mirror of
https://github.com/rdkit/rdkit.git
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5dfd67a22a
* copy in, get building, add some basic tests * complete the testing Except for regiosiomers, which do not work * regioisomers work now * backup commit; things work * remove last of NM macros from hashfunctions.cpp * remove last of NM macros from hashfunctions.cpp * remove dependency on the abstraction layer * typo * start using namespaces clang-format * switch to using enums for the HashFunctions and StripTypes * Add initial python wrapper (and tests) * move the new hashing code to the MolHash library still may want to revise the naming of this * Setup deprecation of the older hashing code * better release notes text * change in response to review
76 lines
3.1 KiB
C++
76 lines
3.1 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 <GraphMol/MolHash/MolHash.h>
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#include <RDBoost/Wrap.h>
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namespace python = boost::python;
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using namespace RDKit;
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namespace {
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std::string GenMolHashString(const ROMol &mol, python::object atomsToUse,
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python::object bondsToUse) {
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std::unique_ptr<std::vector<unsigned>> avect;
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if (atomsToUse) {
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avect = pythonObjectToVect(atomsToUse,
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static_cast<unsigned>(mol.getNumAtoms()));
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}
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std::unique_ptr<std::vector<unsigned>> bvect;
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if (bondsToUse) {
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bvect = pythonObjectToVect(bondsToUse,
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static_cast<unsigned>(mol.getNumBonds()));
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}
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std::string res =
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MolHash::generateMoleculeHashSet(mol, avect.get(), bvect.get());
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return res;
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}
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std::string MolHashHelper(const ROMol &mol, MolHash::HashFunction func) {
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RWMol cpy(mol);
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return MolHash::MolHash(&cpy, func);
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}
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} // namespace
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BOOST_PYTHON_MODULE(rdMolHash) {
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python::scope().attr("__doc__") =
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"Module containing functions to generate hashes for molecules";
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python::enum_<MolHash::HashFunction>("HashFunction")
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.value("AnonymousGraph", MolHash::HashFunction::AnonymousGraph)
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.value("ElementGraph", MolHash::HashFunction::ElementGraph)
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.value("CanonicalSmiles", MolHash::HashFunction::CanonicalSmiles)
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.value("MurckoScaffold", MolHash::HashFunction::MurckoScaffold)
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.value("ExtendedMurcko", MolHash::HashFunction::ExtendedMurcko)
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.value("MolFormula", MolHash::HashFunction::MolFormula)
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.value("AtomBondCounts", MolHash::HashFunction::AtomBondCounts)
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.value("DegreeVector", MolHash::HashFunction::DegreeVector)
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.value("Mesomer", MolHash::HashFunction::Mesomer)
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.value("HetAtomTautomer", MolHash::HashFunction::HetAtomTautomer)
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.value("HetAtomProtomer", MolHash::HashFunction::HetAtomProtomer)
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.value("RedoxPair", MolHash::HashFunction::RedoxPair)
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.value("Regioisomer", MolHash::HashFunction::Regioisomer)
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.value("NetCharge", MolHash::HashFunction::NetCharge)
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.value("SmallWorldIndexBR", MolHash::HashFunction::SmallWorldIndexBR)
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.value("SmallWorldIndexBRL", MolHash::HashFunction::SmallWorldIndexBRL)
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.value("ArthorSubstructureOrder",
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MolHash::HashFunction::ArthorSubstructureOrder);
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std::string docString = "DEPRECATED: please use MolHash() instead";
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python::def("GenerateMoleculeHashString", GenMolHashString,
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(python::arg("mol"), python::arg("atomsToUse") = python::list(),
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python::arg("bondsToUse") = python::list()),
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docString.c_str());
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python::def("MolHash", MolHashHelper,
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(python::arg("mol"), python::arg("func")),
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"Generate a hash for a molecule. The func argument determines "
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"which hash is generated.");
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}
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