robert-m-elder commited on
Commit
bd5fb72
·
1 Parent(s): 7f77ca2

changed all name lookups to report IUPAC name, except when unavailable

Browse files
Files changed (1) hide show
  1. ChemID.py +10 -8
ChemID.py CHANGED
@@ -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.common_name:
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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
@@ -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.common_name
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  except:
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  name = None
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  # then try cirpy
@@ -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.common_name
 
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  origin = 'chemicals'
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  except KeyboardInterrupt:
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  raise
@@ -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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- #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
 
155
  # first try chemicals package
156
  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