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dc4893132b
* fixes #4721 * - store in RingInfo the index of the ring(s) each atom and bond belongs to rather tham just their size - expand the RingInfo API with a few useful methods - identify rings that are certainly aliphatic upfront - avoid unnecessary copying atomRings when RingInfo is already initialized * - code modernization and cleanup - better handling of dummies in aromatic rings - exposed atomMembers() and bondMembers() - added several tests * - avoid order dependency on rings - added test for the above * changes in response to review Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
125 lines
4.1 KiB
C++
125 lines
4.1 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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for (const auto &ring : self->atomRings()) {
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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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for (const auto &ring : self->bondRings()) {
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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 atomMembers(const RingInfo *self, unsigned int idx) {
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return python::tuple(self->atomMembers(idx));
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}
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python::object bondMembers(const RingInfo *self, unsigned int idx) {
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return python::tuple(self->bondMembers(idx));
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}
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python::object atomRingSizes(const RingInfo *self, unsigned int idx) {
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return python::tuple(self->atomRingSizes(idx));
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}
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python::object bondRingSizes(const RingInfo *self, unsigned int idx) {
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return python::tuple(self->bondRingSizes(idx));
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}
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#ifdef RDK_USE_URF
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python::object atomRingFamilies(const RingInfo *self) {
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python::list res;
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for (const auto &ring : self->atomRingFamilies()) {
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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 bondRingFamilies(const RingInfo *self) {
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python::list res;
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for (const auto &ring : self->bondRingFamilies()) {
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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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#endif
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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 =
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python::extract<unsigned int>(bondRing.attr("__len__")());
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if (nAts != nBnds) {
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throw_value_error("list sizes must match");
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}
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if (!self->isInitialized()) {
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self->initialize();
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}
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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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} // namespace
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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("MinAtomRingSize", &RingInfo::minAtomRingSize)
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.def("AreAtomsInSameRing", &RingInfo::areAtomsInSameRing)
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.def("AreAtomsInSameRingOfSize", &RingInfo::areAtomsInSameRingOfSize)
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.def("IsBondInRingOfSize", &RingInfo::isBondInRingOfSize)
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.def("MinBondRingSize", &RingInfo::minBondRingSize)
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.def("AreBondsInSameRing", &RingInfo::areBondsInSameRing)
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.def("AreBondsInSameRingOfSize", &RingInfo::areBondsInSameRingOfSize)
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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("AtomMembers", atomMembers)
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.def("BondMembers", bondMembers)
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.def("AtomRingSizes", atomRingSizes)
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.def("BondRingSizes", bondRingSizes)
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#ifdef RDK_USE_URF
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.def("NumRingFamilies", &RingInfo::numRingFamilies)
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.def("NumRelevantCycles", &RingInfo::numRelevantCycles)
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.def("AtomRingFamilies", atomRingFamilies)
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.def("BondRingFamilies", bondRingFamilies)
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.def("AreRingFamiliesInitialized",
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&RingInfo::areRingFamiliesInitialized)
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#endif
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.def("AddRing", addRing,
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(python::arg("self"), python::arg("atomIds"),
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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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} // namespace RDKit
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void wrap_ringinfo() { RDKit::ringinfo_wrapper::wrap(); }
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