ROMol.h
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//
// Copyright (C) 2003-2018 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 ROMol.h
\brief Defines the primary molecule class \c ROMol as well as associated
typedefs
*/
#include <RDGeneral/export.h>
#ifndef __RD_ROMOL_H__
#define __RD_ROMOL_H__
/// Std stuff
#include <utility>
#include <map>
// boost stuff
#include <RDGeneral/BoostStartInclude.h>
#include <boost/graph/adjacency_list.hpp>
#include <boost/smart_ptr.hpp>
#include <RDGeneral/BoostEndInclude.h>
// our stuff
#include <RDGeneral/types.h>
#include <RDGeneral/RDProps.h>
#include "Atom.h"
#include "Bond.h"
#include "Conformer.h"
#include "SubstanceGroup.h"
#include "StereoGroup.h"
namespace RDKit {
class SubstanceGroup;
class Atom;
class Bond;
//! This is the BGL type used to store the topology:
typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
Atom *, Bond *>
MolGraph;
class MolPickler;
class RWMol;
class QueryAtom;
class QueryBond;
class RingInfo;
template <class T1, class T2>
class AtomIterator_;
class BondIterator_;
class ConstBondIterator_;
template <class T1, class T2>
class AromaticAtomIterator_;
template <class T1, class T2>
class HeteroatomIterator_;
template <class T1, class T2>
class QueryAtomIterator_;
template <class T1, class T2>
class MatchingAtomIterator_;
RDKIT_GRAPHMOL_EXPORT extern const int ci_RIGHTMOST_ATOM;
RDKIT_GRAPHMOL_EXPORT extern const int ci_LEADING_BOND;
RDKIT_GRAPHMOL_EXPORT extern const int ci_ATOM_HOLDER;
//! ROMol is a molecule class that is intended to have a fixed topology
/*!
This is the primary class for most molecule operations.
If you need to be manipulating the molecule (e.g. adding or deleting
atoms or bonds, use an RWMol instead.
<b>Notes:</b>
- each ROMol maintains a Dict of \c properties:
- Each \c property is keyed by name and can store an
arbitrary type.
- \c Properties can be marked as \c calculated, in which case
they will be cleared when the \c clearComputedProps() method
is called.
- Because they have no impact upon chemistry, all \c property
operations are \c const, this allows extra flexibility for
clients who need to store extra data on ROMol objects.
- each ROMol has collections of \c bookmarks for Atoms and Bonds:
- the Atom bookmarks and Bond bookmarks are stored separately
from each other
- each \c bookmark, an integer, can map to more than one
Atom or Bond
- these are currently used in molecule construction, but
could also be useful for reaction mapping and the like
- information about rings (SSSR and the like) is stored in the
molecule's RingInfo pointer.
*/
//! \name C++11 Iterators
template <class Graph, class Vertex>
struct CXXAtomIterator {
Graph *graph;
typename Graph::vertex_iterator vstart, vend;
struct CXXAtomIter {
Graph *graph;
typename Graph::vertex_iterator pos;
Atom *current;
CXXAtomIter(Graph *graph, typename Graph::vertex_iterator pos)
: graph(graph), pos(pos), current(nullptr) {}
Vertex &operator*() {
current = (*graph)[*pos];
return current;
}
CXXAtomIter &operator++() {
++pos;
return *this;
}
bool operator!=(const CXXAtomIter &it) const { return pos != it.pos; }
};
CXXAtomIterator(Graph *graph) : graph(graph) {
auto vs = boost::vertices(*graph);
vstart = vs.first;
vend = vs.second;
}
CXXAtomIter begin() { return {graph, vstart}; }
CXXAtomIter end() { return {graph, vend}; }
};
template <class Graph, class Edge>
struct CXXBondIterator {
Graph *graph;
typename Graph::edge_iterator vstart, vend;
struct CXXBondIter {
Graph *graph;
typename Graph::edge_iterator pos;
Bond *current;
CXXBondIter(Graph *graph, typename Graph::edge_iterator pos)
: graph(graph), pos(pos), current(nullptr) {}
Edge &operator*() {
current = (*graph)[*pos];
return current;
}
CXXBondIter &operator++() {
++pos;
return *this;
}
bool operator!=(const CXXBondIter &it) const { return pos != it.pos; }
};
CXXBondIterator(Graph *graph) : graph(graph) {
auto vs = boost::edges(*graph);
vstart = vs.first;
vend = vs.second;
}
CXXBondIter begin() { return {graph, vstart}; }
CXXBondIter end() { return {graph, vend}; }
};
class RDKIT_GRAPHMOL_EXPORT ROMol : public RDProps {
public:
friend class MolPickler;
friend class RWMol;
//! \cond TYPEDEFS
//! \name typedefs
//@{
typedef MolGraph::vertex_descriptor vertex_descriptor;
typedef MolGraph::edge_descriptor edge_descriptor;
typedef MolGraph::edge_iterator EDGE_ITER;
typedef MolGraph::out_edge_iterator OEDGE_ITER;
typedef MolGraph::vertex_iterator VERTEX_ITER;
typedef MolGraph::adjacency_iterator ADJ_ITER;
typedef std::pair<EDGE_ITER, EDGE_ITER> BOND_ITER_PAIR;
typedef std::pair<OEDGE_ITER, OEDGE_ITER> OBOND_ITER_PAIR;
typedef std::pair<VERTEX_ITER, VERTEX_ITER> ATOM_ITER_PAIR;
typedef std::pair<ADJ_ITER, ADJ_ITER> ADJ_ITER_PAIR;
typedef std::vector<Atom *> ATOM_PTR_VECT;
typedef ATOM_PTR_VECT::iterator ATOM_PTR_VECT_I;
typedef ATOM_PTR_VECT::const_iterator ATOM_PTR_VECT_CI;
typedef std::vector<Bond *> BOND_PTR_VECT;
typedef BOND_PTR_VECT::iterator BOND_PTR_VECT_I;
typedef BOND_PTR_VECT::const_iterator BOND_PTR_VECT_CI;
typedef std::list<Atom *> ATOM_PTR_LIST;
typedef ATOM_PTR_LIST::iterator ATOM_PTR_LIST_I;
typedef ATOM_PTR_LIST::const_iterator ATOM_PTR_LIST_CI;
typedef std::list<Bond *> BOND_PTR_LIST;
typedef BOND_PTR_LIST::iterator BOND_PTR_LIST_I;
typedef BOND_PTR_LIST::const_iterator BOND_PTR_LIST_CI;
// list of conformations
typedef std::list<CONFORMER_SPTR> CONF_SPTR_LIST;
typedef CONF_SPTR_LIST::iterator CONF_SPTR_LIST_I;
typedef CONF_SPTR_LIST::const_iterator CONF_SPTR_LIST_CI;
typedef std::pair<CONF_SPTR_LIST_I, CONF_SPTR_LIST_I> CONFS_I_PAIR;
// ROFIX: these will need to be readonly somehow?
typedef std::map<int, ATOM_PTR_LIST> ATOM_BOOKMARK_MAP;
typedef std::map<int, BOND_PTR_LIST> BOND_BOOKMARK_MAP;
typedef class AtomIterator_<Atom, ROMol> AtomIterator;
typedef class AtomIterator_<const Atom, const ROMol> ConstAtomIterator;
typedef class BondIterator_ BondIterator;
typedef class ConstBondIterator_ ConstBondIterator;
typedef class AromaticAtomIterator_<Atom, ROMol> AromaticAtomIterator;
typedef class AromaticAtomIterator_<const Atom, const ROMol>
ConstAromaticAtomIterator;
typedef class HeteroatomIterator_<Atom, ROMol> HeteroatomIterator;
typedef class HeteroatomIterator_<const Atom, const ROMol>
ConstHeteroatomIterator;
typedef class QueryAtomIterator_<Atom, ROMol> QueryAtomIterator;
typedef class QueryAtomIterator_<const Atom, const ROMol>
ConstQueryAtomIterator;
typedef class MatchingAtomIterator_<Atom, ROMol> MatchingAtomIterator;
typedef class MatchingAtomIterator_<const Atom, const ROMol>
ConstMatchingAtomIterator;
typedef CONF_SPTR_LIST_I ConformerIterator;
typedef CONF_SPTR_LIST_CI ConstConformerIterator;
//@}
//! \endcond
//! C++11 Range iterator
/*!
<b>Usage</b>
\code
for(auto atom : mol.atoms()) {
atom->getIdx();
};
\endcode
*/
CXXAtomIterator<MolGraph, Atom *> atoms() { return {&d_graph}; }
CXXAtomIterator<const MolGraph, Atom *const> atoms() const {
return {&d_graph};
}
/*!
<b>Usage</b>
\code
for(auto bond : mol.bonds()) {
bond->getIdx();
};
\endcode
*/
CXXBondIterator<MolGraph, Bond *> bonds() { return {&d_graph}; }
CXXBondIterator<const MolGraph, Bond *const> bonds() const {
return {&d_graph};
}
ROMol() : RDProps(), numBonds(0) { initMol(); }
//! copy constructor with a twist
/*!
\param other the molecule to be copied
\param quickCopy (optional) if this is true, the resulting ROMol will not
copy any of the properties or bookmarks and conformers from \c other.
This can
make the copy substantially faster (thus the name).
\param confId (optional) if this is >=0, the resulting ROMol will contain
only
the specified conformer from \c other.
*/
ROMol(const ROMol &other, bool quickCopy = false, int confId = -1)
: RDProps() {
dp_ringInfo = 0;
initFromOther(other, quickCopy, confId);
numBonds = rdcast<unsigned int>(boost::num_edges(d_graph));
};
//! construct a molecule from a pickle string
ROMol(const std::string &binStr);
virtual ~ROMol() { destroy(); };
//@}
//! \name Atoms
//@{
//! returns our number of atoms
unsigned int getNumAtoms(bool onlyExplicit = 1) const;
//! returns our number of heavy atoms (atomic number > 1)
unsigned int getNumHeavyAtoms() const;
//! returns a pointer to a particular Atom
Atom *getAtomWithIdx(unsigned int idx);
//! \overload
const Atom *getAtomWithIdx(unsigned int idx) const;
//! \overload
template <class U>
Atom *getAtomWithIdx(const U idx) {
return getAtomWithIdx(rdcast<unsigned int>(idx));
}
//! \overload
template <class U>
const Atom *getAtomWithIdx(const U idx) const {
return getAtomWithIdx(rdcast<unsigned int>(idx));
}
//! returns the degree (number of neighbors) of an Atom in the graph
unsigned int getAtomDegree(const Atom *at) const;
//@}
//! \name Bonds
//@{
//! returns our number of Bonds
unsigned int getNumBonds(bool onlyHeavy = 1) const;
//! returns a pointer to a particular Bond
Bond *getBondWithIdx(unsigned int idx);
//! \overload
const Bond *getBondWithIdx(unsigned int idx) const;
//! \overload
template <class U>
Bond *getBondWithIdx(const U idx) {
return getBondWithIdx(rdcast<unsigned int>(idx));
}
//! \overload
template <class U>
const Bond *getBondWithIdx(const U idx) const {
return getBondWithIdx(rdcast<unsigned int>(idx));
}
//! returns a pointer to the bond between two atoms, Null on failure
Bond *getBondBetweenAtoms(unsigned int idx1, unsigned int idx2);
//! \overload
const Bond *getBondBetweenAtoms(unsigned int idx1, unsigned int idx2) const;
//! \overload
template <class U, class V>
Bond *getBondBetweenAtoms(const U idx1, const V idx2) {
return getBondBetweenAtoms(rdcast<unsigned int>(idx1),
rdcast<unsigned int>(idx2));
}
//! \overload
template <class U, class V>
const Bond *getBondBetweenAtoms(const U idx1, const V idx2) const {
return getBondBetweenAtoms(rdcast<unsigned int>(idx1),
rdcast<unsigned int>(idx2));
}
//@}
//! \name Bookmarks
//@{
//! associates an Atom pointer with a bookmark
void setAtomBookmark(Atom *at, int mark) {
d_atomBookmarks[mark].push_back(at);
};
//! associates an Atom pointer with a bookmark
void replaceAtomBookmark(Atom *at, int mark) {
d_atomBookmarks[mark].clear();
d_atomBookmarks[mark].push_back(at);
};
//! returns the first Atom associated with the \c bookmark provided
Atom *getAtomWithBookmark(int mark);
//! returns the Atom associated with the \c bookmark provided
//! a check is made to ensure it is the only atom with that bookmark
Atom *getUniqueAtomWithBookmark(int mark);
//! returns all Atoms associated with the \c bookmark provided
ATOM_PTR_LIST &getAllAtomsWithBookmark(int mark);
//! removes a \c bookmark from our collection
void clearAtomBookmark(int mark);
//! removes a particular Atom from the list associated with the \c bookmark
void clearAtomBookmark(int mark, const Atom *atom);
//! blows out all atomic \c bookmarks
void clearAllAtomBookmarks() { d_atomBookmarks.clear(); };
//! queries whether or not any atoms are associated with a \c bookmark
bool hasAtomBookmark(int mark) const { return d_atomBookmarks.count(mark); };
//! returns a pointer to all of our atom \c bookmarks
ATOM_BOOKMARK_MAP *getAtomBookmarks() { return &d_atomBookmarks; };
//! associates a Bond pointer with a bookmark
void setBondBookmark(Bond *bond, int mark) {
d_bondBookmarks[mark].push_back(bond);
};
//! returns the first Bond associated with the \c bookmark provided
Bond *getBondWithBookmark(int mark);
//! returns the Bond associated with the \c bookmark provided
//! a check is made to ensure it is the only bond with that bookmark
Bond *getUniqueBondWithBookmark(int mark);
//! returns all bonds associated with the \c bookmark provided
BOND_PTR_LIST &getAllBondsWithBookmark(int mark);
//! removes a \c bookmark from our collection
void clearBondBookmark(int mark);
//! removes a particular Bond from the list associated with the \c bookmark
void clearBondBookmark(int mark, const Bond *bond);
//! blows out all bond \c bookmarks
void clearAllBondBookmarks() { d_bondBookmarks.clear(); };
//! queries whether or not any bonds are associated with a \c bookmark
bool hasBondBookmark(int mark) const { return d_bondBookmarks.count(mark); };
//! returns a pointer to all of our bond \c bookmarks
BOND_BOOKMARK_MAP *getBondBookmarks() { return &d_bondBookmarks; };
//@}
//! \name Conformers
//@{
//! return the conformer with a specified ID
//! if the ID is negative the first conformation will be returned
const Conformer &getConformer(int id = -1) const;
//! return the conformer with a specified ID
//! if the ID is negative the first conformation will be returned
Conformer &getConformer(int id = -1);
//! Delete the conformation with the specified ID
void removeConformer(unsigned int id);
//! Clear all the conformations on the molecule
void clearConformers() { d_confs.clear(); }
//! Add a new conformation to the molecule
/*!
\param conf - conformation to be added to the molecule, this molecule takes
ownership
of the conformer
\param assignId - a unique ID will be assigned to the conformation if
true
otherwise it is assumed that the conformation already has
an (unique) ID set
*/
unsigned int addConformer(Conformer *conf, bool assignId = false);
inline unsigned int getNumConformers() const {
return rdcast<unsigned int>(d_confs.size());
}
//! \name Topology
//@{
//! returns a pointer to our RingInfo structure
//! <b>Note:</b> the client should not delete this.
RingInfo *getRingInfo() const { return dp_ringInfo; };
//! provides access to all neighbors around an Atom
/*!
\param at the atom whose neighbors we are looking for
<b>Usage</b>
\code
... mol is a const ROMol & ...
... atomPtr is a const Atom * ...
... requires #include <boost/range/iterator_range.hpp>
for (const auto &nbri :
boost::make_iterator_range(m.getAtomNeighbors(atomPtr))) {
const auto &nbr = (*m)[nbri];
// nbr is an atom pointer
}
\endcode
*/
ADJ_ITER_PAIR getAtomNeighbors(Atom const *at) const;
//! provides access to all Bond objects connected to an Atom
/*!
\param at the atom whose neighbors we are looking for
<b>Usage</b>
\code
... mol is a const ROMol & ...
... atomPtr is a const Atom * ...
... requires #include <boost/range/iterator_range.hpp>
for (const auto &nbri :
boost::make_iterator_range(m.getAtomBonds(atomPtr))) {
const auto &nbr = (*m)[nbri];
// nbr is a bond pointer
}
\endcode
or, if you need a non-const Bond *:
\code
... mol is a const ROMol & ...
... atomPtr is a const Atom * ...
... requires #include <boost/range/iterator_range.hpp>
for (const auto &nbri :
boost::make_iterator_range(m.getAtomBonds(atomPtr))) {
auto nbr = (*m)[nbri];
// nbr is a bond pointer
}
\endcode
*/
OBOND_ITER_PAIR getAtomBonds(Atom const *at) const;
//! returns an iterator pair for looping over all Atoms
/*!
<b>Usage</b>
\code
ROMol::VERTEX_ITER atBegin,atEnd;
boost::tie(atBegin,atEnd) = mol.getVertices();
while(atBegin!=atEnd){
ATOM_SPTR at2=mol[*atBegin];
... do something with the Atom ...
++atBegin;
}
\endcode
*/
ATOM_ITER_PAIR getVertices();
//! returns an iterator pair for looping over all Bonds
/*!
<b>Usage</b>
\code
ROMol::EDGE_ITER firstB,lastB;
boost::tie(firstB,lastB) = mol.getEdges();
while(firstB!=lastB){
BOND_SPTR bond = mol[*firstB];
... do something with the Bond ...
++firstB;
}
\endcode
*/
BOND_ITER_PAIR getEdges();
//! \overload
ATOM_ITER_PAIR getVertices() const;
//! \overload
BOND_ITER_PAIR getEdges() const;
//! brief returns a pointer to our underlying BGL object
/*!
This can be useful if you need to call other BGL algorithms:
Here's an example:
\code
... mol is a const ROMol ...
... mapping is an INT_VECT ...
mapping.resize(mol.getNumAtoms());
const MolGraph &G_p = mol.getTopology();
int res = boost::connected_components(G_p,&mapping[0]);
\endcode
*/
MolGraph const &getTopology() const { return d_graph; };
//@}
//! \name Iterators
//@{
//! get an AtomIterator pointing at our first Atom
AtomIterator beginAtoms();
//! \overload
ConstAtomIterator beginAtoms() const;
//! get an AtomIterator pointing at the end of our Atoms
AtomIterator endAtoms();
//! \overload
ConstAtomIterator endAtoms() const;
//! get a BondIterator pointing at our first Bond
BondIterator beginBonds();
//! \overload
ConstBondIterator beginBonds() const;
//! get a BondIterator pointing at the end of our Bonds
BondIterator endBonds();
//! \overload
ConstBondIterator endBonds() const;
//! get an AtomIterator pointing at our first aromatic Atom
AromaticAtomIterator beginAromaticAtoms();
//! \overload
ConstAromaticAtomIterator beginAromaticAtoms() const;
//! get an AtomIterator pointing at the end of our Atoms
AromaticAtomIterator endAromaticAtoms();
//! \overload
ConstAromaticAtomIterator endAromaticAtoms() const;
//! get an AtomIterator pointing at our first hetero Atom
HeteroatomIterator beginHeteros();
//! \overload
ConstHeteroatomIterator beginHeteros() const;
//! get an AtomIterator pointing at the end of our Atoms
HeteroatomIterator endHeteros();
//! \overload
ConstHeteroatomIterator endHeteros() const;
//! get an AtomIterator pointing at our first Atom that matches \c query
QueryAtomIterator beginQueryAtoms(QueryAtom const *query);
//! \overload
ConstQueryAtomIterator beginQueryAtoms(QueryAtom const *) const;
//! get an AtomIterator pointing at the end of our Atoms
QueryAtomIterator endQueryAtoms();
//! \overload
ConstQueryAtomIterator endQueryAtoms() const;
//! get an AtomIterator pointing at our first Atom that matches \c query
MatchingAtomIterator beginMatchingAtoms(bool (*query)(Atom *));
//! \overload
ConstMatchingAtomIterator beginMatchingAtoms(
bool (*query)(const Atom *)) const;
//! get an AtomIterator pointing at the end of our Atoms
MatchingAtomIterator endMatchingAtoms();
//! \overload
ConstMatchingAtomIterator endMatchingAtoms() const;
inline ConformerIterator beginConformers() { return d_confs.begin(); }
inline ConformerIterator endConformers() { return d_confs.end(); }
inline ConstConformerIterator beginConformers() const {
return d_confs.begin();
}
inline ConstConformerIterator endConformers() const { return d_confs.end(); }
//@}
//! \name Properties
//@{
//! clears all of our \c computed \c properties
void clearComputedProps(bool includeRings = true) const;
//! calculates any of our lazy \c properties
/*!
<b>Notes:</b>
- this calls \c updatePropertyCache() on each of our Atoms and Bonds
*/
void updatePropertyCache(bool strict = true);
bool needsUpdatePropertyCache() const;
//@}
//! \name Misc
//@{
//! sends some debugging info to a stream
void debugMol(std::ostream &str) const;
//@}
Atom *operator[](const vertex_descriptor &v) { return d_graph[v]; };
const Atom *operator[](const vertex_descriptor &v) const {
return d_graph[v];
};
Bond *operator[](const edge_descriptor &e) { return d_graph[e]; };
const Bond *operator[](const edge_descriptor &e) const { return d_graph[e]; };
//! Gets a reference to the groups of atoms with relative stereochemistry
/*!
Stereo groups are also called enhanced stereochemistry in the SDF/Mol3000
file format.
*/
const std::vector<StereoGroup> &getStereoGroups() const {
return d_stereo_groups;
}
private:
MolGraph d_graph;
ATOM_BOOKMARK_MAP d_atomBookmarks;
BOND_BOOKMARK_MAP d_bondBookmarks;
RingInfo *dp_ringInfo;
CONF_SPTR_LIST d_confs;
std::vector<SubstanceGroup> d_sgroups;
friend RDKIT_GRAPHMOL_EXPORT std::vector<SubstanceGroup> &getSubstanceGroups(
ROMol &);
friend RDKIT_GRAPHMOL_EXPORT const std::vector<SubstanceGroup>
&getSubstanceGroups(const ROMol &);
void clearSubstanceGroups() { d_sgroups.clear(); }
std::vector<StereoGroup> d_stereo_groups;
ROMol &operator=(
const ROMol &); // disable assignment, RWMol's support assignment
protected:
unsigned int numBonds;
#ifndef WIN32
private:
#endif
void initMol();
virtual void destroy();
//! adds an Atom to our collection
/*!
\param atom pointer to the Atom to add
\param updateLabel (optional) if this is true, the new Atom will be
our \c activeAtom
\param takeOwnership (optional) if this is true, we take ownership of \c
atom
instead of copying it.
\return the new number of atoms
*/
unsigned int addAtom(Atom *atom, bool updateLabel = true,
bool takeOwnership = false);
//! adds a Bond to our collection
/*!
\param bond pointer to the Bond to add
\param takeOwnership (optional) if this is true, we take ownership of \c
bond
instead of copying it.
\return the new number of bonds
*/
unsigned int addBond(Bond *bond, bool takeOwnership = false);
//! Sets groups of atoms with relative stereochemistry
/*!
\param stereo_groups the new set of stereo groups. All will be replaced.
Stereo groups are also called enhanced stereochemistry in the SDF/Mol3000
file format. stereo_groups should be std::move()ed into this function.
*/
void setStereoGroups(std::vector<StereoGroup> stereo_groups);
//! adds a Bond to our collection
/*!
\param bond pointer to the Bond to add
\return the new number of bonds
<b>Note:</b> since this is using a smart pointer, we don't need to worry
about
issues of ownership.
*/
void initFromOther(const ROMol &other, bool quickCopy, int confId);
};
typedef std::vector<ROMol> MOL_VECT;
typedef boost::shared_ptr<ROMol> ROMOL_SPTR;
typedef std::vector<ROMol *> MOL_PTR_VECT;
typedef std::vector<ROMOL_SPTR> MOL_SPTR_VECT;
typedef MOL_PTR_VECT::const_iterator MOL_PTR_VECT_CI;
typedef MOL_PTR_VECT::iterator MOL_PTR_VECT_I;
}; // namespace RDKit
#endif
RDKit::ROMol::getRingInfo
RingInfo * getRingInfo() const
Definition: ROMol.h:452
RDKit::ROMol::bonds
CXXBondIterator< MolGraph, Bond * > bonds()
Definition: ROMol.h:264
RDKit::ci_LEADING_BOND
const RDKIT_GRAPHMOL_EXPORT int ci_LEADING_BOND
RDKit::AtomIterator_
A general random access iterator.
Definition: AtomIterators.h:31
RDKit::CXXBondIterator::CXXBondIter::graph
Graph * graph
Definition: ROMol.h:144
RDKit::QueryAtomIterator_
Iterate over atoms matching a query. This is bidirectional.
Definition: AtomIterators.h:141
RDKit::ROMol::ROMol
ROMol()
Definition: ROMol.h:270
RDKit::ROMol::getAtomBookmarks
ATOM_BOOKMARK_MAP * getAtomBookmarks()
returns a pointer to all of our atom bookmarks
Definition: ROMol.h:387
RDKit::ROMol::setBondBookmark
void setBondBookmark(Bond *bond, int mark)
associates a Bond pointer with a bookmark
Definition: ROMol.h:390
RDKit::ROMol::clearAllAtomBookmarks
void clearAllAtomBookmarks()
blows out all atomic bookmarks
Definition: ROMol.h:383
RDKit::ROMol::operator[]
const Bond * operator[](const edge_descriptor &e) const
Definition: ROMol.h:655
RDKit::ROMol::endConformers
ConstConformerIterator endConformers() const
Definition: ROMol.h:623
RDKit::CXXBondIterator::CXXBondIterator
CXXBondIterator(Graph *graph)
Definition: ROMol.h:162
RDKit::CXXAtomIterator::CXXAtomIter
Definition: ROMol.h:110
RDKit::CXXBondIterator::vend
Graph::edge_iterator vend
Definition: ROMol.h:141
types.h
RDKit::CXXBondIterator
Definition: ROMol.h:139
BoostStartInclude.h
Bond.h
RDKit::CXXBondIterator::CXXBondIter
Definition: ROMol.h:143
RDKit::ROMol::getBondWithIdx
const Bond * getBondWithIdx(const U idx) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: ROMol.h:336
RDKit::ROMol::hasBondBookmark
bool hasBondBookmark(int mark) const
queries whether or not any bonds are associated with a bookmark
Definition: ROMol.h:408
RDKit::CXXBondIterator::vstart
Graph::edge_iterator vstart
Definition: ROMol.h:141
StereoGroup.h
Defines the class StereoGroup which stores relationships between the absolute configurations of atoms...
RDKit::ROMol::bonds
CXXBondIterator< const MolGraph, Bond *const > bonds() const
Definition: ROMol.h:266
RDKit::MOL_PTR_VECT_I
MOL_PTR_VECT::iterator MOL_PTR_VECT_I
Definition: ROMol.h:741
RDKit::ROMol::operator[]
Bond * operator[](const edge_descriptor &e)
Definition: ROMol.h:654
RDKit::Bond
class for representing a bond
Definition: Bond.h:47
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:31
RDKit::CXXAtomIterator::CXXAtomIter::current
Atom * current
Definition: ROMol.h:113
RDKit::AromaticAtomIterator_
Iterate over aromatic atoms, this is bidirectional.
Definition: AtomIterators.h:109
RDKit::ROMol::clearConformers
void clearConformers()
Clear all the conformations on the molecule.
Definition: ROMol.h:429
RDKit::CXXBondIterator::begin
CXXBondIter begin()
Definition: ROMol.h:167
RDKit::CXXBondIterator::CXXBondIter::operator!=
bool operator!=(const CXXBondIter &it) const
Definition: ROMol.h:159
RDKit::CXXAtomIterator::CXXAtomIter::pos
Graph::vertex_iterator pos
Definition: ROMol.h:112
RDKit::CXXAtomIterator::vstart
Graph::vertex_iterator vstart
Definition: ROMol.h:108
RDKit::ROMol::getAtomWithIdx
Atom * getAtomWithIdx(const U idx)
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: ROMol.h:308
RDKit::CXXAtomIterator
Definition: ROMol.h:106
RDKit::ROMol::getNumConformers
unsigned int getNumConformers() const
Definition: ROMol.h:443
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:69
BoostEndInclude.h
RDKit::HeteroatomIterator_
Iterate over heteroatoms, this is bidirectional.
Definition: AtomIterators.h:73
RDKit::QueryBond
Class for storing Bond queries.
Definition: QueryBond.h:28
RDKit::ROMol::getBondBetweenAtoms
Bond * getBondBetweenAtoms(const U idx1, const V idx2)
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: ROMol.h:345
Atom.h
Defines the Atom class and associated typedefs.
RDKit::CXXBondIterator::CXXBondIter::CXXBondIter
CXXBondIter(Graph *graph, typename Graph::edge_iterator pos)
Definition: ROMol.h:148
RDKit::RingInfo
A class to store information about a molecule's rings.
Definition: RingInfo.h:28
RDKit::ROMol::beginConformers
ConstConformerIterator beginConformers() const
Definition: ROMol.h:619
RDKit::ROMol
Definition: ROMol.h:171
RDKit::MOL_SPTR_VECT
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
Definition: FragCatParams.h:20
RDKit::ci_RIGHTMOST_ATOM
const RDKIT_GRAPHMOL_EXPORT int ci_RIGHTMOST_ATOM
RDKit::ConstBondIterator_
const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be Rand...
Definition: BondIterators.h:52
RDKIT_GRAPHMOL_EXPORT
#define RDKIT_GRAPHMOL_EXPORT
Definition: export.h:307
RDKit::CXXAtomIterator::end
CXXAtomIter end()
Definition: ROMol.h:135
RDKit::CXXAtomIterator::CXXAtomIter::CXXAtomIter
CXXAtomIter(Graph *graph, typename Graph::vertex_iterator pos)
Definition: ROMol.h:115
RDKit::MOL_VECT
std::vector< ROMol > MOL_VECT
Definition: ROMol.h:735
RDKit::ROMol::numBonds
unsigned int numBonds
Definition: ROMol.h:684
SubstanceGroup.h
Defines the SubstanceGroup class.
RDKit::ROMol::ROMol
ROMol(const ROMol &other, bool quickCopy=false, int confId=-1)
copy constructor with a twist
Definition: ROMol.h:283
RDProps.h
RDKit::CXXBondIterator::graph
Graph * graph
Definition: ROMol.h:140
RDKit::ROMol::replaceAtomBookmark
void replaceAtomBookmark(Atom *at, int mark)
associates an Atom pointer with a bookmark
Definition: ROMol.h:366
RDKit::Conformer
The class for representing 2D or 3D conformation of a molecule.
Definition: Conformer.h:43
RDKit::ROMol::getBondBetweenAtoms
const Bond * getBondBetweenAtoms(const U idx1, const V idx2) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: ROMol.h:351
RDKit::CXXAtomIterator::CXXAtomIter::operator++
CXXAtomIter & operator++()
Definition: ROMol.h:122
RDKit::ci_ATOM_HOLDER
const RDKIT_GRAPHMOL_EXPORT int ci_ATOM_HOLDER
RDKit::ROMol::clearAllBondBookmarks
void clearAllBondBookmarks()
blows out all bond bookmarks
Definition: ROMol.h:406
RDKit::RDProps
Definition: RDProps.h:10
RDKit::MolGraph
boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, Atom *, Bond * > MolGraph
This is the BGL type used to store the topology:
Definition: ROMol.h:43
RDKit::ROMol::beginConformers
ConformerIterator beginConformers()
Definition: ROMol.h:615
RDKit::BondIterator_
iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAcce...
Definition: BondIterators.h:27
RDKit::ROMol::operator[]
Atom * operator[](const vertex_descriptor &v)
Definition: ROMol.h:649
RDKit::ROMol::getBondWithIdx
Bond * getBondWithIdx(const U idx)
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: ROMol.h:331
RDKit::CXXBondIterator::end
CXXBondIter end()
Definition: ROMol.h:168
RDKit::MOL_PTR_VECT_CI
MOL_PTR_VECT::const_iterator MOL_PTR_VECT_CI
Definition: ROMol.h:740
RDKit::CXXBondIterator::CXXBondIter::current
Bond * current
Definition: ROMol.h:146
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::CXXBondIterator::CXXBondIter::operator++
CXXBondIter & operator++()
Definition: ROMol.h:155
RDKit::CXXAtomIterator::vend
Graph::vertex_iterator vend
Definition: ROMol.h:108
RDKit::CXXAtomIterator::CXXAtomIter::graph
Graph * graph
Definition: ROMol.h:111
RDKit::ROMol::operator[]
const Atom * operator[](const vertex_descriptor &v) const
Definition: ROMol.h:650
RDKit::CXXAtomIterator::CXXAtomIter::operator!=
bool operator!=(const CXXAtomIter &it) const
Definition: ROMol.h:126
RDKit::CXXBondIterator::CXXBondIter::operator*
Edge & operator*()
Definition: ROMol.h:151
RDKit::CXXAtomIterator::graph
Graph * graph
Definition: ROMol.h:107
RDKit::MolPickler
handles pickling (serializing) molecules
Definition: MolPickler.h:63
RDKit::MOL_PTR_VECT
std::vector< ROMol * > MOL_PTR_VECT
Definition: ROMol.h:737
RDKit::ROMol::atoms
CXXAtomIterator< MolGraph, Atom * > atoms()
C++11 Range iterator.
Definition: ROMol.h:249
RDKit::ROMol::endConformers
ConformerIterator endConformers()
Definition: ROMol.h:617
RDKit::CXXAtomIterator::begin
CXXAtomIter begin()
Definition: ROMol.h:134
RDKit::ROMol::setAtomBookmark
void setAtomBookmark(Atom *at, int mark)
associates an Atom pointer with a bookmark
Definition: ROMol.h:362
RDKit::ROMol::getStereoGroups
const std::vector< StereoGroup > & getStereoGroups() const
Gets a reference to the groups of atoms with relative stereochemistry.
Definition: ROMol.h:662
RDKit::QueryAtom
Class for storing atomic queries.
Definition: QueryAtom.h:27
RDKit::CXXAtomIterator::CXXAtomIterator
CXXAtomIterator(Graph *graph)
Definition: ROMol.h:129
Conformer.h
RDKit::ROMol::~ROMol
virtual ~ROMol()
Definition: ROMol.h:292
RDKit::ROMol::getBondBookmarks
BOND_BOOKMARK_MAP * getBondBookmarks()
returns a pointer to all of our bond bookmarks
Definition: ROMol.h:410
RDKit::CXXBondIterator::CXXBondIter::pos
Graph::edge_iterator pos
Definition: ROMol.h:145
RDKit::ROMol::getTopology
const MolGraph & getTopology() const
brief returns a pointer to our underlying BGL object
Definition: ROMol.h:555
RDKit::MatchingAtomIterator_
Iterate over atoms matching a query function. This is bidirectional.
Definition: AtomIterators.h:174
RDKit::getSubstanceGroups
RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & getSubstanceGroups(ROMol &mol)
RDKit::ROMol::hasAtomBookmark
bool hasAtomBookmark(int mark) const
queries whether or not any atoms are associated with a bookmark
Definition: ROMol.h:385
RDKit::ROMol::getAtomWithIdx
const Atom * getAtomWithIdx(const U idx) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: ROMol.h:313
RDKit::ROMol::atoms
CXXAtomIterator< const MolGraph, Atom *const > atoms() const
Definition: ROMol.h:251
RDKit::ROMOL_SPTR
boost::shared_ptr< ROMol > ROMOL_SPTR
Definition: ChemTransforms.h:22
RDKit::CXXAtomIterator::CXXAtomIter::operator*
Vertex & operator*()
Definition: ROMol.h:118
export.h