('CN(C)C2=CC=CC=C2',1),
('O=C(C4=CC=CC=C4)C3=CC=CC=C3',0),
('COC1=CC=C(C)C(OC)=C1C',0),
('CN(C)C1=CC=CC=C1OC',2),
('O=C(C2=CC=CC=C2)CC1=CC=CC=C1',0),
('O=C(NC2=CC=CC=C2)CN(C)C1=CC=CC=C1',2),
('O=C(N(C)C2=CC=CC=C2)CC1=CC=CC=C1',1), # methylated amide is included
('C12=CC=CC=C1OCCC2',1),
('C12=CC=CC=C1OC=C2',1), # benzofuran
('C12=CC=CC=C1NC=N2',2), # benzimidazole hydroxylated at 5 position
('CC1=CC=C(C=CO2)C2=C1',0)
]
self._runTest(data,Fragments.fr_para_hydroxylation)
def test11(self):
data = [('C1C(C=C2[C@](C1)([C@]3([C@@](CC2)([C@]4([C@](CC3)([C@@H](CC4)O)C)[H])[H])[H])C)=O',1), # testosterone 6beta hydroxylation includedbut not dienone
('CCC=CCCC',2),
('C=CC',1),
('C=CCO',0)
]
self._runTest(data,Fragments.fr_allylic_oxid)
def test12(self):
data = [('c1ccccc1C',1),
('c1ccccc1CC',1),
('c1(C)cccc(C)c1CC',2),
('c1(N)cccc(O)c1CC',0),
('c1cccc(C)c1CC',2),
('c1ccccc1CN',0),
('c1ccccc1CCN',0),
('c1(C)ccccc1CCN',1)
]
self._runTest(data,Fragments.fr_aryl_methyl)
def test13(self):
data = [('CNC1(CCCCC1=O)C2(=CC=CC=C2Cl)',1), # ketamine
('C1=C(C(=C(C=C1)C)NC(CN(CC)CC)=O)C',1), # lidocaine
('c1(C)ccccc1CCN',0)
]
self._runTest(data,Fragments.fr_Ndealkylation1)
def test14(self):
data = [('C12(=C(N=CC=C1[C@@H](O)C3(N4CC(C(C3)CC4)([H])C=C)[H])C=CC(=C2)OC)',0), # quinine
('N12CCC(CC2)CC1',0), # bridged N
('N1(CCC)CCCCC1',1),
('CCC1(CCCCN(C)C1)C2=CC=CC(O)=C2',1), # meptazinol
('C1(=C2C3=C(C=C1)C[C@@H]4[C@]5([C@@]3([C@H]([C@H](CC5)O)O2)CCN4CC6CCC6)O)O',1), # nalbuphine
('CC1N=C2CCCCN2C(=O)C=1CCN3CCC(CC3)C4=NOC5C=C(F)C=CC4=5',1), # risperidone
('N1CCOCC1',0), # morpholino group
('n1ccccc1',0)
]
self._runTest(data,Fragments.fr_Ndealkylation2)
def test15(self):
data = [('C(COC(NC(C)C)=O)(COC(N)=O)(CCC)C',1), # carisoprodol
('CN(CC3=CSC(C(C)C)=N3)C(N[C@@H]([C@H](C)C)C(N[C@@H](CC4=CC=CC=C4)C[C@H](O)[C@H](CC2=CC=CC=C2)NC(OCC1=CN=CS1)=O)=O)=O',1), # ritonavir
('c1(C)ccccc1CCN',0)
]
self._runTest(data,Fragments.fr_alkyl_carbamate)
def test16(self):
data = [('C1(CCC(O1)=O)(C)CC/C=C\CC',1),
('CN(CC3=CSC(C(C)C)=N3)C(N[C@@H]([C@H](C)C)C(N[C@@H](CC4=CC=CC=C4)C[C@H](O)[C@H](CC2=CC=CC=C2)NC(OCC1=CN=CS1)=O)=O)=O',0), # ritonavir
('c1(C)ccccc1CCN',0)
]
self._runTest(data,Fragments.fr_lactone)
def test17(self):
data = [('O=C(C=CC1=CC=CC=C1)C=CC2=CC=CC=C2',0), # a,b-unsat. dienone
('c1ccccc1-C(=O)-c2ccccc2',0),
('c1ccccc1-C(=O)-CCO',1),
('CC(=O)NCCC',0)
]
self._runTest(data,Fragments.fr_ketone_Topliss)
def test18(self):
data = [('C1=CC(=CC=C1C(N[C@@H](CCC(O)=O)C(O)=O)=O)N(CC2=NC3C(=NC(=NC=3N=C2)N)N)C',2), # methotrexate
('S(NC1=NC=CC=N1)(=O)(=O)C2=CC=C(C=C2)N',1), # sulfadiazine
('S(NC1=NC=CC=N1)(=O)(=O)C2=CC=C(C=C2)',0),
('c1ccccc1-C(=O)-CCO',0),
('NNC(=O)C1C2CCCCC=2N=C3C=CC=CC=13',1),
('NC(=N)C1C2CCCCC=2N=C3C=CC=CC=13',1),
('NNC1C2CCCCC=2N=C3C=CC=CC=13',1),
('NC1C2CCCCC=2N=C3C=CC=CC=13',1) # tacrine
]
self._runTest(data,Fragments.fr_ArN)
def test19(self):
data = [('CC(C)(C)NCC(O)C1=CC(O)=CC(O)=C1',1), # terbulatine
('OCCN1CCN(CC/C=C2\C3=CC=CC=C3SC4C=CC(Cl)=CC2=4)CC1',1), # clopenthixol
('c1ccccc1-C(=O)-CCO',0),
('CC(=O)NCCC',0)
]
self._runTest(data,Fragments.fr_HOCCN)
def test20(self):
data = [('c1ccccc1OC',1),
('c1ccccc1Oc2ccccc2',0),
('c1ccccc1OCC',0),
]
self._runTest(data,Fragments.fr_methoxy)
def test21(self):
data = [('C/C(C(C)=O)=N\O',1),
('C(=N/OC(C(=O)O)(C)C)(/C1=CS[N+](=N1)C)C(N[C@@H]2C(N([C@@H]2C)S(O)(=O)=O)=O)=O',1), # aztreonam
('c1ccccc1OCC',0),
]
self._runTest(data,Fragments.fr_oxime)
def test22(self):
data = [('CCCF',1),
('c1ccccc1C(C)(C)Br',1),
('c1ccccc1CC(C)(C)Cl',1),
]
self._runTest(data,Fragments.fr_alkyl_halide)
if __name__ == '__main__':
unittest.main()
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"""unit testing code for graph-theoretical descriptors
"""
from __future__ import print_function
from rdkit import RDConfig
import unittest,os.path
from rdkit import Chem
from rdkit.Chem import GraphDescriptors,MolSurf,Lipinski,Crippen
def feq(n1,n2,tol=1e-4):
return abs(n1-n2)<=tol
class TestCase(unittest.TestCase):
def setUp(self):
if doLong:
print('\n%s: '%self.shortDescription(),end='')
def testBertzCTShort(self):
""" test calculation of Bertz 'C(T)' index
"""
data = [('C=CC=C',21.01955),
('O=CC=O',25.01955),
('FCC(=O)CF',46.7548875),
('O=C1C=CC(=O)C=C1',148.705216),
('C12C(F)=C(O)C(F)C1C(F)=C(O)C(F)2',315.250442),
('C12CC=CCC1C(=O)C3CC=CCC3C(=O)2',321.539522)]
for smi,CT in data:
m = Chem.MolFromSmiles(smi)
newCT = GraphDescriptors.BertzCT(m, forceDMat = 1)
assert feq(newCT,CT,1e-3),'mol %s (CT calc = %f) should have CT = %f'%(smi,newCT,CT)
def _testBertzCTLong(self):
""" test calculation of Bertz 'C(T)' index
NOTE: this is a backwards compatibility test, because of the changes
w.r.t. the treatment of aromatic atoms in the new version, we need
to ignore molecules with aromatic rings...
"""
col = 1
with open(os.path.join(RDConfig.RDCodeDir,'Chem','test_data','PP_descrs_regress.2.csv'),'r') as inF:
lineNum=0
for line in inF:
lineNum+=1
if line[0] != '#':
splitL = line.split(',')
smi = splitL[0]
try:
m = Chem.MolFromSmiles(smi)
except:
m = None
assert m,'line %d, smiles: %s'%(lineNum,smi)
useIt=1
for atom in m.GetAtoms():
if atom.GetIsAromatic():
useIt=0
break
if useIt:
tgtVal = float(splitL[col])
try:
val = GraphDescriptors.BertzCT(m)
except:
val = 666
assert feq(val,tgtVal,1e-4),'line %d, mol %s (CT calc = %f) should have CT = %f'%(lineNum,smi,val,tgtVal)
def __testDesc(self,fileN,col,func):
with open(os.path.join(RDConfig.RDCodeDir,'Chem','test_data',fileN),'r') as inF:
lineNum=0
for line in inF:
lineNum+=1
if line[0] != '#':
splitL = line.split(',')
smi = splitL[0]
try:
m = Chem.MolFromSmiles(smi)
except:
m = None
assert m,'line %d, smiles: %s'%(lineNum,smi)
useIt=1
if useIt:
tgtVal = float(splitL[col])
if not feq(tgtVal,666.0):
try:
val = func(m)
except:
val = 666
assert feq(val,tgtVal,1e-4),'line %d, mol %s (calc = %f) should have val = %f'%(lineNum,smi,val,tgtVal)
def testChi0Long(self):
""" test calculation of Chi0
"""
col = 2
self.__testDesc('PP_descrs_regress.csv',col,GraphDescriptors.Chi0)
def _testChi0Long2(self):
""" test calculation of Chi0
"""
col = 2
self.__testDesc('PP_descrs_regress.2.csv',col,GraphDescriptors.Chi0)
def testHallKierAlphaLong(self):
""" test calculation of the Hall-Kier Alpha value
"""
col = 3
self.__testDesc('PP_descrs_regress.csv',col,GraphDescriptors.HallKierAlpha)
def _testHallKierAlphaLong2(self):
""" test calculation of the Hall-Kier Alpha value
"""
col = 3
self.__testDesc('PP_descrs_regress.2.csv',col,GraphDescriptors.HallKierAlpha)
def testIpc(self):
""" test calculation of Ipc.
"""
data = [('CCCCC',1.40564,11.24511),('CCC(C)C',1.37878, 9.65148),('CC(C)(C)C',0.72193,3.60964),('CN(CC)CCC',1.67982,31.91664),('C1CCCCC1',1.71997,34.39946),('CC1CCCCC1',1.68562,47.19725),('Cc1ccccc1',1.68562,47.19725),('CC(C)=C(C)C',1.36096,13.60964),('C#N',1.00000,2.00000),('OC#N',0.91830,2.75489)]
for smi,res1,res2 in data:
m = Chem.MolFromSmiles(smi)
Ipc = GraphDescriptors.Ipc(m, forceDMat=1)
Ipc_avg = GraphDescriptors.Ipc(m,avg = 1, forceDMat=1)
assert feq(Ipc_avg,res1,1e-3),'mol %s (Ipc_avg=%f) should have Ipc_avg=%f'%(smi,Ipc_avg,res1)
assert feq(Ipc,res2,1e-3),'mol %s (Ipc=%f) should have Ipc=%f'%(smi,Ipc,res2)
Ipc = GraphDescriptors.Ipc(m)
Ipc_avg = GraphDescriptors.Ipc(m,avg = 1)
assert feq(Ipc_avg,res1,1e-3),'2nd pass: mol %s (Ipc_avg=%f) should have Ipc_avg=%f'%(smi,Ipc_avg,res1)
assert feq(Ipc,res2,1e-3),'2nd pass: mol %s (Ipc=%f) should have Ipc=%f'%(smi,Ipc,res2)
def _testIpcLong(self):
""" test calculation of Ipc
"""
col = 4
self.__testDesc('PP_descrs_regress.csv',col,GraphDescriptors.Ipc)
def _testIpcLong2(self):
""" test calculation of Ipc
"""
col = 4
self.__testDesc('PP_descrs_regress.2.csv',col,GraphDescriptors.Ipc)
def testKappa1(self):
""" test calculation of the Hall-Kier kappa1 value
corrected data from Tables 3 and 6 of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
data = [('C12CC2C3CC13',2.344),
('C1CCC12CC2',3.061),
('C1CCCCC1',4.167),
('CCCCCC',6.000),
('CCC(C)C1CCC(C)CC1',9.091),
('CC(C)CC1CCC(C)CC1',9.091),
('CC(C)C1CCC(C)CCC1',9.091)
]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
kappa = GraphDescriptors.Kappa1(m)
assert feq(kappa,res,1e-3),'mol %s (kappa1=%f) should have kappa1=%f'%(smi,kappa,res)
def testKappa2(self):
""" test calculation of the Hall-Kier kappa2 value
corrected data from Tables 5 and 6 of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
data = [
('[C+2](C)(C)(C)(C)(C)C',0.667),
('[C+](C)(C)(C)(C)(CC)',1.240),
('C(C)(C)(C)(CCC)',2.3444),
('CC(C)CCCC',4.167),
('CCCCCCC',6.000),
('CCCCCC',5.000),
('CCCCCCC',6.000),
('C1CCCC1',1.440),
('C1CCCC1C',1.633),
('C1CCCCC1',2.222),
('C1CCCCCC1',3.061),
('CCCCC',4.00),
('CC=CCCC',4.740),
('C1=CN=CN1',0.884),
('c1ccccc1',1.606),
('c1cnccc1',1.552),
('n1ccncc1',1.500),
('CCCCF',3.930),
('CCCCCl',4.290),
('CCCCBr',4.480),
('CCC(C)C1CCC(C)CC1',4.133),
('CC(C)CC1CCC(C)CC1',4.133),
('CC(C)C1CCC(C)CCC1',4.133)
]
for smi,res in data:
#print smi
m = Chem.MolFromSmiles(smi)
kappa = GraphDescriptors.Kappa2(m)
assert feq(kappa,res,1e-3),'mol %s (kappa2=%f) should have kappa2=%f'%(smi,kappa,res)
def testKappa3(self):
""" test calculation of the Hall-Kier kappa3 value
corrected data from Tables 3 and 6 of Rev. Comp. Chem. vol 2, 367-422, (1991)
"""
data = [
('C[C+](C)(C)(C)C(C)(C)C',2.000),
('CCC(C)C(C)(C)(CC)',2.380),
('CCC(C)CC(C)CC',4.500),
('CC(C)CCC(C)CC',5.878),
('CC(C)CCCC(C)C',8.000),
('CCC(C)C1CCC(C)CC1',2.500),
('CC(C)CC1CCC(C)CC1',3.265),
('CC(C)C1CCC(C)CCC1',2.844)
]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
kappa = GraphDescriptors.Kappa3(m)
assert feq(kappa,res,1e-3),'mol %s (kappa3=%f) should have kappa3=%f'%(smi,kappa,res)
def testKappa3Long(self):
""" test calculation of kappa3
"""
col = 5
self.__testDesc('PP_descrs_regress.csv',col,GraphDescriptors.Kappa3)
def _testKappa3Long2(self):
""" test calculation of kappa3
"""
col = 5
self.__testDesc('PP_descrs_regress.2.csv',col,GraphDescriptors.Kappa3)
def _testLabuteASALong(self):
""" test calculation of Labute's ASA value
"""
col = 6
self.__testDesc('PP_descrs_regress.csv',col,lambda x:MolSurf.LabuteASA(x,includeHs=1))
def _testLabuteASALong2(self):
""" test calculation of Labute's ASA value
"""
col = 6
self.__testDesc('PP_descrs_regress.2.csv',col,lambda x:MolSurf.LabuteASA(x,includeHs=1))
def _testTPSAShortNCI(self):
" Short TPSA test "
inName = RDConfig.RDDataDir+'/NCI/first_200.tpsa.csv'
with open(inName,'r') as inF:
lines = inF.readlines()
for line in lines:
if line[0] != '#':
line.strip()
smi,ans = line.split(',')
ans = float(ans)
mol = Chem.MolFromSmiles(smi)
calc = MolSurf.TPSA(mol)
assert feq(calc,ans),'bad TPSA for SMILES %s (%.2f != %.2f)'%(smi,calc,ans)
def _testTPSALongNCI(self):
" Long TPSA test "
fileN = 'tpsa_regr.csv'
with open(os.path.join(RDConfig.RDCodeDir,'Chem','test_data',fileN),'r') as inF:
lines = inF.readlines()
lineNo = 0
for line in lines:
lineNo+=1
if line[0] != '#':
line.strip()
smi,ans = line.split(',')
ans = float(ans)
try:
mol = Chem.MolFromSmiles(smi)
except:
import traceback
traceback.print_exc()
mol = None
assert mol,"line %d, failed for smiles: %s"%(lineNo,smi)
calc = MolSurf.TPSA(mol)
assert feq(calc,ans),'line %d: bad TPSA for SMILES %s (%.2f != %.2f)'%(lineNo,smi,calc,ans)
def testTPSALong(self):
""" test calculation of TPSA
"""
col = 28
self.__testDesc('PP_descrs_regress.csv',col,MolSurf.TPSA)
def _testTPSALong2(self):
""" test calculation of TPSA
"""
col = 28
self.__testDesc('PP_descrs_regress.2.csv',col,MolSurf.TPSA)
def _testLipinskiLong(self):
""" test calculation of Lipinski params
"""
fName = 'PP_descrs_regress.csv'
# we can't do H Acceptors for these pyridine-containing molecules
# because the values will be wrong for EVERY one.
#col = 29
#self.__testDesc(fName,col,Lipinski.NumHAcceptors)
col = 30
self.__testDesc(fName,col,Lipinski.NumHDonors)
col = 31
self.__testDesc(fName,col,Lipinski.NumHeteroatoms)
col = 32
self.__testDesc(fName,col,Lipinski.NumRotatableBonds)
def _testHAcceptorsLong(self):
""" test calculation of Lipinski params
"""
fName = 'Block_regress.Lip.csv'
col = 1
self.__testDesc(fName,col,Lipinski.NumHAcceptors)
def _testHDonorsLong(self):
""" test calculation of Lipinski params
"""
fName = 'Block_regress.Lip.csv'
col = 2
self.__testDesc(fName,col,Lipinski.NumHDonors)
def _testHeterosLong(self):
""" test calculation of Lipinski params
"""
fName = 'Block_regress.Lip.csv'
col = 3
self.__testDesc(fName,col,Lipinski.NumHeteroatoms)
def _testRotBondsLong(self):
""" test calculation of Lipinski params
"""
fName = 'Block_regress.Lip.csv'
col = 4
self.__testDesc(fName,col,Lipinski.NumRotatableBonds)
def _testLogPLong(self):
""" test calculation of Lipinski params
"""
fName = 'PP_descrs_regress.csv'
col = 33
self.__testDesc(fName,col,lambda x:Crippen.MolLogP(x,includeHs=1))
def _testLogPLong2(self):
""" test calculation of Lipinski params
"""
fName = 'PP_descrs_regress.2.csv'
col = 33
self.__testDesc(fName,col,lambda x:Crippen.MolLogP(x,includeHs=1))
def _testMOELong(self):
""" test calculation of MOE-type descriptors
"""
fName = 'PP_descrs_regress.VSA.csv'
col = 1
self.__testDesc(fName,col,MolSurf.SMR_VSA1)
col = 2
self.__testDesc(fName,col,MolSurf.SMR_VSA10)
col = 3
self.__testDesc(fName,col,MolSurf.SMR_VSA2)
col = 4
self.__testDesc(fName,col,MolSurf.SMR_VSA3)
col = 5
self.__testDesc(fName,col,MolSurf.SMR_VSA4)
col = 6
self.__testDesc(fName,col,MolSurf.SMR_VSA5)
col = 7
self.__testDesc(fName,col,MolSurf.SMR_VSA6)
col = 8
self.__testDesc(fName,col,MolSurf.SMR_VSA7)
col = 9
self.__testDesc(fName,col,MolSurf.SMR_VSA8)
col = 10
self.__testDesc(fName,col,MolSurf.SMR_VSA9)
col = 11
self.__testDesc(fName,col,MolSurf.SlogP_VSA1)
col = 12
self.__testDesc(fName,col,MolSurf.SlogP_VSA10)
col = 13
self.__testDesc(fName,col,MolSurf.SlogP_VSA11)
col = 14
self.__testDesc(fName,col,MolSurf.SlogP_VSA12)
def _testMOELong2(self):
""" test calculation of MOE-type descriptors
"""
fName = 'PP_descrs_regress.VSA.2.csv'
col = 1
self.__testDesc(fName,col,MolSurf.SMR_VSA1)
col = 2
self.__testDesc(fName,col,MolSurf.SMR_VSA10)
col = 11
self.__testDesc(fName,col,MolSurf.SlogP_VSA1)
col = 12
self.__testDesc(fName,col,MolSurf.SlogP_VSA10)
col = 13
self.__testDesc(fName,col,MolSurf.SlogP_VSA11)
col = 14
self.__testDesc(fName,col,MolSurf.SlogP_VSA12)
def testBalabanJ(self):
""" test calculation of the Balaban J value
J values are from Balaban's paper and have had roundoff
errors and typos corrected.
"""
data = [# alkanes
('CC',1.0),('CCC',1.6330),
('CCCC',1.9747),('CC(C)C',2.3238),
('CCCCC',2.1906),('CC(C)CC',2.5396),('CC(C)(C)C',3.0237),
('CCCCCC',2.3391),('CC(C)CCC',2.6272),('CCC(C)CC',2.7542),('CC(C)(C)CC',3.1685),
('CC(C)C(C)C',2.9935),
# cycloalkanes
('C1CCCCC1',2.0000),
('C1C(C)CCCC1',2.1229),
('C1C(CC)CCCC1',2.1250),
('C1C(C)C(C)CCC1',2.2794),
('C1C(C)CC(C)CC1',2.2307),
('C1C(C)CCC(C)C1',2.1924),
('C1C(CCC)CCCC1',2.0779),
('C1C(C(C)C)CCCC1',2.2284),
('C1C(CC)C(C)CCC1',2.2973),
('C1C(CC)CC(C)CC1',2.2317),
('C1C(CC)CCC(C)C1',2.1804),
('C1C(C)C(C)C(C)CC1',2.4133),
('C1C(C)C(C)CC(C)C1',2.3462),
('C1C(C)CC(C)CC1(C)',2.3409),
# aromatics
('c1ccccc1',3.0000),
('c1c(C)cccc1',3.0215),
('c1c(CC)cccc1',2.8321),
('c1c(C)c(C)ccc1',3.1349),
('c1c(C)cc(C)cc1',3.0777),
('c1c(C)ccc(C)c1',3.0325),
('c1c(CCC)cccc1',2.6149),
('c1c(C(C)C)cccc1',2.8483),
('c1c(CC)c(C)ccc1',3.0065),
('c1c(CC)cc(C)cc1',2.9369),
('c1c(CC)ccc(C)c1',2.8816),
('c1c(C)c(C)c(C)cc1',3.2478),
('c1c(C)c(C)cc(C)c1',3.1717),
('c1c(C)cc(C)cc1(C)',3.1657)
]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
j = GraphDescriptors.BalabanJ(m,forceDMat=1)
assert feq(j,res),'mol %s (J=%f) should have J=%f'%(smi,j,res)
j = GraphDescriptors.BalabanJ(m)
assert feq(j,res),'second pass: mol %s (J=%f) should have J=%f'%(smi,j,res)
def _testBalabanJLong(self):
""" test calculation of the balaban j value
"""
fName = 'PP_descrs_regress.rest.2.csv'
col = 1
self.__testDesc(fName,col,GraphDescriptors.BalabanJ)
def _testKappa1Long(self):
""" test calculation of kappa1
"""
fName = 'PP_descrs_regress.rest.2.csv'
col = 31
self.__testDesc(fName,col,GraphDescriptors.Kappa1)
def _testKappa2Long(self):
""" test calculation of kappa2
"""
fName = 'PP_descrs_regress.rest.2.csv'
col = 32
self.__testDesc(fName,col,GraphDescriptors.Kappa2)
def _testChi0Long(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 5
self.__testDesc(fName,col,GraphDescriptors.Chi0)
def _testChi1Long(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 8
self.__testDesc(fName,col,GraphDescriptors.Chi1)
def _testChi0v(self):
""" test calculation of Chi0v
"""
data = [('CCCCCC',4.828),('CCC(C)CC',4.992),('CC(C)CCC',4.992),
('CC(C)C(C)C',5.155),('CC(C)(C)CC',5.207),
('CCCCCO',4.276),('CCC(O)CC',4.439),('CC(O)(C)CC',4.654),('c1ccccc1O',3.834),
('CCCl',2.841),('CCBr',3.671),('CCI',4.242)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi0v(m)
assert feq(chi,res,1e-3),'mol %s (Chi0v=%f) should have Chi0V=%f'%(smi,chi,res)
def _testChi0vLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 7
self.__testDesc(fName,col,GraphDescriptors.Chi0v)
def testChi1v(self):
""" test calculation of Chi1v
"""
data = [('CCCCCC',2.914),('CCC(C)CC',2.808),('CC(C)CCC',2.770),
('CC(C)C(C)C',2.643),('CC(C)(C)CC',2.561),
('CCCCCO',2.523),('CCC(O)CC',2.489),('CC(O)(C)CC',2.284),('c1ccccc1O',2.134)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi1v(m)
assert feq(chi,res,1e-3),'mol %s (Chi1v=%f) should have Chi1V=%f'%(smi,chi,res)
def _testChi1vLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 10
self.__testDesc(fName,col,GraphDescriptors.Chi1v)
def testPathCounts(self):
""" FIX: this should be in some other file
"""
data = [('CCCCCC',(6,5,4,3,2,1)),
('CCC(C)CC',(6,5,5,4,1,0)),
('CC(C)CCC',(6,5,5,3,2,0)),
('CC(C)C(C)C',(6,5,6,4,0,0)),
('CC(C)(C)CC',(6,5,7,3,0,0)),
('CCCCCO',(6,5,4,3,2,1)),
('CCC(O)CC',(6,5,5,4,1,0)),
('CC(O)(C)CC',(6,5,7,3,0,0)),
('c1ccccc1O',(7,7,8,8,8,8)),
]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
for i in range(1,6):
cnt = len(Chem.FindAllPathsOfLengthN(m,i,useBonds=1))
assert cnt==res[i],(smi,i,cnt,res[i],Chem.FindAllPathsOfLengthN(m,i,useBonds=1))
cnt = len(Chem.FindAllPathsOfLengthN(m,i+1,useBonds=0))
assert cnt==res[i],(smi,i,cnt,res[i],Chem.FindAllPathsOfLengthN(m,i+1,useBonds=1))
def testChi2v(self):
""" test calculation of Chi2v
"""
data = [('CCCCCC',1.707),('CCC(C)CC',1.922),('CC(C)CCC',2.183),
('CC(C)C(C)C',2.488),('CC(C)(C)CC',2.914),
('CCCCCO',1.431),('CCC(O)CC',1.470),('CC(O)(C)CC',2.166),('c1ccccc1O',1.336),
]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi2v(m)
assert feq(chi,res,1e-3),'mol %s (Chi2v=%f) should have Chi2V=%f'%(smi,chi,res)
def _testChi2vLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 12
self.__testDesc(fName,col,GraphDescriptors.Chi2v)
def testChi3v(self):
""" test calculation of Chi3v
"""
data = [('CCCCCC',0.957),('CCC(C)CC',1.394),('CC(C)CCC',0.866),('CC(C)C(C)C',1.333),('CC(C)(C)CC',1.061),
('CCCCCO',0.762),('CCC(O)CC',0.943),('CC(O)(C)CC',0.865),('c1ccccc1O',0.756)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi3v(m)
assert feq(chi,res,1e-3),'mol %s (Chi3v=%f) should have Chi3V=%f'%(smi,chi,res)
def _testChi3vLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 14
self.__testDesc(fName,col,GraphDescriptors.Chi3v)
def testChi4v(self):
""" test calculation of Chi4v
"""
data = [('CCCCCC',0.500),('CCC(C)CC',0.289),('CC(C)CCC',0.577),
('CC(C)C(C)C',0.000),('CC(C)(C)CC',0.000),
('CCCCCO',0.362),('CCC(O)CC',0.289),('CC(O)(C)CC',0.000),('c1ccccc1O',0.428)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi4v(m)
assert feq(chi,res,1e-3),'mol %s (Chi4v=%f) should have Chi4V=%f'%(smi,chi,res)
def testChi5v(self):
""" test calculation of Chi5v
"""
data = [('CCCCCC',0.250),('CCC(C)CC',0.000),('CC(C)CCC',0.000),
('CC(C)C(C)C',0.000),('CC(C)(C)CC',0.000),
('CCCCCO',0.112),('CCC(O)CC',0.000),('CC(O)(C)CC',0.000),('c1ccccc1O',0.242)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.ChiNv_(m,5)
assert feq(chi,res,1e-3),'mol %s (Chi5v=%f) should have Chi5V=%f'%(smi,chi,res)
def testChi0n(self):
""" test calculation of Chi0n
"""
data = [('CCCCCC',4.828),('CCC(C)CC',4.992),('CC(C)CCC',4.992),
('CC(C)C(C)C',5.155),('CC(C)(C)CC',5.207),
('CCCCCO',4.276),('CCC(O)CC',4.439),('CC(O)(C)CC',4.654),('c1ccccc1O',3.834),
('CCCl',2.085),('CCBr',2.085),('CCI',2.085),]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi0n(m)
assert feq(chi,res,1e-3),'mol %s (Chi0n=%f) should have Chi0n=%f'%(smi,chi,res)
def _testChi0nLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 6
self.__testDesc(fName,col,GraphDescriptors.Chi0n)
def testChi1n(self):
""" test calculation of Chi1n
"""
data = [('CCCCCC',2.914),('CCC(C)CC',2.808),('CC(C)CCC',2.770),
('CC(C)C(C)C',2.643),('CC(C)(C)CC',2.561),
('CCCCCO',2.523),('CCC(O)CC',2.489),('CC(O)(C)CC',2.284),('c1ccccc1O',2.134)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi1n(m)
assert feq(chi,res,1e-3),'mol %s (Chi1n=%f) should have Chi1N=%f'%(smi,chi,res)
def _testChi1nLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 9
self.__testDesc(fName,col,GraphDescriptors.Chi1n)
def testChi2n(self):
""" test calculation of Chi2n
"""
data = [('CCCCCC',1.707),('CCC(C)CC',1.922),('CC(C)CCC',2.183),
('CC(C)C(C)C',2.488),('CC(C)(C)CC',2.914),
('CCCCCO',1.431),('CCC(O)CC',1.470),('CC(O)(C)CC',2.166),('c1ccccc1O',1.336)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi2n(m)
assert feq(chi,res,1e-3),'mol %s (Chi2n=%f) should have Chi2N=%f'%(smi,chi,res)
def _testChi2nLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 11
self.__testDesc(fName,col,GraphDescriptors.Chi2n)
def testChi3n(self):
""" test calculation of Chi3n
"""
data = [('CCCCCC',0.957),('CCC(C)CC',1.394),('CC(C)CCC',0.866),('CC(C)C(C)C',1.333),('CC(C)(C)CC',1.061),
('CCCCCO',0.762),('CCC(O)CC',0.943),('CC(O)(C)CC',0.865),('c1ccccc1O',0.756)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi3n(m)
assert feq(chi,res,1e-3),'mol %s (Chi3n=%f) should have Chi3N=%f'%(smi,chi,res)
def _testChi3nLong(self):
fName = 'PP_descrs_regress.rest.2.csv'
col = 13
self.__testDesc(fName,col,GraphDescriptors.Chi3n)
def testChi4n(self):
""" test calculation of Chi4n
"""
data = [('CCCCCC',0.500),('CCC(C)CC',0.289),('CC(C)CCC',0.577),
('CC(C)C(C)C',0.000),('CC(C)(C)CC',0.000),
('CCCCCO',0.362),('CCC(O)CC',0.289),('CC(O)(C)CC',0.000),('c1ccccc1O',0.428)]
for smi,res in data:
m = Chem.MolFromSmiles(smi)
chi = GraphDescriptors.Chi4n(m)
assert feq(chi,res,1e-3),'mol %s (Chi4n=%f) should have Chi4N=%f'%(smi,chi,res)
def testIssue125(self):
""" test an issue with calculating BalabanJ
"""
smi = 'O=C(OC)C1=C(C)NC(C)=C(C(OC)=O)C1C2=CC=CC=C2[N+]([O-])=O'
m1 = Chem.MolFromSmiles(smi)
m2 = Chem.MolFromSmiles(smi)
Chem.MolToSmiles(m1)
j1=GraphDescriptors.BalabanJ(m1)
j2=GraphDescriptors.BalabanJ(m2)
assert feq(j1,j2)
def testOrderDepend(self):
""" test order dependence of some descriptors:
"""
data = [('C=CC=C',21.01955,2.73205),
('O=CC=O',25.01955,2.73205),
('FCC(=O)CF',46.7548875,2.98816),
('O=C1C=CC(=O)C=C1',148.705216,2.8265),
('C12C(F)=C(O)C(F)C1C(F)=C(O)C(F)2',315.250442,2.4509),
('C12CC=CCC1C(=O)C3CC=CCC3C(=O)2',321.539522,1.95986)]
for smi,CT,bal in data:
m = Chem.MolFromSmiles(smi)
newBal = GraphDescriptors.BalabanJ(m, forceDMat = 1)
assert feq(newBal,bal,1e-4),'mol %s %f!=%f'%(smi,newBal,bal)
m = Chem.MolFromSmiles(smi)
newCT = GraphDescriptors.BertzCT(m, forceDMat = 1)
assert feq(newCT,CT,1e-4),'mol %s (CT calc = %f) should have CT = %f'%(smi,newCT,CT)
m = Chem.MolFromSmiles(smi)
newCT = GraphDescriptors.BertzCT(m, forceDMat = 1)
assert feq(newCT,CT,1e-4),'mol %s (CT calc = %f) should have CT = %f'%(smi,newCT,CT)
newBal = GraphDescriptors.BalabanJ(m, forceDMat = 1)
assert feq(newBal,bal,1e-4),'mol %s %f!=%f'%(smi,newBal,bal)
m = Chem.MolFromSmiles(smi)
newBal = GraphDescriptors.BalabanJ(m, forceDMat = 1)
assert feq(newBal,bal,1e-4),'mol %s %f!=%f'%(smi,newBal,bal)
newCT = GraphDescriptors.BertzCT(m, forceDMat = 1)
assert feq(newCT,CT,1e-4),'mol %s (CT calc = %f) should have CT = %f'%(smi,newCT,CT)
if __name__ == '__main__':
import sys,getopt,re
doLong=0
if len(sys.argv) >1:
args,extras=getopt.getopt(sys.argv[1:],'l')
for arg,val in args:
if arg=='-l':
doLong=1
sys.argv.remove('-l')
if doLong:
for methName in dir(TestCase):
if re.match('_test',methName):
newName = re.sub('_test','test',methName)
exec('TestCase.%s = TestCase.%s'%(newName,methName))
unittest.main()
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""" unit testing code for Lipinski parameter calculation
This provides a workout for the SMARTS matcher
"""
from __future__ import print_function
from rdkit import RDConfig
import unittest,os
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Lipinski, rdMolDescriptors
NonStrict = "NUM_ROTATABLEBONDS_O"
Strict = "NUM_ROTATABLEBONDS"
class TestCase(unittest.TestCase):
def setUp(self):
print('\n%s: '%self.shortDescription(),end='')
self.inFileName = '%s/NCI/first_200.props.sdf'%(RDConfig.RDDataDir)
def test1(self):
" testing first 200 mols from NCI "
# figure out which rotor version we are using
m = Chem.MolFromSmiles("CC(C)(C)c1cc(O)c(cc1O)C(C)(C)C")
if Lipinski.NumRotatableBonds(m) == 2:
rot_prop = NonStrict
else:
rot_prop = Strict
suppl = Chem.SDMolSupplier(self.inFileName)
idx = 1
oldDonorSmarts = Chem.MolFromSmarts('[NH1,NH2,OH1]')
OldDonorCount = lambda x,y=oldDonorSmarts:Lipinski._NumMatches(x,y)
oldAcceptorSmarts = Chem.MolFromSmarts('[N,O]')
OldAcceptorCount = lambda x,y=oldAcceptorSmarts:Lipinski._NumMatches(x,y)
for m in suppl:
if m:
calc = Lipinski.NHOHCount(m)
orig = int(m.GetProp('NUM_LIPINSKIHDONORS'))
assert calc==orig,'bad num h donors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NOCount(m)
orig = int(m.GetProp('NUM_LIPINSKIHACCEPTORS'))
assert calc==orig,'bad num h acceptors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumHDonors(m)
orig = int(m.GetProp('NUM_HDONORS'))
assert calc==orig,'bad num h donors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumHAcceptors(m)
orig = int(m.GetProp('NUM_HACCEPTORS'))
assert calc==orig,'bad num h acceptors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumHeteroatoms(m)
orig = int(m.GetProp('NUM_HETEROATOMS'))
assert calc==orig,'bad num heteroatoms for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = Lipinski.NumRotatableBonds(m)
orig = int(m.GetProp(rot_prop))
assert calc==orig,'bad num rotors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
# test the underlying numrotatable bonds
calc = rdMolDescriptors.CalcNumRotatableBonds(m, rdMolDescriptors.NumRotatableBondsOptions.NonStrict)
orig = int(m.GetProp(NonStrict))
assert calc==orig,'bad num rotors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
calc = rdMolDescriptors.CalcNumRotatableBonds(m, rdMolDescriptors.NumRotatableBondsOptions.Strict)
orig = int(m.GetProp(Strict))
assert calc==orig,'bad num rotors for mol %d (%s): %d != %d'%(idx,m.GetProp('SMILES'),calc,orig)
idx += 1
def testIssue2183420(self):
" testing a problem with the acceptor definition "
self.assertTrue(Lipinski.NumHAcceptors(Chem.MolFromSmiles('NC'))==1)
self.assertTrue(Lipinski.NumHAcceptors(Chem.MolFromSmiles('CNC'))==1)
self.assertTrue(Lipinski.NumHAcceptors(Chem.MolFromSmiles('CN(C)C'))==1)
self.assertTrue(Lipinski.NumHAcceptors(Chem.MolFromSmiles('NC(=O)'))==1)
self.assertTrue(Lipinski.NumHAcceptors(Chem.MolFromSmiles('NC(=O)C'))==1)
self.assertTrue(Lipinski.NumHAcceptors(Chem.MolFromSmiles('CNC(=O)'))==1)
self.assertTrue(Lipinski.NumHAcceptors(Chem.MolFromSmiles('CNC(=O)C'))==1)
self.assertTrue(Lipinski.NumHAcceptors(Chem.MolFromSmiles('O=CNC(=O)C'))==2)
self.assertTrue(Lipinski.NumHAcceptors(Chem.MolFromSmiles('O=C(C)NC(=O)C'))==2)
if __name__ == '__main__':
unittest.main()
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""" unit testing code for molecule suppliers
"""
from rdkit import RDConfig
import unittest,cPickle,os
from rdkit import Chem
class TestCase(unittest.TestCase):
def setUp(self):
self._files=[]
def tearDown(self):
for fileN in self._files:
try:
os.unlink(fileN)
except OSError:
pass
def test1SDSupplier(self):
fileN = os.path.join(RDConfig.RDCodeDir,'VLib','NodeLib','test_data','NCI_aids.10.sdf')
suppl = Chem.SDMolSupplier(fileN)
ms = [x for x in suppl]
assert len(ms)==10
# test repeating:
ms = [x for x in suppl]
assert len(ms)==10
# test reset:
suppl.reset()
m = suppl.next()
assert m.GetProp('_Name')=='48'
assert m.GetProp('NSC')=='48'
assert m.GetProp('CAS_RN')=='15716-70-8'
m = suppl.next()
assert m.GetProp('_Name')=='78'
assert m.GetProp('NSC')=='78'
assert m.GetProp('CAS_RN')=='6290-84-2'
suppl.reset()
for i in range(10):
m = suppl.next()
try:
m = suppl.next()
except StopIteration:
ok=1
else:
ok=0
assert ok
def test2SmilesSupplier(self):
fileN = os.path.join(RDConfig.RDCodeDir,'VLib','NodeLib','test_data','pgp_20.txt')
suppl = Chem.SmilesMolSupplier(fileN,delimiter='\t',smilesColumn=2,
nameColumn=1,titleLine=1)
ms = [x for x in suppl]
assert len(ms)==20
# test repeating:
ms = [x for x in suppl]
assert len(ms)==20
# test reset:
suppl.reset()
m = suppl.next()
assert m.GetProp('_Name')=='ALDOSTERONE'
assert m.GetProp('ID')=='RD-PGP-0001'
m = suppl.next()
assert m.GetProp('_Name')=='AMIODARONE'
assert m.GetProp('ID')=='RD-PGP-0002'
suppl.reset()
for i in range(20):
m = suppl.next()
try:
m = suppl.next()
except StopIteration:
ok=1
else:
ok=0
assert ok
def test3SmilesSupplier(self):
txt="""C1CC1,1
CC(=O)O,3
fail,4
CCOC,5
"""
import tempfile
fileN = tempfile.mktemp('.csv')
open(fileN,'w+').write(txt)
self._files.append(fileN)
suppl = Chem.SmilesMolSupplier(fileN,delimiter=',',smilesColumn=0,
nameColumn=1,titleLine=0)
ms = [x for x in suppl]
while ms.count(None):
ms.remove(None)
assert len(ms)==3
if __name__ == '__main__':
unittest.main()
| {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/UnitTestSuppliers.py",
"copies": "2",
"size": "2680",
"license": "bsd-3-clause",
"hash": -6046542816694804000,
"line_mean": 22.9285714286,
"line_max": 91,
"alpha_frac": 0.5873134328,
"autogenerated": false,
"ratio": 3.055872291904219,
"config_test": true,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.4643185724704219,
"avg_score": null,
"num_lines": null
} |
""" utility functionality for clustering molecules using fingerprints
includes a command line app for clustering
Sample Usage:
python ClusterMols.py -d data.gdb -t daylight_sig \
--idName="CAS_TF" -o clust1.pkl \
--actTable="dop_test" --actName="moa_quant"
"""
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbInfo,DbUtils
from rdkit.ML.Data import DataUtils
from rdkit.ML.Cluster import Clusters
from rdkit.ML.Cluster import Murtagh
import sys,cPickle
from rdkit.Chem.Fingerprints import FingerprintMols,MolSimilarity
from rdkit import DataStructs
import numpy
_cvsVersion="$Id$"
idx1 = _cvsVersion.find(':')+1
idx2 = _cvsVersion.rfind('$')
__VERSION_STRING="%s"%(_cvsVersion[idx1:idx2])
message=FingerprintMols.message
error=FingerprintMols.error
def GetDistanceMatrix(data,metric,isSimilarity=1):
""" data should be a list of tuples with fingerprints in position 1
(the rest of the elements of the tuple are not important)
Returns the symmetric distance matrix
(see ML.Cluster.Resemblance for layout documentation)
"""
nPts = len(data)
res = numpy.zeros((nPts*(nPts-1)/2),numpy.float)
nSoFar=0
for col in xrange(1,nPts):
for row in xrange(col):
fp1 = data[col][1]
fp2 = data[row][1]
if fp1.GetNumBits()>fp2.GetNumBits():
fp1 = DataStructs.FoldFingerprint(fp1,fp1.GetNumBits()/fp2.GetNumBits())
elif fp2.GetNumBits()>fp1.GetNumBits():
fp2 = DataStructs.FoldFingerprint(fp2,fp2.GetNumBits()/fp1.GetNumBits())
sim = metric(fp1,fp2)
if isSimilarity:
sim = 1.-sim
res[nSoFar] = sim
nSoFar += 1
return res
def ClusterPoints(data,metric,algorithmId,haveLabels=False,haveActs=True,returnDistances=False):
message('Generating distance matrix.\n')
dMat = GetDistanceMatrix(data,metric)
message('Clustering\n')
clustTree = Murtagh.ClusterData(dMat,len(data),algorithmId,
isDistData=1)[0]
acts = []
if haveActs and len(data[0])>2:
# we've got activities... use them:
acts = [int(x[2]) for x in data]
if not haveLabels:
labels = ['Mol: %s'%str(x[0]) for x in data]
else:
labels = [x[0] for x in data]
clustTree._ptLabels = labels
if acts:
clustTree._ptValues = acts
for pt in clustTree.GetPoints():
idx = pt.GetIndex()-1
pt.SetName(labels[idx])
if acts:
try:
pt.SetData(int(acts[idx]))
except:
pass
if not returnDistances:
return clustTree
else:
return clustTree,dMat
def ClusterFromDetails(details):
""" Returns the cluster tree
"""
data = MolSimilarity.GetFingerprints(details)
if details.maxMols > 0:
data = data[:details.maxMols]
if details.outFileName:
try:
outF = open(details.outFileName,'wb+')
except IOError:
error("Error: could not open output file %s for writing\n"%(details.outFileName))
return None
else:
outF = None
if not data:
return None
clustTree = ClusterPoints(data,details.metric,details.clusterAlgo,
haveLabels=0,haveActs=1)
if outF:
cPickle.dump(clustTree,outF)
return clustTree
_usageDoc="""
Usage: ClusterMols.py [args] <fName>
If <fName> is provided and no tableName is specified (see below),
data will be read from the text file <fName>. Text files delimited
with either commas (extension .csv) or tabs (extension .txt) are
supported.
Command line arguments are:
- -d _dbName_: set the name of the database from which
to pull input fingerprint information.
- -t _tableName_: set the name of the database table
from which to pull input fingerprint information
- --idName=val: sets the name of the id column in the input
database. Default is *ID*.
- -o _outFileName_: name of the output file (output will
be a pickle (.pkl) file with the cluster tree)
- --actTable=val: name of table containing activity values
(used to color points in the cluster tree).
- --actName=val: name of column with activities in the activity
table. The values in this column should either be integers or
convertible into integers.
- --SLINK: use the single-linkage clustering algorithm
(default is Ward's minimum variance)
- --CLINK: use the complete-linkage clustering algorithm
(default is Ward's minimum variance)
- --UPGMA: use the group-average clustering algorithm
(default is Ward's minimum variance)
- --dice: use the DICE similarity metric instead of Tanimoto
- --cosine: use the cosine similarity metric instead of Tanimoto
- --fpColName=val: name to use for the column which stores
fingerprints (in pickled format) in the input db table.
Default is *AutoFragmentFP*
- --minPath=val: minimum path length to be included in
fragment-based fingerprints. Default is *2*.
- --maxPath=val: maximum path length to be included in
fragment-based fingerprints. Default is *7*.
- --nBitsPerHash: number of bits to be set in the output
fingerprint for each fragment. Default is *4*.
- --discrim: use of path-based discriminators to hash bits.
Default is *false*.
- -V: include valence information in the fingerprints
Default is *false*.
- -H: include Hs in the fingerprint
Default is *false*.
- --useMACCS: use the public MACCS keys to do the fingerprinting
(instead of a daylight-type fingerprint)
"""
if __name__ == '__main__':
message("This is ClusterMols version %s\n\n"%(__VERSION_STRING))
FingerprintMols._usageDoc=_usageDoc
details = FingerprintMols.ParseArgs()
ClusterFromDetails(details)
| {
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"path": "rdkit/Chem/Fingerprints/ClusterMols.py",
"copies": "2",
"size": "6021",
"license": "bsd-3-clause",
"hash": 8993781663323533000,
"line_mean": 30.1968911917,
"line_max": 96,
"alpha_frac": 0.6799534961,
"autogenerated": false,
"ratio": 3.5564087418783226,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.5236362237978323,
"avg_score": null,
"num_lines": null
} |
""" utility functionality for fingerprinting sets of molecules
includes a command line app for working with fingerprints
and databases
Sample Usage:
python FingerprintMols.py -d data.gdb \
-t 'raw_dop_data' --smilesName="Structure" --idName="Mol_ID" \
--outTable="daylight_sig"
"""
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import MACCSkeys
from rdkit.ML.Cluster import Murtagh
from rdkit import DataStructs
import sys
from rdkit.six.moves import cPickle
_cvsVersion = "$Id$"
idx1 = _cvsVersion.find(':') + 1
idx2 = _cvsVersion.rfind('$')
__VERSION_STRING = "%s" % (_cvsVersion[idx1:idx2])
def error(msg):
sys.stderr.write(msg)
def message(msg):
sys.stderr.write(msg)
def GetRDKFingerprint(mol):
""" uses default parameters """
details = FingerprinterDetails()
return apply(FingerprintMol, (mol, ), details.__dict__)
def FoldFingerprintToTargetDensity(fp, **fpArgs):
nOn = fp.GetNumOnBits()
nTot = fp.GetNumBits()
while (float(nOn) / nTot < fpArgs['tgtDensity']):
if nTot / 2 > fpArgs['minSize']:
fp = DataStructs.FoldFingerprint(fp, 2)
nOn = fp.GetNumOnBits()
nTot = fp.GetNumBits()
else:
break
return fp
def FingerprintMol(mol, fingerprinter=Chem.RDKFingerprint, **fpArgs):
if not fpArgs:
details = FingerprinterDetails()
fpArgs = details.__dict__
if fingerprinter != Chem.RDKFingerprint:
fp = fingerprinter(mol, **fpArgs)
fp = FoldFingerprintToTargetDensity(fp, **fpArgs)
else:
fp = fingerprinter(mol, fpArgs['minPath'], fpArgs['maxPath'], fpArgs['fpSize'],
fpArgs['bitsPerHash'], fpArgs['useHs'], fpArgs['tgtDensity'],
fpArgs['minSize'])
return fp
def FingerprintsFromSmiles(dataSource, idCol, smiCol, fingerprinter=Chem.RDKFingerprint,
reportFreq=10, maxMols=-1, **fpArgs):
""" fpArgs are passed as keyword arguments to the fingerprinter
Returns a list of 2-tuples: (id,fp)
"""
res = []
nDone = 0
for entry in dataSource:
id, smi = str(entry[idCol]), str(entry[smiCol])
mol = Chem.MolFromSmiles(smi)
if mol is not None:
fp = FingerprintMol(mol, fingerprinter, **fpArgs)
res.append((id, fp))
nDone += 1
if reportFreq > 0 and not nDone % reportFreq:
message('Done %d molecules\n' % (nDone))
if maxMols > 0 and nDone >= maxMols:
break
else:
error('Problems parsing SMILES: %s\n' % smi)
return res
def FingerprintsFromMols(mols, fingerprinter=Chem.RDKFingerprint, reportFreq=10, maxMols=-1,
**fpArgs):
""" fpArgs are passed as keyword arguments to the fingerprinter
Returns a list of 2-tuples: (id,fp)
"""
res = []
nDone = 0
for id, mol in mols:
if mol:
fp = FingerprintMol(mol, fingerprinter, **fpArgs)
res.append((id, fp))
nDone += 1
if reportFreq > 0 and not nDone % reportFreq:
message('Done %d molecules\n' % (nDone))
if maxMols > 0 and nDone >= maxMols:
break
else:
error('Problems parsing SMILES: %s\n' % smi)
return res
def FingerprintsFromPickles(dataSource, idCol, pklCol, fingerprinter=Chem.RDKFingerprint,
reportFreq=10, maxMols=-1, **fpArgs):
""" fpArgs are passed as keyword arguments to the fingerprinter
Returns a list of 2-tuples: (id,fp)
"""
res = []
nDone = 0
for entry in dataSource:
id, pkl = str(entry[idCol]), str(entry[pklCol])
mol = Chem.Mol(pkl)
if mol is not None:
fp = FingerprintMol(mol, fingerprinter, **fpArgs)
res.append((id, fp))
nDone += 1
if reportFreq > 0 and not nDone % reportFreq:
message('Done %d molecules\n' % (nDone))
if maxMols > 0 and nDone >= maxMols:
break
else:
error('Problems parsing pickle for id: %s\n' % id)
return res
def FingerprintsFromDetails(details, reportFreq=10):
data = None
if details.dbName and details.tableName:
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbInfo
from rdkit.ML.Data import DataUtils
try:
conn = DbConnect(details.dbName, details.tableName)
except Exception:
import traceback
error('Problems establishing connection to database: %s|%s\n' % (details.dbName,
details.tableName))
traceback.print_exc()
if not details.idName:
details.idName = DbInfo.GetColumnNames(details.dbName, details.tableName)[0]
dataSet = DataUtils.DBToData(details.dbName, details.tableName,
what='%s,%s' % (details.idName, details.smilesName))
idCol = 0
smiCol = 1
elif details.inFileName and details.useSmiles:
from rdkit.ML.Data import DataUtils
conn = None
if not details.idName:
details.idName = 'ID'
try:
dataSet = DataUtils.TextFileToData(details.inFileName,
onlyCols=[details.idName, details.smilesName])
except IOError:
import traceback
error('Problems reading from file %s\n' % (details.inFileName))
traceback.print_exc()
idCol = 0
smiCol = 1
elif details.inFileName and details.useSD:
conn = None
dataset = None
if not details.idName:
details.idName = 'ID'
dataSet = []
try:
s = Chem.SDMolSupplier(details.inFileName)
except Exception:
import traceback
error('Problems reading from file %s\n' % (details.inFileName))
traceback.print_exc()
else:
while 1:
try:
m = s.next()
except StopIteration:
break
if m:
dataSet.append(m)
if reportFreq > 0 and not len(dataSet) % reportFreq:
message('Read %d molecules\n' % (len(dataSet)))
if details.maxMols > 0 and len(dataSet) >= details.maxMols:
break
for i, mol in enumerate(dataSet):
if mol.HasProp(details.idName):
nm = mol.GetProp(details.idName)
else:
nm = mol.GetProp('_Name')
dataSet[i] = (nm, mol)
else:
dataSet = None
fps = None
if dataSet and not details.useSD:
data = dataSet.GetNamedData()
if not details.molPklName:
fps = apply(FingerprintsFromSmiles, (data, idCol, smiCol), details.__dict__)
else:
fps = apply(FingerprintsFromPickles, (data, idCol, smiCol), details.__dict__)
elif dataSet and details.useSD:
fps = apply(FingerprintsFromMols, (dataSet, ), details.__dict__)
if fps:
if details.outFileName:
outF = open(details.outFileName, 'wb+')
for i in range(len(fps)):
cPickle.dump(fps[i], outF)
outF.close()
dbName = details.outDbName or details.dbName
if details.outTableName and dbName:
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbInfo, DbUtils, DbModule
conn = DbConnect(dbName)
#
# We don't have a db open already, so we'll need to figure out
# the types of our columns...
#
colTypes = DbUtils.TypeFinder(data, len(data), len(data[0]))
typeStrs = DbUtils.GetTypeStrings([details.idName, details.smilesName], colTypes,
keyCol=details.idName)
cols = '%s, %s %s' % (typeStrs[0], details.fpColName, DbModule.binaryTypeName)
# FIX: we should really check to see if the table
# is already there and, if so, add the appropriate
# column.
#
# create the new table
#
if details.replaceTable or \
details.outTableName.upper() not in [x.upper() for x in conn.GetTableNames()]:
conn.AddTable(details.outTableName, cols)
#
# And add the data
#
for id, fp in fps:
tpl = id, DbModule.binaryHolder(fp.ToBinary())
conn.InsertData(details.outTableName, tpl)
conn.Commit()
return fps
# ------------------------------------------------
#
# Command line parsing stuff
#
# ------------------------------------------------
class FingerprinterDetails(object):
""" class for storing the details of a fingerprinting run,
generates sensible defaults on construction
"""
def __init__(self):
self._fingerprinterInit()
self._screenerInit()
self._clusterInit()
def _fingerprinterInit(self):
self.fingerprinter = Chem.RDKFingerprint
self.fpColName = "AutoFragmentFP"
self.idName = ''
self.dbName = ''
self.outDbName = ''
self.tableName = ''
self.minSize = 64
self.fpSize = 2048
self.tgtDensity = 0.3
self.minPath = 1
self.maxPath = 7
self.discrimHash = 0
self.useHs = 0
self.useValence = 0
self.bitsPerHash = 2
self.smilesName = 'SMILES'
self.maxMols = -1
self.outFileName = ''
self.outTableName = ''
self.inFileName = ''
self.replaceTable = True
self.molPklName = ''
self.useSmiles = True
self.useSD = False
def _screenerInit(self):
self.metric = DataStructs.TanimotoSimilarity
self.doScreen = ''
self.topN = 10
self.screenThresh = 0.75
self.doThreshold = 0
self.smilesTableName = ''
self.probeSmiles = ''
self.probeMol = None
self.noPickle = 0
def _clusterInit(self):
self.clusterAlgo = Murtagh.WARDS
self.actTableName = ''
self.actName = ''
def GetMetricName(self):
if self.metric == DataStructs.TanimotoSimilarity:
return 'Tanimoto'
elif self.metric == DataStructs.DiceSimilarity:
return 'Dice'
elif self.metric == DataStructs.CosineSimilarity:
return 'Cosine'
elif self.metric:
return self.metric
else:
return 'Unknown'
def SetMetricFromName(self, name):
name = name.upper()
if name == "TANIMOTO":
self.metric = DataStructs.TanimotoSimilarity
elif name == "DICE":
self.metric = DataStructs.DiceSimilarity
elif name == "COSINE":
self.metric = DataStructs.CosineSimilarity
def Usage():
""" prints a usage string and exits
"""
print(_usageDoc)
sys.exit(-1)
_usageDoc = """
Usage: FingerprintMols.py [args] <fName>
If <fName> is provided and no tableName is specified (see below),
data will be read from the text file <fName>. Text files delimited
with either commas (extension .csv) or tabs (extension .txt) are
supported.
Command line arguments are:
- -d _dbName_: set the name of the database from which
to pull input molecule information. If output is
going to a database, this will also be used for that
unless the --outDbName option is used.
- -t _tableName_: set the name of the database table
from which to pull input molecule information
- --smilesName=val: sets the name of the SMILES column
in the input database. Default is *SMILES*.
- --useSD: Assume that the input file is an SD file, not a SMILES
table.
- --idName=val: sets the name of the id column in the input
database. Defaults to be the name of the first db column
(or *ID* for text files).
- -o _outFileName_: name of the output file (output will
be a pickle file with one label,fingerprint entry for each
molecule).
- --outTable=val: name of the output db table used to store
fingerprints. If this table already exists, it will be
replaced.
- --outDbName: name of output database, if it's being used.
Defaults to be the same as the input db.
- --fpColName=val: name to use for the column which stores
fingerprints (in pickled format) in the output db table.
Default is *AutoFragmentFP*
- --maxSize=val: base size of the fingerprints to be generated
Default is *2048*
- --minSize=val: minimum size of the fingerprints to be generated
(limits the amount of folding that happens). Default is *64*
- --density=val: target bit density in the fingerprint. The
fingerprint will be folded until this density is
reached. Default is *0.3*
- --minPath=val: minimum path length to be included in
fragment-based fingerprints. Default is *1*.
- --maxPath=val: maximum path length to be included in
fragment-based fingerprints. Default is *7*.
- --nBitsPerHash: number of bits to be set in the output
fingerprint for each fragment. Default is *2*.
- --discrim: use of path-based discriminators to hash bits.
Default is *false*.
- -V: include valence information in the fingerprints
Default is *false*.
- -H: include Hs in the fingerprint
Default is *false*.
- --maxMols=val: sets the maximum number of molecules to be
fingerprinted.
- --useMACCS: use the public MACCS keys to do the fingerprinting
(instead of a daylight-type fingerprint)
"""
def ParseArgs(details=None):
""" parses the command line arguments and returns a
_FingerprinterDetails_ instance with the results.
**Note**:
- If you make modifications here, please update the global
_usageDoc string so the Usage message is up to date.
- This routine is used by both the fingerprinter, the clusterer and the
screener; not all arguments make sense for all applications.
"""
import sys, getopt
args = sys.argv[1:]
try:
args, extras = getopt.getopt(args,
'HVs:d:t:o:h',
[
'minSize=',
'maxSize=',
'density=',
'minPath=',
'maxPath=',
'bitsPerHash=',
'smilesName=',
'molPkl=',
'useSD',
'idName=',
'discrim',
'outTable=',
'outDbName=',
'fpColName=',
'maxMols=',
'useMACCS',
'keepTable',
# SCREENING:
'smilesTable=',
'doScreen=',
'topN=',
'thresh=',
'smiles=',
'dice',
'cosine',
# CLUSTERING:
'actTable=',
'actName=',
'SLINK',
'CLINK',
'UPGMA',
])
except Exception:
import traceback
traceback.print_exc()
Usage()
if details is None:
details = FingerprinterDetails()
if len(extras):
details.inFileName = extras[0]
for arg, val in args:
if arg == '-H':
details.useHs = 1
elif arg == '-V':
details.useValence = 1
elif arg == '-d':
details.dbName = val
elif arg == '-t':
details.tableName = val
elif arg == '-o':
details.outFileName = val
elif arg == '--minSize':
details.minSize = int(val)
elif arg == '--maxSize':
details.fpSize = int(val)
elif arg == '--density':
details.tgtDensity = float(val)
elif arg == '--outTable':
details.outTableName = val
elif arg == '--outDbName':
details.outDbName = val
elif arg == '--fpColName':
details.fpColName = val
elif arg == '--minPath':
details.minPath = int(val)
elif arg == '--maxPath':
details.maxPath = int(val)
elif arg == '--nBitsPerHash':
details.bitsPerHash = int(val)
elif arg == '--discrim':
details.discrimHash = 1
elif arg == '--smilesName':
details.smilesName = val
elif arg == '--molPkl':
details.molPklName = val
elif arg == '--useSD':
details.useSmiles = False
details.useSD = True
elif arg == '--idName':
details.idName = val
elif arg == '--maxMols':
details.maxMols = int(val)
elif arg == '--useMACCS':
details.fingerprinter = MACCSkeys.GenMACCSKeys
elif arg == '--keepTable':
details.replaceTable = False
# SCREENER:
elif arg == '--smilesTable':
details.smilesTableName = val
elif arg == '--topN':
details.doThreshold = 0
details.topN = int(val)
elif arg == '--thresh':
details.doThreshold = 1
details.screenThresh = float(val)
elif arg == '--smiles':
details.probeSmiles = val
elif arg == '--dice':
details.metric = DataStructs.DiceSimilarity
elif arg == '--cosine':
details.metric = DataStructs.CosineSimilarity
# CLUSTERS:
elif arg == '--SLINK':
details.clusterAlgo = Murtagh.SLINK
elif arg == '--CLINK':
details.clusterAlgo = Murtagh.CLINK
elif arg == '--UPGMA':
details.clusterAlgo = Murtagh.UPGMA
elif arg == '--actTable':
details.actTableName = val
elif arg == '--actName':
details.actName = val
elif arg == '-h':
Usage()
return details
if __name__ == '__main__':
message("This is FingerprintMols version %s\n\n" % (__VERSION_STRING))
details = ParseArgs()
FingerprintsFromDetails(details)
| {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Fingerprints/FingerprintMols.py",
"copies": "1",
"size": "17861",
"license": "bsd-3-clause",
"hash": -1879890710035294000,
"line_mean": 29.6890034364,
"line_max": 92,
"alpha_frac": 0.5855775153,
"autogenerated": false,
"ratio": 3.762586896987571,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.4848164412287571,
"avg_score": null,
"num_lines": null
} |
""" utility functionality for molecular similarity
includes a command line app for screening databases
Sample Usage:
python MolSimilarity.py -d data.gdb -t daylight_sig --idName="Mol_ID" \
--topN=100 --smiles='c1(C=O)ccc(Oc2ccccc2)cc1' --smilesTable=raw_dop_data \
--smilesName="structure" -o results.csv
"""
from rdkit import RDConfig
from rdkit import DataStructs
from rdkit import Chem
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbModule
from rdkit.DataStructs.TopNContainer import TopNContainer
import sys, types
from rdkit.six.moves import cPickle
from rdkit.Chem.Fingerprints import FingerprintMols, DbFpSupplier
try:
from rdkit.VLib.NodeLib.DbPickleSupplier import _lazyDataSeq as _dataSeq
except ImportError:
_dataSeq = None
from rdkit import DataStructs
_cvsVersion = "$Id$"
idx1 = _cvsVersion.find(':') + 1
idx2 = _cvsVersion.rfind('$')
__VERSION_STRING = "%s" % (_cvsVersion[idx1:idx2])
def _ConstructSQL(details, extraFields=''):
fields = '%s.%s' % (details.tableName, details.idName)
join = ''
if details.smilesTableName:
if details.smilesName:
fields = fields + ',%s' % (details.smilesName)
join = 'join %s smi on smi.%s=%s.%s' % (details.smilesTableName, details.idName,
details.tableName, details.idName)
if details.actTableName:
if details.actName:
fields = fields + ',%s' % (details.actName)
join = join + 'join %s act on act.%s=%s.%s' % (details.actTableName, details.idName,
details.tableName, details.idName)
#data = conn.GetData(fields=fields,join=join)
if extraFields:
fields += ',' + extraFields
cmd = 'select %s from %s %s' % (fields, details.tableName, join)
return cmd
def ScreenInDb(details, mol):
try:
probeFp = apply(FingerprintMols.FingerprintMol, (mol, ), details.__dict__)
except Exception:
import traceback
FingerprintMols.error('Error: problems fingerprinting molecule.\n')
traceback.print_exc()
return []
if details.dbName and details.tableName:
try:
conn = DbConnect(details.dbName, details.tableName)
if hasattr(details, 'dbUser'):
conn.user = details.dbUser
if hasattr(details, 'dbPassword'):
conn.password = details.dbPassword
except Exception:
import traceback
FingerprintMols.error('Error: Problems establishing connection to database: %s|%s\n' %
(details.dbName, details.tableName))
traceback.print_exc()
if details.metric not in (DataStructs.TanimotoSimilarity, DataStructs.DiceSimilarity,
DataStructs.CosineSimilarity):
data = GetFingerprints(details)
res = ScreenFingerprints(details, data, mol)
else:
res = []
if details.metric == DataStructs.TanimotoSimilarity:
func = 'rd_tanimoto'
pkl = probeFp.ToBitString()
elif details.metric == DataStructs.DiceSimilarity:
func = 'rd_dice'
pkl = probeFp.ToBitString()
elif details.metric == DataStructs.CosineSimilarity:
func = 'rd_cosine'
pkl = probeFp.ToBitString()
extraFields = "%s(%s,%s) as tani" % (func, DbModule.placeHolder, details.fpColName)
cmd = _ConstructSQL(details, extraFields=extraFields)
if details.doThreshold:
# we need to do a subquery here:
cmd = "select * from (%s) tmp where tani>%f" % (cmd, details.screenThresh)
cmd += " order by tani desc"
if not details.doThreshold and details.topN > 0:
cmd += " limit %d" % details.topN
curs = conn.GetCursor()
curs.execute(cmd, (pkl, ))
res = curs.fetchall()
return res
def GetFingerprints(details):
""" returns an iterable sequence of fingerprints
each fingerprint will have a _fieldsFromDb member whose first entry is
the id.
"""
if details.dbName and details.tableName:
try:
conn = DbConnect(details.dbName, details.tableName)
if hasattr(details, 'dbUser'):
conn.user = details.dbUser
if hasattr(details, 'dbPassword'):
conn.password = details.dbPassword
except Exception:
import traceback
FingerprintMols.error('Error: Problems establishing connection to database: %s|%s\n' %
(details.dbName, details.tableName))
traceback.print_exc()
cmd = _ConstructSQL(details, extraFields=details.fpColName)
curs = conn.GetCursor()
#curs.execute(cmd)
#print 'CURSOR:',curs,curs.closed
if _dataSeq:
suppl = _dataSeq(curs, cmd, depickle=not details.noPickle, klass=DataStructs.ExplicitBitVect)
_dataSeq._conn = conn
else:
suppl = DbFpSupplier.ForwardDbFpSupplier(data, fpColName=details.fpColName)
elif details.inFileName:
conn = None
try:
inF = open(details.inFileName, 'r')
except IOError:
import traceback
FingerprintMols.error('Error: Problems reading from file %s\n' % (details.inFileName))
traceback.print_exc()
suppl = []
done = 0
while not done:
try:
id, fp = cPickle.load(inF)
except Exception:
done = 1
else:
fp._fieldsFromDb = [id]
suppl.append(fp)
else:
suppl = None
return suppl
def ScreenFingerprints(details, data, mol=None, probeFp=None):
""" Returns a list of results
"""
if probeFp is None:
try:
probeFp = apply(FingerprintMols.FingerprintMol, (mol, ), details.__dict__)
except Exception:
import traceback
FingerprintMols.error('Error: problems fingerprinting molecule.\n')
traceback.print_exc()
return []
if not probeFp:
return []
res = []
if not details.doThreshold and details.topN > 0:
topN = TopNContainer(details.topN)
else:
topN = []
res = []
count = 0
for pt in data:
fp1 = probeFp
if not details.noPickle:
if type(pt) in (types.TupleType, types.ListType):
id, fp = pt
else:
fp = pt
id = pt._fieldsFromDb[0]
score = DataStructs.FingerprintSimilarity(fp1, fp, details.metric)
else:
id, pkl = pt
score = details.metric(fp1, str(pkl))
if topN:
topN.Insert(score, id)
elif not details.doThreshold or \
(details.doThreshold and score>=details.screenThresh):
res.append((id, score))
count += 1
if hasattr(details, 'stopAfter') and count >= details.stopAfter:
break
for score, id in topN:
res.append((id, score))
return res
def ScreenFromDetails(details, mol=None):
""" Returns a list of results
"""
if not mol:
if not details.probeMol:
smi = details.probeSmiles
try:
mol = Chem.MolFromSmiles(smi)
except Exception:
import traceback
FingerprintMols.error('Error: problems generating molecule for smiles: %s\n' % (smi))
traceback.print_exc()
return
else:
mol = details.probeMol
if not mol:
return
if details.outFileName:
try:
outF = open(details.outFileName, 'w+')
except IOError:
FingerprintMols.error("Error: could not open output file %s for writing\n" %
(details.outFileName))
return None
else:
outF = None
if not hasattr(details, 'useDbSimilarity') or not details.useDbSimilarity:
data = GetFingerprints(details)
res = ScreenFingerprints(details, data, mol)
else:
res = ScreenInDb(details, mol)
if outF:
for pt in res:
outF.write(','.join([str(x) for x in pt]))
outF.write('\n')
return res
_usageDoc = """
Usage: MolSimilarity.py [args] <fName>
If <fName> is provided and no tableName is specified (see below),
data will be read from the pickled file <fName>. This file should
contain a series of pickled (id,fingerprint) tuples.
NOTE: at the moment the user is responsible for ensuring that the
fingerprint parameters given at run time (used to fingerprint the
probe molecule) match those used to generate the input fingerprints.
Command line arguments are:
- --smiles=val: sets the SMILES for the input molecule. This is
a required argument.
- -d _dbName_: set the name of the database from which
to pull input fingerprint information.
- -t _tableName_: set the name of the database table
from which to pull input fingerprint information
- --smilesTable=val: sets the name of the database table
which contains SMILES for the input fingerprints. If this
information is provided along with smilesName (see below),
the output file will contain SMILES data
- --smilesName=val: sets the name of the SMILES column
in the input database. Default is *SMILES*.
- --topN=val: sets the number of results to return.
Default is *10*.
- --thresh=val: sets the similarity threshold.
- --idName=val: sets the name of the id column in the input
database. Default is *ID*.
- -o _outFileName_: name of the output file (output will
be a CSV file with one line for each of the output molecules
- --dice: use the DICE similarity metric instead of Tanimoto
- --cosine: use the cosine similarity metric instead of Tanimoto
- --fpColName=val: name to use for the column which stores
fingerprints (in pickled format) in the output db table.
Default is *AutoFragmentFP*
- --minPath=val: minimum path length to be included in
fragment-based fingerprints. Default is *1*.
- --maxPath=val: maximum path length to be included in
fragment-based fingerprints. Default is *7*.
- --nBitsPerHash: number of bits to be set in the output
fingerprint for each fragment. Default is *4*.
- --discrim: use of path-based discriminators to hash bits.
Default is *false*.
- -V: include valence information in the fingerprints
Default is *false*.
- -H: include Hs in the fingerprint
Default is *false*.
- --useMACCS: use the public MACCS keys to do the fingerprinting
(instead of a daylight-type fingerprint)
"""
if __name__ == '__main__':
FingerprintMols.message("This is MolSimilarity version %s\n\n" % (__VERSION_STRING))
FingerprintMols._usageDoc = _usageDoc
details = FingerprintMols.ParseArgs()
ScreenFromDetails(details)
| {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Fingerprints/MolSimilarity.py",
"copies": "1",
"size": "10616",
"license": "bsd-3-clause",
"hash": -5818794250270112000,
"line_mean": 30.9759036145,
"line_max": 99,
"alpha_frac": 0.6589110776,
"autogenerated": false,
"ratio": 3.641852487135506,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 0.9712496407467367,
"avg_score": 0.01765343145362771,
"num_lines": 332
} |
"""
"""
from __future__ import print_function
import copy
import random
import numpy
from rdkit.DataStructs.VectCollection import VectCollection
from rdkit.ML import InfoTheory
from rdkit.ML.DecTree import SigTree
try:
from rdkit.ML.FeatureSelect import CMIM
except ImportError:
CMIM = None
def _GenerateRandomEnsemble(nToInclude, nBits):
""" Generates a random subset of a group of indices
**Arguments**
- nToInclude: the size of the desired set
- nBits: the maximum index to be included in the set
**Returns**
a list of indices
"""
# Before Python 2.3 added the random.sample() function, this was
# way more complicated:
return random.sample(range(nBits), nToInclude)
def BuildSigTree(examples, nPossibleRes, ensemble=None, random=0,
metric=InfoTheory.InfoType.BIASENTROPY, biasList=[1], depth=0, maxDepth=-1,
useCMIM=0, allowCollections=False, verbose=0, **kwargs):
"""
**Arguments**
- examples: the examples to be classified. Each example
should be a sequence at least three entries long, with
entry 0 being a label, entry 1 a BitVector and entry -1
an activity value
- nPossibleRes: the number of result codes possible
- ensemble: (optional) if this argument is provided, it
should be a sequence which is used to limit the bits
which are actually considered as potential descriptors.
The default is None (use all bits).
- random: (optional) If this argument is nonzero, it
specifies the number of bits to be randomly selected
for consideration at this node (i.e. this toggles the
growth of Random Trees).
The default is 0 (no random descriptor selection)
- metric: (optional) This is an _InfoTheory.InfoType_ and
sets the metric used to rank the bits.
The default is _InfoTheory.InfoType.BIASENTROPY_
- biasList: (optional) If provided, this provides a bias
list for the bit ranker.
See the _InfoTheory.InfoBitRanker_ docs for an explanation
of bias.
The default value is [1], which biases towards actives.
- maxDepth: (optional) the maximum depth to which the tree
will be grown
The default is -1 (no depth limit).
- useCMIM: (optional) if this is >0, the CMIM algorithm
(conditional mutual information maximization) will be
used to select the descriptors used to build the trees.
The value of the variable should be set to the number
of descriptors to be used. This option and the
ensemble option are mutually exclusive (CMIM will not be
used if the ensemble is set), but it happily coexsts
with the random argument (to only consider random subsets
of the top N CMIM bits)
The default is 0 (do not use CMIM)
- depth: (optional) the current depth in the tree
This is used in the recursion and should not be set
by the client.
**Returns**
a SigTree.SigTreeNode with the root of the decision tree
"""
if verbose:
print(' ' * depth, 'Build')
tree = SigTree.SigTreeNode(None, 'node', level=depth)
tree.SetData(-666)
# tree.SetExamples(examples)
# counts of each result code:
# resCodes = map(lambda x:int(x[-1]),examples)
resCodes = [int(x[-1]) for x in examples]
# print('resCodes:',resCodes)
counts = [0] * nPossibleRes
for res in resCodes:
counts[res] += 1
# print(' '*depth,'counts:',counts)
nzCounts = numpy.nonzero(counts)[0]
if verbose:
print(' ' * depth, '\tcounts:', counts)
if len(nzCounts) == 1:
# bottomed out because there is only one result code left
# with any counts (i.e. there's only one type of example
# left... this is GOOD!).
res = nzCounts[0]
tree.SetLabel(res)
tree.SetName(str(res))
tree.SetTerminal(1)
elif maxDepth >= 0 and depth > maxDepth:
# Bottomed out: max depth hit
# We don't really know what to do here, so
# use the heuristic of picking the most prevalent
# result
v = numpy.argmax(counts)
tree.SetLabel(v)
tree.SetName('%d?' % v)
tree.SetTerminal(1)
else:
# find the variable which gives us the best improvement
# We do this with an InfoBitRanker:
fp = examples[0][1]
nBits = fp.GetNumBits()
ranker = InfoTheory.InfoBitRanker(nBits, nPossibleRes, metric)
if biasList:
ranker.SetBiasList(biasList)
if CMIM is not None and useCMIM > 0 and not ensemble:
ensemble = CMIM.SelectFeatures(examples, useCMIM, bvCol=1)
if random:
if ensemble:
if len(ensemble) > random:
picks = _GenerateRandomEnsemble(random, len(ensemble))
availBits = list(numpy.take(ensemble, picks))
else:
availBits = list(range(len(ensemble)))
else:
availBits = _GenerateRandomEnsemble(random, nBits)
else:
availBits = None
if availBits:
ranker.SetMaskBits(availBits)
# print(' 2:'*depth,availBits)
useCollections = isinstance(examples[0][1], VectCollection)
for example in examples:
# print(' '*depth,example[1].ToBitString(),example[-1])
if not useCollections:
ranker.AccumulateVotes(example[1], example[-1])
else:
example[1].Reset()
ranker.AccumulateVotes(example[1].orVect, example[-1])
try:
bitInfo = ranker.GetTopN(1)[0]
best = int(bitInfo[0])
gain = bitInfo[1]
except Exception:
import traceback
traceback.print_exc()
print('get top n failed')
gain = -1.0
if gain <= 0.0:
v = numpy.argmax(counts)
tree.SetLabel(v)
tree.SetName('?%d?' % v)
tree.SetTerminal(1)
return tree
best = int(bitInfo[0])
# print(' '*depth,'\tbest:',bitInfo)
if verbose:
print(' ' * depth, '\tbest:', bitInfo)
# set some info at this node
tree.SetName('Bit-%d' % (best))
tree.SetLabel(best)
# tree.SetExamples(examples)
tree.SetTerminal(0)
# loop over possible values of the new variable and
# build a subtree for each one
onExamples = []
offExamples = []
for example in examples:
if example[1][best]:
if allowCollections and useCollections:
sig = copy.copy(example[1])
sig.DetachVectsNotMatchingBit(best)
ex = [example[0], sig]
if len(example) > 2:
ex.extend(example[2:])
example = ex
onExamples.append(example)
else:
offExamples.append(example)
# print(' '*depth,len(offExamples),len(onExamples))
for ex in (offExamples, onExamples):
if len(ex) == 0:
v = numpy.argmax(counts)
tree.AddChild('%d??' % v, label=v, data=0.0, isTerminal=1)
else:
child = BuildSigTree(ex, nPossibleRes, random=random, ensemble=ensemble, metric=metric,
biasList=biasList, depth=depth + 1, maxDepth=maxDepth, verbose=verbose)
if child is None:
v = numpy.argmax(counts)
tree.AddChild('%d???' % v, label=v, data=0.0, isTerminal=1)
else:
tree.AddChildNode(child)
return tree
def SigTreeBuilder(examples, attrs, nPossibleVals, initialVar=None, ensemble=None,
randomDescriptors=0, **kwargs):
nRes = nPossibleVals[-1]
return BuildSigTree(examples, nRes, random=randomDescriptors, **kwargs)
| {
"repo_name": "rvianello/rdkit",
"path": "rdkit/ML/DecTree/BuildSigTree.py",
"copies": "4",
"size": "7570",
"license": "bsd-3-clause",
"hash": 7574152487346788000,
"line_mean": 31.6293103448,
"line_max": 100,
"alpha_frac": 0.6389696169,
"autogenerated": false,
"ratio": 3.680116674769081,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 1,
"avg_score": 0.011142782735495446,
"num_lines": 232
} |
""" command line utility for working with FragmentCatalogs (CASE-type analysis)
**Usage**
BuildFragmentCatalog [optional args] <filename>
filename, the name of a delimited text file containing InData, is required
for some modes of operation (see below)
**Command Line Arguments**
- -n *maxNumMols*: specify the maximum number of molecules to be processed
- -b: build the catalog and OnBitLists
*requires InData*
- -s: score compounds
*requires InData and a Catalog, can use OnBitLists*
- -g: calculate info gains
*requires Scores*
- -d: show details about high-ranking fragments
*requires a Catalog and Gains*
- --catalog=*filename*: filename with the pickled catalog.
If -b is provided, this file will be overwritten.
- --onbits=*filename*: filename to hold the pickled OnBitLists.
If -b is provided, this file will be overwritten
- --scores=*filename*: filename to hold the text score data.
If -s is provided, this file will be overwritten
- --gains=*filename*: filename to hold the text gains data.
If -g is provided, this file will be overwritten
- --details=*filename*: filename to hold the text details data.
If -d is provided, this file will be overwritten.
- --minPath=2: specify the minimum length for a path
- --maxPath=6: specify the maximum length for a path
- --smiCol=1: specify which column in the input data file contains
SMILES
- --actCol=-1: specify which column in the input data file contains
activities
- --nActs=2: specify the number of possible activity values
- --nBits=-1: specify the maximum number of bits to show details for
"""
from __future__ import print_function
import sys,os
from rdkit.six.moves import cPickle #@UnresolvedImport #pylint: disable=F0401
from rdkit.six import next
from rdkit import Chem
from rdkit import RDConfig
from rdkit.Chem import FragmentCatalog
from rdkit.Dbase.DbConnection import DbConnect
import numpy
from rdkit.ML import InfoTheory
import types
_cvsVersion="$Revision$"
idx1 = _cvsVersion.find(':')+1
idx2 = _cvsVersion.rfind('$')
__VERSION_STRING="%s"%(_cvsVersion[idx1:idx2])
def message(msg,dest=sys.stdout):
dest.write(msg)
def BuildCatalog(suppl,maxPts=-1,groupFileName=None,
minPath=2,maxPath=6,reportFreq=10):
""" builds a fragment catalog from a set of molecules in a delimited text block
**Arguments**
- suppl: a mol supplier
- maxPts: (optional) if provided, this will set an upper bound on the
number of points to be considered
- groupFileName: (optional) name of the file containing functional group
information
- minPath, maxPath: (optional) names of the minimum and maximum path lengths
to be considered
- reportFreq: (optional) how often to display status information
**Returns**
a FragmentCatalog
"""
if groupFileName is None:
groupFileName = os.path.join(RDConfig.RDDataDir,"FunctionalGroups.txt")
fpParams = FragmentCatalog.FragCatParams(minPath,maxPath,groupFileName)
catalog = FragmentCatalog.FragCatalog(fpParams)
fgen = FragmentCatalog.FragCatGenerator()
if maxPts >0:
nPts = maxPts
else:
if hasattr(suppl,'__len__'):
nPts = len(suppl)
else:
nPts = -1
for i,mol in enumerate(suppl):
if i == nPts:
break
if i and not i%reportFreq:
if nPts>-1:
message('Done %d of %d, %d paths\n'%(i,nPts,catalog.GetFPLength()))
else:
message('Done %d, %d paths\n'%(i,catalog.GetFPLength()))
fgen.AddFragsFromMol(mol,catalog)
return catalog
def ScoreMolecules(suppl,catalog,maxPts=-1,actName='',acts=None,
nActs=2,reportFreq=10):
""" scores the compounds in a supplier using a catalog
**Arguments**
- suppl: a mol supplier
- catalog: the FragmentCatalog
- maxPts: (optional) the maximum number of molecules to be
considered
- actName: (optional) the name of the molecule's activity property.
If this is not provided, the molecule's last property will be used.
- acts: (optional) a sequence of activity values (integers).
If not provided, the activities will be read from the molecules.
- nActs: (optional) number of possible activity values
- reportFreq: (optional) how often to display status information
**Returns**
a 2-tuple:
1) the results table (a 3D array of ints nBits x 2 x nActs)
2) a list containing the on bit lists for each molecule
"""
nBits = catalog.GetFPLength()
resTbl = numpy.zeros((nBits,2,nActs),numpy.int)
obls = []
if not actName and not acts:
actName = suppl[0].GetPropNames()[-1]
fpgen = FragmentCatalog.FragFPGenerator()
suppl.reset()
i = 1
for mol in suppl:
if i and not i%reportFreq:
message('Done %d.\n'%(i))
if mol:
if not acts:
act = int(mol.GetProp(actName))
else:
act = acts[i-1]
fp = fpgen.GetFPForMol(mol,catalog)
obls.append([x for x in fp.GetOnBits()])
for j in range(nBits):
resTbl[j,0,act] += 1
for id in obls[i-1]:
resTbl[id-1,0,act] -= 1
resTbl[id-1,1,act] += 1
else:
obls.append([])
i+=1
return resTbl,obls
def ScoreFromLists(bitLists,suppl,catalog,maxPts=-1,actName='',acts=None,
nActs=2,reportFreq=10):
""" similar to _ScoreMolecules()_, but uses pre-calculated bit lists
for the molecules (this speeds things up a lot)
**Arguments**
- bitLists: sequence of on bit sequences for the input molecules
- suppl: the input supplier (we read activities from here)
- catalog: the FragmentCatalog
- maxPts: (optional) the maximum number of molecules to be
considered
- actName: (optional) the name of the molecule's activity property.
If this is not provided, the molecule's last property will be used.
- nActs: (optional) number of possible activity values
- reportFreq: (optional) how often to display status information
**Returns**
the results table (a 3D array of ints nBits x 2 x nActs)
"""
nBits = catalog.GetFPLength()
if maxPts >0:
nPts = maxPts
else:
nPts = len(bitLists)
resTbl = numpy.zeros((nBits,2,nActs),numpy.int)
if not actName and not acts:
actName = suppl[0].GetPropNames()[-1]
suppl.reset()
for i in range(1,nPts+1):
mol = next(suppl)
if not acts:
act = int(mol.GetProp(actName))
else:
act = acts[i-1]
if i and not i%reportFreq:
message('Done %d of %d\n'%(i,nPts))
ids = set()
for id in bitLists[i-1]:
ids.add(id-1)
for j in range(nBits):
resTbl[j,0,act] += 1
for id in ids:
resTbl[id,0,act] -= 1
resTbl[id,1,act] += 1
return resTbl
def CalcGains(suppl,catalog,topN=-1,actName='',acts=None,
nActs=2,reportFreq=10,biasList=None,collectFps=0):
""" calculates info gains by constructing fingerprints
*DOC*
Returns a 2-tuple:
1) gains matrix
2) list of fingerprints
"""
nBits = catalog.GetFPLength()
if topN < 0:
topN = nBits
if not actName and not acts:
actName = suppl[0].GetPropNames()[-1]
gains = [0]*nBits
if hasattr(suppl,'__len__'):
nMols = len(suppl)
else:
nMols = -1
fpgen = FragmentCatalog.FragFPGenerator()
#ranker = InfoTheory.InfoBitRanker(nBits,nActs,InfoTheory.InfoType.ENTROPY)
if biasList:
ranker = InfoTheory.InfoBitRanker(nBits,nActs,InfoTheory.InfoType.BIASENTROPY)
ranker.SetBiasList(biasList)
else:
ranker = InfoTheory.InfoBitRanker(nBits,nActs,InfoTheory.InfoType.ENTROPY)
i = 0
fps = []
for mol in suppl:
if not acts:
try:
act = int(mol.GetProp(actName))
except KeyError:
message('ERROR: Molecule has no property: %s\n'%(actName))
message('\tAvailable properties are: %s\n'%(str(mol.GetPropNames())))
raise KeyError(actName)
else:
act = acts[i]
if i and not i%reportFreq:
if nMols>0:
message('Done %d of %d.\n'%(i,nMols))
else:
message('Done %d.\n'%(i))
fp = fpgen.GetFPForMol(mol,catalog)
ranker.AccumulateVotes(fp,act)
i+=1;
if collectFps:
fps.append(fp)
gains = ranker.GetTopN(topN)
return gains,fps
def CalcGainsFromFps(suppl,fps,topN=-1,actName='',acts=None,
nActs=2,reportFreq=10,biasList=None):
""" calculates info gains from a set of fingerprints
*DOC*
"""
nBits = len(fps[0])
if topN < 0:
topN = nBits
if not actName and not acts:
actName = suppl[0].GetPropNames()[-1]
gains = [0]*nBits
if hasattr(suppl,'__len__'):
nMols = len(suppl)
else:
nMols = -1
if biasList:
ranker = InfoTheory.InfoBitRanker(nBits,nActs,InfoTheory.InfoType.BIASENTROPY)
ranker.SetBiasList(biasList)
else:
ranker = InfoTheory.InfoBitRanker(nBits,nActs,InfoTheory.InfoType.ENTROPY)
for i,mol in enumerate(suppl):
if not acts:
try:
act = int(mol.GetProp(actName))
except KeyError:
message('ERROR: Molecule has no property: %s\n'%(actName))
message('\tAvailable properties are: %s\n'%(str(mol.GetPropNames())))
raise KeyError(actName)
else:
act = acts[i]
if i and not i%reportFreq:
if nMols>0:
message('Done %d of %d.\n'%(i,nMols))
else:
message('Done %d.\n'%(i))
fp = fps[i]
ranker.AccumulateVotes(fp,act)
gains = ranker.GetTopN(topN)
return gains
def OutputGainsData(outF,gains,cat,nActs=2):
actHeaders = ['Act-%d'%(x) for x in range(nActs)]
if cat:
outF.write('id,Description,Gain,%s\n'%(','.join(actHeaders)))
else:
outF.write('id,Gain,%s\n'%(','.join(actHeaders)))
for entry in gains:
id = int(entry[0])
outL = [str(id)]
if cat:
descr = cat.GetBitDescription(id)
outL.append(descr)
outL.append('%.6f'%entry[1])
outL += ['%d'%x for x in entry[2:]]
outF.write(','.join(outL))
outF.write('\n')
def ProcessGainsData(inF,delim=',',idCol=0,gainCol=1):
""" reads a list of ids and info gains out of an input file
"""
res = []
inL = inF.readline()
for line in inF.xreadlines():
splitL = line.strip().split(delim)
res.append((splitL[idCol],float(splitL[gainCol])))
return res
def ShowDetails(catalog,gains,nToDo=-1,outF=sys.stdout,idCol=0,gainCol=1,
outDelim=','):
"""
gains should be a sequence of sequences. The idCol entry of each
sub-sequence should be a catalog ID. _ProcessGainsData()_ provides
suitable input.
"""
if nToDo < 0:
nToDo = len(gains)
for i in range(nToDo):
id = int(gains[i][idCol])
gain = float(gains[i][gainCol])
descr = catalog.GetFragDescription(id)
if descr:
outF.write('%s\n'%(outDelim.join((str(id),descr,str(gain)))))
def SupplierFromDetails(details):
from rdkit.VLib.NodeLib.DbMolSupply import DbMolSupplyNode
from rdkit.VLib.NodeLib.SmilesSupply import SmilesSupplyNode
if details.dbName:
conn = DbConnect(details.dbName,details.tableName)
suppl = DbMolSupplyNode(conn.GetData())
else:
suppl = SmilesSupplyNode(details.inFileName,delim=details.delim,
nameColumn=details.nameCol,
smilesColumn=details.smiCol,
titleLine=details.hasTitle)
if type(details.actCol)==types.IntType:
suppl.reset()
m = next(suppl)
actName = m.GetPropNames()[details.actCol]
details.actCol = actName
if type(details.nameCol)==types.IntType:
suppl.reset()
m = next(suppl)
nameName = m.GetPropNames()[details.nameCol]
details.nameCol = nameName
suppl.reset()
if type(details.actCol)==types.IntType:
suppl.reset()
m = next(suppl)
actName = m.GetPropNames()[details.actCol]
details.actCol = actName
if type(details.nameCol)==types.IntType:
suppl.reset()
m = next(suppl)
nameName = m.GetPropNames()[details.nameCol]
details.nameCol = nameName
suppl.reset()
return suppl
def Usage():
print("This is BuildFragmentCatalog version %s"%(__VERSION_STRING))
print('usage error')
#print(__doc__)
sys.exit(-1)
class RunDetails(object):
numMols=-1
doBuild=0
doSigs=0
doScore=0
doGains=0
doDetails=0
catalogName=None
onBitsName=None
scoresName=None
gainsName=None
dbName=''
tableName=None
detailsName=None
inFileName=None
fpName=None
minPath=2
maxPath=6
smiCol=1
actCol=-1
nameCol=-1
hasTitle=1
nActs = 2
nBits=-1
delim=','
biasList=None
topN=-1
def ParseArgs(details):
import getopt
try:
args,extras = getopt.getopt(sys.argv[1:],'n:d:cst',
['catalog=','onbits=',
'scoresFile=','gainsFile=','detailsFile=','fpFile=',
'minPath=','maxPath=','smiCol=','actCol=','nameCol=','nActs=',
'nBits=','biasList=','topN=',
'build','sigs','gains','details','score','noTitle'])
except Exception:
sys.stderr.write('Error parsing command line:\n')
import traceback
traceback.print_exc()
Usage()
for arg,val in args:
if arg=='-n':
details.numMols=int(val)
elif arg=='-c':
details.delim=','
elif arg=='-s':
details.delim=' '
elif arg=='-t':
details.delim='\t'
elif arg=='-d':
details.dbName=val
elif arg=='--build':
details.doBuild=1
elif arg=='--score':
details.doScore=1
elif arg=='--gains':
details.doGains=1
elif arg=='--sigs':
details.doSigs=1
elif arg=='-details':
details.doDetails=1
elif arg=='--catalog':
details.catalogName=val
elif arg=='--onbits':
details.onBitsName=val
elif arg=='--scoresFile':
details.scoresName=val
elif arg=='--gainsFile':
details.gainsName=val
elif arg=='--detailsFile':
details.detailsName=val
elif arg=='--fpFile':
details.fpName=val
elif arg=='--minPath':
details.minPath=int(val)
elif arg=='--maxPath':
details.maxPath=int(val)
elif arg=='--smiCol':
try:
details.smiCol=int(val)
except ValueError:
details.smiCol=val
elif arg=='--actCol':
try:
details.actCol=int(val)
except ValueError:
details.actCol=val
elif arg=='--nameCol':
try:
details.nameCol=int(val)
except ValueError:
details.nameCol=val
elif arg=='--nActs':
details.nActs=int(val)
elif arg=='--nBits':
details.nBits=int(val)
elif arg=='--noTitle':
details.hasTitle=0
elif arg=='--biasList':
details.biasList=tuple(eval(val))
elif arg=='--topN':
details.topN=int(val)
elif arg=='-h':
Usage()
sys.exit(0)
else:
Usage()
if len(extras):
if details.dbName:
details.tableName=extras[0]
else:
details.inFileName = extras[0]
else:
Usage()
if __name__=='__main__':
import time
details = RunDetails()
ParseArgs(details)
from io import StringIO
suppl = SupplierFromDetails(details)
cat = None
obls = None
if details.doBuild:
if not suppl:
message("We require inData to generate a catalog\n")
sys.exit(-2)
message("Building catalog\n")
t1 = time.time()
cat = BuildCatalog(suppl,maxPts=details.numMols,
minPath=details.minPath,maxPath=details.maxPath)
t2 = time.time()
message("\tThat took %.2f seconds.\n"%(t2-t1))
if details.catalogName:
message("Dumping catalog data\n")
cPickle.dump(cat,open(details.catalogName,'wb+'))
elif details.catalogName:
message("Loading catalog\n")
cat = cPickle.load(open(details.catalogName,'rb'))
if details.onBitsName:
try:
obls = cPickle.load(open(details.onBitsName,'rb'))
except Exception:
obls = None
else:
if len(obls)<(inD.count('\n')-1):
obls = None
scores = None
if details.doScore:
if not suppl:
message("We require inData to score molecules\n")
sys.exit(-2)
if not cat:
message("We require a catalog to score molecules\n")
sys.exit(-2)
message("Scoring compounds\n")
if not obls or len(obls)<details.numMols:
scores,obls = ScoreMolecules(suppl,cat,maxPts=details.numMols,
actName=details.actCol,
nActs=details.nActs)
if details.scoresName:
cPickle.dump(scores,open(details.scoresName,'wb+'))
if details.onBitsName:
cPickle.dump(obls,open(details.onBitsName,'wb+'))
else:
scores = ScoreFromLists(obls,suppl,cat,maxPts=details.numMols,
actName=details.actCol,
nActs=details.nActs)
elif details.scoresName:
scores = cPickle.load(open(details.scoresName,'rb'))
if details.fpName and os.path.exists(details.fpName) and not details.doSigs:
message("Reading fingerprints from file.\n")
fps = cPickle.load(open(details.fpName,'rb'))
else:
fps = []
gains = None
if details.doGains:
if not suppl:
message("We require inData to calculate gains\n")
sys.exit(-2)
if not (cat or fps):
message("We require either a catalog or fingerprints to calculate gains\n")
sys.exit(-2)
message("Calculating Gains\n")
t1 = time.time()
if details.fpName:
collectFps=1
else:
collectFps=0
if not fps:
gains,fps = CalcGains(suppl,cat,topN=details.topN,actName=details.actCol,
nActs=details.nActs,biasList=details.biasList,
collectFps=collectFps)
if details.fpName:
message("Writing fingerprint file.\n")
tmpF=open(details.fpName,'wb+')
cPickle.dump(fps,tmpF,1)
tmpF.close()
else:
gains = CalcGainsFromFps(suppl,fps,topN=details.topN,actName=details.actCol,
nActs=details.nActs,biasList=details.biasList)
t2=time.time()
message("\tThat took %.2f seconds.\n"%(t2-t1))
if details.gainsName:
outF = open(details.gainsName,'w+')
OutputGainsData(outF,gains,cat,nActs=details.nActs)
else:
if details.gainsName:
inF = open(details.gainsName,'r')
gains = ProcessGainsData(inF)
if details.doDetails:
if not cat:
message("We require a catalog to get details\n")
sys.exit(-2)
if not gains:
message("We require gains data to get details\n")
sys.exit(-2)
io = StringIO()
io.write('id,SMILES,gain\n')
ShowDetails(cat,gains,nToDo=details.nBits,outF=io)
if details.detailsName:
open(details.detailsName,'w+').write(io.getvalue())
else:
sys.stderr.write(io.getvalue())
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""" contains factory class for producing signatures
"""
from __future__ import print_function, division
from rdkit.DataStructs import SparseBitVect,IntSparseIntVect,LongSparseIntVect
from rdkit.Chem.Pharm2D import Utils
import copy
import numpy
_verbose = False
class SigFactory(object):
"""
SigFactory's are used by creating one, setting the relevant
parameters, then calling the GetSignature() method each time a
signature is required.
"""
def __init__(self,featFactory,useCounts=False,minPointCount=2,maxPointCount=3,
shortestPathsOnly=True,includeBondOrder=False,skipFeats=None,
trianglePruneBins=True):
self.featFactory = featFactory
self.useCounts=useCounts
self.minPointCount=minPointCount
self.maxPointCount=maxPointCount
self.shortestPathsOnly=shortestPathsOnly
self.includeBondOrder=includeBondOrder
self.trianglePruneBins=trianglePruneBins
if skipFeats is None:
self.skipFeats=[]
else:
self.skipFeats=skipFeats
self._bins = None
self.sigKlass=None
def SetBins(self,bins):
""" bins should be a list of 2-tuples """
self._bins = copy.copy(bins)
self.Init()
def GetBins(self):
return self._bins
def GetNumBins(self):
return len(self._bins)
def GetSignature(self):
return self.sigKlass(self._sigSize)
def _GetBitSummaryData(self,bitIdx):
nPts,combo,scaffold = self.GetBitInfo(bitIdx)
fams=self.GetFeatFamilies()
labels = [fams[x] for x in combo]
dMat = numpy.zeros((nPts,nPts),numpy.int)
dVect = Utils.nPointDistDict[nPts]
for idx in range(len(dVect)):
i,j = dVect[idx]
dMat[i,j] = scaffold[idx]
dMat[j,i] = scaffold[idx]
return nPts,combo,scaffold,labels,dMat
def GetBitDescriptionAsText(self,bitIdx,includeBins=0,fullPage=1):
""" returns text with a description of the bit
**Arguments**
- bitIdx: an integer bit index
- includeBins: (optional) if nonzero, information about the bins will be
included as well
- fullPage: (optional) if nonzero, html headers and footers will
be included (so as to make the output a complete page)
**Returns**
a string with the HTML
"""
nPts,combo,scaffold,labels,dMat=self._GetBitSummaryData(bitIdx)
def GetBitDescription(self,bitIdx):
""" returns a text description of the bit
**Arguments**
- bitIdx: an integer bit index
**Returns**
a string
"""
nPts,combo,scaffold,labels,dMat=self._GetBitSummaryData(bitIdx)
res = " ".join(labels)+ " "
for row in dMat:
res += "|"+" ".join([str(x) for x in row])
res += "|"
return res
def _findBinIdx(self,dists,bins,scaffolds):
""" OBSOLETE: this has been rewritten in C++
Internal use only
Returns the index of a bin defined by a set of distances.
**Arguments**
- dists: a sequence of distances (not binned)
- bins: a sorted sequence of distance bins (2-tuples)
- scaffolds: a list of possible scaffolds (bin combinations)
**Returns**
an integer bin index
**Note**
the value returned here is not an index in the overall
signature. It is, rather, an offset of a scaffold in the
possible combinations of distance bins for a given
proto-pharmacophore.
"""
nBins = len(bins)
nDists = len(dists)
whichBins = [0]*nDists
# This would be a ton easier if we had contiguous bins
# i.e. if we could maintain the bins as a list of bounds)
# because then we could use Python's bisect module.
# Since we can't do that, we've got to do our own binary
# search here.
for i in range(nDists):
dist = dists[i]
where = -1
# do a simple binary search:
startP,endP = 0,len(bins)
while startP<endP:
midP = (startP+endP) // 2
begBin,endBin = bins[midP]
if dist < begBin:
endP = midP
elif dist >= endBin:
startP = midP+1
else:
where = midP
break
if where < 0:
return None
whichBins[i] = where
res = scaffolds.index(tuple(whichBins))
if _verbose:
print('----- _fBI -----------')
print(' scaffolds:',scaffolds)
print(' bins:',whichBins)
print(' res:',res)
return res
def GetFeatFamilies(self):
fams = [fam for fam in self.featFactory.GetFeatureFamilies() if fam not in self.skipFeats]
fams.sort()
return fams
def GetMolFeats(self,mol):
featFamilies=self.GetFeatFamilies()
featMatches = {}
for fam in featFamilies:
featMatches[fam] = []
feats = self.featFactory.GetFeaturesForMol(mol,includeOnly=fam)
for feat in feats:
featMatches[fam].append(feat.GetAtomIds())
return [featMatches[x] for x in featFamilies]
def GetBitIdx(self,featIndices,dists,sortIndices=True):
""" returns the index for a pharmacophore described using a set of
feature indices and distances
**Arguments***
- featIndices: a sequence of feature indices
- dists: a sequence of distance between the features, only the
unique distances should be included, and they should be in the
order defined in Utils.
- sortIndices : sort the indices
**Returns**
the integer bit index
"""
nPoints = len(featIndices)
if nPoints>3:
raise NotImplementedError('>3 points not supported')
if nPoints < self.minPointCount: raise IndexError('bad number of points')
if nPoints > self.maxPointCount: raise IndexError('bad number of points')
# this is the start of the nPoint-point pharmacophores
startIdx = self._starts[nPoints]
#
# now we need to map the pattern indices to an offset from startIdx
#
if sortIndices:
tmp = list(featIndices)
tmp.sort()
featIndices = tmp
if featIndices[0]<0: raise IndexError('bad feature index')
if max(featIndices)>=self._nFeats: raise IndexError('bad feature index')
if nPoints==3:
featIndices,dists=Utils.OrderTriangle(featIndices,dists)
offset = Utils.CountUpTo(self._nFeats,nPoints,featIndices)
if _verbose: print('offset for feature %s: %d'%(str(featIndices),offset))
offset *= len(self._scaffolds[len(dists)])
try:
if _verbose:
print('>>>>>>>>>>>>>>>>>>>>>>>')
print('\tScaffolds:',repr(self._scaffolds[len(dists)]),type(self._scaffolds[len(dists)]))
print('\tDists:',repr(dists),type(dists))
print('\tbins:',repr(self._bins),type(self._bins))
bin = self._findBinIdx(dists,self._bins,self._scaffolds[len(dists)])
except ValueError:
fams = self.GetFeatFamilies()
fams = [fams[x] for x in featIndices]
raise IndexError('distance bin not found: feats: %s; dists=%s; bins=%s; scaffolds: %s'%(fams,dists,self._bins,self._scaffolds))
return startIdx + offset + bin
def GetBitInfo(self,idx):
""" returns information about the given bit
**Arguments**
- idx: the bit index to be considered
**Returns**
a 3-tuple:
1) the number of points in the pharmacophore
2) the proto-pharmacophore (tuple of pattern indices)
3) the scaffold (tuple of distance indices)
"""
if idx >= self._sigSize:
raise IndexError('bad index (%d) queried. %d is the max'%(idx,self._sigSize))
# first figure out how many points are in the p'cophore
nPts = self.minPointCount
while nPts < self.maxPointCount and self._starts[nPts+1]<=idx:
nPts+=1
# how far are we in from the start point?
offsetFromStart = idx - self._starts[nPts]
if _verbose:
print('\t %d Points, %d offset'%(nPts,offsetFromStart))
# lookup the number of scaffolds
nDists = len(Utils.nPointDistDict[nPts])
scaffolds = self._scaffolds[nDists]
nScaffolds = len(scaffolds)
# figure out to which proto-pharmacophore we belong:
protoIdx = offsetFromStart // nScaffolds
indexCombos = Utils.GetIndexCombinations(self._nFeats,nPts)
combo = tuple(indexCombos[protoIdx])
if _verbose:
print('\t combo: %s'%(str(combo)))
# and which scaffold:
scaffoldIdx = offsetFromStart % nScaffolds
scaffold = scaffolds[scaffoldIdx]
if _verbose:
print('\t scaffold: %s'%(str(scaffold)))
return nPts,combo,scaffold
def Init(self):
""" Initializes internal parameters. This **must** be called after
making any changes to the signature parameters
"""
accum = 0
self._scaffolds = [0]*(len(Utils.nPointDistDict[self.maxPointCount+1]))
self._starts = {}
if not self.skipFeats:
self._nFeats = len(self.featFactory.GetFeatureFamilies())
else:
self._nFeats = 0
for fam in self.featFactory.GetFeatureFamilies():
if fam not in self.skipFeats:
self._nFeats+=1
for i in range(self.minPointCount,self.maxPointCount+1):
self._starts[i] = accum
nDistsHere = len(Utils.nPointDistDict[i])
scaffoldsHere = Utils.GetPossibleScaffolds(i,self._bins,
useTriangleInequality=self.trianglePruneBins)
nBitsHere = len(scaffoldsHere)
self._scaffolds[nDistsHere] = scaffoldsHere
pointsHere = Utils.NumCombinations(self._nFeats,i) * nBitsHere
accum += pointsHere
self._sigSize = accum
if not self.useCounts:
self.sigKlass = SparseBitVect
elif self._sigSize<2**31:
self.sigKlass = IntSparseIntVect
else:
self.sigKlass = LongSparseIntVect
def GetSigSize(self):
return self._sigSize
try:
from rdkit.Chem.Pharmacophores import cUtils
except ImportError:
pass
else:
SigFactory._findBinIdx = cUtils.FindBinIdx
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""" contains factory class for producing signatures
"""
from __future__ import print_function, division
from rdkit.DataStructs import SparseBitVect, IntSparseIntVect, LongSparseIntVect
from rdkit.Chem.Pharm2D import Utils
import copy
import numpy
_verbose = False
class SigFactory(object):
"""
SigFactory's are used by creating one, setting the relevant
parameters, then calling the GetSignature() method each time a
signature is required.
"""
def __init__(self, featFactory, useCounts=False, minPointCount=2, maxPointCount=3,
shortestPathsOnly=True, includeBondOrder=False, skipFeats=None,
trianglePruneBins=True):
self.featFactory = featFactory
self.useCounts = useCounts
self.minPointCount = minPointCount
self.maxPointCount = maxPointCount
self.shortestPathsOnly = shortestPathsOnly
self.includeBondOrder = includeBondOrder
self.trianglePruneBins = trianglePruneBins
if skipFeats is None:
self.skipFeats = []
else:
self.skipFeats = skipFeats
self._bins = None
self.sigKlass = None
def SetBins(self, bins):
""" bins should be a list of 2-tuples """
self._bins = copy.copy(bins)
self.Init()
def GetBins(self):
return self._bins
def GetNumBins(self):
return len(self._bins)
def GetSignature(self):
return self.sigKlass(self._sigSize)
def _GetBitSummaryData(self, bitIdx):
nPts, combo, scaffold = self.GetBitInfo(bitIdx)
fams = self.GetFeatFamilies()
labels = [fams[x] for x in combo]
dMat = numpy.zeros((nPts, nPts), numpy.int)
dVect = Utils.nPointDistDict[nPts]
for idx in range(len(dVect)):
i, j = dVect[idx]
dMat[i, j] = scaffold[idx]
dMat[j, i] = scaffold[idx]
return nPts, combo, scaffold, labels, dMat
def GetBitDescriptionAsText(self, bitIdx, includeBins=0, fullPage=1):
""" returns text with a description of the bit
**Arguments**
- bitIdx: an integer bit index
- includeBins: (optional) if nonzero, information about the bins will be
included as well
- fullPage: (optional) if nonzero, html headers and footers will
be included (so as to make the output a complete page)
**Returns**
a string with the HTML
"""
nPts, combo, scaffold, labels, dMat = self._GetBitSummaryData(bitIdx)
def GetBitDescription(self, bitIdx):
""" returns a text description of the bit
**Arguments**
- bitIdx: an integer bit index
**Returns**
a string
"""
nPts, combo, scaffold, labels, dMat = self._GetBitSummaryData(bitIdx)
res = " ".join(labels) + " "
for row in dMat:
res += "|" + " ".join([str(x) for x in row])
res += "|"
return res
def _findBinIdx(self, dists, bins, scaffolds):
""" OBSOLETE: this has been rewritten in C++
Internal use only
Returns the index of a bin defined by a set of distances.
**Arguments**
- dists: a sequence of distances (not binned)
- bins: a sorted sequence of distance bins (2-tuples)
- scaffolds: a list of possible scaffolds (bin combinations)
**Returns**
an integer bin index
**Note**
the value returned here is not an index in the overall
signature. It is, rather, an offset of a scaffold in the
possible combinations of distance bins for a given
proto-pharmacophore.
"""
nBins = len(bins)
nDists = len(dists)
whichBins = [0] * nDists
# This would be a ton easier if we had contiguous bins
# i.e. if we could maintain the bins as a list of bounds)
# because then we could use Python's bisect module.
# Since we can't do that, we've got to do our own binary
# search here.
for i in range(nDists):
dist = dists[i]
where = -1
# do a simple binary search:
startP, endP = 0, len(bins)
while startP < endP:
midP = (startP + endP) // 2
begBin, endBin = bins[midP]
if dist < begBin:
endP = midP
elif dist >= endBin:
startP = midP + 1
else:
where = midP
break
if where < 0:
return None
whichBins[i] = where
res = scaffolds.index(tuple(whichBins))
if _verbose:
print('----- _fBI -----------')
print(' scaffolds:', scaffolds)
print(' bins:', whichBins)
print(' res:', res)
return res
def GetFeatFamilies(self):
fams = [fam for fam in self.featFactory.GetFeatureFamilies() if fam not in self.skipFeats]
fams.sort()
return fams
def GetMolFeats(self, mol):
featFamilies = self.GetFeatFamilies()
featMatches = {}
for fam in featFamilies:
featMatches[fam] = []
feats = self.featFactory.GetFeaturesForMol(mol, includeOnly=fam)
for feat in feats:
featMatches[fam].append(feat.GetAtomIds())
return [featMatches[x] for x in featFamilies]
def GetBitIdx(self, featIndices, dists, sortIndices=True):
""" returns the index for a pharmacophore described using a set of
feature indices and distances
**Arguments***
- featIndices: a sequence of feature indices
- dists: a sequence of distance between the features, only the
unique distances should be included, and they should be in the
order defined in Utils.
- sortIndices : sort the indices
**Returns**
the integer bit index
"""
nPoints = len(featIndices)
if nPoints > 3:
raise NotImplementedError('>3 points not supported')
if nPoints < self.minPointCount:
raise IndexError('bad number of points')
if nPoints > self.maxPointCount:
raise IndexError('bad number of points')
# this is the start of the nPoint-point pharmacophores
startIdx = self._starts[nPoints]
#
# now we need to map the pattern indices to an offset from startIdx
#
if sortIndices:
tmp = list(featIndices)
tmp.sort()
featIndices = tmp
if featIndices[0] < 0:
raise IndexError('bad feature index')
if max(featIndices) >= self._nFeats:
raise IndexError('bad feature index')
if nPoints == 3:
featIndices, dists = Utils.OrderTriangle(featIndices, dists)
offset = Utils.CountUpTo(self._nFeats, nPoints, featIndices)
if _verbose:
print('offset for feature %s: %d' % (str(featIndices), offset))
offset *= len(self._scaffolds[len(dists)])
try:
if _verbose:
print('>>>>>>>>>>>>>>>>>>>>>>>')
print('\tScaffolds:', repr(self._scaffolds[len(dists)]), type(self._scaffolds[len(dists)]))
print('\tDists:', repr(dists), type(dists))
print('\tbins:', repr(self._bins), type(self._bins))
bin = self._findBinIdx(dists, self._bins, self._scaffolds[len(dists)])
except ValueError:
fams = self.GetFeatFamilies()
fams = [fams[x] for x in featIndices]
raise IndexError('distance bin not found: feats: %s; dists=%s; bins=%s; scaffolds: %s' %
(fams, dists, self._bins, self._scaffolds))
return startIdx + offset + bin
def GetBitInfo(self, idx):
""" returns information about the given bit
**Arguments**
- idx: the bit index to be considered
**Returns**
a 3-tuple:
1) the number of points in the pharmacophore
2) the proto-pharmacophore (tuple of pattern indices)
3) the scaffold (tuple of distance indices)
"""
if idx >= self._sigSize:
raise IndexError('bad index (%d) queried. %d is the max' % (idx, self._sigSize))
# first figure out how many points are in the p'cophore
nPts = self.minPointCount
while nPts < self.maxPointCount and self._starts[nPts + 1] <= idx:
nPts += 1
# how far are we in from the start point?
offsetFromStart = idx - self._starts[nPts]
if _verbose:
print('\t %d Points, %d offset' % (nPts, offsetFromStart))
# lookup the number of scaffolds
nDists = len(Utils.nPointDistDict[nPts])
scaffolds = self._scaffolds[nDists]
nScaffolds = len(scaffolds)
# figure out to which proto-pharmacophore we belong:
protoIdx = offsetFromStart // nScaffolds
indexCombos = Utils.GetIndexCombinations(self._nFeats, nPts)
combo = tuple(indexCombos[protoIdx])
if _verbose:
print('\t combo: %s' % (str(combo)))
# and which scaffold:
scaffoldIdx = offsetFromStart % nScaffolds
scaffold = scaffolds[scaffoldIdx]
if _verbose:
print('\t scaffold: %s' % (str(scaffold)))
return nPts, combo, scaffold
def Init(self):
""" Initializes internal parameters. This **must** be called after
making any changes to the signature parameters
"""
accum = 0
self._scaffolds = [0] * (len(Utils.nPointDistDict[self.maxPointCount + 1]))
self._starts = {}
if not self.skipFeats:
self._nFeats = len(self.featFactory.GetFeatureFamilies())
else:
self._nFeats = 0
for fam in self.featFactory.GetFeatureFamilies():
if fam not in self.skipFeats:
self._nFeats += 1
for i in range(self.minPointCount, self.maxPointCount + 1):
self._starts[i] = accum
nDistsHere = len(Utils.nPointDistDict[i])
scaffoldsHere = Utils.GetPossibleScaffolds(i, self._bins,
useTriangleInequality=self.trianglePruneBins)
nBitsHere = len(scaffoldsHere)
self._scaffolds[nDistsHere] = scaffoldsHere
pointsHere = Utils.NumCombinations(self._nFeats, i) * nBitsHere
accum += pointsHere
self._sigSize = accum
if not self.useCounts:
self.sigKlass = SparseBitVect
elif self._sigSize < 2**31:
self.sigKlass = IntSparseIntVect
else:
self.sigKlass = LongSparseIntVect
def GetSigSize(self):
return self._sigSize
try:
from rdkit.Chem.Pharmacophores import cUtils
except ImportError:
pass
else:
SigFactory._findBinIdx = cUtils.FindBinIdx
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""" contains factory class for producing signatures
"""
from rdkit.DataStructs import SparseBitVect,IntSparseIntVect,LongSparseIntVect
from rdkit.Chem.Pharm2D import Utils
import copy
import numpy
_verbose = False
class SigFactory(object):
"""
SigFactory's are used by creating one, setting the relevant
parameters, then calling the GetSignature() method each time a
signature is required.
"""
def __init__(self,featFactory,useCounts=False,minPointCount=2,maxPointCount=3,
shortestPathsOnly=True,includeBondOrder=False,skipFeats=None,
trianglePruneBins=True):
self.featFactory = featFactory
self.useCounts=useCounts
self.minPointCount=minPointCount
self.maxPointCount=maxPointCount
self.shortestPathsOnly=shortestPathsOnly
self.includeBondOrder=includeBondOrder
self.trianglePruneBins=trianglePruneBins
if skipFeats is None:
self.skipFeats=[]
else:
self.skipFeats=skipFeats
self._bins = None
self.sigKlass=None
def SetBins(self,bins):
""" bins should be a list of 2-tuples """
self._bins = copy.copy(bins)
self.Init()
def GetBins(self):
return self._bins
def GetNumBins(self):
return len(self._bins)
def GetSignature(self):
return self.sigKlass(self._sigSize)
def _GetBitSummaryData(self,bitIdx):
nPts,combo,scaffold = self.GetBitInfo(bitIdx)
fams=self.GetFeatFamilies()
labels = [fams[x] for x in combo]
dMat = numpy.zeros((nPts,nPts),numpy.int)
dVect = Utils.nPointDistDict[nPts]
for idx in range(len(dVect)):
i,j = dVect[idx]
dMat[i,j] = scaffold[idx]
dMat[j,i] = scaffold[idx]
return nPts,combo,scaffold,labels,dMat
def GetBitDescriptionAsText(self,bitIdx,includeBins=0,fullPage=1):
""" returns text with a description of the bit
**Arguments**
- bitIdx: an integer bit index
- includeBins: (optional) if nonzero, information about the bins will be
included as well
- fullPage: (optional) if nonzero, html headers and footers will
be included (so as to make the output a complete page)
**Returns**
a string with the HTML
"""
nPts,combo,scaffold,labels,dMat=self._GetBitSummaryData(bitIdx)
def GetBitDescription(self,bitIdx):
""" returns a text description of the bit
**Arguments**
- bitIdx: an integer bit index
**Returns**
a string
"""
nPts,combo,scaffold,labels,dMat=self._GetBitSummaryData(bitIdx)
res = " ".join(labels)+ " "
for row in dMat:
res += "|"+" ".join([str(x) for x in row])
res += "|"
return res
def _findBinIdx(self,dists,bins,scaffolds):
""" OBSOLETE: this has been rewritten in C++
Internal use only
Returns the index of a bin defined by a set of distances.
**Arguments**
- dists: a sequence of distances (not binned)
- bins: a sorted sequence of distance bins (2-tuples)
- scaffolds: a list of possible scaffolds (bin combinations)
**Returns**
an integer bin index
**Note**
the value returned here is not an index in the overall
signature. It is, rather, an offset of a scaffold in the
possible combinations of distance bins for a given
proto-pharmacophore.
"""
nBins = len(bins)
nDists = len(dists)
whichBins = [0]*nDists
# This would be a ton easier if we had contiguous bins
# i.e. if we could maintain the bins as a list of bounds)
# because then we could use Python's bisect module.
# Since we can't do that, we've got to do our own binary
# search here.
for i in range(nDists):
dist = dists[i]
where = -1
# do a simple binary search:
startP,endP = 0,len(bins)
while startP<endP:
midP = (startP+endP) // 2
begBin,endBin = bins[midP]
if dist < begBin:
endP = midP
elif dist >= endBin:
startP = midP+1
else:
where = midP
break
if where < 0:
return None
whichBins[i] = where
res = scaffolds.index(tuple(whichBins))
if _verbose:
print '----- _fBI -----------'
print ' scaffolds:',scaffolds
print ' bins:',whichBins
print ' res:',res
return res
def GetFeatFamilies(self):
fams = [fam for fam in self.featFactory.GetFeatureFamilies() if fam not in self.skipFeats]
fams.sort()
return fams
def GetMolFeats(self,mol):
featFamilies=self.GetFeatFamilies()
featMatches = {}
for fam in featFamilies:
featMatches[fam] = []
feats = self.featFactory.GetFeaturesForMol(mol,includeOnly=fam)
for feat in feats:
featMatches[fam].append(feat.GetAtomIds())
return [featMatches[x] for x in featFamilies]
def GetBitIdx(self,featIndices,dists,sortIndices=True):
""" returns the index for a pharmacophore described using a set of
feature indices and distances
**Arguments***
- featIndices: a sequence of feature indices
- dists: a sequence of distance between the features, only the
unique distances should be included, and they should be in the
order defined in Utils.
- sortIndices : sort the indices
**Returns**
the integer bit index
"""
nPoints = len(featIndices)
if nPoints>3:
raise NotImplementedError,'>3 points not supported'
if nPoints < self.minPointCount: raise IndexError,'bad number of points'
if nPoints > self.maxPointCount: raise IndexError,'bad number of points'
# this is the start of the nPoint-point pharmacophores
startIdx = self._starts[nPoints]
#
# now we need to map the pattern indices to an offset from startIdx
#
if sortIndices:
tmp = list(featIndices)
tmp.sort()
featIndices = tmp
if featIndices[0]<0: raise IndexError,'bad feature index'
if max(featIndices)>=self._nFeats: raise IndexError,'bad feature index'
if nPoints==3:
featIndices,dists=Utils.OrderTriangle(featIndices,dists)
offset = Utils.CountUpTo(self._nFeats,nPoints,featIndices)
if _verbose: print 'offset for feature %s: %d'%(str(featIndices),offset)
offset *= len(self._scaffolds[len(dists)])
try:
if _verbose:
print '>>>>>>>>>>>>>>>>>>>>>>>'
print '\tScaffolds:',repr(self._scaffolds[len(dists)]),type(self._scaffolds[len(dists)])
print '\tDists:',repr(dists),type(dists)
print '\tbins:',repr(self._bins),type(self._bins)
bin = self._findBinIdx(dists,self._bins,self._scaffolds[len(dists)])
except ValueError:
fams = self.GetFeatFamilies()
fams = [fams[x] for x in featIndices]
raise IndexError,'distance bin not found: feats: %s; dists=%s; bins=%s; scaffolds: %s'%(fams,dists,self._bins,self._scaffolds)
return startIdx + offset + bin
def GetBitInfo(self,idx):
""" returns information about the given bit
**Arguments**
- idx: the bit index to be considered
**Returns**
a 3-tuple:
1) the number of points in the pharmacophore
2) the proto-pharmacophore (tuple of pattern indices)
3) the scaffold (tuple of distance indices)
"""
if idx >= self._sigSize:
raise IndexError,'bad index (%d) queried. %d is the max'%(idx,self._sigSize)
# first figure out how many points are in the p'cophore
nPts = self.minPointCount
while nPts < self.maxPointCount and self._starts[nPts+1]<=idx:
nPts+=1
# how far are we in from the start point?
offsetFromStart = idx - self._starts[nPts]
if _verbose:
print '\t %d Points, %d offset'%(nPts,offsetFromStart)
# lookup the number of scaffolds
nDists = len(Utils.nPointDistDict[nPts])
scaffolds = self._scaffolds[nDists]
nScaffolds = len(scaffolds)
# figure out to which proto-pharmacophore we belong:
protoIdx = offsetFromStart / nScaffolds
indexCombos = Utils.GetIndexCombinations(self._nFeats,nPts)
combo = tuple(indexCombos[protoIdx])
if _verbose:
print '\t combo: %s'%(str(combo))
# and which scaffold:
scaffoldIdx = offsetFromStart % nScaffolds
scaffold = scaffolds[scaffoldIdx]
if _verbose:
print '\t scaffold: %s'%(str(scaffold))
return nPts,combo,scaffold
def Init(self):
""" Initializes internal parameters. This **must** be called after
making any changes to the signature parameters
"""
accum = 0
self._scaffolds = [0]*(len(Utils.nPointDistDict[self.maxPointCount+1]))
self._starts = {}
if not self.skipFeats:
self._nFeats = len(self.featFactory.GetFeatureFamilies())
else:
self._nFeats = 0
for fam in self.featFactory.GetFeatureFamilies():
if fam not in self.skipFeats:
self._nFeats+=1
for i in range(self.minPointCount,self.maxPointCount+1):
self._starts[i] = accum
nDistsHere = len(Utils.nPointDistDict[i])
scaffoldsHere = Utils.GetPossibleScaffolds(i,self._bins,
useTriangleInequality=self.trianglePruneBins)
nBitsHere = len(scaffoldsHere)
self._scaffolds[nDistsHere] = scaffoldsHere
pointsHere = Utils.NumCombinations(self._nFeats,i) * nBitsHere
accum += pointsHere
self._sigSize = accum
if not self.useCounts:
self.sigKlass = SparseBitVect
elif self._sigSize<2**31:
self.sigKlass = IntSparseIntVect
else:
self.sigKlass = LongSparseIntVect
def GetSigSize(self):
return self._sigSize
try:
from rdkit.Chem.Pharmacophores import cUtils
except ImportError:
pass
else:
SigFactory._findBinIdx = cUtils.FindBinIdx
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""" Definitions for 2D Pharmacophores from:
Gobbi and Poppinger, Biotech. Bioeng. _61_ 47-54 (1998)
"""
from rdkit import Chem
from rdkit.Chem.Pharm2D.SigFactory import SigFactory
from rdkit.Chem import ChemicalFeatures
fdef = """
DefineFeature Hydrophobic [$([C;H2,H1](!=*)[C;H2,H1][C;H2,H1][$([C;H1,H2,H3]);!$(C=*)]),$(C([C;H2,H3])([C;H2,H3])[C;H2,H3])]
Family LH
Weights 1.0
EndFeature
DefineFeature Donor [$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]
Family HD
Weights 1.0
EndFeature
DefineFeature Acceptor [$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N&v3;H1,H2]-[!$(*=[O,N,P,S])]),$([N;v3;H0]),$([n,o,s;+0]),F]
Family HA
Weights 1.0
EndFeature
DefineFeature AromaticAttachment [$([a;D3](@*)(@*)*)]
Family AR
Weights 1.0
EndFeature
DefineFeature AliphaticAttachment [$([A;D3](@*)(@*)*)]
Family RR
Weights 1.0
EndFeature
DefineFeature UnusualAtom [!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53]
Family X
Weights 1.0
EndFeature
DefineFeature BasicGroup [$([N;H2&+0][$([C,a]);!$([C,a](=O))]),$([N;H1&+0]([$([C,a]);!$([C,a](=O))])[$([C,a]);!$([C,a](=O))]),$([N;H0&+0]([C;!$(C(=O))])([C;!$(C(=O))])[C;!$(C(=O))]),$([N,n;X2;+0])]
Family BG
Weights 1.0
EndFeature
DefineFeature AcidicGroup [$([C,S](=[O,S,P])-[O;H1])]
Family AG
Weights 1.0
EndFeature
"""
defaultBins = [(2, 3), (3, 4), (4, 5), (5, 6), (6, 7), (7, 8), (8, 100)]
def _init():
global labels, patts, factory
featFactory = ChemicalFeatures.BuildFeatureFactoryFromString(fdef)
factory = SigFactory(featFactory, minPointCount=2, maxPointCount=3)
factory.SetBins(defaultBins)
factory.Init()
_init()
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from rdkit import Chem
from rdfragcatalog import *
import sys
def message(msg,dest=sys.stdout):
dest.write(msg)
class BitGainsInfo(object):
id=-1
description=''
gain=0.0
nPerClass=None
def ProcessGainsFile(fileName,nToDo=-1,delim=',',haveDescriptions=1):
inFile = open(fileName,'r')
nRead = 0
res = []
for line in inFile.xreadlines():
nRead += 1
splitL = [x.strip() for x in line.split(delim)]
if nRead != 1 and len(splitL):
bit = BitGainsInfo()
bit.id = int(splitL[0])
col = 1
if haveDescriptions:
bit.description = splitL[col]
col += 1
bit.gain = float(splitL[col])
col += 1
nPerClass = []
for entry in splitL[col:]:
nPerClass.append(int(entry))
bit.nPerClass = nPerClass
res.append(bit)
if len(res)==nToDo:
break
return res
def BuildAdjacencyList(catalog,bits,limitInclusion=1,orderLevels=0):
adjs = {}
levels = {}
bitIds = [bit.id for bit in bits]
for bitId in bitIds:
entry = catalog.GetBitEntryId(bitId)
tmp = []
order = catalog.GetEntryOrder(entry)
s = levels.get(order,set())
s.add(bitId)
levels[order] = s
for down in catalog.GetEntryDownIds(entry):
id = catalog.GetEntryBitId(down)
if not limitInclusion or id in bitIds:
tmp.append(id)
order = catalog.GetEntryOrder(down)
s = levels.get(order,set())
s.add(id)
levels[order] = s
adjs[bitId] = tmp
if orderLevels:
# we'll play a little game and sort the indices in each level by
# the number of downlinks they have:
for order in levels.keys():
ids = levels[order]
counts = [len(adjs[id]) for id in ids]
countOrder = argsort(counts)
l = [ids[x] for x in countOrder]
l.reverse()
levels[order] = l
return adjs,levels
def GetMolsMatchingBit(mols,bit,fps):
res = []
if isinstance(bit,BitGainsInfo):
bitId = bit.id
else:
bitId = bit
for i,mol in enumerate(mols):
fp = fps[i]
if fp[bitId]:
res.append(mol)
return res
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""" functionality for finding pharmacophore matches in molecules
See Docs/Chem/Pharm2D.triangles.jpg for an illustration of the way
pharmacophores are broken into triangles and labelled.
See Docs/Chem/Pharm2D.signatures.jpg for an illustration of bit
numbering
"""
from rdkit import Chem
from rdkit.Chem.Pharm2D import Utils
import types
import exceptions
class MatchError(exceptions.Exception):
pass
_verbose = 0
def GetAtomsMatchingBit(sigFactory,bitIdx,mol,dMat=None,justOne=0,matchingAtoms=None):
""" Returns a list of lists of atom indices for a bit
**Arguments**
- sigFactory: a SigFactory
- bitIdx: the bit to be queried
- mol: the molecule to be examined
- dMat: (optional) the distance matrix of the molecule
- justOne: (optional) if this is nonzero, only the first match
will be returned.
- matchingAtoms: (optional) if this is nonzero, it should
contain a sequence of sequences with the indices of atoms in
the molecule which match each of the patterns used by the
signature.
**Returns**
a list of tuples with the matching atoms
"""
assert sigFactory.shortestPathsOnly,'not implemented for non-shortest path signatures'
nPts,featCombo,scaffold = sigFactory.GetBitInfo(bitIdx)
if _verbose:
print 'info:',nPts
print '\t',featCombo
print '\t',scaffold
if matchingAtoms is None:
matchingAtoms = sigFactory.GetMolFeats(mol)
# find the atoms that match each features
fams = sigFactory.GetFeatFamilies()
choices = []
for featIdx in featCombo:
tmp = matchingAtoms[featIdx]
if tmp:
choices.append(tmp)
else:
# one of the patterns didn't find a match, we
# can return now
if _verbose: print 'no match found for feature:',featIdx
return []
if _verbose:
print 'choices:'
print choices
if dMat is None:
dMat = Chem.GetDistanceMatrix(mol,sigFactory.includeBondOrder)
matches = []
distsToCheck = Utils.nPointDistDict[nPts]
protoPharmacophores = Utils.GetAllCombinations(choices,noDups=1)
res = []
for protoPharm in protoPharmacophores:
if _verbose: print 'protoPharm:',protoPharm
for i in range(len(distsToCheck)):
dLow,dHigh = sigFactory.GetBins()[scaffold[i]]
a1,a2 = distsToCheck[i]
#
# FIX: this is making all kinds of assumptions about
# things being single-atom matches (or at least that
# only the first atom matters
#
idx1,idx2 = protoPharm[a1][0],protoPharm[a2][0]
dist = dMat[idx1,idx2]
if _verbose: print '\t dist: %d->%d = %d (%d,%d)'%(idx1,idx2,dist,dLow,dHigh)
if dist < dLow or dist >= dHigh:
break
else:
if _verbose: print 'Found one'
# we found it
protoPharm.sort()
protoPharm = tuple(protoPharm)
if protoPharm not in res:
res.append(protoPharm)
if justOne: break
return res
if __name__ == '__main__':
from rdkit import Chem
from rdkit.Chem.Pharm2D import SigFactory,Generate
factory = SigFactory.SigFactory()
factory.SetBins([(1,2),(2,5),(5,8)])
factory.SetPatternsFromSmarts(['O','N'])
factory.SetMinCount(2)
factory.SetMaxCount(3)
sig = factory.GetSignature()
mol = Chem.MolFromSmiles('OCC(=O)CCCN')
Generate.Gen2DFingerprint(mol,sig)
print 'onbits:',list(sig.GetOnBits())
_verbose=0
for bit in sig.GetOnBits():
atoms = GetAtomsMatchingBit(sig,bit,mol)
print '\tBit %d: '%(bit),atoms
print '--------------------------'
sig = factory.GetSignature()
sig.SetIncludeBondOrder(1)
Generate.Gen2DFingerprint(mol,sig)
print 'onbits:',list(sig.GetOnBits())
for bit in sig.GetOnBits():
atoms = GetAtomsMatchingBit(sig,bit,mol)
print '\tBit %d: '%(bit),atoms
| {
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"few_assignments": false,
"quality_score": 0.5077332085733888,
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} |
import sys
from rdkit import Chem
from rdkit.Chem.rdfragcatalog import *
def message(msg, dest=sys.stdout):
dest.write(msg)
class BitGainsInfo(object):
id = -1
description = ''
gain = 0.0
nPerClass = None
def ProcessGainsFile(fileName, nToDo=-1, delim=',', haveDescriptions=1):
inFile = open(fileName, 'r')
nRead = 0
res = []
for line in inFile.xreadlines():
nRead += 1
splitL = [x.strip() for x in line.split(delim)]
if nRead != 1 and len(splitL):
bit = BitGainsInfo()
bit.id = int(splitL[0])
col = 1
if haveDescriptions:
bit.description = splitL[col]
col += 1
bit.gain = float(splitL[col])
col += 1
nPerClass = []
for entry in splitL[col:]:
nPerClass.append(int(entry))
bit.nPerClass = nPerClass
res.append(bit)
if len(res) == nToDo:
break
return res
def BuildAdjacencyList(catalog, bits, limitInclusion=1, orderLevels=0):
adjs = {}
levels = {}
bitIds = [bit.id for bit in bits]
for bitId in bitIds:
entry = catalog.GetBitEntryId(bitId)
tmp = []
order = catalog.GetEntryOrder(entry)
s = levels.get(order, set())
s.add(bitId)
levels[order] = s
for down in catalog.GetEntryDownIds(entry):
id = catalog.GetEntryBitId(down)
if not limitInclusion or id in bitIds:
tmp.append(id)
order = catalog.GetEntryOrder(down)
s = levels.get(order, set())
s.add(id)
levels[order] = s
adjs[bitId] = tmp
if orderLevels:
# we'll play a little game and sort the indices in each level by
# the number of downlinks they have:
for order in levels.keys():
ids = levels[order]
counts = [len(adjs[id]) for id in ids]
countOrder = argsort(counts)
l = [ids[x] for x in countOrder]
l.reverse()
levels[order] = l
return adjs, levels
def GetMolsMatchingBit(mols, bit, fps):
res = []
if isinstance(bit, BitGainsInfo):
bitId = bit.id
else:
bitId = bit
for i, mol in enumerate(mols):
fp = fps[i]
if fp[bitId]:
res.append(mol)
return res
| {
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"autogenerated": false,
"ratio": 3.1758530183727034,
"config_test": false,
"has_no_keywords": false,
"few_assignments": false,
"quality_score": 1,
"avg_score": 0.021880169004199396,
"num_lines": 97
} |