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//
// Copyright (C) 2014 Novartis Institutes for BioMedical Research
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDBoost/python.h>
#include <GraphMol/ROMol.h>
#include <RDBoost/Wrap.h>
#include <GraphMol/FMCS/FMCS.h>
namespace python = boost::python;
namespace RDKit {
void SetMCSAtomTyper(MCSParameters &p, AtomComparator atomComp) {
switch (atomComp) {
case AtomCompareAny:
p.AtomTyper = MCSAtomCompareAny;
break;
case AtomCompareElements:
p.AtomTyper = MCSAtomCompareElements;
break;
case AtomCompareIsotopes:
p.AtomTyper = MCSAtomCompareIsotopes;
break;
}
}
void SetMCSBondTyper(MCSParameters &p, BondComparator bondComp) {
switch (bondComp) {
case BondCompareAny:
p.BondTyper = MCSBondCompareAny;
break;
case BondCompareOrder:
p.BondTyper = MCSBondCompareOrder;
break;
case BondCompareOrderExact:
p.BondTyper = MCSBondCompareOrderExact;
break;
}
}
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,
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;
SetMCSAtomTyper(p, atomComp);
SetMCSBondTyper(p, bondComp);
p.BondCompareParameters.RingMatchesRingOnly = ringMatchesRingOnly;
p.BondCompareParameters.CompleteRingsOnly = completeRingsOnly;
MCSResult *res = nullptr;
{
NOGIL gil;
res = new MCSResult(findMCS(ms, &p));
}
return res;
}
MCSResult *FindMCSWrapper2(python::object mols, const MCSParameters ¶ms) {
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;
{
NOGIL gil;
res = new MCSResult(findMCS(ms, ¶ms));
}
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("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);
python::enum_<RDKit::BondComparator>("BondCompare")
.value("CompareAny", RDKit::BondCompareAny)
.value("CompareOrder", RDKit::BondCompareOrder)
.value("CompareOrderExact", RDKit::BondCompareOrderExact);
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("seedSmarts") = ""),
python::return_value_policy<python::manage_new_object>(),
docString.c_str());
python::class_<RDKit::MCSParameters, boost::noncopyable>(
"MCSParameters", "Parameters controlling how the MCS is constructed")
.def_readwrite("MaximizeBonds", &RDKit::MCSParameters::MaximizeBonds,
"toggles maximizing the number of bonds (instead of the "
"number of atoms)")
.def_readwrite("Threshold", &RDKit::MCSParameters::Threshold,
"fraction of the dataset that must contain the MCS")
.def_readwrite("Timeout", &RDKit::MCSParameters::Timeout,
"timeout (in seconds) for the calculation")
.def_readwrite("Verbose", &RDKit::MCSParameters::Verbose,
"toggles verbose mode")
.def_readwrite("AtomCompareParameters",
&RDKit::MCSParameters::AtomCompareParameters,
"parameters for comparing atoms")
.def_readwrite("BondCompareParameters",
&RDKit::MCSParameters::BondCompareParameters,
"parameters for comparing bonds")
// haven't been able to get these properly working
// .def_readwrite("AtomTyper", &RDKit::MCSParameters::AtomTyper,
// "function for comparing atoms")
// .def_readwrite("BondTyper", &RDKit::MCSParameters::BondTyper,
// "function for comparing bonds")
.def_readwrite("InitialSeed", &RDKit::MCSParameters::InitialSeed,
"SMILES string to be used as the seed of the MCS")
.def("SetAtomTyper", RDKit::SetMCSAtomTyper,
(python::arg("self"), python::arg("comparator")),
"sets the atom typer to be used. The argument should be one of the "
"members of the rdFMCS.AtomCompare class.")
.def("SetBondTyper", RDKit::SetMCSBondTyper,
(python::arg("self"), python::arg("comparator")),
"sets the bond typer to be used. The argument should be one of the "
"members of the rdFMCS.BondCompare class.");
;
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");
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("MatchStereo",
&RDKit::MCSBondCompareParameters::MatchStereo,
"include bond stereo in the comparison");
docString = "Find the MCS for a set of molecules";
python::def("FindMCS", RDKit::FindMCSWrapper2,
(python::arg("mols"), python::arg("parameters")),
python::return_value_policy<python::manage_new_object>(),
docString.c_str());
}
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