mirror of
https://github.com/rdkit/rdkit.git
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ebd384347c
* Changed the callback() and compare() functions to operator() (C++) and __call__() (Python) for consistency. The old functions are deprecated and will be removed in Release 2021.01 * changes in response to review
844 lines
36 KiB
C++
844 lines
36 KiB
C++
//
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// Copyright (C) 2014 Novartis Institutes for BioMedical Research
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDBoost/python.h>
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#include <GraphMol/ROMol.h>
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#include <RDBoost/Wrap.h>
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#include <GraphMol/FMCS/FMCS.h>
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#include <GraphMol/FMCS/RingMatchTableSet.h>
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#define COMPARE_FUNC_NAME "__call__"
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#define CALLBACK_FUNC_NAME "__call__"
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// DEPRECATED: remove from here in release 2021.01
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#define COMPARE_DEPRECATED_FUNC_NAME "compare"
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#define CALLBACK_DEPRECATED_FUNC_NAME "callback"
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// DEPRECATED: remove until here in release 2021.01
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namespace python = boost::python;
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namespace RDKit {
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struct PyMCSAtomCompare : public boost::python::wrapper<PyMCSAtomCompare> {
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inline bool checkAtomRingMatch(const MCSAtomCompareParameters& p,
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const ROMol& mol1, unsigned int atom1,
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const ROMol& mol2, unsigned int atom2) const {
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return RDKit::checkAtomRingMatch(p, mol1, atom1, mol2, atom2);
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}
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inline bool checkAtomCharge(const MCSAtomCompareParameters& p,
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const ROMol& mol1, unsigned int atom1,
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const ROMol& mol2, unsigned int atom2) const {
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return RDKit::checkAtomCharge(p, mol1, atom1, mol2, atom2);
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}
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inline bool checkAtomChirality(const MCSAtomCompareParameters& p,
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const ROMol& mol1, unsigned int atom1,
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const ROMol& mol2, unsigned int atom2) const {
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return RDKit::checkAtomChirality(p, mol1, atom1, mol2, atom2);
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}
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virtual bool operator()(const MCSAtomCompareParameters&,
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const ROMol&, unsigned int, const ROMol&, unsigned int) {
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PyErr_SetString(PyExc_AttributeError,
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"The " COMPARE_FUNC_NAME "() method "
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"must be overridden in the rdFMCS.MCSAtomCompare subclass");
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python::throw_error_already_set();
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return false;
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}
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// DEPRECATED: remove the following compare() method in release 2021.01
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virtual bool compare(const MCSAtomCompareParameters&,
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const ROMol&, unsigned int, const ROMol&, unsigned int) {
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PyErr_SetString(PyExc_AttributeError,
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"The " COMPARE_DEPRECATED_FUNC_NAME "() method (DEPRECATED) "
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"must be overridden in the rdFMCS.MCSAtomCompare subclass");
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python::throw_error_already_set();
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return false;
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}
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bool hasPythonOverride(const char *attrName) {
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auto obj = get_override(attrName);
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return PyCallable_Check(obj.ptr());
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}
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};
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struct PyMCSBondCompare : public boost::python::wrapper<PyMCSBondCompare> {
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inline bool checkBondStereo(const MCSBondCompareParameters& p,
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const ROMol& mol1, unsigned int bond1,
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const ROMol& mol2, unsigned int bond2) const {
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return RDKit::checkBondStereo(p, mol1, bond1, mol2, bond2);
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}
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inline bool checkBondRingMatch(const MCSBondCompareParameters& p,
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const ROMol& mol1, unsigned int bond1,
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const ROMol& mol2, unsigned int bond2) {
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if (!ringMatchTablesMols.count(&mol1)) {
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ringMatchTables.init(&mol1);
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ringMatchTables.computeRingMatchTable(&mol1, &mol1, *mcsParameters);
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ringMatchTablesMols.insert(&mol1);
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}
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if (!ringMatchTablesMols.count(&mol2)) {
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ringMatchTables.computeRingMatchTable(&mol1, &mol2, *mcsParameters);
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ringMatchTables.addTargetBondRingsIndeces(&mol2);
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ringMatchTablesMols.insert(&mol2);
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}
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return RDKit::checkBondRingMatch(p, mol1, bond1, mol2, bond2, &ringMatchTables);
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}
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bool hasPythonOverride(const char *attrName) {
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auto obj = get_override(attrName);
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return PyCallable_Check(obj.ptr());
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}
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virtual bool operator()(const MCSBondCompareParameters&,
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const ROMol&, unsigned int, const ROMol&, unsigned int) {
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PyErr_SetString(PyExc_AttributeError,
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"The " COMPARE_FUNC_NAME "() method "
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"must be overridden in the rdFMCS.MCSBondCompare subclass");
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python::throw_error_already_set();
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return false;
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}
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// DEPRECATED: remove the following compare() method in release 2021.01
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virtual bool compare(const MCSBondCompareParameters&,
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const ROMol&, unsigned int, const ROMol&, unsigned int) {
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PyErr_SetString(PyExc_AttributeError,
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"The " COMPARE_DEPRECATED_FUNC_NAME "() method (DEPRECATED) "
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"must be overridden in the rdFMCS.MCSBondCompare subclass");
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python::throw_error_already_set();
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return false;
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}
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const MCSParameters *mcsParameters;
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std::set<const ROMol *> ringMatchTablesMols;
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FMCS::RingMatchTableSet ringMatchTables;
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};
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struct PyAtomBondCompData {
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std::string atomCompFuncName;
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std::string bondCompFuncName;
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python::object pyAtomComp;
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python::object pyBondComp;
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};
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struct PyCompareFunctionUserData {
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const MCSParameters *mcsParameters;
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std::set<const ROMol *> *ringMatchTablesMols;
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FMCS::RingMatchTableSet *ringMatchTables;
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PyAtomBondCompData pyAtomBondCompData;
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};
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struct PyProgressCallbackUserData {
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const MCSProgressData *mcsProgressData;
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std::string callbackFuncName;
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python::object pyMCSProgress;
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PyAtomBondCompData pyAtomBondCompData;
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};
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struct PyMCSProgress : public boost::python::wrapper<PyMCSProgress> {
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bool hasPythonOverride(const char *attrName) {
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auto obj = get_override(attrName);
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return PyCallable_Check(obj.ptr());
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}
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virtual bool operator()(const MCSProgressData&,
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const MCSParameters&) {
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PyErr_SetString(PyExc_AttributeError,
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"The " CALLBACK_FUNC_NAME "() method "
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"must be overridden in the rdFMCS.MCSProgress subclass");
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python::throw_error_already_set();
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return false;
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}
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// DEPRECATED: remove the following callback() method in release 2021.01
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virtual bool callback(const MCSProgressData&,
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const MCSParameters&) {
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PyErr_SetString(PyExc_AttributeError,
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"The " CALLBACK_DEPRECATED_FUNC_NAME "() method "
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"must be overridden in the rdFMCS.MCSProgress subclass");
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python::throw_error_already_set();
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return false;
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}
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};
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class PyMCSProgressData {
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public:
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PyMCSProgressData() :
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pd(new MCSProgressData()),
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pcud(new PyProgressCallbackUserData()) {
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pcud->mcsProgressData = pd.get();
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}
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PyMCSProgressData(const MCSProgressData &other) :
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PyMCSProgressData() {
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*pd = other;
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}
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unsigned int getNumAtoms() const {
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return pd->NumAtoms;
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}
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unsigned int getNumBonds() const {
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return pd->NumBonds;
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}
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unsigned int getSeedProcessed() const {
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return pd->SeedProcessed;
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}
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private:
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std::unique_ptr<MCSProgressData> pd;
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std::unique_ptr<PyProgressCallbackUserData> pcud;
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};
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class PyMCSParameters {
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public:
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PyMCSParameters() :
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p(new MCSParameters()),
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cfud(new PyCompareFunctionUserData()),
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pcud(new PyProgressCallbackUserData()) {
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cfud->mcsParameters = p.get();
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pcud->mcsProgressData = nullptr;
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}
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PyMCSParameters(const MCSParameters &other,
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const PyProgressCallbackUserData &pcudOther) :
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PyMCSParameters() {
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*p = other;
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pcud->pyMCSProgress = pcudOther.pyMCSProgress;
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cfud->pyAtomBondCompData = pcudOther.pyAtomBondCompData;
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}
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const MCSParameters *get() const {
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return p.get();
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}
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bool getMaximizeBonds() const {
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return p->MaximizeBonds;
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}
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void setMaximizeBonds(bool value) {
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p->MaximizeBonds = value;
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}
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double getThreshold() const {
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return p->Threshold;
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}
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void setThreshold(double value) {
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p->Threshold = value;
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}
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unsigned int getTimeout() const {
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return p->Timeout;
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}
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void setTimeout(unsigned int value) {
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p->Timeout = value;
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}
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bool getVerbose() const {
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return p->Verbose;
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}
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void setVerbose(bool value) {
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p->Verbose = value;
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}
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const MCSAtomCompareParameters& getAtomCompareParameters() const {
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return p->AtomCompareParameters;
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}
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void setAtomCompareParameters(const MCSAtomCompareParameters &value) {
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p->AtomCompareParameters = value;
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}
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const MCSBondCompareParameters& getBondCompareParameters() const {
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return p->BondCompareParameters;
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}
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void setBondCompareParameters(const MCSBondCompareParameters &value) {
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p->BondCompareParameters = value;
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}
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std::string getInitialSeed() const {
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return p->InitialSeed;
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}
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void setInitialSeed(const std::string &value) {
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p->InitialSeed = value;
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}
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void errorNotDefined(const char *className, const char *funcName) {
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// should never happen as the method is virtual but not pure in the C++ class
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std::stringstream ss;
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ss << "The " << funcName << "() method must be defined "
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"in the " << className << " subclass";
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PyErr_SetString(PyExc_AttributeError, ss.str().c_str());
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python::throw_error_already_set();
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}
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void errorNotCallable(const char *className, const char *funcName) {
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std::stringstream ss;
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ss << "The " << funcName << " attribute in the "
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<< className << " subclass is not a callable method";
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PyErr_SetString(PyExc_TypeError, ss.str().c_str());
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python::throw_error_already_set();
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}
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void errorNotOverridden(const char *className, const char *funcName) {
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std::stringstream ss;
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ss << "The " << funcName << " method must be overridden in the "
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<< className << " subclass";
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PyErr_SetString(PyExc_TypeError, ss.str().c_str());
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python::throw_error_already_set();
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}
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void setMCSAtomTyper(PyObject *atomComp) {
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PRECONDITION(atomComp, "atomComp must not be NULL");
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python::object atomCompObject(python::handle<>(python::borrowed(atomComp)));
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python::extract<AtomComparator> extractAtomComparator(atomCompObject);
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if (extractAtomComparator.check()) {
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AtomComparator ac(extractAtomComparator());
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p->setMCSAtomTyperFromEnum(ac);
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}
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else {
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python::extract<PyMCSAtomCompare *> extractPyMCSAtomCompare(atomCompObject);
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if (extractPyMCSAtomCompare.check()) {
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PyObject *callable = PyObject_GetAttrString(atomCompObject.ptr(), COMPARE_FUNC_NAME);
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if (!callable) {
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errorNotDefined(COMPARE_FUNC_NAME, "rdFMCS.MCSAtomCompare");
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}
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if (!PyCallable_Check(callable)) {
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errorNotCallable(COMPARE_FUNC_NAME, "rdFMCS.MCSAtomCompare");
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}
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if (!extractPyMCSAtomCompare()->hasPythonOverride(COMPARE_FUNC_NAME)) {
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// DEPRECATED: remove from here in release 2021.01
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callable = PyObject_GetAttrString(atomCompObject.ptr(), COMPARE_DEPRECATED_FUNC_NAME);
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if (!callable) {
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errorNotDefined(COMPARE_DEPRECATED_FUNC_NAME, "rdFMCS.MCSAtomCompare");
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}
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if (!PyCallable_Check(callable)) {
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errorNotCallable(COMPARE_DEPRECATED_FUNC_NAME, "rdFMCS.MCSAtomCompare");
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}
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if (!extractPyMCSAtomCompare()->hasPythonOverride(COMPARE_DEPRECATED_FUNC_NAME)) {
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errorNotOverridden(COMPARE_FUNC_NAME, "rdFMCS.MCSAtomCompare");
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}
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else {
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cfud->pyAtomBondCompData.atomCompFuncName = COMPARE_DEPRECATED_FUNC_NAME;
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}
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// DEPRECATED: remove until here in release 2021.01
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// uncomment the following line in release 2021.01
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// errorNotOverridden(COMPARE_FUNC_NAME, "rdFMCS.MCSAtomCompare");
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}
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else {
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cfud->pyAtomBondCompData.atomCompFuncName = COMPARE_FUNC_NAME;
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}
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p->CompareFunctionsUserData = cfud.get();
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p->AtomTyper = MCSAtomComparePyFunc;
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cfud->pyAtomBondCompData.pyAtomComp = atomCompObject;
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cfud->mcsParameters = p.get();
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}
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else {
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PyErr_SetString(PyExc_TypeError,
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"expected an instance of a rdFMCS.MCSAtomCompare subclass "
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"or a member of the AtomCompare class");
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python::throw_error_already_set();
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}
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}
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}
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python::object getMCSAtomTyper() {
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static const std::map<RDKit::MCSAtomCompareFunction,
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RDKit::AtomComparator> atomTyperToComp = {
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{ MCSAtomCompareAny, AtomCompareAny },
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{ MCSAtomCompareElements, AtomCompareElements },
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{ MCSAtomCompareIsotopes, AtomCompareIsotopes },
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{ MCSAtomCompareAnyHeavyAtom, AtomCompareAnyHeavyAtom }
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};
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if (!cfud->pyAtomBondCompData.pyAtomComp.is_none()) {
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return cfud->pyAtomBondCompData.pyAtomComp;
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}
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python::object res;
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try {
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res = python::object(atomTyperToComp.at(p->AtomTyper));
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}
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catch(const std::out_of_range&) {
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PyErr_SetString(PyExc_TypeError,
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"Unknown AtomTyper");
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python::throw_error_already_set();
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}
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return res;
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}
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void setMCSBondTyper(PyObject *bondComp) {
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PRECONDITION(bondComp, "bondComp must not be NULL");
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python::object bondCompObject(python::handle<>(python::borrowed(bondComp)));
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python::extract<BondComparator> extractBondComparator(bondCompObject);
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if (extractBondComparator.check()) {
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BondComparator bc(extractBondComparator());
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p->setMCSBondTyperFromEnum(bc);
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}
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else {
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python::extract<PyMCSBondCompare *> extractPyMCSBondCompare(bondCompObject);
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if (extractPyMCSBondCompare.check()) {
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PyObject *callable = PyObject_GetAttrString(bondCompObject.ptr(), COMPARE_FUNC_NAME);
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if (!callable) {
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errorNotDefined(COMPARE_FUNC_NAME, "rdFMCS.MCSBondCompare");
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}
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if (!PyCallable_Check(callable)) {
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errorNotCallable(COMPARE_FUNC_NAME, "rdFMCS.MCSBondCompare");
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}
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if (!extractPyMCSBondCompare()->hasPythonOverride(COMPARE_FUNC_NAME)) {
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// DEPRECATED: remove from here in release 2021.01
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callable = PyObject_GetAttrString(bondCompObject.ptr(), COMPARE_DEPRECATED_FUNC_NAME);
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if (!callable) {
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errorNotDefined(COMPARE_DEPRECATED_FUNC_NAME, "rdFMCS.MCSBondCompare");
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}
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if (!PyCallable_Check(callable)) {
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errorNotCallable(COMPARE_DEPRECATED_FUNC_NAME, "rdFMCS.MCSBondCompare");
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}
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if (!extractPyMCSBondCompare()->hasPythonOverride(COMPARE_DEPRECATED_FUNC_NAME)) {
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errorNotOverridden(COMPARE_FUNC_NAME, "rdFMCS.MCSBondCompare");
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}
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else {
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cfud->pyAtomBondCompData.bondCompFuncName = COMPARE_DEPRECATED_FUNC_NAME;
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}
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// DEPRECATED: remove until here in release 2021.01
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// uncomment the following line in release 2021.01
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// errorNotOverridden(COMPARE_FUNC_NAME, "rdFMCS.MCSBondCompare");
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}
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else {
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cfud->pyAtomBondCompData.bondCompFuncName = COMPARE_FUNC_NAME;
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}
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p->CompareFunctionsUserData = cfud.get();
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p->BondTyper = MCSBondComparePyFunc;
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cfud->pyAtomBondCompData.pyBondComp = bondCompObject;
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PyMCSBondCompare *bc = extractPyMCSBondCompare();
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bc->mcsParameters = p.get();
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cfud->mcsParameters = p.get();
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cfud->ringMatchTablesMols = &bc->ringMatchTablesMols;
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cfud->ringMatchTables = &bc->ringMatchTables;
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}
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else {
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PyErr_SetString(PyExc_TypeError,
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"expected an instance of a rdFMCS.MCSBondCompare subclass "
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"or a member of the BondCompare class");
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python::throw_error_already_set();
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}
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}
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}
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python::object getMCSBondTyper() {
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static const std::map<RDKit::MCSBondCompareFunction,
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RDKit::BondComparator> bondTyperToComp = {
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{ MCSBondCompareAny, BondCompareAny },
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{ MCSBondCompareOrder, BondCompareOrder },
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{ MCSBondCompareOrderExact, BondCompareOrderExact }
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};
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if (!cfud->pyAtomBondCompData.pyBondComp.is_none()) {
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return cfud->pyAtomBondCompData.pyBondComp;
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}
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python::object res;
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try {
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res = python::object(bondTyperToComp.at(p->BondTyper));
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}
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catch(const std::out_of_range&) {
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PyErr_SetString(PyExc_TypeError,
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"Unknown BondTyper");
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python::throw_error_already_set();
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}
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return res;
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}
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void setMCSProgressCallback(PyObject *progress) {
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PRECONDITION(progress, "progress must not be NULL");
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python::object progressObject(python::handle<>(python::borrowed(progress)));
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python::extract<PyMCSProgress *> extractMCSProgress(progressObject);
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if (extractMCSProgress.check()) {
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PyObject *callable = PyObject_GetAttrString(progressObject.ptr(), CALLBACK_FUNC_NAME);
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if (!callable) {
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errorNotDefined(CALLBACK_FUNC_NAME, "rdFMCS.MCSProgress");
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}
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if (!PyCallable_Check(callable)) {
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errorNotCallable(CALLBACK_FUNC_NAME, "rdFMCS.MCSProgress");
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}
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if (!extractMCSProgress()->hasPythonOverride(CALLBACK_FUNC_NAME)) {
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// DEPRECATED: remove from here in release 2021.01
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callable = PyObject_GetAttrString(progressObject.ptr(), CALLBACK_DEPRECATED_FUNC_NAME);
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if (!callable) {
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errorNotDefined(CALLBACK_DEPRECATED_FUNC_NAME, "rdFMCS.MCSProgress");
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}
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if (!PyCallable_Check(callable)) {
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errorNotCallable(CALLBACK_DEPRECATED_FUNC_NAME, "rdFMCS.MCSProgress");
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|
}
|
|
if (!extractMCSProgress()->hasPythonOverride(CALLBACK_DEPRECATED_FUNC_NAME)) {
|
|
errorNotOverridden(CALLBACK_FUNC_NAME, "rdFMCS.MCSProgress");
|
|
}
|
|
else {
|
|
pcud->callbackFuncName = CALLBACK_DEPRECATED_FUNC_NAME;
|
|
}
|
|
// DEPRECATED: remove until here in release 2021.01
|
|
// uncomment the following line in release 2021.01
|
|
// errorNotOverridden(COMPARE_FUNC_NAME, "rdFMCS.MCSAtomCompare");
|
|
}
|
|
else {
|
|
pcud->callbackFuncName = CALLBACK_FUNC_NAME;
|
|
}
|
|
p->ProgressCallbackUserData = pcud.get();
|
|
p->ProgressCallback = MCSProgressCallbackPyFunc;
|
|
pcud->pyMCSProgress = progressObject;
|
|
pcud->pyAtomBondCompData = cfud->pyAtomBondCompData;
|
|
}
|
|
else {
|
|
PyErr_SetString(PyExc_TypeError,
|
|
"expected an instance of a rdFMCS.MCSProgress subclass");
|
|
python::throw_error_already_set();
|
|
}
|
|
}
|
|
python::object getMCSProgressCallback() {
|
|
if (!pcud->pyMCSProgress.is_none()) {
|
|
return pcud->pyMCSProgress;
|
|
}
|
|
return python::object();
|
|
}
|
|
void clearRingTableCache() {
|
|
if (cfud->ringMatchTablesMols) {
|
|
cfud->ringMatchTablesMols->clear();
|
|
}
|
|
if (cfud->ringMatchTables) {
|
|
cfud->ringMatchTables->clear();
|
|
}
|
|
}
|
|
private:
|
|
static bool MCSAtomComparePyFunc(const MCSAtomCompareParameters& p,
|
|
const ROMol& mol1, unsigned int atom1,
|
|
const ROMol& mol2, unsigned int atom2,
|
|
void* userData) {
|
|
PRECONDITION(userData, "userData must not be NULL");
|
|
PyCompareFunctionUserData *cfud = static_cast<PyCompareFunctionUserData *>(userData);
|
|
bool res = false;
|
|
{
|
|
PyGILStateHolder h;
|
|
res = python::call_method<bool>(cfud->pyAtomBondCompData.pyAtomComp.ptr(),
|
|
cfud->pyAtomBondCompData.atomCompFuncName.c_str(),
|
|
boost::ref(p), boost::ref(mol1),
|
|
atom1, boost::ref(mol2), atom2);
|
|
}
|
|
return res;
|
|
}
|
|
static bool MCSBondComparePyFunc(const MCSBondCompareParameters& p,
|
|
const ROMol& mol1, unsigned int bond1,
|
|
const ROMol& mol2, unsigned int bond2,
|
|
void* userData) {
|
|
PRECONDITION(userData, "userData must not be NULL");
|
|
PyCompareFunctionUserData *cfud = static_cast<PyCompareFunctionUserData *>(userData);
|
|
bool res = false;
|
|
{
|
|
PyGILStateHolder h;
|
|
res = python::call_method<bool>(cfud->pyAtomBondCompData.pyBondComp.ptr(),
|
|
cfud->pyAtomBondCompData.bondCompFuncName.c_str(),
|
|
boost::ref(p), boost::ref(mol1),
|
|
bond1, boost::ref(mol2), bond2);
|
|
}
|
|
return res;
|
|
}
|
|
static bool MCSProgressCallbackPyFunc(const MCSProgressData& stat,
|
|
const MCSParameters& params, void* userData) {
|
|
PRECONDITION(userData, "userData must not be NULL");
|
|
PyProgressCallbackUserData *pcud = static_cast<PyProgressCallbackUserData *>(userData);
|
|
bool res = false;
|
|
{
|
|
PyMCSParameters ps(params, *pcud);
|
|
PyMCSProgressData pd(stat);
|
|
PyGILStateHolder h;
|
|
res = python::call_method<bool>(pcud->pyMCSProgress.ptr(), pcud->callbackFuncName.c_str(),
|
|
boost::ref(pd), boost::ref(ps));
|
|
}
|
|
return res;
|
|
}
|
|
std::unique_ptr<MCSParameters> p;
|
|
std::unique_ptr<PyCompareFunctionUserData> cfud;
|
|
std::unique_ptr<PyProgressCallbackUserData> pcud;
|
|
};
|
|
|
|
MCSResult *FindMCSWrapper(python::object mols, bool maximizeBonds,
|
|
double threshold, unsigned timeout, bool verbose,
|
|
bool matchValences, bool ringMatchesRingOnly,
|
|
bool completeRingsOnly, bool matchChiralTag,
|
|
AtomComparator atomComp, BondComparator bondComp,
|
|
RingComparator ringComp, std::string seedSmarts) {
|
|
std::vector<ROMOL_SPTR> ms;
|
|
unsigned int nElems = python::extract<unsigned int>(mols.attr("__len__")());
|
|
ms.resize(nElems);
|
|
for (unsigned int i = 0; i < nElems; ++i) {
|
|
if (!mols[i]) {
|
|
throw_value_error("molecule is None");
|
|
}
|
|
ms[i] = python::extract<ROMOL_SPTR>(mols[i]);
|
|
}
|
|
MCSParameters p;
|
|
p.Threshold = threshold;
|
|
p.MaximizeBonds = maximizeBonds;
|
|
p.Timeout = timeout;
|
|
p.Verbose = verbose;
|
|
p.InitialSeed = seedSmarts;
|
|
p.AtomCompareParameters.MatchValences = matchValences;
|
|
p.AtomCompareParameters.MatchChiralTag = matchChiralTag;
|
|
p.AtomCompareParameters.RingMatchesRingOnly = ringMatchesRingOnly;
|
|
p.setMCSAtomTyperFromEnum(atomComp);
|
|
p.setMCSBondTyperFromEnum(bondComp);
|
|
p.BondCompareParameters.RingMatchesRingOnly = ringMatchesRingOnly;
|
|
p.BondCompareParameters.CompleteRingsOnly = completeRingsOnly;
|
|
p.BondCompareParameters.MatchFusedRings = (ringComp != IgnoreRingFusion);
|
|
p.BondCompareParameters.MatchFusedRingsStrict = (ringComp == StrictRingFusion);
|
|
|
|
MCSResult *res = nullptr;
|
|
{
|
|
NOGIL gil;
|
|
res = new MCSResult(findMCS(ms, &p));
|
|
}
|
|
return res;
|
|
}
|
|
|
|
MCSResult *FindMCSWrapper2(python::object mols, PyMCSParameters &pyMcsParams) {
|
|
std::vector<ROMOL_SPTR> ms;
|
|
unsigned int nElems = python::extract<unsigned int>(mols.attr("__len__")());
|
|
ms.resize(nElems);
|
|
for (unsigned int i = 0; i < nElems; ++i) {
|
|
if (!mols[i]) {
|
|
throw_value_error("molecule is None");
|
|
}
|
|
ms[i] = python::extract<ROMOL_SPTR>(mols[i]);
|
|
}
|
|
|
|
MCSResult *res = nullptr;
|
|
pyMcsParams.clearRingTableCache();
|
|
{
|
|
NOGIL gil;
|
|
res = new MCSResult(findMCS(ms, pyMcsParams.get()));
|
|
}
|
|
return res;
|
|
}
|
|
} // namespace RDKit
|
|
namespace {
|
|
struct mcsresult_wrapper {
|
|
static void wrap() {
|
|
python::class_<RDKit::MCSResult>("MCSResult", "used to return MCS results",
|
|
python::no_init)
|
|
.def_readonly("numAtoms", &RDKit::MCSResult::NumAtoms,
|
|
"number of atoms in MCS")
|
|
.def_readonly("numBonds", &RDKit::MCSResult::NumBonds,
|
|
"number of bonds in MCS")
|
|
.def_readonly("queryMol", &RDKit::MCSResult::QueryMol,
|
|
"query molecule for the MCS")
|
|
.def_readonly("smartsString", &RDKit::MCSResult::SmartsString,
|
|
"SMARTS string for the MCS")
|
|
.def_readonly("canceled", &RDKit::MCSResult::Canceled,
|
|
"if True, the MCS calculation did not finish");
|
|
}
|
|
};
|
|
} // namespace
|
|
|
|
BOOST_PYTHON_MODULE(rdFMCS) {
|
|
python::scope().attr("__doc__") =
|
|
"Module containing a C++ implementation of the FMCS algorithm";
|
|
mcsresult_wrapper::wrap();
|
|
|
|
python::enum_<RDKit::AtomComparator>("AtomCompare")
|
|
.value("CompareAny", RDKit::AtomCompareAny)
|
|
.value("CompareElements", RDKit::AtomCompareElements)
|
|
.value("CompareIsotopes", RDKit::AtomCompareIsotopes)
|
|
.value("CompareAnyHeavyAtom", RDKit::AtomCompareAnyHeavyAtom);
|
|
python::enum_<RDKit::BondComparator>("BondCompare")
|
|
.value("CompareAny", RDKit::BondCompareAny)
|
|
.value("CompareOrder", RDKit::BondCompareOrder)
|
|
.value("CompareOrderExact", RDKit::BondCompareOrderExact);
|
|
python::enum_<RDKit::RingComparator>("RingCompare")
|
|
.value("IgnoreRingFusion", RDKit::IgnoreRingFusion)
|
|
.value("PermissiveRingFusion", RDKit::PermissiveRingFusion)
|
|
.value("StrictRingFusion", RDKit::StrictRingFusion);
|
|
|
|
std::string docString = "Find the MCS for a set of molecules";
|
|
python::def(
|
|
"FindMCS", RDKit::FindMCSWrapper,
|
|
(python::arg("mols"), python::arg("maximizeBonds") = true,
|
|
python::arg("threshold") = 1.0, python::arg("timeout") = 3600,
|
|
python::arg("verbose") = false, python::arg("matchValences") = false,
|
|
python::arg("ringMatchesRingOnly") = false,
|
|
python::arg("completeRingsOnly") = false,
|
|
python::arg("matchChiralTag") = false,
|
|
python::arg("atomCompare") = RDKit::AtomCompareElements,
|
|
python::arg("bondCompare") = RDKit::BondCompareOrder,
|
|
python::arg("ringCompare") = RDKit::IgnoreRingFusion,
|
|
python::arg("seedSmarts") = ""),
|
|
python::return_value_policy<python::manage_new_object>(),
|
|
docString.c_str());
|
|
|
|
python::class_<RDKit::PyMCSParameters, boost::noncopyable>(
|
|
"MCSParameters", "Parameters controlling how the MCS is constructed")
|
|
.add_property("MaximizeBonds",
|
|
&RDKit::PyMCSParameters::getMaximizeBonds,
|
|
&RDKit::PyMCSParameters::setMaximizeBonds,
|
|
"toggles maximizing the number of bonds (instead of the "
|
|
"number of atoms)")
|
|
.add_property("Threshold",
|
|
&RDKit::PyMCSParameters::getThreshold,
|
|
&RDKit::PyMCSParameters::setThreshold,
|
|
"fraction of the dataset that must contain the MCS")
|
|
.add_property("Timeout",
|
|
&RDKit::PyMCSParameters::getTimeout,
|
|
&RDKit::PyMCSParameters::setTimeout,
|
|
"timeout (in seconds) for the calculation")
|
|
.add_property("Verbose",
|
|
&RDKit::PyMCSParameters::getVerbose,
|
|
&RDKit::PyMCSParameters::setVerbose,
|
|
"toggles verbose mode")
|
|
.add_property("AtomCompareParameters", python::make_function(
|
|
&RDKit::PyMCSParameters::getAtomCompareParameters,
|
|
python::return_internal_reference<>()),
|
|
&RDKit::PyMCSParameters::setAtomCompareParameters,
|
|
"parameters for comparing atoms")
|
|
.add_property("BondCompareParameters", python::make_function(
|
|
&RDKit::PyMCSParameters::getBondCompareParameters,
|
|
python::return_internal_reference<>()),
|
|
&RDKit::PyMCSParameters::setBondCompareParameters,
|
|
"parameters for comparing bonds")
|
|
.add_property("AtomTyper",
|
|
&RDKit::PyMCSParameters::getMCSAtomTyper,
|
|
&RDKit::PyMCSParameters::setMCSAtomTyper,
|
|
"atom typer to be used. Must be one of the "
|
|
"members of the rdFMCS.AtomCompare class or "
|
|
"an instance of a user-defined subclass of "
|
|
"rdFMCS.MCSAtomCompare")
|
|
.add_property("BondTyper",
|
|
&RDKit::PyMCSParameters::getMCSBondTyper,
|
|
&RDKit::PyMCSParameters::setMCSBondTyper,
|
|
"bond typer to be used. Must be one of the "
|
|
"members of the rdFMCS.BondCompare class or "
|
|
"an instance of a user-defined subclass of "
|
|
"rdFMCS.MCSBondCompare")
|
|
.add_property("ProgressCallback",
|
|
&RDKit::PyMCSParameters::getMCSProgressCallback,
|
|
&RDKit::PyMCSParameters::setMCSProgressCallback,
|
|
"progress callback class. Must be a "
|
|
"user-defined subclass of rdFMCS.Progress")
|
|
.add_property("InitialSeed",
|
|
&RDKit::PyMCSParameters::getInitialSeed,
|
|
&RDKit::PyMCSParameters::setInitialSeed,
|
|
"SMILES string to be used as the seed of the MCS")
|
|
.def("SetAtomTyper", &RDKit::PyMCSParameters::setMCSAtomTyper,
|
|
(python::arg("self"), python::arg("comparator")),
|
|
"DEPRECATED: please use the AtomTyper property instead. "
|
|
"Sets the atom typer to be used. The argument must be one "
|
|
"of the members of the rdFMCS.MCSAtomCompare class or an "
|
|
"instance of a user-defined subclass of rdFMCS.MCSAtomCompare")
|
|
.def("SetBondTyper", &RDKit::PyMCSParameters::setMCSBondTyper,
|
|
(python::arg("self"), python::arg("comparator")),
|
|
"DEPRECATED: please use the BondTyper property instead. "
|
|
"Sets the bond typer to be used. The argument must be one "
|
|
"of the members of the rdFMCS.MCSBondCompare class or an "
|
|
"instance of a user-defined subclass of rdFMCS.MCSBondCompare");
|
|
|
|
python::class_<RDKit::MCSAtomCompareParameters, boost::noncopyable>(
|
|
"MCSAtomCompareParameters",
|
|
"Parameters controlling how atom-atom matching is done")
|
|
.def_readwrite("MatchValences",
|
|
&RDKit::MCSAtomCompareParameters::MatchValences,
|
|
"include atom valences in the match")
|
|
.def_readwrite("MatchChiralTag",
|
|
&RDKit::MCSAtomCompareParameters::MatchChiralTag,
|
|
"include atom chirality in the match")
|
|
.def_readwrite("MatchFormalCharge",
|
|
&RDKit::MCSAtomCompareParameters::MatchFormalCharge,
|
|
"include formal charge in the match")
|
|
.def_readwrite("RingMatchesRingOnly",
|
|
&RDKit::MCSAtomCompareParameters::RingMatchesRingOnly,
|
|
"ring atoms are only allowed to match other ring atoms")
|
|
.def_readwrite("MatchIsotope",
|
|
&RDKit::MCSAtomCompareParameters::MatchIsotope,
|
|
"use isotope atom queries in MCSResults");
|
|
|
|
python::class_<RDKit::MCSBondCompareParameters, boost::noncopyable>(
|
|
"MCSBondCompareParameters",
|
|
"Parameters controlling how bond-bond matching is done")
|
|
.def_readwrite("RingMatchesRingOnly",
|
|
&RDKit::MCSBondCompareParameters::RingMatchesRingOnly,
|
|
"ring bonds are only allowed to match other ring bonds")
|
|
.def_readwrite("CompleteRingsOnly",
|
|
&RDKit::MCSBondCompareParameters::CompleteRingsOnly,
|
|
"results cannot include partial rings")
|
|
.def_readwrite("MatchFusedRings",
|
|
&RDKit::MCSBondCompareParameters::MatchFusedRings,
|
|
"enforce check on ring fusion, i.e. alpha-methylnaphthalene "
|
|
"won't match beta-methylnaphtalene, but decalin "
|
|
"will match cyclodecane unless MatchFusedRingsStrict is True")
|
|
.def_readwrite("MatchFusedRingsStrict",
|
|
&RDKit::MCSBondCompareParameters::MatchFusedRingsStrict,
|
|
"only enforced if MatchFusedRings is True; the ring fusion "
|
|
"must be the same in both query and target, i.e. decalin "
|
|
"won't match cyclodecane")
|
|
.def_readwrite("MatchStereo",
|
|
&RDKit::MCSBondCompareParameters::MatchStereo,
|
|
"include bond stereo in the comparison");
|
|
|
|
python::class_<RDKit::PyMCSProgress, boost::noncopyable>(
|
|
"MCSProgress", "Base class. Subclass and override "
|
|
"MCSProgress." CALLBACK_FUNC_NAME "() "
|
|
"to define a custom callback function")
|
|
.def(CALLBACK_FUNC_NAME, &RDKit::PyMCSProgress::operator(),
|
|
(python::arg("self"), python::arg("stat"),
|
|
python::arg("parameters")),
|
|
"override to implement a custom progress callback")
|
|
// DEPRECATED: remove from here in release 2021.01
|
|
.def(CALLBACK_DEPRECATED_FUNC_NAME, &RDKit::PyMCSProgress::callback,
|
|
(python::arg("self"), python::arg("stat"),
|
|
python::arg("parameters")),
|
|
"DEPRECATED: override " CALLBACK_FUNC_NAME " instead.\n"
|
|
"override to implement a custom progress callback.\n")
|
|
// DEPRECATED: remove until here in release 2021.01
|
|
;
|
|
|
|
python::class_<RDKit::PyMCSProgressData, boost::noncopyable>(
|
|
"MCSProgressData", "Information about the MCS progress")
|
|
.add_property("numAtoms", &RDKit::PyMCSProgressData::getNumAtoms,
|
|
"number of atoms in MCS")
|
|
.add_property("numBonds", &RDKit::PyMCSProgressData::getNumBonds,
|
|
"number of bonds in MCS")
|
|
.add_property("seedProcessed", &RDKit::PyMCSProgressData::getSeedProcessed,
|
|
"number of processed seeds");
|
|
|
|
python::class_<RDKit::PyMCSAtomCompare, boost::noncopyable>(
|
|
"MCSAtomCompare", "Base class. Subclass and override "
|
|
"MCSAtomCompare." COMPARE_FUNC_NAME "() to define custom "
|
|
"atom compare functions, then set MCSParameters.AtomTyper "
|
|
"to an instance of the subclass")
|
|
.def("CheckAtomRingMatch", &RDKit::PyMCSAtomCompare::checkAtomRingMatch,
|
|
(python::arg("self"), python::arg("parameters"),
|
|
python::arg("mol1"), python::arg("atom1"),
|
|
python::arg("mol2"), python::arg("atom2")),
|
|
"Return True if both atoms are, or are not, in a ring")
|
|
.def("CheckAtomCharge", &RDKit::PyMCSAtomCompare::checkAtomCharge,
|
|
(python::arg("self"), python::arg("parameters"),
|
|
python::arg("mol1"), python::arg("atom1"),
|
|
python::arg("mol2"), python::arg("atom2")),
|
|
"Return True if both atoms have the same formal charge")
|
|
.def("CheckAtomChirality", &RDKit::PyMCSAtomCompare::checkAtomChirality,
|
|
(python::arg("self"), python::arg("parameters"),
|
|
python::arg("mol1"), python::arg("atom1"),
|
|
python::arg("mol2"), python::arg("atom2")),
|
|
"Return True if both atoms have, or have not, a chiral tag")
|
|
.def(COMPARE_FUNC_NAME, &RDKit::PyMCSAtomCompare::operator(),
|
|
(python::arg("self"), python::arg("parameters"),
|
|
python::arg("mol1"), python::arg("atom1"),
|
|
python::arg("mol2"), python::arg("atom2")),
|
|
"override to implement custom atom comparison")
|
|
// DEPRECATED: remove from here in release 2020.03
|
|
.def(COMPARE_DEPRECATED_FUNC_NAME, &RDKit::PyMCSAtomCompare::compare,
|
|
(python::arg("self"), python::arg("parameters"),
|
|
python::arg("mol1"), python::arg("atom1"),
|
|
python::arg("mol2"), python::arg("atom2")),
|
|
"override to implement custom atom comparison")
|
|
// DEPRECATED: remove until here in release 2020.03
|
|
;
|
|
|
|
python::class_<RDKit::PyMCSBondCompare, boost::noncopyable>(
|
|
"MCSBondCompare", "Base class. Subclass and override "
|
|
"MCSBondCompare." COMPARE_FUNC_NAME "() to define custom "
|
|
"bond compare functions, then set MCSParameters.BondTyper "
|
|
"to an instance of the subclass")
|
|
.def("CheckBondStereo", &RDKit::PyMCSBondCompare::checkBondStereo,
|
|
(python::arg("self"), python::arg("parameters"),
|
|
python::arg("mol1"), python::arg("bond1"),
|
|
python::arg("mol2"), python::arg("bond2")),
|
|
"Return True if both bonds have, or have not, a stereo descriptor")
|
|
.def("CheckBondRingMatch", &RDKit::PyMCSBondCompare::checkBondRingMatch,
|
|
(python::arg("self"), python::arg("parameters"),
|
|
python::arg("mol1"), python::arg("bond1"),
|
|
python::arg("mol2"), python::arg("bond2")),
|
|
"Return True if both bonds are, or are not, part of a ring")
|
|
.def(COMPARE_FUNC_NAME, &RDKit::PyMCSBondCompare::operator(),
|
|
(python::arg("self"), python::arg("parameters"),
|
|
python::arg("mol1"), python::arg("bond1"),
|
|
python::arg("mol2"), python::arg("bond2")),
|
|
"override to implement custom bond comparison")
|
|
// DEPRECATED: remove from here in release 2020.03
|
|
.def(COMPARE_DEPRECATED_FUNC_NAME, &RDKit::PyMCSBondCompare::compare,
|
|
(python::arg("self"), python::arg("parameters"),
|
|
python::arg("mol1"), python::arg("bond1"),
|
|
python::arg("mol2"), python::arg("bond2")),
|
|
"override to implement custom bond comparison")
|
|
// DEPRECATED: remove until here in release 2020.03
|
|
;
|
|
|
|
python::def("FindMCS", RDKit::FindMCSWrapper2,
|
|
(python::arg("mols"), python::arg("parameters")),
|
|
python::return_value_policy<python::manage_new_object>(),
|
|
docString.c_str());
|
|
}
|