mirror of
https://github.com/rdkit/rdkit.git
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5cf8a6a9b7
* expose addRing to python * backup commit * basics of atom and bond loading * basics of atom and bond loading * do bond stereo too * Loads of cleanups Read conformers and molecule properties Better tests update one of the test values so that we aren't always testing ccw * enable auto-download of rapidjson distrib * reader now mostly done (still missing atomic/bond properties) * a bit of optimization * a bit of cleanup * a bit more optimization * backup * test zero-order bonds * prep work for writer (not done) * add isotope support * backup * getting there with the writing * progress on writing; still need to do the RDKit part though * can now roundtrip, including chirality. double bond stereo needs to wait for backend fixes * add a timing test for benchmarking * add a timing test for benchmarking * add another template * add parse params; optionally set bond types to aromatic; add python wrapper * disable benchmark run by default * write conformers * refactoring * docs * port to commonchem * switch representation * start reading and writing properties * fix a memory problem * set a common_property for gasteiger charges * parse partial charges * add partial charge writing * reformatting * add support for disabling parts of the parsing * remove the "name" property from files * editing * more post-review changes * make the molinterchange build optional * make them really optional
73 lines
2.4 KiB
C++
73 lines
2.4 KiB
C++
//
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// Copyright (C) Greg Landrum 2007-2017
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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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#define NO_IMPORT_ARRAY
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#include <RDBoost/python.h>
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#include <RDBoost/Wrap.h>
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#include <GraphMol/RDKitBase.h>
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#include <RDGeneral/types.h>
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namespace python = boost::python;
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namespace {
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using namespace RDKit;
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python::object atomRings(const RingInfo *self) {
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python::list res;
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VECT_INT_VECT rings = self->atomRings();
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for (auto &ring : rings) {
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res.append(python::tuple(ring));
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}
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return python::tuple(res);
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}
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python::object bondRings(const RingInfo *self) {
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python::list res;
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VECT_INT_VECT rings = self->bondRings();
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for (auto &ring : rings) {
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res.append(python::tuple(ring));
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}
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return python::tuple(res);
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}
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void addRing(RingInfo *self,python::object atomRing, python::object bondRing){
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unsigned int nAts = python::extract<unsigned int>(atomRing.attr("__len__")());
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unsigned int nBnds = python::extract<unsigned int>(bondRing.attr("__len__")());
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if(nAts != nBnds) throw_value_error("list sizes must match");
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if(!self->isInitialized()) self->initialize();
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INT_VECT aring(nAts);
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INT_VECT bring(nAts);
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for (unsigned int i = 0; i < nAts; ++i) {
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aring[i] = python::extract<int>(atomRing[i])();
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bring[i] = python::extract<int>(bondRing[i])();
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}
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self->addRing(aring,bring);
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}
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}
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namespace RDKit {
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std::string classDoc = "contains information about a molecule's rings\n";
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struct ringinfo_wrapper {
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static void wrap() {
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python::class_<RingInfo>("RingInfo", classDoc.c_str(), python::no_init)
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.def("IsAtomInRingOfSize", &RingInfo::isAtomInRingOfSize)
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.def("IsBondInRingOfSize", &RingInfo::isBondInRingOfSize)
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.def("IsBondInRingOfSize", &RingInfo::isBondInRingOfSize)
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.def("NumAtomRings", &RingInfo::numAtomRings)
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.def("NumBondRings", &RingInfo::numBondRings)
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.def("NumRings", &RingInfo::numRings)
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.def("AtomRings", atomRings)
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.def("BondRings", bondRings)
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.def("AddRing", addRing, (python::arg("self"),python::arg("atomIds"),python::arg("bondIds")),
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"Adds a ring to the set. Be very careful with this operation.");
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};
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};
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} // end of namespace
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void wrap_ringinfo() { RDKit::ringinfo_wrapper::wrap(); }
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