#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

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 &)

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

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.

◆ 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.

◆ 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 RDKit::RDProps::clear().

◆ ~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.

◆ 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.

◆ atomNeighbors() [1/2]

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

inline

Definition at line 289 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 284 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 277 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 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(*)(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 316 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 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.

◆ 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 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.

◆ 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 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

◆ 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.

◆ 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.

◆ getAtomWithIdx() [3/4]

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

returns a pointer to a particular Atom

Referenced by 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 470 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 476 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().

◆ 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.

◆ 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.

◆ 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.

◆ 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

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.

Referenced by RDKit::FileParserUtils::applyMolListPropToAtoms(), RDKit::Canon::BreakTies(), RDKit::FMCS::TargetMatch::init(), RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST(), 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::FMCS::TargetMatch::init().

◆ getNumConformers()

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

inline

Definition at line 568 of file ROMol.h.

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::queryAtomRingMembership(), 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 790 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.

◆ 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.

◆ 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

◆ operator=() [2/2]

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

inlinenoexcept

Definition at line 373 of file ROMol.h.

◆ operator[]() [1/4]

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

inline

Definition at line 782 of file ROMol.h.

◆ operator[]() [2/4]

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

inline

Definition at line 783 of file ROMol.h.

◆ operator[]() [3/4]

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

inline

Definition at line 777 of file ROMol.h.

◆ operator[]() [4/4]

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

inline

Definition at line 778 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.

◆ 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.

◆ 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 & )

friend

◆ getSubstanceGroups [2/2]

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

friend

◆ MolPickler

friend class MolPickler

friend

Definition at line 201 of file ROMol.h.

◆ RWMol

friend class RWMol

friend

Definition at line 202 of file ROMol.h.

Member Data Documentation

◆ numBonds

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

protected

Definition at line 832 of file ROMol.h.

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

ROMol.h

Public Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ ROMol() [1/5]

◆ ROMol() [2/5]

◆ ROMol() [3/5]

◆ ROMol() [4/5]

◆ ROMol() [5/5]

◆ ~ROMol()

Member Function Documentation

◆ addConformer()

◆ atomBonds() [1/2]

◆ atomBonds() [2/2]

◆ atomNeighbors() [1/2]

◆ atomNeighbors() [2/2]

◆ atoms() [1/2]

◆ atoms() [2/2]

◆ beginAromaticAtoms() [1/2]

◆ beginAromaticAtoms() [2/2]

◆ beginAtoms() [1/2]

◆ beginAtoms() [2/2]

◆ beginBonds() [1/2]

◆ beginBonds() [2/2]

◆ beginConformers() [1/2]

◆ beginConformers() [2/2]

◆ beginHeteros() [1/2]

◆ beginHeteros() [2/2]

◆ beginMatchingAtoms() [1/2]

◆ beginMatchingAtoms() [2/2]

◆ beginQueryAtoms() [1/2]

◆ beginQueryAtoms() [2/2]

◆ bonds() [1/2]

◆ bonds() [2/2]

◆ clearAllAtomBookmarks()

◆ clearAllBondBookmarks()

◆ clearAtomBookmark() [1/2]

◆ clearAtomBookmark() [2/2]

◆ clearBondBookmark() [1/2]

◆ clearBondBookmark() [2/2]

◆ clearComputedProps()

◆ clearConformers()

◆ debugMol()

◆ endAromaticAtoms() [1/2]

◆ endAromaticAtoms() [2/2]

◆ endAtoms() [1/2]

◆ endAtoms() [2/2]

◆ endBonds() [1/2]

◆ endBonds() [2/2]

◆ endConformers() [1/2]

◆ endConformers() [2/2]

◆ endHeteros() [1/2]

◆ endHeteros() [2/2]

◆ endMatchingAtoms() [1/2]

◆ endMatchingAtoms() [2/2]

◆ endQueryAtoms() [1/2]

◆ endQueryAtoms() [2/2]

◆ getAllAtomsWithBookmark()

◆ getAllBondsWithBookmark()

◆ getAtomBonds()

◆ getAtomBookmarks()

◆ getAtomDegree()

◆ getAtomNeighbors()

◆ getAtomWithBookmark()

◆ getAtomWithIdx() [1/4]

◆ getAtomWithIdx() [2/4]

◆ getAtomWithIdx() [3/4]

◆ getAtomWithIdx() [4/4]

◆ getBondBetweenAtoms() [1/4]

◆ getBondBetweenAtoms() [2/4]

◆ getBondBetweenAtoms() [3/4]

◆ getBondBetweenAtoms() [4/4]

◆ getBondBookmarks()

◆ getBondWithBookmark()

◆ getBondWithIdx() [1/4]

◆ getBondWithIdx() [2/4]

◆ getBondWithIdx() [3/4]

◆ getBondWithIdx() [4/4]

◆ getConformer() [1/2]