mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
Allow converting mol blocks directly to InChI (#2262)
* basics of enabling molblock -> InChI * first pass at python wrapper * test that options work
This commit is contained in:
Greg Landrum
committed by
Brian Kelley
Brian Kelley
parent
cb35234f8c
commit
bebf0c9002
32
External/INCHI-API/Wrap/pyInchi.cpp
vendored
32
External/INCHI-API/Wrap/pyInchi.cpp
vendored
@@ -44,6 +44,16 @@ namespace {
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rv.auxInfoPtr);
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}
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boost::python::tuple MolBlockToInchi(const std::string &molblock, std::string options)
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{
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RDKit::ExtraInchiReturnValues rv;
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const char* _options = NULL;
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if (options.size())
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_options = options.c_str();
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std::string inchi = RDKit::MolBlockToInchi(molblock, rv, _options);
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return boost::python::make_tuple(inchi, rv.returnCode, rv.messagePtr, rv.logPtr,
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rv.auxInfoPtr);
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}
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boost::python::tuple InchiToMol(const std::string &inchi, bool sanitize,
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bool removeHs)
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{
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@@ -95,6 +105,28 @@ BOOST_PYTHON_MODULE(rdinchi) {
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boost::python::arg("options")=std::string()),
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docString.c_str()
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);
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docString = "return the InChI for a ROMol molecule.\n\
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\n\
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Arguments:\n\
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- molblock: the mol block to use.\n\
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- options: the InChI generation options.\n\
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Options should be prefixed with either a - or a /\n\
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Available options are explained in the InChI technical FAQ:\n\
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http://www.inchi-trust.org/fileadmin/user_upload/html/inchifaq/inchi-faq.html#15.14\n\
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and the User Guide:\n\
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http://www.inchi-trust.org/fileadmin/user_upload/software/inchi-v1.04/InChI_UserGuide.pdf\n\
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Returns:\n\
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a tuple with:\n\
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- the InChI\n\
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- the return code from the InChI conversion\n\
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- a string with any messages from the InChI conversion\n\
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- a string with any log messages from the InChI conversion\n\
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- a string with the InChI AuxInfo\n";
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boost::python::def("MolBlockToInchi", MolBlockToInchi,
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(boost::python::arg("molblock"),
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boost::python::arg("options")=std::string()),
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docString.c_str()
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);
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docString = "return the InChI key for an InChI string";
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boost::python::def("InchiToInchiKey", RDKit::InchiToInchiKey,
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(boost::python::arg("inchi")),
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35
External/INCHI-API/inchi.cpp
vendored
35
External/INCHI-API/inchi.cpp
vendored
@@ -1960,6 +1960,41 @@ std::string MolToInchi(const ROMol& mol, ExtraInchiReturnValues& rv,
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return inchi;
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}
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std::string MolBlockToInchi(const std::string &molBlock, ExtraInchiReturnValues& rv,
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const char* options) {
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// create output
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inchi_Output output;
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memset((void *)&output, 0, sizeof(output));
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// call DLL
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std::string inchi;
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{
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#if RDK_TEST_MULTITHREADED
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std::lock_guard<std::mutex> lock(inchiMutex);
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#endif
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char *_options = nullptr;
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if (options) {
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_options = new char[strlen(options) + 1];
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fixOptionSymbol(options, _options);
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options = _options;
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}
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int retcode = MakeINCHIFromMolfileText( molBlock.c_str(), (char *)options, &output );
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// generate output
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rv.returnCode = retcode;
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if (output.szInChI) inchi = std::string(output.szInChI);
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if (output.szMessage) rv.messagePtr = std::string(output.szMessage);
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if (output.szLog) rv.logPtr = std::string(output.szLog);
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if (output.szAuxInfo) rv.auxInfoPtr = std::string(output.szAuxInfo);
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// clean up
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FreeINCHI(&output);
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delete [] _options;
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}
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return inchi;
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}
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std::string InchiToInchiKey(const std::string& inchi) {
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char inchiKey[29];
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char xtra1[65], xtra2[65];
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15
External/INCHI-API/inchi.h
vendored
15
External/INCHI-API/inchi.h
vendored
@@ -67,6 +67,21 @@ namespace RDKit {
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*/
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RDKIT_RDINCHILIB_EXPORT std::string MolToInchi(const ROMol& mol, ExtraInchiReturnValues& rv,
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const char *options=NULL);
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/*! Get the InChI string for a given mol block
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* \param mol The input mol block
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* \param rv An ExtraInchiReturnValues struct instance that is used to receive
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* extra return values such as InChI Auxiliary Information and error messages
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* from InChI API.
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* \param options An null-terminated character string of space-deliminated
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* InChI options that is passed to InChI API as is (except that / is naively
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* converted to - to non-Windows platforms and - is converted to / on Windows)
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* Available options are explained in the InChI technical FAQ:
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* http://www.inchi-trust.org/fileadmin/user_upload/html/inchifaq/inchi-faq.html#15.14
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* and the User Guide:
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* http://www.inchi-trust.org/fileadmin/user_upload/software/inchi-v1.04/InChI_UserGuide.pdf
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*/
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RDKIT_RDINCHILIB_EXPORT std::string MolBlockToInchi(const std::string & mol, ExtraInchiReturnValues& rv,
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const char *options=NULL);
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/*! Get the InChI Key for an input InChI string
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* \param inchi The input InChI string, which can be standard or not.
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*/
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61
External/INCHI-API/python/inchi.py
vendored
61
External/INCHI-API/python/inchi.py
vendored
@@ -1,4 +1,3 @@
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# $Id$
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#
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# Copyright (c) 2011, Novartis Institutes for BioMedical Research Inc.
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# All rights reserved.
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@@ -123,6 +122,37 @@ def MolToInchiAndAuxInfo(mol, options="", logLevel=None, treatWarningAsError=Fal
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raise InchiReadWriteError(inchi, aux, message)
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return inchi, aux
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def MolBlockToInchiAndAuxInfo(molblock, options="", logLevel=None, treatWarningAsError=False):
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"""Returns the standard InChI string and InChI auxInfo for a mol block
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Keyword arguments:
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logLevel -- the log level used for logging logs and messages from InChI
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API. set to None to diable the logging completely
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treatWarningAsError -- set to True to raise an exception in case of a
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molecule that generates warning in calling InChI API. The resultant InChI
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string and AuxInfo string as well as the error message are encoded in the
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exception.
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Returns:
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a tuple of the standard InChI string and the auxInfo string returned by
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InChI API, in that order, for the input molecule
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"""
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inchi, retcode, message, logs, aux = rdinchi.MolBlockToInchi(molblock, options)
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if logLevel is not None:
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if logLevel not in logLevelToLogFunctionLookup:
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raise ValueError("Unsupported log level: %d" % logLevel)
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log = logLevelToLogFunctionLookup[logLevel]
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if retcode == 0:
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log(message)
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if retcode != 0:
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if retcode == 1:
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logger.warning(message)
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else:
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logger.error(message)
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if treatWarningAsError and retcode != 0:
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raise InchiReadWriteError(inchi, aux, message)
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return inchi, aux
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def MolToInchi(mol, options="", logLevel=None, treatWarningAsError=False):
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"""Returns the standard InChI string for a molecule
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@@ -152,6 +182,33 @@ def MolToInchi(mol, options="", logLevel=None, treatWarningAsError=False):
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raise InchiReadWriteError(inchi, message)
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return inchi
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def MolBlockToInchi(molblock, options="", logLevel=None, treatWarningAsError=False):
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"""Returns the standard InChI string for a mol block
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Keyword arguments:
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logLevel -- the log level used for logging logs and messages from InChI
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API. set to None to diable the logging completely
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treatWarningAsError -- set to True to raise an exception in case of a
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molecule that generates warning in calling InChI API. The resultant InChI
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string and AuxInfo string as well as the error message are encoded in the
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exception.
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Returns:
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the standard InChI string returned by InChI API for the input molecule
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"""
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if options.find('AuxNone') == -1:
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if options:
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options += " /AuxNone"
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else:
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options += "/AuxNone"
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try:
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inchi, aux = MolBlockToInchiAndAuxInfo(molblock, options, logLevel=logLevel,
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treatWarningAsError=treatWarningAsError)
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except InchiReadWriteError as inst:
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inchi, aux, message = inst.args
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raise InchiReadWriteError(inchi, message)
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return inchi
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def InchiToInchiKey(inchi):
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"""Return the InChI key for the given InChI string. Return None on error"""
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@@ -173,5 +230,5 @@ def MolToInchiKey(mol, options=""):
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__all__ = ['MolToInchiAndAuxInfo', 'MolToInchi', 'MolFromInchi', 'InchiReadWriteError',
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__all__ = ['MolToInchiAndAuxInfo', 'MolToInchi', 'MolBlockToInchiAndAuxInfo', 'MolBlockToInchi', 'MolFromInchi', 'InchiReadWriteError',
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'InchiToInchiKey', 'MolToInchiKey', 'INCHI_AVAILABLE']
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148
External/INCHI-API/test.cpp
vendored
148
External/INCHI-API/test.cpp
vendored
@@ -566,6 +566,151 @@ void testGithubIssue1572() {
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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}
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void testMolBlockToInchi() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog)
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<< "testing mol block to InChI"
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<< std::endl;
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{
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std::string molb = R"MOL(
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Mrv1824 02111920092D
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6 6 0 0 0 0 999 V2000
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-5.5134 3.5259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-6.2279 3.1134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-6.2279 2.2884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-5.5134 1.8759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-4.7989 2.2884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-4.7989 3.1134 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 1 0 0 0 0
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3 4 1 0 0 0 0
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4 5 1 0 0 0 0
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5 6 1 0 0 0 0
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1 6 1 0 0 0 0
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2 3 2 0 0 0 0
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M END
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)MOL";
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ExtraInchiReturnValues tmp;
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std::string inchi = MolBlockToInchi(molb, tmp);
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TEST_ASSERT(inchi=="InChI=1S/C5H8O/c1-2-4-6-5-3-1/h1-2H,3-5H2");
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}
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{
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std::string molb=R"MOL(BDBM163075
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RDKit 2D
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27 30 0 0 0 0 0 0 0 0999 V2000
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1.6146 -5.5162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.9260 -4.0489 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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7.0484 1.6535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-7.2594 1.8470 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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6.4379 3.0237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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6.1670 0.4398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-6.6489 0.4769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-6.3781 3.0608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.9796 -3.6396 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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4.9460 3.1800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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4.6752 0.5961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-5.1571 0.3205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-4.8863 2.9045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-3.0946 -2.6362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.4878 -3.7959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.5729 2.1226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.7839 1.3780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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4.0647 1.9663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-4.2758 1.5343 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0711 -1.5187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.6916 0.9089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.6816 -0.1486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.4207 -1.6751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.1734 0.0078 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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0.1997 1.0652 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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2.3020 -0.4613 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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0.8110 -3.0456 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 1 0
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2 27 1 0
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3 5 2 0
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3 6 1 0
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4 7 2 0
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4 8 1 0
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5 10 1 0
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6 11 2 0
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7 12 1 0
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8 13 2 0
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9 14 2 0
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9 15 1 0
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10 18 2 0
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11 18 1 0
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12 19 2 0
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13 19 1 0
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14 20 1 0
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15 27 1 0
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16 18 1 0
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16 21 1 0
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17 19 1 0
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17 24 1 0
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20 22 2 0
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20 23 1 0
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21 25 2 0
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21 26 1 0
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22 24 1 0
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22 25 1 0
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23 26 2 0
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23 27 1 0
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M CHG 2 15 -1 27 1
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M END
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)MOL";
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ExtraInchiReturnValues tmp;
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std::string inchi = MolBlockToInchi(molb, tmp);
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TEST_ASSERT(inchi=="InChI=1S/C23H23N3O/c1-2-27-15-9-14-20-22(24-17-19-12-7-4-8-13-19)25-21(26-23(20)27)16-18-10-5-3-6-11-18/h3-15H,2,16-17H2,1H3,(H,24,25,26)");
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TEST_ASSERT(tmp.messagePtr == "Charges were rearranged; Accepted unusual valence(s): O(4)");
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}
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{
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std::string molb=R"MOL(
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Mrv1824 02121905282D
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10 11 0 0 0 0 999 V2000
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-4.6875 -1.1393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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-5.4020 -1.5518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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-5.4020 -2.3768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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-4.6875 -2.7893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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-3.9730 -2.3768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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-3.9730 -1.5518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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-3.2586 -2.7893 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
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-2.5441 -1.5518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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-2.5441 -2.3768 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
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-1.9608 -0.9684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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1 2 2 0 0 0 0
|
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2 3 1 0 0 0 0
|
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3 4 2 0 0 0 0
|
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4 5 1 0 0 0 0
|
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5 6 2 0 0 0 0
|
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1 6 1 0 0 0 0
|
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7 9 1 0 0 0 0
|
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6 8 1 0 0 0 0
|
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7 5 1 0 0 0 0
|
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8 10 1 0 0 0 0
|
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8 9 2 0 0 0 0
|
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M END
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)MOL";
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{
|
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ExtraInchiReturnValues tmp;
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std::string inchi = MolBlockToInchi(molb, tmp);
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TEST_ASSERT(inchi=="InChI=1S/C8H8N2/c1-6-7-4-2-3-5-8(7)10-9-6/h2-5H,1H3,(H,9,10)");
|
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}
|
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{
|
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ExtraInchiReturnValues tmp;
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std::string inchi = MolBlockToInchi(molb, tmp, "/FixedH");
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TEST_ASSERT(inchi=="InChI=1/C8H8N2/c1-6-7-4-2-3-5-8(7)10-9-6/h2-5H,1H3,(H,9,10)/f/h10H");
|
||||
}
|
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}
|
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
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}
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|
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|
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//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
|
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//
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//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
|
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@@ -582,6 +727,7 @@ int main() {
|
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testGithubIssue437();
|
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testGithubIssue562();
|
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testGithubIssue614();
|
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#endif
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testGithubIssue1572();
|
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#endif
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testMolBlockToInchi();
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}
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@@ -46,7 +46,7 @@ from rdkit.Chem import MolFromMolBlock, MolToMolBlock
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from rdkit.Chem import INCHI_AVAILABLE
|
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if INCHI_AVAILABLE:
|
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from rdkit.Chem import InchiReadWriteError
|
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from rdkit.Chem import MolToInchi, MolFromInchi, InchiToInchiKey, MolToInchiKey
|
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from rdkit.Chem import MolToInchi, MolBlockToInchi, MolFromInchi, InchiToInchiKey, MolToInchiKey
|
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|
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COLOR_RED = '\033[31m'
|
||||
COLOR_GREEN = '\033[32m'
|
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@@ -273,6 +273,57 @@ class TestCase(unittest.TestCase):
|
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k2 = MolToInchiKey(m)
|
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self.assertEqual(k1, k2)
|
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|
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def test5MolBlockToInchi(self):
|
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mb = """
|
||||
Mrv1824 02111920092D
|
||||
|
||||
6 6 0 0 0 0 999 V2000
|
||||
-5.5134 3.5259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.2279 3.1134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-6.2279 2.2884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.5134 1.8759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.7989 2.2884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.7989 3.1134 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 1 0 0 0 0
|
||||
3 4 1 0 0 0 0
|
||||
4 5 1 0 0 0 0
|
||||
5 6 1 0 0 0 0
|
||||
1 6 1 0 0 0 0
|
||||
2 3 2 0 0 0 0
|
||||
M END"""
|
||||
inchi = MolBlockToInchi(mb)
|
||||
self.assertEqual(inchi,"InChI=1S/C5H8O/c1-2-4-6-5-3-1/h1-2H,3-5H2")
|
||||
# make sure that options work
|
||||
mb2 = """
|
||||
Mrv1824 02121905282D
|
||||
|
||||
10 11 0 0 0 0 999 V2000
|
||||
-4.6875 -1.1393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.4020 -1.5518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.4020 -2.3768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.6875 -2.7893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.9730 -2.3768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.9730 -1.5518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.2586 -2.7893 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.5441 -1.5518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.5441 -2.3768 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.9608 -0.9684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 2 0 0 0 0
|
||||
2 3 1 0 0 0 0
|
||||
3 4 2 0 0 0 0
|
||||
4 5 1 0 0 0 0
|
||||
5 6 2 0 0 0 0
|
||||
1 6 1 0 0 0 0
|
||||
7 9 1 0 0 0 0
|
||||
6 8 1 0 0 0 0
|
||||
7 5 1 0 0 0 0
|
||||
8 10 1 0 0 0 0
|
||||
8 9 2 0 0 0 0
|
||||
M END"""
|
||||
inchi2 = MolBlockToInchi(mb2,options="/FixedH")
|
||||
self.assertEqual(inchi2,"InChI=1/C8H8N2/c1-6-7-4-2-3-5-8(7)10-9-6/h2-5H,1H3,(H,9,10)/f/h10H")
|
||||
|
||||
|
||||
|
||||
if __name__ == '__main__': # pragma: nocover
|
||||
# only run the test if InChI is available
|
||||
|
||||
Reference in New Issue
Block a user