Delete evaluation

evaluation/prepare_receptor4.py

@@ -1,183 +0,0 @@
-#!/usr/bin/env python
-#
-# 
-#
-# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/Utilities24/prepare_receptor4.py,v 1.11 2007/11/28 22:40:22 rhuey Exp $
-#
-import os 
-
-from MolKit import Read
-import MolKit.molecule
-import MolKit.protein
-from AutoDockTools.MoleculePreparation import AD4ReceptorPreparation
-
-
-if __name__ == '__main__':
-    import sys
-    import getopt
-
-
-    def usage():
-        "Print helpful, accurate usage statement to stdout."
-        print "Usage: prepare_receptor4.py -r filename"
-        print
-        print "    Description of command..."
-        print "         -r   receptor_filename "
-        print "        supported file types include pdb,mol2,pdbq,pdbqs,pdbqt, possibly pqr,cif"
-        print "    Optional parameters:"
-        print "        [-v]  verbose output (default is minimal output)"
-        print "        [-o pdbqt_filename]  (default is 'molecule_name.pdbqt')"
-        print "        [-A]  type(s) of repairs to make: "
-        print "             'bonds_hydrogens': build bonds and add hydrogens "
-        print "             'bonds': build a single bond from each atom with no bonds to its closest neighbor" 
-        print "             'hydrogens': add hydrogens"
-        print "             'checkhydrogens': add hydrogens only if there are none already"
-        print "             'None': do not make any repairs "
-        print "             (default is 'checkhydrogens')"
-        print "        [-C]  preserve all input charges ie do not add new charges "
-        print "             (default is addition of gasteiger charges)"
-        print "        [-p]  preserve input charges on specific atom types, eg -p Zn -p Fe"
-        print "        [-U]  cleanup type:"
-        print "             'nphs': merge charges and remove non-polar hydrogens"
-        print "             'lps': merge charges and remove lone pairs"
-        print "             'waters': remove water residues"
-        print "             'nonstdres': remove chains composed entirely of residues of"
-        print "                      types other than the standard 20 amino acids"
-        print "             'deleteAltB': remove XX@B atoms and rename XX@A atoms->XX"
-        print "             (default is 'nphs_lps_waters_nonstdres') "
-        print "        [-e]  delete every nonstd residue from any chain"
-        print "              'True': any residue whose name is not in this list:"
-        print "                      ['CYS','ILE','SER','VAL','GLN','LYS','ASN', "
-        print "                      'PRO','THR','PHE','ALA','HIS','GLY','ASP', "
-        print "                      'LEU', 'ARG', 'TRP', 'GLU', 'TYR','MET', "
-        print "                      'HID', 'HSP', 'HIE', 'HIP', 'CYX', 'CSS']"
-        print "              will be deleted from any chain. "
-        print "              NB: there are no  nucleic acid residue names at all "
-        print "              in the list and no metals. "
-        print "             (default is False which means not to do this)"
-        print "        [-M]  interactive "
-        print "             (default is 'automatic': outputfile is written with no further user input)"
-
-
-    # process command arguments
-    try:
-        opt_list, args = getopt.getopt(sys.argv[1:], 'r:vo:A:Cp:U:eM:')
-
-    except getopt.GetoptError, msg:
-        print 'prepare_receptor4.py: %s' %msg
-        usage()
-        sys.exit(2)
-
-    # initialize required parameters
-    #-s: receptor
-    receptor_filename =  None
-
-    # optional parameters
-    verbose = None
-    #-A: repairs to make: add bonds and/or hydrogens or checkhydrogens
-    repairs = ''
-    #-C default: add gasteiger charges 
-    charges_to_add = 'gasteiger'
-    #-p preserve charges on specific atom types
-    preserve_charge_types=None
-    #-U: cleanup by merging nphs_lps, nphs, lps, waters, nonstdres
-    cleanup  = "nphs_lps_waters_nonstdres"
-    #-o outputfilename
-    outputfilename = None
-    #-m mode 
-    mode = 'automatic'
-    #-e delete every nonstd residue from each chain
-    delete_single_nonstd_residues = None
-
-    #'r:vo:A:Cp:U:eMh'
-    for o, a in opt_list:
-        if o in ('-r', '--r'):
-            receptor_filename = a
-            if verbose: print 'set receptor_filename to ', a
-        if o in ('-v', '--v'):
-            verbose = True
-            if verbose: print 'set verbose to ', True
-        if o in ('-o', '--o'):
-            outputfilename = a
-            if verbose: print 'set outputfilename to ', a
-        if o in ('-A', '--A'):
-            repairs = a
-            if verbose: print 'set repairs to ', a
-        if o in ('-C', '--C'):
-            charges_to_add = None
-            if verbose: print 'do not add charges'
-        if o in ('-p', '--p'):
-            if not preserve_charge_types:
-                preserve_charge_types = a
-            else:
-                preserve_charge_types = preserve_charge_types + ','+ a
-            if verbose: print 'preserve initial charges on ', preserve_charge_types
-        if o in ('-U', '--U'):
-            cleanup  = a
-            if verbose: print 'set cleanup to ', a
-        if o in ('-e', '--e'):
-            delete_single_nonstd_residues  = True
-            if verbose: print 'set delete_single_nonstd_residues to True'
-        if o in ('-M', '--M'):
-            mode = a
-            if verbose: print 'set mode to ', a
-        if o in ('-h', '--'):
-            usage()
-            sys.exit()
-
-
-    if not receptor_filename:
-        print 'prepare_receptor4: receptor filename must be specified.'
-        usage()
-        sys.exit()
-
-    #what about nucleic acids???
-
-    mols = Read(receptor_filename)
-    if verbose: print 'read ', receptor_filename
-    mol = mols[0]
-    preserved = {}
-    if charges_to_add is not None and preserve_charge_types is not None:
-        preserved_types = preserve_charge_types.split(',') 
-        if verbose: print "preserved_types=", preserved_types
-        for t in preserved_types:
-            if verbose: print 'preserving charges on type->', t
-            if not len(t): continue
-            ats = mol.allAtoms.get(lambda x: x.autodock_element==t)
-            if verbose: print "preserving charges on ", ats.name
-            for a in ats:
-                if a.chargeSet is not None:
-                    preserved[a] = [a.chargeSet, a.charge]
-
-    if len(mols)>1:
-        if verbose: print "more than one molecule in file"
-        #use the molecule with the most atoms
-        ctr = 1
-        for m in mols[1:]:
-            ctr += 1
-            if len(m.allAtoms)>len(mol.allAtoms):
-                mol = m
-                if verbose: print "mol set to ", ctr, "th molecule with", len(mol.allAtoms), "atoms"
-    mol.buildBondsByDistance()
-
-    if verbose:
-        print "setting up RPO with mode=", mode,
-        print "and outputfilename= ", outputfilename
-        print "charges_to_add=", charges_to_add
-        print "delete_single_nonstd_residues=", delete_single_nonstd_residues
-
-    RPO = AD4ReceptorPreparation(mol, mode, repairs, charges_to_add, 
-                        cleanup, outputfilename=outputfilename,
-                        preserved=preserved, 
-                        delete_single_nonstd_residues=delete_single_nonstd_residues)    
-
-    if charges_to_add is not None:
-        #restore any previous charges
-        for atom, chargeList in preserved.items():
-            atom._charges[chargeList[0]] = chargeList[1]
-            atom.chargeSet = chargeList[0]
-
-
-# To execute this command type:
-# prepare_receptor4.py -r pdb_file -o outputfilename -A checkhydrogens 
-

evaluation/vina_score.py

@@ -1,35 +0,0 @@
-from vina import Vina
-from rdkit.Chem.rdForceFieldHelpers import UFFOptimizeMolecule
-from rdkit import Chem
-import numpy as np
-import os
-
-for i in range(100):
-    path = './' + str(i) + '.sdf'
-    if os.path.exists(path):
-        print(path)
-        v = Vina(sf_name='vina')
-        v.set_receptor('2rma_protein.pdbqt')
-        v.set_ligand_from_file('2rma_ligand'+'.pdbqt')
-
-        # Calculate the docking center
-        mol = Chem.MolFromMolFile(path, sanitize=True)
-        mol = Chem.AddHs(mol, addCoords=True)
-        UFFOptimizeMolecule(mol)
-        pos = mol.GetConformer(0).GetPositions()
-        center = np.mean(pos, 0)
-
-        v.compute_vina_maps(center=center, box_size=[20, 20, 20])
-
-        # Score the current pose
-        energy = v.score()
-        print('Score before minimization: %.3f (kcal/mol)' % energy[0])
-
-        # Minimized locally the current pose
-        energy_minimized = v.optimize()
-        print('Score after minimization : %.3f (kcal/mol)' % energy_minimized[0])
-        v.write_pose('ligand_minimized.pdbqt', overwrite=True)
-
-        # Dock the ligand
-        v.dock(exhaustiveness=64, n_poses=30)
-        v.write_poses('out.pdbqt', n_poses=5, overwrite=True)