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d41752d558
* run clang-tidy with readability-braces-around-statements clang-format the results clean up all the parts that clang-tidy-8 broke * fix problem on windows
240 lines
10 KiB
C++
240 lines
10 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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namespace python = boost::python;
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namespace RDKit {
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void SetMCSAtomTyper(MCSParameters &p, AtomComparator atomComp) {
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switch (atomComp) {
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case AtomCompareAny:
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p.AtomTyper = MCSAtomCompareAny;
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break;
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case AtomCompareElements:
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p.AtomTyper = MCSAtomCompareElements;
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break;
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case AtomCompareIsotopes:
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p.AtomTyper = MCSAtomCompareIsotopes;
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break;
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case AtomCompareAnyHeavyAtom:
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p.AtomTyper = MCSAtomCompareAnyHeavyAtom;
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break;
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}
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}
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void SetMCSBondTyper(MCSParameters &p, BondComparator bondComp) {
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switch (bondComp) {
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case BondCompareAny:
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p.BondTyper = MCSBondCompareAny;
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break;
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case BondCompareOrder:
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p.BondTyper = MCSBondCompareOrder;
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break;
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case BondCompareOrderExact:
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p.BondTyper = MCSBondCompareOrderExact;
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break;
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}
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}
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MCSResult *FindMCSWrapper(python::object mols, bool maximizeBonds,
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double threshold, unsigned timeout, bool verbose,
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bool matchValences, bool ringMatchesRingOnly,
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bool completeRingsOnly, bool matchChiralTag,
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AtomComparator atomComp, BondComparator bondComp,
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RingComparator ringComp, std::string seedSmarts) {
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std::vector<ROMOL_SPTR> ms;
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unsigned int nElems = python::extract<unsigned int>(mols.attr("__len__")());
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ms.resize(nElems);
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for (unsigned int i = 0; i < nElems; ++i) {
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if (!mols[i]) {
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throw_value_error("molecule is None");
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}
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ms[i] = python::extract<ROMOL_SPTR>(mols[i]);
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}
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MCSParameters p;
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p.Threshold = threshold;
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p.MaximizeBonds = maximizeBonds;
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p.Timeout = timeout;
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p.Verbose = verbose;
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p.InitialSeed = seedSmarts;
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p.AtomCompareParameters.MatchValences = matchValences;
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p.AtomCompareParameters.MatchChiralTag = matchChiralTag;
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p.AtomCompareParameters.RingMatchesRingOnly = ringMatchesRingOnly;
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SetMCSAtomTyper(p, atomComp);
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SetMCSBondTyper(p, bondComp);
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p.BondCompareParameters.RingMatchesRingOnly = ringMatchesRingOnly;
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p.BondCompareParameters.CompleteRingsOnly = completeRingsOnly;
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p.BondCompareParameters.MatchFusedRings = (ringComp != IgnoreRingFusion);
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p.BondCompareParameters.MatchFusedRingsStrict = (ringComp == StrictRingFusion);
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MCSResult *res = nullptr;
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{
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NOGIL gil;
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res = new MCSResult(findMCS(ms, &p));
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}
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return res;
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}
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MCSResult *FindMCSWrapper2(python::object mols, const MCSParameters ¶ms) {
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std::vector<ROMOL_SPTR> ms;
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unsigned int nElems = python::extract<unsigned int>(mols.attr("__len__")());
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ms.resize(nElems);
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for (unsigned int i = 0; i < nElems; ++i) {
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if (!mols[i]) {
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throw_value_error("molecule is None");
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}
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ms[i] = python::extract<ROMOL_SPTR>(mols[i]);
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}
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MCSResult *res = nullptr;
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{
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NOGIL gil;
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res = new MCSResult(findMCS(ms, ¶ms));
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}
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return res;
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}
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} // namespace RDKit
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namespace {
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struct mcsresult_wrapper {
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static void wrap() {
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python::class_<RDKit::MCSResult>("MCSResult", "used to return MCS results",
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python::no_init)
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.def_readonly("numAtoms", &RDKit::MCSResult::NumAtoms,
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"number of atoms in MCS")
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.def_readonly("numBonds", &RDKit::MCSResult::NumBonds,
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"number of bonds in MCS")
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.def_readonly("queryMol", &RDKit::MCSResult::QueryMol,
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"query molecule for the MCS")
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.def_readonly("smartsString", &RDKit::MCSResult::SmartsString,
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"SMARTS string for the MCS")
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.def_readonly("canceled", &RDKit::MCSResult::Canceled,
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"if True, the MCS calculation did not finish");
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}
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};
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} // namespace
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BOOST_PYTHON_MODULE(rdFMCS) {
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python::scope().attr("__doc__") =
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"Module containing a C++ implementation of the FMCS algorithm";
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mcsresult_wrapper::wrap();
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python::enum_<RDKit::AtomComparator>("AtomCompare")
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.value("CompareAny", RDKit::AtomCompareAny)
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.value("CompareElements", RDKit::AtomCompareElements)
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.value("CompareIsotopes", RDKit::AtomCompareIsotopes)
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.value("CompareAnyHeavyAtom", RDKit::AtomCompareAnyHeavyAtom);
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python::enum_<RDKit::BondComparator>("BondCompare")
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.value("CompareAny", RDKit::BondCompareAny)
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.value("CompareOrder", RDKit::BondCompareOrder)
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.value("CompareOrderExact", RDKit::BondCompareOrderExact);
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python::enum_<RDKit::RingComparator>("RingCompare")
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.value("IgnoreRingFusion", RDKit::IgnoreRingFusion)
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.value("PermissiveRingFusion", RDKit::PermissiveRingFusion)
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.value("StrictRingFusion", RDKit::StrictRingFusion);
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std::string docString = "Find the MCS for a set of molecules";
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python::def(
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"FindMCS", RDKit::FindMCSWrapper,
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(python::arg("mols"), python::arg("maximizeBonds") = true,
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python::arg("threshold") = 1.0, python::arg("timeout") = 3600,
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python::arg("verbose") = false, python::arg("matchValences") = false,
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python::arg("ringMatchesRingOnly") = false,
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python::arg("completeRingsOnly") = false,
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python::arg("matchChiralTag") = false,
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python::arg("atomCompare") = RDKit::AtomCompareElements,
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python::arg("bondCompare") = RDKit::BondCompareOrder,
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python::arg("ringCompare") = RDKit::IgnoreRingFusion,
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python::arg("seedSmarts") = ""),
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python::return_value_policy<python::manage_new_object>(),
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docString.c_str());
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python::class_<RDKit::MCSParameters, boost::noncopyable>(
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"MCSParameters", "Parameters controlling how the MCS is constructed")
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.def_readwrite("MaximizeBonds", &RDKit::MCSParameters::MaximizeBonds,
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"toggles maximizing the number of bonds (instead of the "
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"number of atoms)")
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.def_readwrite("Threshold", &RDKit::MCSParameters::Threshold,
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"fraction of the dataset that must contain the MCS")
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.def_readwrite("Timeout", &RDKit::MCSParameters::Timeout,
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"timeout (in seconds) for the calculation")
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.def_readwrite("Verbose", &RDKit::MCSParameters::Verbose,
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"toggles verbose mode")
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.def_readwrite("AtomCompareParameters",
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&RDKit::MCSParameters::AtomCompareParameters,
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"parameters for comparing atoms")
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.def_readwrite("BondCompareParameters",
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&RDKit::MCSParameters::BondCompareParameters,
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"parameters for comparing bonds")
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// haven't been able to get these properly working
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// .def_readwrite("AtomTyper", &RDKit::MCSParameters::AtomTyper,
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// "function for comparing atoms")
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// .def_readwrite("BondTyper", &RDKit::MCSParameters::BondTyper,
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// "function for comparing bonds")
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.def_readwrite("InitialSeed", &RDKit::MCSParameters::InitialSeed,
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"SMILES string to be used as the seed of the MCS")
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.def("SetAtomTyper", RDKit::SetMCSAtomTyper,
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(python::arg("self"), python::arg("comparator")),
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"sets the atom typer to be used. The argument should be one of the "
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"members of the rdFMCS.AtomCompare class.")
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.def("SetBondTyper", RDKit::SetMCSBondTyper,
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(python::arg("self"), python::arg("comparator")),
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"sets the bond typer to be used. The argument should be one of the "
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"members of the rdFMCS.BondCompare class.");
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;
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python::class_<RDKit::MCSAtomCompareParameters, boost::noncopyable>(
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"MCSAtomCompareParameters",
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"Parameters controlling how atom-atom matching is done")
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.def_readwrite("MatchValences",
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&RDKit::MCSAtomCompareParameters::MatchValences,
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"include atom valences in the match")
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.def_readwrite("MatchChiralTag",
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&RDKit::MCSAtomCompareParameters::MatchChiralTag,
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"include atom chirality in the match")
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.def_readwrite("MatchFormalCharge",
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&RDKit::MCSAtomCompareParameters::MatchFormalCharge,
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"include formal charge in the match")
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.def_readwrite("RingMatchesRingOnly",
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&RDKit::MCSAtomCompareParameters::RingMatchesRingOnly,
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"ring atoms are only allowed to match other ring atoms");
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python::class_<RDKit::MCSBondCompareParameters, boost::noncopyable>(
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"MCSBondCompareParameters",
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"Parameters controlling how bond-bond matching is done")
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.def_readwrite("RingMatchesRingOnly",
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&RDKit::MCSBondCompareParameters::RingMatchesRingOnly,
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"ring bonds are only allowed to match other ring bonds")
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.def_readwrite("CompleteRingsOnly",
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&RDKit::MCSBondCompareParameters::CompleteRingsOnly,
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"results cannot include partial rings")
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.def_readwrite("MatchFusedRings",
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&RDKit::MCSBondCompareParameters::MatchFusedRings,
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"enforce check on ring fusion, i.e. alpha-methylnaphthalene "
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"won't match beta-methylnaphtalene, but decalin "
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"will match cyclodecane unless MatchFusedRingsStrict is True")
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.def_readwrite("MatchFusedRingsStrict",
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&RDKit::MCSBondCompareParameters::MatchFusedRingsStrict,
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"only enforced if MatchFusedRings is True; the ring fusion "
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"must be the same in both query and target, i.e. decalin "
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"won't match cyclodecane")
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.def_readwrite("MatchStereo",
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&RDKit::MCSBondCompareParameters::MatchStereo,
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"include bond stereo in the comparison");
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docString = "Find the MCS for a set of molecules";
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python::def("FindMCS", RDKit::FindMCSWrapper2,
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(python::arg("mols"), python::arg("parameters")),
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python::return_value_policy<python::manage_new_object>(),
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docString.c_str());
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}
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