def process_pubchem_command(matchobj):
"""Function to process match of ``pubchem`` in molecule block."""
string = matchobj.group(2)
if re.match(r'^\s*[0-9]+\s*$', string):
# This is just a number - must be a CID
pcobj = pubchem.PubChemObj(int(string), '', '')
try:
return pcobj.getMoleculeString()
except Exception as e:
return e.message
else:
# Search pubchem for the provided string
try:
results = pubchem.getPubChemResults(string)
except Exception as e:
return e.message
# N.B. Anything starting with PubchemError will be handled correctly by the molecule parser
# in libmints, which will just print the rest of the string and exit gracefully.
if not results:
# Nothing!
return "PubchemError\n\tNo results were found when searching PubChem for %s.\n" % (
string)
elif len(results) == 1:
# There's only 1 result - use it
return results[0].getMoleculeString()
else:
# There are multiple results. Print and exit
msg = "\tPubchemError\n"
msg += "\tMultiple pubchem results were found. Replace\n\n\t\tpubchem:%s\n\n" % (
string)
msg += "\twith the Chemical ID number or exact name from one of the following and re-run.\n\n"
msg += "\t Chemical ID IUPAC Name\n\n"
for result in results:
msg += "%s" % (result)
if result.name().lower() == string.lower():
#We've found an exact match!
return result.getMoleculeString()
return msg
def process_pubchem_command(matchobj):
"""Function to process match of ``pubchem`` in molecule block."""
string = matchobj.group(2)
if re.match(r'^\s*[0-9]+\s*$', string):
# This is just a number - must be a CID
pcobj = pubchem.PubChemObj(int(string), '', '')
try:
return pcobj.getMoleculeString()
except Exception as e:
return e.message
else:
# Search pubchem for the provided string
try:
results = pubchem.getPubChemResults(string)
except Exception as e:
return e.message
# N.B. Anything starting with PubchemError will be handled correctly by the molecule parser
# in libmints, which will just print the rest of the string and exit gracefully.
if not results:
# Nothing!
return "PubchemError\n\tNo results were found when searching PubChem for %s.\n" % (string)
elif len(results) == 1:
# There's only 1 result - use it
return results[0].getMoleculeString()
else:
# There are multiple results. Print and exit
msg = "\tPubchemError\n"
msg += "\tMultiple pubchem results were found. Replace\n\n\t\tpubchem:%s\n\n" % (string)
msg += "\twith the Chemical ID number or exact name from one of the following and re-run.\n\n"
msg += "\t Chemical ID IUPAC Name\n\n"
for result in results:
msg += "%s" % (result)
if result.name().lower() == string.lower():
#We've found an exact match!
return result.getMoleculeString()
return msg