AtomIterators.h
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//
// Copyright (C) 2002-2006 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.
//
/*! \file AtomIterators.h
\brief various tools for iterating over a molecule's Atoms.
<b>WARNING:</b> If you go changing the molecule underneath one of
these iterators you will be sad...
*/
#include <RDGeneral/export.h>
#ifndef __RD_ATOM_ITERATORS_H__
#define __RD_ATOM_ITERATORS_H__
#ifdef _MSC_VER
#pragma warning(disable : 4661) // no suitable definition provided for explicit
// template instantiation request
#endif
namespace RDKit {
class QueryAtom;
//! A general random access iterator
template <class Atom_, class Mol_>
class RDKIT_GRAPHMOL_EXPORT AtomIterator_ {
public:
typedef AtomIterator_<Atom_, Mol_> ThisType;
AtomIterator_() : _pos(-1), _max(-1), _mol(nullptr){};
AtomIterator_(Mol_ *mol);
AtomIterator_(Mol_ *mol, int pos);
AtomIterator_(const ThisType &other);
AtomIterator_ &operator=(const ThisType &other);
AtomIterator_ &operator+=(int val);
AtomIterator_ &operator-=(int val);
AtomIterator_ operator+(int val) const;
AtomIterator_ operator-(int val) const;
// iterator subtraction
int operator-(ThisType &other) const;
// dereference
Atom_ *operator*() const;
// random access
Atom_ *operator[](const int which) const;
bool operator==(const ThisType &other) const;
bool operator!=(const ThisType &other) const;
bool operator<(const ThisType &other) const;
bool operator<=(const ThisType &other) const;
bool operator>(const ThisType &other) const;
bool operator>=(const ThisType &other) const;
// pre-increment
ThisType &operator++();
ThisType operator++(int);
// pre-decrement
ThisType &operator--();
ThisType operator--(int);
private:
int _pos, _max;
Mol_ *_mol;
};
//! Iterate over heteroatoms, this is bidirectional
template <class Atom_, class Mol_>
class RDKIT_GRAPHMOL_EXPORT HeteroatomIterator_ {
public:
typedef HeteroatomIterator_<Atom_, Mol_> ThisType;
HeteroatomIterator_() : _end(-1), _pos(-1), _mol(nullptr){};
HeteroatomIterator_(Mol_ *mol);
HeteroatomIterator_(Mol_ *mol, int pos);
~HeteroatomIterator_();
HeteroatomIterator_(const ThisType &other);
HeteroatomIterator_ &operator=(const ThisType &other);
bool operator==(const ThisType &other) const;
bool operator!=(const ThisType &other) const;
Atom_ *operator*() const;
// pre-increment
ThisType &operator++();
ThisType operator++(int);
// pre-decrement
ThisType &operator--();
ThisType operator--(int);
private:
int _end, _pos;
Mol_ *_mol;
// FIX: somehow changing the following to a pointer make the regression test
// pass
// QueryAtom _qA;
QueryAtom *_qA;
int _findNext(int from);
int _findPrev(int from);
};
//! Iterate over aromatic atoms, this is bidirectional
template <class Atom_, class Mol_>
class RDKIT_GRAPHMOL_EXPORT AromaticAtomIterator_ {
public:
typedef AromaticAtomIterator_<Atom_, Mol_> ThisType;
AromaticAtomIterator_() : _end(-1), _pos(-1), _mol(nullptr){};
AromaticAtomIterator_(Mol_ *mol);
AromaticAtomIterator_(Mol_ *mol, int pos);
~AromaticAtomIterator_();
AromaticAtomIterator_(const ThisType &other);
AromaticAtomIterator_ &operator=(const ThisType &other);
bool operator==(const ThisType &other) const;
bool operator!=(const ThisType &other) const;
Atom_ *operator*() const;
// pre-increment
ThisType &operator++();
ThisType operator++(int);
// pre-decrement
ThisType &operator--();
ThisType operator--(int);
private:
int _end, _pos;
Mol_ *_mol;
int _findNext(int from);
int _findPrev(int from);
};
//! Iterate over atoms matching a query. This is bidirectional.
template <class Atom_, class Mol_>
class RDKIT_GRAPHMOL_EXPORT QueryAtomIterator_ {
public:
typedef QueryAtomIterator_<Atom_, Mol_> ThisType;
QueryAtomIterator_() : _end(-1), _pos(-1), _mol(nullptr), _qA(nullptr){};
QueryAtomIterator_(Mol_ *mol, QueryAtom const *what);
QueryAtomIterator_(Mol_ *mol, int pos);
~QueryAtomIterator_();
QueryAtomIterator_(const ThisType &other);
QueryAtomIterator_ &operator=(const ThisType &other);
bool operator==(const ThisType &other) const;
bool operator!=(const ThisType &other) const;
Atom_ *operator*() const;
// pre-increment
ThisType &operator++();
ThisType operator++(int);
// pre-decrement
ThisType &operator--();
ThisType operator--(int);
private:
int _end, _pos;
Mol_ *_mol;
QueryAtom *_qA;
int _findNext(int from);
int _findPrev(int from);
};
//! Iterate over atoms matching a query function. This is bidirectional.
template <class Atom_, class Mol_>
class RDKIT_GRAPHMOL_EXPORT MatchingAtomIterator_ {
public:
typedef MatchingAtomIterator_<Atom_, Mol_> ThisType;
MatchingAtomIterator_() : _end(-1), _pos(-1), _mol(nullptr), _qF(nullptr){};
MatchingAtomIterator_(Mol_ *mol, bool (*fn)(Atom_ *));
MatchingAtomIterator_(Mol_ *mol, int pos);
~MatchingAtomIterator_();
MatchingAtomIterator_(const ThisType &other);
MatchingAtomIterator_ &operator=(const ThisType &other);
bool operator==(const ThisType &other) const;
bool operator!=(const ThisType &other) const;
Atom_ *operator*() const;
// pre-increment
ThisType &operator++();
ThisType operator++(int);
// pre-decrement
ThisType &operator--();
ThisType operator--(int);
private:
int _end, _pos;
Mol_ *_mol;
bool (*_qF)(Atom_ *);
int _findNext(int from);
int _findPrev(int from);
};
} // namespace RDKit
#endif
RDKit::AtomIterator_
A general random access iterator.
Definition: AtomIterators.h:31
RDKit::QueryAtomIterator_
Iterate over atoms matching a query. This is bidirectional.
Definition: AtomIterators.h:141
RDKit::operator+
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect operator+(const DiscreteValueVect &p1, const DiscreteValueVect &p2)
RDKit::MatchingAtomIterator_::MatchingAtomIterator_
MatchingAtomIterator_()
Definition: AtomIterators.h:177
RDKit::AtomIterator_::ThisType
AtomIterator_< Atom_, Mol_ > ThisType
Definition: AtomIterators.h:33
RDKit::HeteroatomIterator_::HeteroatomIterator_
HeteroatomIterator_()
Definition: AtomIterators.h:76
RDKit::AromaticAtomIterator_
Iterate over aromatic atoms, this is bidirectional.
Definition: AtomIterators.h:109
RDKit::AromaticAtomIterator_::ThisType
AromaticAtomIterator_< Atom_, Mol_ > ThisType
Definition: AtomIterators.h:111
RDKit::HeteroatomIterator_::ThisType
HeteroatomIterator_< Atom_, Mol_ > ThisType
Definition: AtomIterators.h:75
RDKit::HeteroatomIterator_
Iterate over heteroatoms, this is bidirectional.
Definition: AtomIterators.h:73
RDKIT_GRAPHMOL_EXPORT
#define RDKIT_GRAPHMOL_EXPORT
Definition: export.h:307
RDKit::QueryAtomIterator_::QueryAtomIterator_
QueryAtomIterator_()
Definition: AtomIterators.h:144
RDKit::MatchingAtomIterator_::ThisType
MatchingAtomIterator_< Atom_, Mol_ > ThisType
Definition: AtomIterators.h:176
RDKit::operator-
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect operator-(const DiscreteValueVect &p1, const DiscreteValueVect &p2)
RDKit::QueryAtomIterator_::ThisType
QueryAtomIterator_< Atom_, Mol_ > ThisType
Definition: AtomIterators.h:143
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::AromaticAtomIterator_::AromaticAtomIterator_
AromaticAtomIterator_()
Definition: AtomIterators.h:112
RDGeom::operator*
RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Point3D operator*(const RDGeom::Point3D &p1, double v)
RDKit::QueryAtom
Class for storing atomic queries.
Definition: QueryAtom.h:27
RDKit::MatchingAtomIterator_
Iterate over atoms matching a query function. This is bidirectional.
Definition: AtomIterators.h:174
RDKit::AtomIterator_::AtomIterator_
AtomIterator_()
Definition: AtomIterators.h:34
export.h