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 <boost/dynamic_bitset.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,
class Iterator = typename Graph::vertex_iterator>
struct CXXAtomIterator {
Graph *graph;
Iterator vstart, vend;
struct CXXAtomIter {
Graph *graph;
Iterator pos;
Atom *current;
CXXAtomIter(Graph *graph, 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;
}
CXXAtomIterator(Graph *graph, Iterator start, Iterator end)
: graph(graph), vstart(start), vend(end){};
CXXAtomIter begin() { return {graph, vstart}; }
CXXAtomIter end() { return {graph, vend}; }
};
template <class Graph, class Edge,
class Iterator = typename Graph::edge_iterator>
struct CXXBondIterator {
Graph *graph;
Iterator vstart, vend;
struct CXXBondIter {
Graph *graph;
Iterator pos;
Bond *current;
CXXBondIter(Graph *graph, 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;
}
CXXBondIterator(Graph *graph, Iterator start, Iterator end)
: graph(graph), vstart(start), vend(end){};
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};
}
CXXAtomIterator<const MolGraph, Atom *const, MolGraph::adjacency_iterator>
atomNeighbors(Atom const *at) const {
auto pr = getAtomNeighbors(at);
return {&d_graph, pr.first, pr.second};
}
CXXAtomIterator<MolGraph, Atom *, MolGraph::adjacency_iterator> atomNeighbors(
Atom const *at) {
auto pr = getAtomNeighbors(at);
return {&d_graph, pr.first, pr.second};
}
CXXBondIterator<const MolGraph, Bond *const, MolGraph::out_edge_iterator>
atomBonds(Atom const *at) const {
auto pr = getAtomBonds(at);
return {&d_graph, pr.first, pr.second};
}
CXXBondIterator<MolGraph, Bond *, MolGraph::out_edge_iterator> atomBonds(
Atom const *at) {
auto pr = getAtomBonds(at);
return {&d_graph, pr.first, pr.second};
}
/*!
<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() { 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 = nullptr;
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);
//! construct a molecule from a pickle string
ROMol(const std::string &binStr, unsigned int propertyFlags);
virtual ~ROMol() { destroy(); }
//@}
//! \name Atoms
//@{
//! returns our number of atoms
inline unsigned int getNumAtoms() const {
return rdcast<unsigned int>(boost::num_vertices(d_graph));
}
unsigned int getNumAtoms(bool onlyExplicit) 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 = nullptr;
CONF_SPTR_LIST d_confs;
std::vector<SubstanceGroup> d_sgroups;
std::vector<StereoGroup> d_stereo_groups;
std::unique_ptr<boost::dynamic_bitset<>> dp_delAtoms = nullptr;
std::unique_ptr<boost::dynamic_bitset<>> dp_delBonds = nullptr;
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(); }
ROMol &operator=(
const ROMol &); // disable assignment, RWMol's support assignment
protected:
unsigned int numBonds{0};
#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
Atom.h
Defines the Atom class and associated typedefs.
Bond.h
BoostEndInclude.h
BoostStartInclude.h
Conformer.h
RDProps.h
StereoGroup.h
Defines the class StereoGroup which stores relationships between the absolute configurations of atoms...
SubstanceGroup.h
Defines the SubstanceGroup class.
RDKit::AromaticAtomIterator_
Iterate over aromatic atoms, this is bidirectional.
Definition: AtomIterators.h:111
RDKit::AtomIterator_
A general random access iterator.
Definition: AtomIterators.h:31
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:68
RDKit::BondIterator_
iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAcce...
Definition: BondIterators.h:27
RDKit::Bond
class for representing a bond
Definition: Bond.h:46
RDKit::Conformer
The class for representing 2D or 3D conformation of a molecule.
Definition: Conformer.h:45
RDKit::ConstBondIterator_
const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be Rand...
Definition: BondIterators.h:52
RDKit::HeteroatomIterator_
Iterate over heteroatoms, this is bidirectional.
Definition: AtomIterators.h:74
RDKit::MatchingAtomIterator_
Iterate over atoms matching a query function. This is bidirectional.
Definition: AtomIterators.h:178
RDKit::MolPickler
handles pickling (serializing) molecules
Definition: MolPickler.h:68
RDKit::QueryAtomIterator_
Iterate over atoms matching a query. This is bidirectional.
Definition: AtomIterators.h:144
RDKit::QueryAtom
Class for storing atomic queries.
Definition: QueryAtom.h:27
RDKit::QueryBond
Class for storing Bond queries.
Definition: QueryBond.h:28
RDKit::RDProps
Definition: RDProps.h:14
RDKit::ROMol
Definition: ROMol.h:178
RDKit::ROMol::endAromaticAtoms
ConstAromaticAtomIterator endAromaticAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::bonds
CXXBondIterator< MolGraph, Bond * > bonds()
Definition: ROMol.h:295
RDKit::ROMol::getAtomNeighbors
ADJ_ITER_PAIR getAtomNeighbors(Atom const *at) const
provides access to all neighbors around an Atom
RDKit::ROMol::endQueryAtoms
ConstQueryAtomIterator endQueryAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::operator[]
const Bond * operator[](const edge_descriptor &e) const
Definition: ROMol.h:691
RDKit::ROMol::needsUpdatePropertyCache
bool needsUpdatePropertyCache() const
RDKit::ROMol::getAtomBonds
OBOND_ITER_PAIR getAtomBonds(Atom const *at) const
provides access to all Bond objects connected to an Atom
RDKit::ROMol::getNumBonds
unsigned int getNumBonds(bool onlyHeavy=1) const
returns our number of Bonds
RDKit::ROMol::bonds
CXXBondIterator< const MolGraph, Bond *const > bonds() const
Definition: ROMol.h:297
RDKit::ROMol::clearAtomBookmark
void clearAtomBookmark(int mark)
removes a bookmark from our collection
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:381
RDKit::ROMol::getNumHeavyAtoms
unsigned int getNumHeavyAtoms() const
returns our number of heavy atoms (atomic number > 1)
RDKit::ROMol::clearAtomBookmark
void clearAtomBookmark(int mark, const Atom *atom)
removes a particular Atom from the list associated with the bookmark
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:349
RDKit::ROMol::getNumConformers
unsigned int getNumConformers() const
Definition: ROMol.h:479
RDKit::ROMol::endAtoms
AtomIterator endAtoms()
get an AtomIterator pointing at the end of our Atoms
RDKit::ROMol::getBondWithIdx
Bond * getBondWithIdx(unsigned int idx)
returns a pointer to a particular Bond
RDKit::ROMol::getRingInfo
RingInfo * getRingInfo() const
Definition: ROMol.h:488
RDKit::ROMol::endAtoms
ConstAtomIterator endAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::beginBonds
BondIterator beginBonds()
get a BondIterator pointing at our first Bond
RDKit::ROMol::hasAtomBookmark
bool hasAtomBookmark(int mark) const
queries whether or not any atoms are associated with a bookmark
Definition: ROMol.h:421
RDKit::ROMol::getTopology
MolGraph const & getTopology() const
brief returns a pointer to our underlying BGL object
Definition: ROMol.h:591
RDKit::ROMol::beginQueryAtoms
ConstQueryAtomIterator beginQueryAtoms(QueryAtom const *) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::getNumAtoms
unsigned int getNumAtoms() const
returns our number of atoms
Definition: ROMol.h:332
RDKit::ROMol::endConformers
ConstConformerIterator endConformers() const
Definition: ROMol.h:659
RDKit::ROMol::beginMatchingAtoms
ConstMatchingAtomIterator beginMatchingAtoms(bool(*query)(const Atom *)) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::ROMol
ROMol(const ROMol &other, bool quickCopy=false, int confId=-1)
copy constructor with a twist
Definition: ROMol.h:314
RDKit::ROMol::endMatchingAtoms
ConstMatchingAtomIterator endMatchingAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::getEdges
BOND_ITER_PAIR getEdges()
returns an iterator pair for looping over all Bonds
RDKit::ROMol::clearConformers
void clearConformers()
Clear all the conformations on the molecule.
Definition: ROMol.h:465
RDKit::ROMol::setBondBookmark
void setBondBookmark(Bond *bond, int mark)
associates a Bond pointer with a bookmark
Definition: ROMol.h:426
RDKit::ROMol::updatePropertyCache
void updatePropertyCache(bool strict=true)
calculates any of our lazy properties
RDKit::ROMol::getAllAtomsWithBookmark
ATOM_PTR_LIST & getAllAtomsWithBookmark(int mark)
returns all Atoms associated with the bookmark provided
RDKit::ROMol::getBondWithBookmark
Bond * getBondWithBookmark(int mark)
returns the first Bond associated with the bookmark provided
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:387
RDKit::ROMol::getBondBookmarks
BOND_BOOKMARK_MAP * getBondBookmarks()
returns a pointer to all of our bond bookmarks
Definition: ROMol.h:446
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:344
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:372
RDKit::ROMol::endQueryAtoms
QueryAtomIterator endQueryAtoms()
get an AtomIterator pointing at the end of our Atoms
RDKit::ROMol::getAllBondsWithBookmark
BOND_PTR_LIST & getAllBondsWithBookmark(int mark)
returns all bonds associated with the bookmark provided
RDKit::ROMol::addConformer
unsigned int addConformer(Conformer *conf, bool assignId=false)
Add a new conformation to the molecule.
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:367
RDKit::ROMol::clearAllBondBookmarks
void clearAllBondBookmarks()
blows out all bond bookmarks
Definition: ROMol.h:442
RDKit::ROMol::getVertices
ATOM_ITER_PAIR getVertices()
returns an iterator pair for looping over all Atoms
RDKit::ROMol::getEdges
BOND_ITER_PAIR getEdges() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::getSubstanceGroups
friend RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & getSubstanceGroups(ROMol &)
RDKit::ROMol::clearComputedProps
void clearComputedProps(bool includeRings=true) const
clears all of our computed properties
RDKit::ROMol::operator[]
Atom * operator[](const vertex_descriptor &v)
Definition: ROMol.h:685
RDKit::ROMol::ROMol
ROMol(const std::string &binStr, unsigned int propertyFlags)
construct a molecule from a pickle string
RDKit::ROMol::beginAtoms
ConstAtomIterator beginAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::getBondWithIdx
const Bond * getBondWithIdx(unsigned int idx) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::beginAromaticAtoms
ConstAromaticAtomIterator beginAromaticAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::debugMol
void debugMol(std::ostream &str) const
sends some debugging info to a stream
RDKit::ROMol::getBondBetweenAtoms
const Bond * getBondBetweenAtoms(unsigned int idx1, unsigned int idx2) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::setAtomBookmark
void setAtomBookmark(Atom *at, int mark)
associates an Atom pointer with a bookmark
Definition: ROMol.h:398
RDKit::ROMol::getStereoGroups
const std::vector< StereoGroup > & getStereoGroups() const
Gets a reference to the groups of atoms with relative stereochemistry.
Definition: ROMol.h:698
RDKit::ROMol::endMatchingAtoms
MatchingAtomIterator endMatchingAtoms()
get an AtomIterator pointing at the end of our Atoms
RDKit::ROMol::beginBonds
ConstBondIterator beginBonds() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::atoms
CXXAtomIterator< MolGraph, Atom * > atoms()
C++11 Range iterator.
Definition: ROMol.h:256
RDKit::ROMol::endBonds
BondIterator endBonds()
get a BondIterator pointing at the end of our Bonds
RDKit::ROMol::ROMol
ROMol(const std::string &binStr)
construct a molecule from a pickle string
RDKit::ROMol::getUniqueAtomWithBookmark
Atom * getUniqueAtomWithBookmark(int mark)
RDKit::ROMol::beginQueryAtoms
QueryAtomIterator beginQueryAtoms(QueryAtom const *query)
get an AtomIterator pointing at our first Atom that matches query
RDKit::ROMol::endHeteros
ConstHeteroatomIterator endHeteros() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::getAtomWithIdx
Atom * getAtomWithIdx(unsigned int idx)
returns a pointer to a particular Atom
RDKit::ROMol::getAtomWithBookmark
Atom * getAtomWithBookmark(int mark)
returns the first Atom associated with the bookmark provided
RDKit::ROMol::atoms
CXXAtomIterator< const MolGraph, Atom *const > atoms() const
Definition: ROMol.h:258
RDKit::ROMol::replaceAtomBookmark
void replaceAtomBookmark(Atom *at, int mark)
associates an Atom pointer with a bookmark
Definition: ROMol.h:402
RDKit::ROMol::atomBonds
CXXBondIterator< MolGraph, Bond *, MolGraph::out_edge_iterator > atomBonds(Atom const *at)
Definition: ROMol.h:280
RDKit::ROMol::getAtomDegree
unsigned int getAtomDegree(const Atom *at) const
returns the degree (number of neighbors) of an Atom in the graph
RDKit::ROMol::endAromaticAtoms
AromaticAtomIterator endAromaticAtoms()
get an AtomIterator pointing at the end of our Atoms
RDKit::ROMol::clearAllAtomBookmarks
void clearAllAtomBookmarks()
blows out all atomic bookmarks
Definition: ROMol.h:419
RDKit::ROMol::~ROMol
virtual ~ROMol()
Definition: ROMol.h:325
RDKit::ROMol::beginConformers
ConformerIterator beginConformers()
Definition: ROMol.h:651
RDKit::ROMol::endBonds
ConstBondIterator endBonds() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::getNumAtoms
unsigned int getNumAtoms(bool onlyExplicit) const
RDKit::ROMol::atomBonds
CXXBondIterator< const MolGraph, Bond *const, MolGraph::out_edge_iterator > atomBonds(Atom const *at) const
Definition: ROMol.h:275
RDKit::ROMol::ROMol
ROMol()
Definition: ROMol.h:301
RDKit::ROMol::operator[]
const Atom * operator[](const vertex_descriptor &v) const
Definition: ROMol.h:686
RDKit::ROMol::endHeteros
HeteroatomIterator endHeteros()
get an AtomIterator pointing at the end of our Atoms
RDKit::ROMol::getBondBetweenAtoms
Bond * getBondBetweenAtoms(unsigned int idx1, unsigned int idx2)
returns a pointer to the bond between two atoms, Null on failure
RDKit::ROMol::beginConformers
ConstConformerIterator beginConformers() const
Definition: ROMol.h:655
RDKit::ROMol::clearBondBookmark
void clearBondBookmark(int mark, const Bond *bond)
removes a particular Bond from the list associated with the bookmark
RDKit::ROMol::getConformer
Conformer & getConformer(int id=-1)
RDKit::ROMol::getSubstanceGroups
friend RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > & getSubstanceGroups(const ROMol &)
RDKit::ROMol::getAtomBookmarks
ATOM_BOOKMARK_MAP * getAtomBookmarks()
returns a pointer to all of our atom bookmarks
Definition: ROMol.h:423
RDKit::ROMol::beginMatchingAtoms
MatchingAtomIterator beginMatchingAtoms(bool(*query)(Atom *))
get an AtomIterator pointing at our first Atom that matches query
RDKit::ROMol::atomNeighbors
CXXAtomIterator< const MolGraph, Atom *const, MolGraph::adjacency_iterator > atomNeighbors(Atom const *at) const
Definition: ROMol.h:263
RDKit::ROMol::hasBondBookmark
bool hasBondBookmark(int mark) const
queries whether or not any bonds are associated with a bookmark
Definition: ROMol.h:444
RDKit::ROMol::operator[]
Bond * operator[](const edge_descriptor &e)
Definition: ROMol.h:690
RDKit::ROMol::atomNeighbors
CXXAtomIterator< MolGraph, Atom *, MolGraph::adjacency_iterator > atomNeighbors(Atom const *at)
Definition: ROMol.h:268
RDKit::ROMol::beginAtoms
AtomIterator beginAtoms()
get an AtomIterator pointing at our first Atom
RDKit::ROMol::getUniqueBondWithBookmark
Bond * getUniqueBondWithBookmark(int mark)
RDKit::ROMol::removeConformer
void removeConformer(unsigned int id)
Delete the conformation with the specified ID.
RDKit::ROMol::beginAromaticAtoms
AromaticAtomIterator beginAromaticAtoms()
get an AtomIterator pointing at our first aromatic Atom
RDKit::ROMol::beginHeteros
ConstHeteroatomIterator beginHeteros() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::getConformer
const Conformer & getConformer(int id=-1) const
RDKit::ROMol::endConformers
ConformerIterator endConformers()
Definition: ROMol.h:653
RDKit::ROMol::getVertices
ATOM_ITER_PAIR getVertices() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::ROMol::clearBondBookmark
void clearBondBookmark(int mark)
removes a bookmark from our collection
RDKit::ROMol::beginHeteros
HeteroatomIterator beginHeteros()
get an AtomIterator pointing at our first hetero Atom
RDKit::ROMol::getAtomWithIdx
const Atom * getAtomWithIdx(unsigned int idx) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
RDKit::RingInfo
A class to store information about a molecule's rings.
Definition: RingInfo.h:28
export.h
RDKIT_GRAPHMOL_EXPORT
#define RDKIT_GRAPHMOL_EXPORT
Definition: export.h:209
RDKit
Std stuff.
Definition: Abbreviations.h:18
RDKit::MOL_VECT
std::vector< ROMol > MOL_VECT
Definition: ROMol.h:774
RDKit::MOL_PTR_VECT_CI
MOL_PTR_VECT::const_iterator MOL_PTR_VECT_CI
Definition: ROMol.h:779
RDKit::ci_RIGHTMOST_ATOM
RDKIT_GRAPHMOL_EXPORT const int ci_RIGHTMOST_ATOM
RDKit::ci_ATOM_HOLDER
RDKIT_GRAPHMOL_EXPORT const int ci_ATOM_HOLDER
RDKit::MOL_PTR_VECT
std::vector< ROMol * > MOL_PTR_VECT
Definition: ROMol.h:776
RDKit::ROMOL_SPTR
boost::shared_ptr< ROMol > ROMOL_SPTR
Definition: ChemTransforms.h:22
RDKit::MOL_PTR_VECT_I
MOL_PTR_VECT::iterator MOL_PTR_VECT_I
Definition: ROMol.h:780
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:44
RDKit::MOL_SPTR_VECT
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
Definition: FragCatParams.h:20
RDKit::ci_LEADING_BOND
RDKIT_GRAPHMOL_EXPORT const int ci_LEADING_BOND
RDKit::CXXAtomIterator::CXXAtomIter
Definition: ROMol.h:112
RDKit::CXXAtomIterator::CXXAtomIter::current
Atom * current
Definition: ROMol.h:115
RDKit::CXXAtomIterator::CXXAtomIter::operator*
Vertex & operator*()
Definition: ROMol.h:120
RDKit::CXXAtomIterator::CXXAtomIter::graph
Graph * graph
Definition: ROMol.h:113
RDKit::CXXAtomIterator::CXXAtomIter::CXXAtomIter
CXXAtomIter(Graph *graph, Iterator pos)
Definition: ROMol.h:117
RDKit::CXXAtomIterator::CXXAtomIter::operator++
CXXAtomIter & operator++()
Definition: ROMol.h:124
RDKit::CXXAtomIterator::CXXAtomIter::pos
Iterator pos
Definition: ROMol.h:114
RDKit::CXXAtomIterator::CXXAtomIter::operator!=
bool operator!=(const CXXAtomIter &it) const
Definition: ROMol.h:128
RDKit::CXXAtomIterator
Definition: ROMol.h:108
RDKit::CXXAtomIterator::graph
Graph * graph
Definition: ROMol.h:109
RDKit::CXXAtomIterator::vstart
Iterator vstart
Definition: ROMol.h:110
RDKit::CXXAtomIterator::vend
Iterator vend
Definition: ROMol.h:110
RDKit::CXXAtomIterator::end
CXXAtomIter end()
Definition: ROMol.h:139
RDKit::CXXAtomIterator::CXXAtomIterator
CXXAtomIterator(Graph *graph, Iterator start, Iterator end)
Definition: ROMol.h:136
RDKit::CXXAtomIterator::CXXAtomIterator
CXXAtomIterator(Graph *graph)
Definition: ROMol.h:131
RDKit::CXXAtomIterator::begin
CXXAtomIter begin()
Definition: ROMol.h:138
RDKit::CXXBondIterator::CXXBondIter
Definition: ROMol.h:148
RDKit::CXXBondIterator::CXXBondIter::current
Bond * current
Definition: ROMol.h:151
RDKit::CXXBondIterator::CXXBondIter::CXXBondIter
CXXBondIter(Graph *graph, Iterator pos)
Definition: ROMol.h:153
RDKit::CXXBondIterator::CXXBondIter::graph
Graph * graph
Definition: ROMol.h:149
RDKit::CXXBondIterator::CXXBondIter::operator!=
bool operator!=(const CXXBondIter &it) const
Definition: ROMol.h:164
RDKit::CXXBondIterator::CXXBondIter::pos
Iterator pos
Definition: ROMol.h:150
RDKit::CXXBondIterator::CXXBondIter::operator*
Edge & operator*()
Definition: ROMol.h:156
RDKit::CXXBondIterator::CXXBondIter::operator++
CXXBondIter & operator++()
Definition: ROMol.h:160
RDKit::CXXBondIterator
Definition: ROMol.h:144
RDKit::CXXBondIterator::graph
Graph * graph
Definition: ROMol.h:145
RDKit::CXXBondIterator::begin
CXXBondIter begin()
Definition: ROMol.h:174
RDKit::CXXBondIterator::vstart
Iterator vstart
Definition: ROMol.h:146
RDKit::CXXBondIterator::vend
Iterator vend
Definition: ROMol.h:146
RDKit::CXXBondIterator::CXXBondIterator
CXXBondIterator(Graph *graph)
Definition: ROMol.h:167
RDKit::CXXBondIterator::CXXBondIterator
CXXBondIterator(Graph *graph, Iterator start, Iterator end)
Definition: ROMol.h:172
RDKit::CXXBondIterator::end
CXXBondIter end()
Definition: ROMol.h:175
types.h