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# $Id$
#
# Copyright (c) 2011, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
INCHI_AVAILABLE = True
import logging
from rdkit.Chem import rdinchi
from rdkit import RDLogger
logger = RDLogger.logger()
logLevelToLogFunctionLookup = {
logging.INFO: logger.info,
logging.DEBUG: logger.debug,
logging.WARNING: logger.warning,
logging.CRITICAL: logger.critical,
logging.ERROR: logger.error
}
class InchiReadWriteError(Exception):
pass
def MolFromInchi(inchi, sanitize=True, removeHs=True, logLevel=None, treatWarningAsError=False):
"""Construct a molecule from a InChI string
Keyword arguments:
sanitize -- set to True to enable sanitization of the molecule. Default is
True
removeHs -- set to True to remove Hydrogens from a molecule. This only
makes sense when sanitization is enabled
logLevel -- the log level used for logging logs and messages from InChI
API. set to None to diable the logging completely
treatWarningAsError -- set to True to raise an exception in case of a
molecule that generates warning in calling InChI API. The resultant
molecule and error message are part of the excpetion
Returns:
a rdkit.Chem.rdchem.Mol instance
"""
try:
mol, retcode, message, log = rdinchi.InchiToMol(inchi, sanitize, removeHs)
except ValueError as e:
logger.error(str(e))
return None
if logLevel is not None:
if logLevel not in logLevelToLogFunctionLookup:
raise ValueError("Unsupported log level: %d" % logLevel)
log = logLevelToLogFunctionLookup[logLevel]
if retcode == 0:
log(message)
if retcode != 0:
if retcode == 1:
logger.warning(message)
else:
logger.error(message)
if treatWarningAsError and retcode != 0:
raise InchiReadWriteError(mol, message)
return mol
def MolToInchiAndAuxInfo(mol, options="", logLevel=None, treatWarningAsError=False):
"""Returns the standard InChI string and InChI auxInfo for a molecule
Keyword arguments:
logLevel -- the log level used for logging logs and messages from InChI
API. set to None to diable the logging completely
treatWarningAsError -- set to True to raise an exception in case of a
molecule that generates warning in calling InChI API. The resultant InChI
string and AuxInfo string as well as the error message are encoded in the
exception.
Returns:
a tuple of the standard InChI string and the auxInfo string returned by
InChI API, in that order, for the input molecule
"""
inchi, retcode, message, logs, aux = rdinchi.MolToInchi(mol, options)
if logLevel is not None:
if logLevel not in logLevelToLogFunctionLookup:
raise ValueError("Unsupported log level: %d" % logLevel)
log = logLevelToLogFunctionLookup[logLevel]
if retcode == 0:
log(message)
if retcode != 0:
if retcode == 1:
logger.warning(message)
else:
logger.error(message)
if treatWarningAsError and retcode != 0:
raise InchiReadWriteError(inchi, aux, message)
return inchi, aux
def MolToInchi(mol, options="", logLevel=None, treatWarningAsError=False):
"""Returns the standard InChI string for a molecule
Keyword arguments:
logLevel -- the log level used for logging logs and messages from InChI
API. set to None to diable the logging completely
treatWarningAsError -- set to True to raise an exception in case of a
molecule that generates warning in calling InChI API. The resultant InChI
string and AuxInfo string as well as the error message are encoded in the
exception.
Returns:
the standard InChI string returned by InChI API for the input molecule
"""
if options.find('AuxNone') == -1:
if options:
options += " /AuxNone"
else:
options += "/AuxNone"
try:
inchi, aux = MolToInchiAndAuxInfo(mol, options, logLevel=logLevel,
treatWarningAsError=treatWarningAsError)
except InchiReadWriteError as inst:
inchi, aux, message = inst.args
raise InchiReadWriteError(inchi, message)
return inchi
def InchiToInchiKey(inchi):
"""Return the InChI key for the given InChI string. Return None on error"""
ret = rdinchi.InchiToInchiKey(inchi)
if ret:
return ret
else:
return None
def MolToInchiKey(mol, options=""):
"""Returns the standard InChI key for a molecule
Returns:
the standard InChI key returned by InChI API for the input molecule
"""
return rdinchi.MolToInchiKey(mol,options)
__all__ = ['MolToInchiAndAuxInfo', 'MolToInchi', 'MolFromInchi', 'InchiReadWriteError',
'InchiToInchiKey', 'MolToInchiKey', 'INCHI_AVAILABLE']
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