Commit ·
bd5fb72
1
Parent(s): 7f77ca2
changed all name lookups to report IUPAC name, except when unavailable
Browse files
ChemID.py
CHANGED
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@@ -155,10 +155,10 @@ def smiles2name(smiles):
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# first try chemicals package
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try:
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cm = chemicals.search_chemical(smiles)
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-
if cm.
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-
name = cm.common_name
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-
elif cm.iupac_name:
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name = cm.iupac_name
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except:
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name = None
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# then try pubchem for compounds
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@@ -237,7 +237,7 @@ def cas2name(cas):
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if not name:
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try:
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cm = chemicals.search_chemical(cas)
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-
name = cm.
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except:
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name = None
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# then try cirpy
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@@ -268,7 +268,8 @@ def string2name(string):
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# try chemicals package
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try:
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cm = chemicals.search_chemical(string)
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-
name = cm.
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origin = 'chemicals'
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except KeyboardInterrupt:
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raise
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@@ -280,10 +281,11 @@ def string2name(string):
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try:
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compounds = pcp.get_compounds(string, namespace='name')
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c = compounds[0]
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-
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-
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# have seen empty iupac_name before, try synonyms if this happens
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-
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origin = 'PubChem'
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except:
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name = None
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# first try chemicals package
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try:
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cm = chemicals.search_chemical(smiles)
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+
if cm.iupac_name:
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name = cm.iupac_name
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elif cm.common_name:
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name = cm.common_name
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except:
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name = None
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# then try pubchem for compounds
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if not name:
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try:
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cm = chemicals.search_chemical(cas)
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name = cm.iupac_name
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except:
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name = None
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# then try cirpy
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# try chemicals package
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try:
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cm = chemicals.search_chemical(string)
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name = cm.iupac_name
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#name = cm.common_name
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origin = 'chemicals'
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except KeyboardInterrupt:
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raise
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try:
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compounds = pcp.get_compounds(string, namespace='name')
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c = compounds[0]
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if c.iupac_name:
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name = c.iupac_name
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if not name:
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# have seen empty iupac_name before, try synonyms if this happens
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name = c.synonyms[0]
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origin = 'PubChem'
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except:
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name = None
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