mirror of
https://github.com/rdkit/rdkit.git
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122 lines
4.2 KiB
C++
122 lines
4.2 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 <boost/python.hpp>
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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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typedef enum {
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AtomCompareAny,
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AtomCompareElements,
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AtomCompareIsotopes
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} AtomComparator_;
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typedef enum {
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BondCompareAny,
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BondCompareOrder,
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BondCompareOrderExact
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} BondComparator_;
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MCSResult *FindMCSWrapper(python::object mols,bool maximizeBonds,double threshold,
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unsigned timeout,bool verbose,
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bool ringMatchesRingOnly,bool completeRingsOnly,
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AtomComparator_ atomComp, BondComparator_ bondComp) {
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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]) throw_value_error("molecule is None");
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ms[i] = python::extract<ROMOL_SPTR>(mols[i]);
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}
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MCSParameters *ps=new MCSParameters();
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ps->MaximizeBonds=maximizeBonds;
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ps->Threshold=threshold;
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ps->Timeout=timeout;
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ps->Verbose=verbose;
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switch(atomComp) {
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case AtomCompareAny:
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ps->AtomTyper=MCSAtomCompareAny;
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break;
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case AtomCompareElements:
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ps->AtomTyper=MCSAtomCompareElements;
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break;
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case AtomCompareIsotopes:
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ps->AtomTyper=MCSAtomCompareIsotopes;
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break;
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}
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switch(bondComp) {
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case BondCompareAny:
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ps->BondTyper=MCSBondCompareAny;
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break;
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case BondCompareOrder:
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ps->BondTyper=MCSBondCompareOrder;
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break;
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case BondCompareOrderExact:
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ps->BondTyper=MCSBondCompareOrderExact;
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break;
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}
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ps->BondCompareParameters.RingMatchesRingOnly=ringMatchesRingOnly;
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ps->BondCompareParameters.CompleteRingsOnly=completeRingsOnly;
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MCSResult *res=new MCSResult(findMCS(ms,ps));
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delete ps;
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return res;
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}
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}
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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","stores MCS results",python::no_init)
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.def_readonly("numAtoms",&RDKit::MCSResult::NumAtoms)
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.def_readonly("numBonds",&RDKit::MCSResult::NumBonds)
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.def_readonly("smartsString",&RDKit::MCSResult::SmartsString)
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.def_readonly("canceled",&RDKit::MCSResult::Canceled)
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;
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}
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};
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}
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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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;
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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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;
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std::string docString = "Find the MCS for a set of molecules";
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python::def("FindMCS", RDKit::FindMCSWrapper,
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(python::arg("mols"),
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python::arg("maximizeBonds")=true,
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python::arg("threshold")=1.0,
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python::arg("timeout")=3600,
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python::arg("verbose")=false,
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python::arg("ringMatchesRingOnly")=false,
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python::arg("completeRingsOnly")=false,
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python::arg("atomCompare")=RDKit::AtomCompareElements,
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python::arg("bondCompare")=RDKit::BondCompareOrder
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),
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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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