RDKit::ROMol Class Reference

#include <ROMol.h>

Inheritance diagram for RDKit::ROMol:

Public Member Functions
CXXAtomIterator< MolGraph, Atom * >	atoms ()
	C++11 Range iterator.
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
	ROMol (const std::string &binStr)
	construct a molecule from a pickle string
	ROMol (const std::string &binStr, unsigned int propertyFlags)
	construct a molecule from a pickle string
	ROMol (ROMol &&o) noexcept
ROMol &	operator= (ROMol &&o) noexcept
ROMol &	operator= (const ROMol &)=delete
virtual	~ROMol ()
Atom *	operator[] (const vertex_descriptor &v)
const Atom *	operator[] (const vertex_descriptor &v) const
Bond *	operator[] (const edge_descriptor &e)
const Bond *	operator[] (const edge_descriptor &e) const
const std::vector< StereoGroup > &	getStereoGroups () const
	Gets a reference to the groups of atoms with relative stereochemistry.
void	setStereoGroups (std::vector< StereoGroup > stereo_groups)
	Sets groups of atoms with relative stereochemistry.
Atoms
unsigned int	getNumAtoms () const
	returns our number of atoms
unsigned int	getNumAtoms (bool onlyExplicit) const
unsigned int	getNumHeavyAtoms () const
	returns our number of heavy atoms (atomic number > 1)
Atom *	getAtomWithIdx (unsigned int idx)
	returns a pointer to a particular Atom
const Atom *	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.
template<class U>
Atom *	getAtomWithIdx (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.
template<class U>
const Atom *	getAtomWithIdx (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.
unsigned int	getAtomDegree (const Atom *at) const
	returns the degree (number of neighbors) of an Atom in the graph
Bonds
unsigned int	getNumBonds (bool onlyHeavy=1) const
	returns our number of Bonds
Bond *	getBondWithIdx (unsigned int idx)
	returns a pointer to a particular Bond
const Bond *	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.
template<class U>
Bond *	getBondWithIdx (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.
template<class U>
const Bond *	getBondWithIdx (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.
Bond *	getBondBetweenAtoms (unsigned int idx1, unsigned int idx2)
	returns a pointer to the bond between two atoms, Null on failure
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 only in what argument(s) it accepts.
template<class U, class V>
Bond *	getBondBetweenAtoms (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.
template<class U, class V>
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 only in what argument(s) it accepts.
Bookmarks
void	setAtomBookmark (Atom *at, int mark)
	associates an Atom pointer with a bookmark
void	replaceAtomBookmark (Atom *at, int mark)
	associates an Atom pointer with a bookmark
Atom *	getAtomWithBookmark (int mark)
	returns the first Atom associated with the bookmark provided
Atom *	getUniqueAtomWithBookmark (int mark)
ATOM_PTR_LIST &	getAllAtomsWithBookmark (int mark)
	returns all Atoms associated with the bookmark provided
void	clearAtomBookmark (int mark)
	removes a bookmark from our collection
void	clearAtomBookmark (int mark, const Atom *atom)
	removes a particular Atom from the list associated with the bookmark
void	clearAllAtomBookmarks ()
	blows out all atomic bookmarks
bool	hasAtomBookmark (int mark) const
	queries whether or not any atoms are associated with a bookmark
ATOM_BOOKMARK_MAP *	getAtomBookmarks ()
	returns a pointer to all of our atom bookmarks
void	setBondBookmark (Bond *bond, int mark)
	associates a Bond pointer with a bookmark
Bond *	getBondWithBookmark (int mark)
	returns the first Bond associated with the bookmark provided
Bond *	getUniqueBondWithBookmark (int mark)
BOND_PTR_LIST &	getAllBondsWithBookmark (int mark)
	returns all bonds associated with the bookmark provided
void	clearBondBookmark (int mark)
	removes a bookmark from our collection
void	clearBondBookmark (int mark, const Bond *bond)
	removes a particular Bond from the list associated with the bookmark
void	clearAllBondBookmarks ()
	blows out all bond bookmarks
bool	hasBondBookmark (int mark) const
	queries whether or not any bonds are associated with a bookmark
BOND_BOOKMARK_MAP *	getBondBookmarks ()
	returns a pointer to all of our bond bookmarks
Conformers
const Conformer &	getConformer (int id=-1) const
Conformer &	getConformer (int id=-1)
void	removeConformer (unsigned int id)
	Delete the conformation with the specified ID.
void	clearConformers ()
	Clear all the conformations on the molecule.
unsigned int	addConformer (Conformer *conf, bool assignId=false)
	Add a new conformation to the molecule.
unsigned int	getNumConformers () const
Topology
RingInfo *	getRingInfo () const
ADJ_ITER_PAIR	getAtomNeighbors (Atom const *at) const
	provides access to all neighbors around an Atom
OBOND_ITER_PAIR	getAtomBonds (Atom const *at) const
	provides access to all Bond objects connected to an Atom
ATOM_ITER_PAIR	getVertices ()
	returns an iterator pair for looping over all Atoms
BOND_ITER_PAIR	getEdges ()
	returns an iterator pair for looping over all Bonds
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.
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.
MolGraph const &	getTopology () const
	brief returns a pointer to our underlying BGL object
Iterators
AtomIterator	beginAtoms ()
	get an AtomIterator pointing at our first Atom
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.
AtomIterator	endAtoms ()
	get an AtomIterator pointing at the end of our Atoms
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.
BondIterator	beginBonds ()
	get a BondIterator pointing at our first Bond
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.
BondIterator	endBonds ()
	get a BondIterator pointing at the end of our Bonds
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.
AromaticAtomIterator	beginAromaticAtoms ()
	get an AtomIterator pointing at our first aromatic Atom
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.
AromaticAtomIterator	endAromaticAtoms ()
	get an AtomIterator pointing at the end of our Atoms
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.
HeteroatomIterator	beginHeteros ()
	get an AtomIterator pointing at our first hetero Atom
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.
HeteroatomIterator	endHeteros ()
	get an AtomIterator pointing at the end of our Atoms
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.
bool	hasQuery () const
	if the Mol has any Query atoms or bonds
QueryAtomIterator	beginQueryAtoms (QueryAtom const *query)
	get an AtomIterator pointing at our first Atom that matches query
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.
QueryAtomIterator	endQueryAtoms ()
	get an AtomIterator pointing at the end of our Atoms
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.
MatchingAtomIterator	beginMatchingAtoms (bool(*query)(Atom *))
	get an AtomIterator pointing at our first Atom that matches query
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.
MatchingAtomIterator	endMatchingAtoms ()
	get an AtomIterator pointing at the end of our Atoms
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.
ConformerIterator	beginConformers ()
ConformerIterator	endConformers ()
ConstConformerIterator	beginConformers () const
ConstConformerIterator	endConformers () const
Properties
void	clearComputedProps (bool includeRings=true) const
	clears all of our computed properties
void	updatePropertyCache (bool strict=true)
	calculates any of our lazy properties
bool	needsUpdatePropertyCache () const
void	clearPropertyCache ()
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)
RDProps &	operator= (const RDProps &rhs)
	RDProps (RDProps &&o) noexcept=default
RDProps &	operator= (RDProps &&rhs) noexcept=default
void	clear ()
const Dict &	getDict () const
	gets the underlying Dictionary
Dict &	getDict ()
STR_VECT	getPropList (bool includePrivate=true, bool includeComputed=true) const
	returns a list with the names of our properties
template<typename T>
void	setProp (const std::string &key, T val, bool computed=false) const
	sets a property value
template<typename T>
void	getProp (const std::string &key, T &res) const
	allows retrieval of a particular property value
template<typename T>
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.
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.
void	clearProp (const std::string &key) const
	clears the value of a property
void	clearComputedProps () const
	clears all of our computed properties
void	updateProps (const RDProps &source, bool preserveExisting=false)
	update the properties from another

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

Detailed Description

Definition at line 199 of file ROMol.h.

Constructor & Destructor Documentation

ROMol() [1/5]

RDKit::ROMol::ROMol ( )

inline

Definition at line 322 of file ROMol.h.

References RDKit::RDProps::RDProps().

Referenced by getSubstanceGroups, getSubstanceGroups, RDKit::RWMol::insertMol(), operator=(), operator=(), ROMol(), ROMol(), RWMol, RDKit::RWMol::RWMol(), RDKit::RWMol::RWMol(), RDKit::RWMol::RWMol(), and RDKit::RWMol::RWMol().

ROMol() [2/5]

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

inline

copy constructor with a twist

Parameters

other	the 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 335 of file ROMol.h.

References numBonds, rdcast, RDKit::RDProps::RDProps(), and ROMol().

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 346 of file ROMol.h.

References atoms(), bonds(), numBonds, RDKit::RDProps::RDProps(), and ROMol().

~ROMol()

virtual RDKit::ROMol::~ROMol ( )

inlinevirtual

Definition at line 414 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 301 of file ROMol.h.

References getAtomBonds().

atomBonds() [2/2]

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

inline

Definition at line 296 of file ROMol.h.

References getAtomBonds().

atomNeighbors() [1/2]

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

inline

Definition at line 289 of file ROMol.h.

References getAtomNeighbors().

atomNeighbors() [2/2]

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

inline

Definition at line 284 of file ROMol.h.

References getAtomNeighbors().

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 277 of file ROMol.h.

Referenced by RDKit::MolDraw2D_detail::addAtomIndices(), RDKit::FileParserUtils::createAtomBoolPropertyList(), RDKit::FileParserUtils::createAtomDoublePropertyList(), RDKit::FileParserUtils::createAtomIntPropertyList(), RDKit::FileParserUtils::createAtomStringPropertyList(), RDKit::FileParserUtils::getAtomPropertyList(), operator=(), and ROMol().

atoms() [2/2]

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

inline

Definition at line 279 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 743 of file ROMol.h.

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

beginConformers() [2/2]

ConstConformerIterator RDKit::ROMol::beginConformers ( ) const

inline

Definition at line 747 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(*

query )(Atom *)

)

get an AtomIterator pointing at our first Atom that matches query

beginMatchingAtoms() [2/2]

ConstMatchingAtomIterator RDKit::ROMol::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.

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 316 of file ROMol.h.

Referenced by RDKit::MolDraw2D_detail::addBondIndices(), RDKit::FileParserUtils::createBondBoolPropertyList(), RDKit::FileParserUtils::createBondDoublePropertyList(), RDKit::FileParserUtils::createBondIntPropertyList(), RDKit::FileParserUtils::createBondStringPropertyList(), operator=(), and ROMol().

bonds() [2/2]

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

inline

Definition at line 318 of file ROMol.h.

clearAllAtomBookmarks()

void RDKit::ROMol::clearAllAtomBookmarks ( )

inline

blows out all atomic bookmarks

Definition at line 508 of file ROMol.h.

clearAllBondBookmarks()

void RDKit::ROMol::clearAllBondBookmarks ( )

inline

blows out all bond bookmarks

Definition at line 531 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 554 of file ROMol.h.

clearPropertyCache()

void RDKit::ROMol::clearPropertyCache

(

)

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

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 745 of file ROMol.h.

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

endConformers() [2/2]

ConstConformerIterator RDKit::ROMol::endConformers ( ) const

inline

Definition at line 751 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

at	the 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 atomBonds(), atomBonds(), 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 512 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

at	the 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 atomNeighbors(), atomNeighbors(), 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 433 of file ROMol.h.

References getAtomWithIdx(), and rdcast.

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 438 of file ROMol.h.

References getAtomWithIdx(), and rdcast.

getAtomWithIdx() [3/4]

Atom * RDKit::ROMol::getAtomWithIdx

(

unsigned int

idx

)

returns a pointer to a particular Atom

Referenced by RDKit::SLNParse::addBranchToMol(), RDKit::FileParserUtils::applyMolListPropsToAtoms(), RDKit::FileParserUtils::applyMolListPropToAtoms(), getAtomWithIdx(), getAtomWithIdx(), RDKit::RWMol::getLastAtom(), and RDKit::FileParserUtils::processMolPropertyList().

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 470 of file ROMol.h.

References getBondBetweenAtoms(), and rdcast.

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 476 of file ROMol.h.

References getBondBetweenAtoms(), and rdcast.

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 getBondBetweenAtoms(), getBondBetweenAtoms(), and RDKit::MolEnumerator::utils::getMolLinkNodes().

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 535 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 456 of file ROMol.h.

References getBondWithIdx(), and rdcast.

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 461 of file ROMol.h.

References getBondWithIdx(), and rdcast.

getBondWithIdx() [3/4]

Bond * RDKit::ROMol::getBondWithIdx

(

unsigned int

idx

)

returns a pointer to a particular Bond

Referenced by getBondWithIdx(), getBondWithIdx(), and RDKit::FileParserUtils::processMolPropertyList().

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

Referenced by RDKit::ForceFieldsHelper::createEmptyForceFieldForMol().

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() [1/2]

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

inline

returns our number of atoms

Definition at line 421 of file ROMol.h.

References rdcast.

Referenced by RDKit::SLNParse::addBranchToMol(), RDKit::FileParserUtils::applyMolListPropsToAtoms(), RDKit::FileParserUtils::applyMolListPropToAtoms(), RDKit::Canon::BreakTies(), RDKit::RWMol::getLastAtom(), RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST(), RDKit::FileParserUtils::processMolPropertyList(), and RDKit::Canon::RefinePartitions().

getNumAtoms() [2/2]

unsigned int RDKit::ROMol::getNumAtoms

(

bool

onlyExplicit

)

const

getNumBonds()

unsigned int RDKit::ROMol::getNumBonds

(

bool

onlyHeavy = 1

)

const

returns our number of Bonds

Referenced by RDKit::FileParserUtils::getV3000CTAB(), and RDKit::FileParserUtils::processMolPropertyList().

getNumConformers()

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

inline

Definition at line 568 of file ROMol.h.

References rdcast.

Referenced by RDKit::MMFF::MMFFOptimizeMoleculeConfs(), RDKit::ForceFieldsHelper::OptimizeMoleculeConfs(), and RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST().

getNumHeavyAtoms()

unsigned int RDKit::ROMol::getNumHeavyAtoms

(

)

const

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

getRingInfo()

RingInfo * RDKit::ROMol::getRingInfo ( ) const

inline

returns a pointer to our RingInfo structure Note: the client should not delete this.

Definition at line 577 of file ROMol.h.

Referenced by RDKit::queryAtomHasRingBond(), RDKit::queryAtomIsInRingOfSize(), RDKit::queryAtomMinRingSize(), RDKit::queryAtomRingBondCount(), RDKit::queryBondIsInRingOfSize(), RDKit::queryBondMinRingSize(), RDKit::queryIsAtomInNRings(), RDKit::queryIsAtomInRing(), RDKit::queryIsBondInNRings(), and RDKit::queryIsBondInRing().

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 791 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]);

Definition at line 680 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 510 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 533 of file ROMol.h.

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

hasQuery()

bool RDKit::ROMol::hasQuery

(

)

const

if the Mol has any Query atoms or bonds

needsUpdatePropertyCache()

bool RDKit::ROMol::needsUpdatePropertyCache

(

)

const

operator=() [1/2]

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

delete

References ROMol().

operator=() [2/2]

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

inlinenoexcept

Definition at line 373 of file ROMol.h.

References atoms(), bonds(), numBonds, RDKit::RDProps::operator=(), and ROMol().

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

operator[]() [1/4]

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

inline

Definition at line 783 of file ROMol.h.

operator[]() [2/4]

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

inline

Definition at line 784 of file ROMol.h.

operator[]() [3/4]

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

inline

Definition at line 778 of file ROMol.h.

operator[]() [4/4]

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

inline

Definition at line 779 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 491 of file ROMol.h.

setAtomBookmark()

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

inline

associates an Atom pointer with a bookmark

Definition at line 487 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 515 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_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.

updatePropertyCache()

void RDKit::ROMol::updatePropertyCache

(

bool

strict = true

)

calculates any of our lazy properties

Notes:

• this calls updatePropertyCache() on each of our Atoms and Bonds

Friends And Related Symbol Documentation

getSubstanceGroups [1/2]

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

friend

References ROMol().

getSubstanceGroups [2/2]

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

friend

References RDKIT_GRAPHMOL_EXPORT, and ROMol().

MolPickler

friend class MolPickler

friend

Definition at line 201 of file ROMol.h.

References MolPickler.

Referenced by MolPickler.

RWMol

friend class RWMol

friend

Definition at line 202 of file ROMol.h.

References ROMol(), and RWMol.

Referenced by RWMol.

Member Data Documentation

numBonds

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

protected

Definition at line 833 of file ROMol.h.

Referenced by RDKit::RWMol::clear(), operator=(), ROMol(), and ROMol().

---

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

• ROMol.h