QueryAtom.h
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//
// Copyright (C) 2001-2017 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 <RDGeneral/export.h>
#ifndef _RD_QUERYATOM_H_
#define _RD_QUERYATOM_H_
#include "Atom.h"
#include <Query/QueryObjects.h>
#include <GraphMol/QueryOps.h>
namespace RDKit {
//! Class for storing atomic queries
/*!
QueryAtom objects are derived from Atom objects, so they can be
added to molecules and the like, but they have much fancier
querying capabilities.
*/
class RDKIT_GRAPHMOL_EXPORT QueryAtom : public Atom {
public:
typedef Queries::Query<int, Atom const *, true> QUERYATOM_QUERY;
QueryAtom() : Atom() {}
explicit QueryAtom(int num) : Atom(num), dp_query(makeAtomNumQuery(num)) {}
explicit QueryAtom(const Atom &other)
: Atom(other), dp_query(makeAtomNumQuery(other.getAtomicNum())) {
if (other.getIsotope()) {
this->expandQuery(makeAtomIsotopeQuery(other.getIsotope()),
Queries::CompositeQueryType::COMPOSITE_AND);
}
if (other.getFormalCharge()) {
this->expandQuery(makeAtomFormalChargeQuery(other.getFormalCharge()),
Queries::CompositeQueryType::COMPOSITE_AND);
}
if (other.getNumRadicalElectrons()) {
this->expandQuery(
makeAtomNumRadicalElectronsQuery(other.getNumRadicalElectrons()),
Queries::CompositeQueryType::COMPOSITE_AND);
}
}
QueryAtom(const QueryAtom &other) : Atom(other) {
if (other.dp_query) {
dp_query = other.dp_query->copy();
} else {
dp_query = nullptr;
}
}
QueryAtom &operator=(const QueryAtom &other) {
if (this == &other) return *this;
Atom::operator=(other);
delete dp_query;
if (other.dp_query) {
dp_query = other.dp_query->copy();
} else {
dp_query = nullptr;
}
return *this;
}
~QueryAtom() override;
//! returns a copy of this query, owned by the caller
Atom *copy() const override;
// This method can be used to distinguish query atoms from standard atoms:
bool hasQuery() const override { return dp_query != nullptr; }
//! replaces our current query with the value passed in
void setQuery(QUERYATOM_QUERY *what) override {
delete dp_query;
dp_query = what;
}
//! returns our current query
QUERYATOM_QUERY *getQuery() const override { return dp_query; }
//! expands our current query
/*!
\param what the Queries::Query to be added. The ownership of
the query is passed to the current object, where it
might be deleted, so that the pointer should not be
used again in the calling code.
\param how the operator to be used in the expansion
\param maintainOrder (optional) flags whether the relative order of
the queries needs to be maintained, if this is
false, the order is reversed
<b>Notes:</b>
- \c what should probably be constructed using one of the functions
defined in QueryOps.h
- the \c maintainOrder option can be useful because the combination
operators short circuit when possible.
*/
void expandQuery(QUERYATOM_QUERY *what,
Queries::CompositeQueryType how = Queries::COMPOSITE_AND,
bool maintainOrder = true) override;
//! returns true if we match Atom \c what
bool Match(Atom const *what) const override;
//! returns true if our query details match those of QueryAtom \c what
bool QueryMatch(QueryAtom const *what) const;
private:
QUERYATOM_QUERY *dp_query{nullptr};
}; // end o' class
namespace detail {
inline std::string qhelper(Atom::QUERYATOM_QUERY *q, unsigned int depth) {
std::string res = "";
if (q) {
for (unsigned int i = 0; i < depth; ++i) res += " ";
res += q->getFullDescription() + "\n";
for (Atom::QUERYATOM_QUERY::CHILD_VECT_CI ci = q->beginChildren();
ci != q->endChildren(); ++ci) {
res += qhelper((*ci).get(), depth + 1);
}
}
return res;
}
} // namespace detail
inline std::string describeQuery(const Atom *atom) {
PRECONDITION(atom, "bad atom");
std::string res = "";
if (atom->hasQuery()) {
res = detail::qhelper(atom->getQuery(), 0);
}
return res;
}
}; // namespace RDKit
#endif
Atom.h
Defines the Atom class and associated typedefs.
PRECONDITION
#define PRECONDITION(expr, mess)
Definition: Invariant.h:109
QueryObjects.h
Pulls in all the query types.
QueryOps.h
Queries::Query
Base class for all queries.
Definition: Query.h:45
Queries::Query::getFullDescription
virtual std::string getFullDescription() const
returns a fuller text description
Definition: Query.h:72
Queries::Query::endChildren
CHILD_VECT_CI endChildren() const
returns an iterator for the end of our child vector
Definition: Query.h:106
Queries::Query::beginChildren
CHILD_VECT_CI beginChildren() const
returns an iterator for the beginning of our child vector
Definition: Query.h:104
Queries::Query::copy
virtual Query< MatchFuncArgType, DataFuncArgType, needsConversion > * copy() const
returns a copy of this Query
Definition: Query.h:128
Queries::Query::CHILD_VECT_CI
typename CHILD_VECT::const_iterator CHILD_VECT_CI
Definition: Query.h:51
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:68
RDKit::Atom::operator=
Atom & operator=(const Atom &other)
RDKit::Atom::getNumRadicalElectrons
unsigned int getNumRadicalElectrons() const
returns the number of radical electrons for this Atom
Definition: Atom.h:199
RDKit::Atom::getQuery
virtual QUERYATOM_QUERY * getQuery() const
NOT CALLABLE.
RDKit::Atom::hasQuery
virtual bool hasQuery() const
Definition: Atom.h:260
RDKit::Atom::getFormalCharge
int getFormalCharge() const
returns the formal charge of this atom
Definition: Atom.h:203
RDKit::Atom::getIsotope
unsigned int getIsotope() const
returns our isotope number
Definition: Atom.h:229
RDKit::QueryAtom
Class for storing atomic queries.
Definition: QueryAtom.h:27
RDKit::QueryAtom::hasQuery
bool hasQuery() const override
Definition: QueryAtom.h:73
RDKit::QueryAtom::QueryMatch
bool QueryMatch(QueryAtom const *what) const
returns true if our query details match those of QueryAtom what
RDKit::QueryAtom::getQuery
QUERYATOM_QUERY * getQuery() const override
returns our current query
Definition: QueryAtom.h:81
RDKit::QueryAtom::setQuery
void setQuery(QUERYATOM_QUERY *what) override
replaces our current query with the value passed in
Definition: QueryAtom.h:76
RDKit::QueryAtom::QueryAtom
QueryAtom(int num)
Definition: QueryAtom.h:32
RDKit::QueryAtom::copy
Atom * copy() const override
returns a copy of this query, owned by the caller
RDKit::QueryAtom::Match
bool Match(Atom const *what) const override
returns true if we match Atom what
RDKit::QueryAtom::QueryAtom
QueryAtom()
Definition: QueryAtom.h:31
RDKit::QueryAtom::QUERYATOM_QUERY
Queries::Query< int, Atom const *, true > QUERYATOM_QUERY
Definition: QueryAtom.h:29
RDKit::QueryAtom::operator=
QueryAtom & operator=(const QueryAtom &other)
Definition: QueryAtom.h:56
RDKit::QueryAtom::QueryAtom
QueryAtom(const QueryAtom &other)
Definition: QueryAtom.h:49
RDKit::QueryAtom::QueryAtom
QueryAtom(const Atom &other)
Definition: QueryAtom.h:33
RDKit::QueryAtom::~QueryAtom
~QueryAtom() override
RDKit::QueryAtom::expandQuery
void expandQuery(QUERYATOM_QUERY *what, Queries::CompositeQueryType how=Queries::COMPOSITE_AND, bool maintainOrder=true) override
expands our current query
export.h
RDKIT_GRAPHMOL_EXPORT
#define RDKIT_GRAPHMOL_EXPORT
Definition: export.h:209
Queries::CompositeQueryType
CompositeQueryType
Definition: QueryObjects.h:36
Queries::COMPOSITE_AND
@ COMPOSITE_AND
Definition: QueryObjects.h:36
RDKit::detail::qhelper
std::string qhelper(Atom::QUERYATOM_QUERY *q, unsigned int depth)
Definition: QueryAtom.h:116
RDKit
Std stuff.
Definition: Abbreviations.h:18
RDKit::makeAtomFormalChargeQuery
T * makeAtomFormalChargeQuery(int what, const std::string &descr)
returns a Query for matching formal charge
Definition: QueryOps.h:487
RDKit::describeQuery
std::string describeQuery(const Atom *atom)
Definition: QueryAtom.h:129
RDKit::makeAtomIsotopeQuery
T * makeAtomIsotopeQuery(int what, const std::string &descr)
returns a Query for matching atoms with a particular isotope
Definition: QueryOps.h:479
RDKit::makeAtomNumQuery
T * makeAtomNumQuery(int what, const std::string &descr)
returns a Query for matching atomic number
Definition: QueryOps.h:364
RDKit::makeAtomNumRadicalElectronsQuery
T * makeAtomNumRadicalElectronsQuery(int what, const std::string &descr)
returns a Query for matching the number of radical electrons
Definition: QueryOps.h:513