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
 
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...
 
virtual ~ROMol ()
 
Atoms
unsigned int getNumAtoms (bool onlyExplicit=1) const
 returns our number of atoms More...
 
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...
 
const MolGraphgetTopology () 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
 
- Public Member Functions inherited from RDKit::RDProps
 RDProps ()
 
 RDProps (const RDProps &rhs)
 
RDPropsoperator= (const RDProps &rhs)
 
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...
 

Friends

class MolPickler
 
class RWMol
 

Misc

RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & getSubstanceGroups (ROMol &)
 
const RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & getSubstanceGroups (const ROMol &)
 
unsigned int numBonds
 
void debugMol (std::ostream &str) const
 sends some debugging info to a stream More...
 
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...
 

Additional Inherited Members

- Protected Attributes inherited from RDKit::RDProps
Dict d_props
 

Detailed Description

Definition at line 171 of file ROMol.h.

Constructor & Destructor Documentation

◆ ROMol() [1/3]

RDKit::ROMol::ROMol ( )
inline

Definition at line 270 of file ROMol.h.

◆ ROMol() [2/3]

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 283 of file ROMol.h.

◆ ROMol() [3/3]

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

construct a molecule from a pickle string

◆ ~ROMol()

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

Definition at line 292 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

◆ 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 249 of file ROMol.h.

Referenced by RDKit::FileParserUtils::getAtomPropertyList().

◆ atoms() [2/2]

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

Definition at line 251 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

◆ 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 615 of file ROMol.h.

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

◆ beginConformers() [2/2]

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

Definition at line 619 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 264 of file ROMol.h.

◆ bonds() [2/2]

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

Definition at line 266 of file ROMol.h.

◆ clearAllAtomBookmarks()

void RDKit::ROMol::clearAllAtomBookmarks ( )
inline

blows out all atomic bookmarks

Definition at line 383 of file ROMol.h.

◆ clearAllBondBookmarks()

void RDKit::ROMol::clearAllBondBookmarks ( )
inline

blows out all bond bookmarks

Definition at line 406 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 429 of file ROMol.h.

◆ debugMol()

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

sends some debugging info to a stream

◆ 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

◆ 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 617 of file ROMol.h.

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

◆ endConformers() [2/2]

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

Definition at line 623 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
}

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 387 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::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 308 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 313 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 345 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 351 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::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 410 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 331 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 336 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;
}

◆ 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()

◆ getNumBonds()

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

◆ getNumConformers()

unsigned int RDKit::ROMol::getNumConformers ( ) const
inline

◆ 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 662 of file ROMol.h.

◆ getTopology()

const MolGraph& 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]);

Definition at line 555 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 385 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 408 of file ROMol.h.

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

◆ needsUpdatePropertyCache()

bool RDKit::ROMol::needsUpdatePropertyCache ( ) const

◆ operator[]() [1/4]

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

Definition at line 654 of file ROMol.h.

◆ operator[]() [2/4]

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

Definition at line 655 of file ROMol.h.

◆ operator[]() [3/4]

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

Definition at line 649 of file ROMol.h.

◆ operator[]() [4/4]

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

Definition at line 650 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 366 of file ROMol.h.

◆ setAtomBookmark()

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

associates an Atom pointer with a bookmark

Definition at line 362 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 390 of file ROMol.h.

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

◆ updatePropertyCache()

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

calculates any of our lazy properties

Notes:

Referenced by RDKit::CachedTrustedSmilesMolHolder::getMol().

Friends And Related Function Documentation

◆ getSubstanceGroups [1/2]

const RDKIT_GRAPHMOL_EXPORT 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 173 of file ROMol.h.

◆ RWMol

friend class RWMol
friend

Definition at line 174 of file ROMol.h.

Member Data Documentation

◆ numBonds

unsigned int RDKit::ROMol::numBonds
protected

Definition at line 684 of file ROMol.h.


The documentation for this class was generated from the following file:
RDKit::ROMol::ROMol
ROMol()
Definition: ROMol.h:270
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition: types.h:254
boost
Definition: RDLog.h:21
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