mirror of
https://github.com/rdkit/rdkit.git
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ba12d98ad0
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers * Actually delete atoms and bonds... * RWMol::clear now calls destroy to handle atom/bond deletion * Changes broken Atom lookup for windows/gcc * Adds tests for running with valgrind * Adds test designed for valgrind and molecule deletions * Removes RNG, actually tests bond deletions * update swig wrappers * deal with most recent changes on the main branch
110 lines
3.6 KiB
C++
110 lines
3.6 KiB
C++
// $Id$
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//
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// Copyright (C) 2003-2010 Greg Landrum and Rational Discovery LLC
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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 "SubstructUtils.h"
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#include <RDGeneral/utils.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <boost/dynamic_bitset.hpp>
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namespace RDKit {
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bool atomCompat(const Atom* a1, const Atom* a2,
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bool useQueryQueryMatches) {
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PRECONDITION(a1, "bad atom");
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PRECONDITION(a2, "bad atom");
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// std::cerr << "\t\tatomCompat: "<< a1 << " " << a1->getIdx() << "-" << a2 <<
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// " " << a2->getIdx() << std::endl;
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bool res;
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if (useQueryQueryMatches && a1->hasQuery() && a2->hasQuery()) {
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res = static_cast<const QueryAtom *>(a1)->QueryMatch(
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static_cast<const QueryAtom *>(a2));
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} else {
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res = a1->Match(a2);
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}
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return res;
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std::cerr << "\t\tatomCompat: " << a1 << " " << a1->getIdx() << "-" << a2
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<< " " << a2->getIdx() << std::endl;
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std::cerr << "\t\t " << res << std::endl;
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return res;
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}
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bool chiralAtomCompat(const Atom* &a1, const Atom* &a2) {
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PRECONDITION(a1, "bad atom");
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PRECONDITION(a2, "bad atom");
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bool res = a1->Match(a2);
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if (res) {
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std::string s1, s2;
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bool hascode1 = a1->getPropIfPresent(common_properties::_CIPCode, s1);
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bool hascode2 = a2->getPropIfPresent(common_properties::_CIPCode, s2);
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if (hascode1 || hascode2) {
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res = hascode1 && hascode2 && s1 == s2;
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}
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}
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std::cerr << "\t\tchiralAtomCompat: " << a1 << " " << a1->getIdx() << "-"
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<< a2 << " " << a2->getIdx() << std::endl;
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std::cerr << "\t\t " << res << std::endl;
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return res;
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}
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bool bondCompat(const Bond* b1, const Bond* b2,
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bool useQueryQueryMatches) {
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PRECONDITION(b1, "bad bond");
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PRECONDITION(b2, "bad bond");
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bool res;
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if (useQueryQueryMatches && b1->hasQuery() && b2->hasQuery()) {
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res = static_cast<const QueryBond *>(b1)->QueryMatch(
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static_cast<const QueryBond *>(b2));
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} else {
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res = b1->Match(b2);
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}
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if (res && b1->getBondType() == Bond::DATIVE &&
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b2->getBondType() == Bond::DATIVE) {
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// for dative bonds we need to make sure that the direction also matches:
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if (!b1->getBeginAtom()->Match(b1->getBeginAtom()) ||
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!b1->getEndAtom()->Match(b2->getEndAtom())) {
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res = false;
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}
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}
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// std::cout << "\t\tbondCompat: "<< b1->getIdx() << "-" << b2->getIdx() << ":
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// " << res << std::endl;
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return res;
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}
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void removeDuplicates(std::vector<MatchVectType> &v, unsigned int nAtoms) {
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//
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// This works by tracking the indices of the atoms in each match vector.
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// This can lead to unexpected behavior when looking at rings and queries
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// that don't specify bond orders. For example querying this molecule:
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// C1CCC=1
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// with the pattern constructed from SMARTS C~C~C~C will return a
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// single match, despite the fact that there are 4 different paths
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// when valence is considered. The defense of this behavior is
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// that the 4 paths are equivalent in the semantics of the query.
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// Also, OELib returns the same results
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//
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std::vector<boost::dynamic_bitset<> > seen;
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std::vector<MatchVectType> res;
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for (std::vector<MatchVectType>::const_iterator i = v.begin(); i != v.end();
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++i) {
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boost::dynamic_bitset<> val(nAtoms);
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for (const auto &ci : *i) {
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val.set(ci.second);
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}
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if (std::find(seen.begin(), seen.end(), val) == seen.end()) {
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// it's something new
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res.push_back(*i);
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seen.push_back(val);
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}
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}
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v = res;
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}
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}
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