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// $Id$
//
// Copyright (C) 2001-2006 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 <GraphMol/QueryAtom.h>
#include <GraphMol/QueryOps.h>
#include <Query/NullQueryAlgebra.h>
namespace RDKit {
QueryAtom::~QueryAtom() {
delete dp_query;
dp_query = nullptr;
};
Atom *QueryAtom::copy() const {
auto *res = new QueryAtom(*this);
return static_cast<Atom *>(res);
}
void QueryAtom::expandQuery(QUERYATOM_QUERY *what,
Queries::CompositeQueryType how,
bool maintainOrder) {
PRECONDITION(dp_query, "Can't expand empty query");
bool thisIsNullQuery = dp_query->getDescription() == "AtomNull";
bool otherIsNullQuery = what->getDescription() == "AtomNull";
if (thisIsNullQuery || otherIsNullQuery) {
mergeNullQueries(dp_query, thisIsNullQuery, what, otherIsNullQuery, how);
delete what;
return;
}
QUERYATOM_QUERY *origQ = dp_query;
std::string descrip;
switch (how) {
case Queries::COMPOSITE_AND:
dp_query = new ATOM_AND_QUERY;
descrip = "AtomAnd";
break;
case Queries::COMPOSITE_OR:
dp_query = new ATOM_OR_QUERY;
descrip = "AtomOr";
break;
case Queries::COMPOSITE_XOR:
dp_query = new ATOM_XOR_QUERY;
descrip = "AtomXor";
break;
default:
UNDER_CONSTRUCTION("unrecognized combination query");
}
dp_query->setDescription(descrip);
if (maintainOrder) {
dp_query->addChild(QUERYATOM_QUERY::CHILD_TYPE(origQ));
dp_query->addChild(QUERYATOM_QUERY::CHILD_TYPE(what));
} else {
dp_query->addChild(QUERYATOM_QUERY::CHILD_TYPE(what));
dp_query->addChild(QUERYATOM_QUERY::CHILD_TYPE(origQ));
}
}
namespace {
bool localMatch(ATOM_EQUALS_QUERY const *q1, ATOM_EQUALS_QUERY const *q2) {
if (q1->getNegation() == q2->getNegation()) {
return q1->getVal() == q2->getVal();
} else {
return q1->getVal() != q2->getVal();
}
}
bool queriesMatch(QueryAtom::QUERYATOM_QUERY const *q1,
QueryAtom::QUERYATOM_QUERY const *q2) {
PRECONDITION(q1, "no q1");
PRECONDITION(q2, "no q2");
static const unsigned int nQueries = 20;
static std::string equalityQueries[nQueries] = {"AtomType",
"AtomRingBondCount",
"AtomRingSize",
"AtomMinRingSize",
"AtomImplicitValence",
"AtomExplicitValence",
"AtomTotalValence",
"AtomAtomicNum",
"AtomExplicitDegree",
"AtomTotalDegree",
"AtomHCount",
"AtomIsAromatic",
"AtomIsAliphatic",
"AtomUnsaturated",
"AtomMass",
"AtomFormalCharge",
"AtomNegativeFormalCharge",
"AtomHybridization",
"AtomInRing",
"AtomInNRings"};
bool res = false;
std::string d1 = q1->getDescription();
std::string d2 = q2->getDescription();
if (d1 == "AtomNull" || d2 == "AtomNull") {
res = true;
} else if (d1 == "AtomOr") {
// FIX: handle negation on AtomOr and AtomAnd
for (auto iter1 = q1->beginChildren(); iter1 != q1->endChildren();
++iter1) {
if (d2 == "AtomOr") {
for (auto iter2 = q2->beginChildren(); iter2 != q2->endChildren();
++iter2) {
if (queriesMatch(iter1->get(), iter2->get())) {
res = true;
break;
}
}
} else {
if (queriesMatch(iter1->get(), q2)) {
res = true;
}
}
if (res) {
break;
}
}
} else if (d1 == "AtomAnd") {
res = true;
for (auto iter1 = q1->beginChildren(); iter1 != q1->endChildren();
++iter1) {
bool matched = false;
if (d2 == "AtomAnd") {
for (auto iter2 = q2->beginChildren(); iter2 != q2->endChildren();
++iter2) {
if (queriesMatch(iter1->get(), iter2->get())) {
matched = true;
break;
}
}
} else {
matched = queriesMatch(iter1->get(), q2);
}
if (!matched) {
res = false;
break;
}
}
// FIX : handle AtomXOr
} else if (d2 == "AtomOr") {
// FIX: handle negation on AtomOr and AtomAnd
for (auto iter2 = q2->beginChildren(); iter2 != q2->endChildren();
++iter2) {
if (queriesMatch(q1, iter2->get())) {
res = true;
break;
}
}
} else if (d2 == "AtomAnd") {
res = true;
for (auto iter2 = q2->beginChildren(); iter2 != q2->endChildren();
++iter2) {
if (!queriesMatch(q1, iter2->get())) {
res = false;
break;
}
}
} else if (d1 == d2) {
if (std::find(&equalityQueries[0], &equalityQueries[nQueries], d1) !=
&equalityQueries[nQueries]) {
res = localMatch(static_cast<ATOM_EQUALS_QUERY const *>(q1),
static_cast<ATOM_EQUALS_QUERY const *>(q2));
}
} else {
}
return res;
}
} // namespace
bool QueryAtom::Match(Atom const *what) const {
PRECONDITION(what, "bad query atom");
PRECONDITION(dp_query, "no query set");
return dp_query->Match(what);
}
bool QueryAtom::QueryMatch(QueryAtom const *what) const {
PRECONDITION(what, "bad query atom");
PRECONDITION(dp_query, "no query set");
if (!what->hasQuery()) {
return dp_query->Match(what);
} else {
return queriesMatch(dp_query, what->getQuery());
}
}
}; // namespace RDKit
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