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// $Id$
//
// Copyright (C) 2003-2010 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "SubstructUtils.h"
#include <RDGeneral/utils.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <boost/dynamic_bitset.hpp>
namespace RDKit {
bool atomCompat(const Atom* a1, const Atom* a2,
bool useQueryQueryMatches) {
PRECONDITION(a1, "bad atom");
PRECONDITION(a2, "bad atom");
// std::cerr << "\t\tatomCompat: "<< a1 << " " << a1->getIdx() << "-" << a2 <<
// " " << a2->getIdx() << std::endl;
bool res;
if (useQueryQueryMatches && a1->hasQuery() && a2->hasQuery()) {
res = static_cast<const QueryAtom *>(a1)->QueryMatch(
static_cast<const QueryAtom *>(a2));
} else {
res = a1->Match(a2);
}
return res;
std::cerr << "\t\tatomCompat: " << a1 << " " << a1->getIdx() << "-" << a2
<< " " << a2->getIdx() << std::endl;
std::cerr << "\t\t " << res << std::endl;
return res;
}
bool chiralAtomCompat(const Atom* &a1, const Atom* &a2) {
PRECONDITION(a1, "bad atom");
PRECONDITION(a2, "bad atom");
bool res = a1->Match(a2);
if (res) {
std::string s1, s2;
bool hascode1 = a1->getPropIfPresent(common_properties::_CIPCode, s1);
bool hascode2 = a2->getPropIfPresent(common_properties::_CIPCode, s2);
if (hascode1 || hascode2) {
res = hascode1 && hascode2 && s1 == s2;
}
}
std::cerr << "\t\tchiralAtomCompat: " << a1 << " " << a1->getIdx() << "-"
<< a2 << " " << a2->getIdx() << std::endl;
std::cerr << "\t\t " << res << std::endl;
return res;
}
bool bondCompat(const Bond* b1, const Bond* b2,
bool useQueryQueryMatches) {
PRECONDITION(b1, "bad bond");
PRECONDITION(b2, "bad bond");
bool res;
if (useQueryQueryMatches && b1->hasQuery() && b2->hasQuery()) {
res = static_cast<const QueryBond *>(b1)->QueryMatch(
static_cast<const QueryBond *>(b2));
} else {
res = b1->Match(b2);
}
if (res && b1->getBondType() == Bond::DATIVE &&
b2->getBondType() == Bond::DATIVE) {
// for dative bonds we need to make sure that the direction also matches:
if (!b1->getBeginAtom()->Match(b1->getBeginAtom()) ||
!b1->getEndAtom()->Match(b2->getEndAtom())) {
res = false;
}
}
// std::cout << "\t\tbondCompat: "<< b1->getIdx() << "-" << b2->getIdx() << ":
// " << res << std::endl;
return res;
}
void removeDuplicates(std::vector<MatchVectType> &v, unsigned int nAtoms) {
//
// This works by tracking the indices of the atoms in each match vector.
// This can lead to unexpected behavior when looking at rings and queries
// that don't specify bond orders. For example querying this molecule:
// C1CCC=1
// with the pattern constructed from SMARTS C~C~C~C will return a
// single match, despite the fact that there are 4 different paths
// when valence is considered. The defense of this behavior is
// that the 4 paths are equivalent in the semantics of the query.
// Also, OELib returns the same results
//
std::vector<boost::dynamic_bitset<> > seen;
std::vector<MatchVectType> res;
for (std::vector<MatchVectType>::const_iterator i = v.begin(); i != v.end();
++i) {
boost::dynamic_bitset<> val(nAtoms);
for (const auto &ci : *i) {
val.set(ci.second);
}
if (std::find(seen.begin(), seen.end(), val) == seen.end()) {
// it's something new
res.push_back(*i);
seen.push_back(val);
}
}
v = res;
}
}
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