RDKit
Open-source cheminformatics and machine learning.
RDKit::ROMol Class Reference

#include <ROMol.h>

Inheritance diagram for RDKit::ROMol:
RDKit::RDProps RDKit::RWMol

Public Member Functions

CXXAtomIterator< MolGraph, Atom * > atoms ()
 C++11 Range iterator. More...
 
CXXAtomIterator< const MolGraph, Atom *const > atoms () const
 
CXXAtomIterator< const MolGraph, Atom *const, MolGraph::adjacency_iterator > atomNeighbors (Atom const *at) const
 
CXXAtomIterator< MolGraph, Atom *, MolGraph::adjacency_iterator > atomNeighbors (Atom const *at)
 
CXXBondIterator< const MolGraph, Bond *const, MolGraph::out_edge_iterator > atomBonds (Atom const *at) const
 
CXXBondIterator< MolGraph, Bond *, MolGraph::out_edge_iterator > atomBonds (Atom const *at)
 
CXXBondIterator< MolGraph, Bond * > bonds ()
 
CXXBondIterator< const MolGraph, Bond *const > bonds () const
 
 ROMol ()
 
 ROMol (const ROMol &other, bool quickCopy=false, int confId=-1)
 copy constructor with a twist More...
 
 ROMol (const std::string &binStr)
 construct a molecule from a pickle string More...
 
 ROMol (const std::string &binStr, unsigned int propertyFlags)
 construct a molecule from a pickle string More...
 
 ROMol (ROMol &&o) noexcept
 
ROMoloperator= (ROMol &&o) noexcept
 
ROMoloperator= (const ROMol &)=delete
 
virtual ~ROMol ()
 
Atomoperator[] (const vertex_descriptor &v)
 
const Atomoperator[] (const vertex_descriptor &v) const
 
Bondoperator[] (const edge_descriptor &e)
 
const Bondoperator[] (const edge_descriptor &e) const
 
const std::vector< StereoGroup > & getStereoGroups () const
 Gets a reference to the groups of atoms with relative stereochemistry. More...
 
void setStereoGroups (std::vector< StereoGroup > stereo_groups)
 Sets groups of atoms with relative stereochemistry. More...
 
Atoms
unsigned int getNumAtoms () const
 returns our number of atoms More...
 
unsigned int getNumAtoms (bool onlyExplicit) const
 
unsigned int getNumHeavyAtoms () const
 returns our number of heavy atoms (atomic number > 1) More...
 
AtomgetAtomWithIdx (unsigned int idx)
 returns a pointer to a particular Atom More...
 
const AtomgetAtomWithIdx (unsigned int idx) const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
template<class U >
AtomgetAtomWithIdx (const U idx)
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
template<class U >
const AtomgetAtomWithIdx (const U idx) const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
unsigned int getAtomDegree (const Atom *at) const
 returns the degree (number of neighbors) of an Atom in the graph More...
 
Bonds
unsigned int getNumBonds (bool onlyHeavy=1) const
 returns our number of Bonds More...
 
BondgetBondWithIdx (unsigned int idx)
 returns a pointer to a particular Bond More...
 
const BondgetBondWithIdx (unsigned int idx) const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
template<class U >
BondgetBondWithIdx (const U idx)
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
template<class U >
const BondgetBondWithIdx (const U idx) const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
BondgetBondBetweenAtoms (unsigned int idx1, unsigned int idx2)
 returns a pointer to the bond between two atoms, Null on failure More...
 
const BondgetBondBetweenAtoms (unsigned int idx1, unsigned int idx2) const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
template<class U , class V >
BondgetBondBetweenAtoms (const U idx1, const V idx2)
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
template<class U , class V >
const BondgetBondBetweenAtoms (const U idx1, const V idx2) const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
Bookmarks
void setAtomBookmark (Atom *at, int mark)
 associates an Atom pointer with a bookmark More...
 
void replaceAtomBookmark (Atom *at, int mark)
 associates an Atom pointer with a bookmark More...
 
AtomgetAtomWithBookmark (int mark)
 returns the first Atom associated with the bookmark provided More...
 
AtomgetUniqueAtomWithBookmark (int mark)
 
ATOM_PTR_LIST & getAllAtomsWithBookmark (int mark)
 returns all Atoms associated with the bookmark provided More...
 
void clearAtomBookmark (int mark)
 removes a bookmark from our collection More...
 
void clearAtomBookmark (int mark, const Atom *atom)
 removes a particular Atom from the list associated with the bookmark More...
 
void clearAllAtomBookmarks ()
 blows out all atomic bookmarks More...
 
bool hasAtomBookmark (int mark) const
 queries whether or not any atoms are associated with a bookmark More...
 
ATOM_BOOKMARK_MAP * getAtomBookmarks ()
 returns a pointer to all of our atom bookmarks More...
 
void setBondBookmark (Bond *bond, int mark)
 associates a Bond pointer with a bookmark More...
 
BondgetBondWithBookmark (int mark)
 returns the first Bond associated with the bookmark provided More...
 
BondgetUniqueBondWithBookmark (int mark)
 
BOND_PTR_LIST & getAllBondsWithBookmark (int mark)
 returns all bonds associated with the bookmark provided More...
 
void clearBondBookmark (int mark)
 removes a bookmark from our collection More...
 
void clearBondBookmark (int mark, const Bond *bond)
 removes a particular Bond from the list associated with the bookmark More...
 
void clearAllBondBookmarks ()
 blows out all bond bookmarks More...
 
bool hasBondBookmark (int mark) const
 queries whether or not any bonds are associated with a bookmark More...
 
BOND_BOOKMARK_MAP * getBondBookmarks ()
 returns a pointer to all of our bond bookmarks More...
 
Conformers
const ConformergetConformer (int id=-1) const
 
ConformergetConformer (int id=-1)
 
void removeConformer (unsigned int id)
 Delete the conformation with the specified ID. More...
 
void clearConformers ()
 Clear all the conformations on the molecule. More...
 
unsigned int addConformer (Conformer *conf, bool assignId=false)
 Add a new conformation to the molecule. More...
 
unsigned int getNumConformers () const
 
Topology
RingInfogetRingInfo () const
 
ADJ_ITER_PAIR getAtomNeighbors (Atom const *at) const
 provides access to all neighbors around an Atom More...
 
OBOND_ITER_PAIR getAtomBonds (Atom const *at) const
 provides access to all Bond objects connected to an Atom More...
 
ATOM_ITER_PAIR getVertices ()
 returns an iterator pair for looping over all Atoms More...
 
BOND_ITER_PAIR getEdges ()
 returns an iterator pair for looping over all Bonds More...
 
ATOM_ITER_PAIR getVertices () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
BOND_ITER_PAIR getEdges () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
MolGraph const & getTopology () const
 brief returns a pointer to our underlying BGL object More...
 
Iterators
AtomIterator beginAtoms ()
 get an AtomIterator pointing at our first Atom More...
 
ConstAtomIterator beginAtoms () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
AtomIterator endAtoms ()
 get an AtomIterator pointing at the end of our Atoms More...
 
ConstAtomIterator endAtoms () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
BondIterator beginBonds ()
 get a BondIterator pointing at our first Bond More...
 
ConstBondIterator beginBonds () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
BondIterator endBonds ()
 get a BondIterator pointing at the end of our Bonds More...
 
ConstBondIterator endBonds () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
AromaticAtomIterator beginAromaticAtoms ()
 get an AtomIterator pointing at our first aromatic Atom More...
 
ConstAromaticAtomIterator beginAromaticAtoms () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
AromaticAtomIterator endAromaticAtoms ()
 get an AtomIterator pointing at the end of our Atoms More...
 
ConstAromaticAtomIterator endAromaticAtoms () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
HeteroatomIterator beginHeteros ()
 get an AtomIterator pointing at our first hetero Atom More...
 
ConstHeteroatomIterator beginHeteros () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
HeteroatomIterator endHeteros ()
 get an AtomIterator pointing at the end of our Atoms More...
 
ConstHeteroatomIterator endHeteros () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
QueryAtomIterator beginQueryAtoms (QueryAtom const *query)
 get an AtomIterator pointing at our first Atom that matches query More...
 
ConstQueryAtomIterator beginQueryAtoms (QueryAtom const *) const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
QueryAtomIterator endQueryAtoms ()
 get an AtomIterator pointing at the end of our Atoms More...
 
ConstQueryAtomIterator endQueryAtoms () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
MatchingAtomIterator beginMatchingAtoms (bool(*query)(Atom *))
 get an AtomIterator pointing at our first Atom that matches query More...
 
ConstMatchingAtomIterator beginMatchingAtoms (bool(*query)(const Atom *)) const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
MatchingAtomIterator endMatchingAtoms ()
 get an AtomIterator pointing at the end of our Atoms More...
 
ConstMatchingAtomIterator endMatchingAtoms () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
ConformerIterator beginConformers ()
 
ConformerIterator endConformers ()
 
ConstConformerIterator beginConformers () const
 
ConstConformerIterator endConformers () const
 
Properties
void clearComputedProps (bool includeRings=true) const
 clears all of our computed properties More...
 
void updatePropertyCache (bool strict=true)
 calculates any of our lazy properties More...
 
bool needsUpdatePropertyCache () const
 
Misc

sends some debugging info to a stream

void debugMol (std::ostream &str) const
 
- Public Member Functions inherited from RDKit::RDProps
 RDProps ()
 
 RDProps (const RDProps &rhs)
 
RDPropsoperator= (const RDProps &rhs)
 
 RDProps (RDProps &&o) noexcept=default
 
RDPropsoperator= (RDProps &&rhs) noexcept=default
 
void clear ()
 
const DictgetDict () const
 gets the underlying Dictionary More...
 
DictgetDict ()
 
STR_VECT getPropList (bool includePrivate=true, bool includeComputed=true) const
 returns a list with the names of our properties More...
 
template<typename T >
void setProp (const std::string &key, T val, bool computed=false) const
 sets a property value More...
 
template<typename T >
void getProp (const std::string &key, T &res) const
 allows retrieval of a particular property value More...
 
template<typename T >
getProp (const std::string &key) const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
template<typename T >
bool getPropIfPresent (const std::string &key, T &res) const
 
bool hasProp (const std::string &key) const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
void clearProp (const std::string &key) const
 clears the value of a property More...
 
void clearComputedProps () const
 clears all of our computed properties More...
 
void updateProps (const RDProps &source, bool preserveExisting=false)
 update the properties from another More...
 

Protected Attributes

unsigned int numBonds {0}
 
- Protected Attributes inherited from RDKit::RDProps
Dict d_props
 

Friends

class MolPickler
 
class RWMol
 
RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & getSubstanceGroups (ROMol &)
 
RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > & getSubstanceGroups (const ROMol &)
 

Detailed Description

Definition at line 197 of file ROMol.h.

Constructor & Destructor Documentation

◆ ROMol() [1/5]

RDKit::ROMol::ROMol ( )
inline

Definition at line 320 of file ROMol.h.

◆ ROMol() [2/5]

RDKit::ROMol::ROMol ( const ROMol other,
bool  quickCopy = false,
int  confId = -1 
)
inline

copy constructor with a twist

Parameters
otherthe molecule to be copied
quickCopy(optional) if this is true, the resulting ROMol will not copy any of the properties or bookmarks and conformers from other. This can make the copy substantially faster (thus the name).
confId(optional) if this is >=0, the resulting ROMol will contain only the specified conformer from other.

Definition at line 333 of file ROMol.h.

◆ ROMol() [3/5]

RDKit::ROMol::ROMol ( const std::string &  binStr)

construct a molecule from a pickle string

◆ ROMol() [4/5]

RDKit::ROMol::ROMol ( const std::string &  binStr,
unsigned int  propertyFlags 
)

construct a molecule from a pickle string

◆ ROMol() [5/5]

RDKit::ROMol::ROMol ( ROMol &&  o)
inlinenoexcept

Definition at line 344 of file ROMol.h.

References RDKit::RDProps::clear().

◆ ~ROMol()

virtual RDKit::ROMol::~ROMol ( )
inlinevirtual

Definition at line 406 of file ROMol.h.

Member Function Documentation

◆ addConformer()

unsigned int RDKit::ROMol::addConformer ( Conformer conf,
bool  assignId = false 
)

Add a new conformation to the molecule.

Parameters
conf- conformation to be added to the molecule, this molecule takes ownership of the conformer
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

◆ atomBonds() [1/2]

CXXBondIterator< MolGraph, Bond *, MolGraph::out_edge_iterator > RDKit::ROMol::atomBonds ( Atom const *  at)
inline

Definition at line 299 of file ROMol.h.

◆ atomBonds() [2/2]

CXXBondIterator< const MolGraph, Bond *const, MolGraph::out_edge_iterator > RDKit::ROMol::atomBonds ( Atom const *  at) const
inline

Definition at line 294 of file ROMol.h.

◆ atomNeighbors() [1/2]

CXXAtomIterator< MolGraph, Atom *, MolGraph::adjacency_iterator > RDKit::ROMol::atomNeighbors ( Atom const *  at)
inline

Definition at line 287 of file ROMol.h.

◆ atomNeighbors() [2/2]

CXXAtomIterator< const MolGraph, Atom *const, MolGraph::adjacency_iterator > RDKit::ROMol::atomNeighbors ( Atom const *  at) const
inline

Definition at line 282 of file ROMol.h.

◆ atoms() [1/2]

CXXAtomIterator< MolGraph, Atom * > RDKit::ROMol::atoms ( )
inline

C++11 Range iterator.

Usage

for(auto atom : mol.atoms()) {
atom->getIdx();
};

Definition at line 275 of file ROMol.h.

Referenced by RDKit::MolDraw2D_detail::addAtomIndices(), and RDKit::FileParserUtils::getAtomPropertyList().

◆ atoms() [2/2]

CXXAtomIterator< const MolGraph, Atom *const > RDKit::ROMol::atoms ( ) const
inline

Definition at line 277 of file ROMol.h.

◆ beginAromaticAtoms() [1/2]

AromaticAtomIterator RDKit::ROMol::beginAromaticAtoms ( )

get an AtomIterator pointing at our first aromatic Atom

◆ beginAromaticAtoms() [2/2]

ConstAromaticAtomIterator RDKit::ROMol::beginAromaticAtoms ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ beginAtoms() [1/2]

AtomIterator RDKit::ROMol::beginAtoms ( )

get an AtomIterator pointing at our first Atom

Referenced by RDKit::RGroupDecompData::relabelRGroup().

◆ beginAtoms() [2/2]

ConstAtomIterator RDKit::ROMol::beginAtoms ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ beginBonds() [1/2]

BondIterator RDKit::ROMol::beginBonds ( )

get a BondIterator pointing at our first Bond

◆ beginBonds() [2/2]

ConstBondIterator RDKit::ROMol::beginBonds ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ beginConformers() [1/2]

ConformerIterator RDKit::ROMol::beginConformers ( )
inline

Definition at line 732 of file ROMol.h.

Referenced by RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST().

◆ beginConformers() [2/2]

ConstConformerIterator RDKit::ROMol::beginConformers ( ) const
inline

Definition at line 736 of file ROMol.h.

◆ beginHeteros() [1/2]

HeteroatomIterator RDKit::ROMol::beginHeteros ( )

get an AtomIterator pointing at our first hetero Atom

◆ beginHeteros() [2/2]

ConstHeteroatomIterator RDKit::ROMol::beginHeteros ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ beginMatchingAtoms() [1/2]

MatchingAtomIterator RDKit::ROMol::beginMatchingAtoms ( bool(*)(Atom *)  query)

get an AtomIterator pointing at our first Atom that matches query

◆ beginMatchingAtoms() [2/2]

ConstMatchingAtomIterator RDKit::ROMol::beginMatchingAtoms ( bool(*)(const Atom *)  query) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ beginQueryAtoms() [1/2]

ConstQueryAtomIterator RDKit::ROMol::beginQueryAtoms ( QueryAtom const *  ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ beginQueryAtoms() [2/2]

QueryAtomIterator RDKit::ROMol::beginQueryAtoms ( QueryAtom const *  query)

get an AtomIterator pointing at our first Atom that matches query

◆ bonds() [1/2]

CXXBondIterator< MolGraph, Bond * > RDKit::ROMol::bonds ( )
inline

Usage

for(auto bond : mol.bonds()) {
bond->getIdx();
};

Definition at line 314 of file ROMol.h.

Referenced by RDKit::MolDraw2D_detail::addBondIndices().

◆ bonds() [2/2]

CXXBondIterator< const MolGraph, Bond *const > RDKit::ROMol::bonds ( ) const
inline

Definition at line 316 of file ROMol.h.

◆ clearAllAtomBookmarks()

void RDKit::ROMol::clearAllAtomBookmarks ( )
inline

blows out all atomic bookmarks

Definition at line 500 of file ROMol.h.

◆ clearAllBondBookmarks()

void RDKit::ROMol::clearAllBondBookmarks ( )
inline

blows out all bond bookmarks

Definition at line 523 of file ROMol.h.

◆ clearAtomBookmark() [1/2]

void RDKit::ROMol::clearAtomBookmark ( int  mark)

removes a bookmark from our collection

◆ clearAtomBookmark() [2/2]

void RDKit::ROMol::clearAtomBookmark ( int  mark,
const Atom atom 
)

removes a particular Atom from the list associated with the bookmark

◆ clearBondBookmark() [1/2]

void RDKit::ROMol::clearBondBookmark ( int  mark)

removes a bookmark from our collection

◆ clearBondBookmark() [2/2]

void RDKit::ROMol::clearBondBookmark ( int  mark,
const Bond bond 
)

removes a particular Bond from the list associated with the bookmark

◆ clearComputedProps()

void RDKit::ROMol::clearComputedProps ( bool  includeRings = true) const

clears all of our computed properties

◆ clearConformers()

void RDKit::ROMol::clearConformers ( )
inline

Clear all the conformations on the molecule.

Definition at line 546 of file ROMol.h.

◆ debugMol()

void RDKit::ROMol::debugMol ( std::ostream &  str) const

◆ endAromaticAtoms() [1/2]

AromaticAtomIterator RDKit::ROMol::endAromaticAtoms ( )

get an AtomIterator pointing at the end of our Atoms

◆ endAromaticAtoms() [2/2]

ConstAromaticAtomIterator RDKit::ROMol::endAromaticAtoms ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ endAtoms() [1/2]

AtomIterator RDKit::ROMol::endAtoms ( )

get an AtomIterator pointing at the end of our Atoms

Referenced by RDKit::RGroupDecompData::relabelRGroup().

◆ endAtoms() [2/2]

ConstAtomIterator RDKit::ROMol::endAtoms ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ endBonds() [1/2]

BondIterator RDKit::ROMol::endBonds ( )

get a BondIterator pointing at the end of our Bonds

◆ endBonds() [2/2]

ConstBondIterator RDKit::ROMol::endBonds ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ endConformers() [1/2]

ConformerIterator RDKit::ROMol::endConformers ( )
inline

Definition at line 734 of file ROMol.h.

Referenced by RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST().

◆ endConformers() [2/2]

ConstConformerIterator RDKit::ROMol::endConformers ( ) const
inline

Definition at line 740 of file ROMol.h.

◆ endHeteros() [1/2]

HeteroatomIterator RDKit::ROMol::endHeteros ( )

get an AtomIterator pointing at the end of our Atoms

◆ endHeteros() [2/2]

ConstHeteroatomIterator RDKit::ROMol::endHeteros ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ endMatchingAtoms() [1/2]

MatchingAtomIterator RDKit::ROMol::endMatchingAtoms ( )

get an AtomIterator pointing at the end of our Atoms

◆ endMatchingAtoms() [2/2]

ConstMatchingAtomIterator RDKit::ROMol::endMatchingAtoms ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ endQueryAtoms() [1/2]

QueryAtomIterator RDKit::ROMol::endQueryAtoms ( )

get an AtomIterator pointing at the end of our Atoms

◆ endQueryAtoms() [2/2]

ConstQueryAtomIterator RDKit::ROMol::endQueryAtoms ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ getAllAtomsWithBookmark()

ATOM_PTR_LIST & RDKit::ROMol::getAllAtomsWithBookmark ( int  mark)

returns all Atoms associated with the bookmark provided

◆ getAllBondsWithBookmark()

BOND_PTR_LIST & RDKit::ROMol::getAllBondsWithBookmark ( int  mark)

returns all bonds associated with the bookmark provided

◆ getAtomBonds()

OBOND_ITER_PAIR RDKit::ROMol::getAtomBonds ( Atom const *  at) const

provides access to all Bond objects connected to an Atom

Parameters
atthe atom whose neighbors we are looking for

Usage

... 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
}
The class for representing atoms.
Definition: Atom.h:68
Definition: RDLog.h:24

or, if you need a non-const Bond *:

... 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
}

Referenced by RDKit::queryAtomHasRingBond(), and RDKit::queryAtomRingBondCount().

◆ getAtomBookmarks()

ATOM_BOOKMARK_MAP * RDKit::ROMol::getAtomBookmarks ( )
inline

returns a pointer to all of our atom bookmarks

Definition at line 504 of file ROMol.h.

Referenced by RDKit::SLNParse::addBranchToMol().

◆ getAtomDegree()

unsigned int RDKit::ROMol::getAtomDegree ( const Atom at) const

returns the degree (number of neighbors) of an Atom in the graph

◆ getAtomNeighbors()

ADJ_ITER_PAIR RDKit::ROMol::getAtomNeighbors ( Atom const *  at) const

provides access to all neighbors around an Atom

Parameters
atthe atom whose neighbors we are looking for

Usage

... 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
}

Referenced by RDKit::queryAtomHasAliphaticHeteroatomNbrs(), RDKit::queryAtomHasHeteroatomNbrs(), RDKit::queryAtomHeavyAtomDegree(), RDKit::queryAtomNonHydrogenDegree(), RDKit::queryAtomNumAliphaticHeteroatomNbrs(), and RDKit::queryAtomNumHeteroatomNbrs().

◆ getAtomWithBookmark()

Atom * RDKit::ROMol::getAtomWithBookmark ( int  mark)

returns the first Atom associated with the bookmark provided

Referenced by RDKit::SLNParse::closeRingBond().

◆ getAtomWithIdx() [1/4]

template<class U >
Atom * RDKit::ROMol::getAtomWithIdx ( const U  idx)
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 425 of file ROMol.h.

◆ getAtomWithIdx() [2/4]

template<class U >
const Atom * RDKit::ROMol::getAtomWithIdx ( const U  idx) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 430 of file ROMol.h.

◆ getAtomWithIdx() [3/4]

Atom * RDKit::ROMol::getAtomWithIdx ( unsigned int  idx)

returns a pointer to a particular Atom

Referenced by RDKit::SLNParse::addBranchToMol(), and RDKit::FileParserUtils::applyMolListPropToAtoms().

◆ getAtomWithIdx() [4/4]

const Atom * RDKit::ROMol::getAtomWithIdx ( unsigned int  idx) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ getBondBetweenAtoms() [1/4]

template<class U , class V >
Bond * RDKit::ROMol::getBondBetweenAtoms ( const U  idx1,
const V  idx2 
)
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 462 of file ROMol.h.

◆ getBondBetweenAtoms() [2/4]

template<class U , class V >
const Bond * RDKit::ROMol::getBondBetweenAtoms ( const U  idx1,
const V  idx2 
) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 468 of file ROMol.h.

◆ getBondBetweenAtoms() [3/4]

Bond * RDKit::ROMol::getBondBetweenAtoms ( unsigned int  idx1,
unsigned int  idx2 
)

returns a pointer to the bond between two atoms, Null on failure

Referenced by RDKit::MolEnumerator::utils::getMolLinkNodes(), and RDKit::FMCS::TargetMatch::init().

◆ getBondBetweenAtoms() [4/4]

const Bond * RDKit::ROMol::getBondBetweenAtoms ( unsigned int  idx1,
unsigned int  idx2 
) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ getBondBookmarks()

BOND_BOOKMARK_MAP * RDKit::ROMol::getBondBookmarks ( )
inline

returns a pointer to all of our bond bookmarks

Definition at line 527 of file ROMol.h.

Referenced by RDKit::SLNParse::addBranchToMol().

◆ getBondWithBookmark()

Bond * RDKit::ROMol::getBondWithBookmark ( int  mark)

returns the first Bond associated with the bookmark provided

◆ getBondWithIdx() [1/4]

template<class U >
Bond * RDKit::ROMol::getBondWithIdx ( const U  idx)
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 448 of file ROMol.h.

◆ getBondWithIdx() [2/4]

template<class U >
const Bond * RDKit::ROMol::getBondWithIdx ( const U  idx) const
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 453 of file ROMol.h.

◆ getBondWithIdx() [3/4]

Bond * RDKit::ROMol::getBondWithIdx ( unsigned int  idx)

returns a pointer to a particular Bond

◆ getBondWithIdx() [4/4]

const Bond * RDKit::ROMol::getBondWithIdx ( unsigned int  idx) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ getConformer() [1/2]

Conformer & RDKit::ROMol::getConformer ( int  id = -1)

return the conformer with a specified ID if the ID is negative the first conformation will be returned

◆ getConformer() [2/2]

const Conformer & RDKit::ROMol::getConformer ( int  id = -1) const

return the conformer with a specified ID if the ID is negative the first conformation will be returned

◆ getEdges() [1/2]

BOND_ITER_PAIR RDKit::ROMol::getEdges ( )

returns an iterator pair for looping over all Bonds

Usage

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;
}
class for representing a bond
Definition: Bond.h:47

◆ getEdges() [2/2]

BOND_ITER_PAIR RDKit::ROMol::getEdges ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ getNumAtoms() [1/2]

◆ getNumAtoms() [2/2]

unsigned int RDKit::ROMol::getNumAtoms ( bool  onlyExplicit) const

◆ getNumBonds()

unsigned int RDKit::ROMol::getNumBonds ( bool  onlyHeavy = 1) const

◆ getNumConformers()

◆ getNumHeavyAtoms()

unsigned int RDKit::ROMol::getNumHeavyAtoms ( ) const

returns our number of heavy atoms (atomic number > 1)

◆ getRingInfo()

◆ getStereoGroups()

const std::vector< StereoGroup > & RDKit::ROMol::getStereoGroups ( ) const
inline

Gets a reference to the groups of atoms with relative stereochemistry.

Stereo groups are also called enhanced stereochemistry in the SDF/Mol3000 file format.

Definition at line 779 of file ROMol.h.

◆ getTopology()

MolGraph const & RDKit::ROMol::getTopology ( ) const
inline

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:

... 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]);
MolGraph const & getTopology() const
brief returns a pointer to our underlying BGL object
Definition: ROMol.h:672
std::vector< int > INT_VECT
Definition: types.h:278
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:55

Definition at line 672 of file ROMol.h.

Referenced by RDKit::queryAtomHasRingBond(), and RDKit::queryAtomRingBondCount().

◆ getUniqueAtomWithBookmark()

Atom * RDKit::ROMol::getUniqueAtomWithBookmark ( int  mark)

returns the Atom associated with the bookmark provided a check is made to ensure it is the only atom with that bookmark

◆ getUniqueBondWithBookmark()

Bond * RDKit::ROMol::getUniqueBondWithBookmark ( int  mark)

returns the Bond associated with the bookmark provided a check is made to ensure it is the only bond with that bookmark

◆ getVertices() [1/2]

ATOM_ITER_PAIR RDKit::ROMol::getVertices ( )

returns an iterator pair for looping over all Atoms

Usage

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;
}

◆ getVertices() [2/2]

ATOM_ITER_PAIR RDKit::ROMol::getVertices ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ hasAtomBookmark()

bool RDKit::ROMol::hasAtomBookmark ( int  mark) const
inline

queries whether or not any atoms are associated with a bookmark

Definition at line 502 of file ROMol.h.

Referenced by RDKit::SLNParse::addBranchToMol(), and RDKit::SLNParse::closeRingBond().

◆ hasBondBookmark()

bool RDKit::ROMol::hasBondBookmark ( int  mark) const
inline

queries whether or not any bonds are associated with a bookmark

Definition at line 525 of file ROMol.h.

Referenced by RDKit::SLNParse::addBranchToMol().

◆ needsUpdatePropertyCache()

bool RDKit::ROMol::needsUpdatePropertyCache ( ) const

◆ operator=() [1/2]

ROMol & RDKit::ROMol::operator= ( const ROMol )
delete

◆ operator=() [2/2]

ROMol & RDKit::ROMol::operator= ( ROMol &&  o)
inlinenoexcept

Definition at line 368 of file ROMol.h.

References RDKit::RDProps::operator=().

Referenced by RDKit::RWMol::operator=().

◆ operator[]() [1/4]

Bond * RDKit::ROMol::operator[] ( const edge_descriptor &  e)
inline

Definition at line 771 of file ROMol.h.

◆ operator[]() [2/4]

const Bond * RDKit::ROMol::operator[] ( const edge_descriptor &  e) const
inline

Definition at line 772 of file ROMol.h.

◆ operator[]() [3/4]

Atom * RDKit::ROMol::operator[] ( const vertex_descriptor &  v)
inline

Definition at line 766 of file ROMol.h.

◆ operator[]() [4/4]

const Atom * RDKit::ROMol::operator[] ( const vertex_descriptor &  v) const
inline

Definition at line 767 of file ROMol.h.

◆ removeConformer()

void RDKit::ROMol::removeConformer ( unsigned int  id)

Delete the conformation with the specified ID.

◆ replaceAtomBookmark()

void RDKit::ROMol::replaceAtomBookmark ( Atom at,
int  mark 
)
inline

associates an Atom pointer with a bookmark

Definition at line 483 of file ROMol.h.

◆ setAtomBookmark()

void RDKit::ROMol::setAtomBookmark ( Atom at,
int  mark 
)
inline

associates an Atom pointer with a bookmark

Definition at line 479 of file ROMol.h.

Referenced by RDKit::SLNParse::addBranchToMol().

◆ setBondBookmark()

void RDKit::ROMol::setBondBookmark ( Bond bond,
int  mark 
)
inline

associates a Bond pointer with a bookmark

Definition at line 507 of file ROMol.h.

Referenced by RDKit::SLNParse::addBranchToMol(), and RDKit::SLNParse::closeRingBond().

◆ setStereoGroups()

void RDKit::ROMol::setStereoGroups ( std::vector< StereoGroup stereo_groups)

Sets groups of atoms with relative stereochemistry.

Parameters
stereo_groupsthe 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.

◆ updatePropertyCache()

void RDKit::ROMol::updatePropertyCache ( bool  strict = true)

calculates any of our lazy properties

Notes:

Referenced by RDKit::RGroupDecompData::relabelCore(), and RDKit::RGroupDecompData::relabelRGroup().

Friends And Related Function Documentation

◆ getSubstanceGroups [1/2]

RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > & getSubstanceGroups ( const ROMol )
friend

◆ getSubstanceGroups [2/2]

RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & getSubstanceGroups ( ROMol )
friend

◆ MolPickler

friend class MolPickler
friend

Definition at line 199 of file ROMol.h.

◆ RWMol

friend class RWMol
friend

Definition at line 200 of file ROMol.h.

Member Data Documentation

◆ numBonds

unsigned int RDKit::ROMol::numBonds {0}
protected

Definition at line 821 of file ROMol.h.


The documentation for this class was generated from the following file: