ROMol is a molecule class that is intended to have a fixed topology. More...

#include <ROMol.h>

Inheritance diagram for RDKit::ROMol:

Public Member Functions
	ROMol ()
	ROMol (const ROMol &other, bool quickCopy=false)
	copy constructor with a twist
	ROMol (const std::string &binStr)
	construct a molecule from a pickle string
virtual	~ROMol ()
ATOM_SPTR	operator[] (const vertex_descriptor &v)
const ATOM_SPTR	operator[] (const vertex_descriptor &v) const
BOND_SPTR	operator[] (const edge_descriptor &e)
const BOND_SPTR	operator[] (const edge_descriptor &e) const
Atoms

unsigned int	getNumAtoms (bool onlyHeavy=1) const
	returns our number of Atoms
Atom *	getAtomWithIdx (unsigned int idx)
	returns a pointer to a particular Atom
const Atom *	getAtomWithIdx (unsigned int idx) const
unsigned int	getAtomDegree (const Atom *at) const
	returns the degree (number of neighbors) of an Atom in the graph
unsigned int	getAtomDegree (ATOM_SPTR at) const
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
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
Bookmarks

void	setAtomBookmark (ATOM_SPTR at, int mark)
	associates an Atom pointer with a bookmark
void	setAtomBookmark (Atom *at, int mark)
Atom *	getAtomWithBookmark (int mark)
	returns the first Atom associated with the `bookmark` provided
ATOM_PTR_LIST &	getAllAtomsWithBookmark (int mark)
	returns all Atoms associated with the `bookmark` provided
void	clearAtomBookmark (const int mark)
	removes a `bookmark` from our collection
void	clearAtomBookmark (const int mark, const Atom *atom)
	removes a particular Atom from the list associated with the `bookmark`
void	clearAtomBookmark (const int mark, ATOM_SPTR atom)
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_SPTR bond, int mark)
	associates a Bond pointer with a bookmark
void	setBondBookmark (Bond *bond, int mark)
Bond *	getBondWithBookmark (int mark)
	returns the first Bond associated with the `bookmark` provided
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	clearBondBookmark (int mark, BOND_SPTR bond)
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
ADJ_ITER_PAIR	getAtomNeighbors (ATOM_SPTR at) const
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
BOND_ITER_PAIR	getEdges () const
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
AtomIterator	endAtoms ()
	get an AtomIterator pointing at the end of our Atoms
ConstAtomIterator	endAtoms () const
BondIterator	beginBonds ()
	get a BondIterator pointing at our first Bond
ConstBondIterator	beginBonds () const
BondIterator	endBonds ()
	get a BondIterator pointing at the end of our Bonds
ConstBondIterator	endBonds () const
AromaticAtomIterator	beginAromaticAtoms ()
	get an AtomIterator pointing at our first aromatic Atom
ConstAromaticAtomIterator	beginAromaticAtoms () const
AromaticAtomIterator	endAromaticAtoms ()
	get an AtomIterator pointing at the end of our Atoms
ConstAromaticAtomIterator	endAromaticAtoms () const
HeteroatomIterator	beginHeteros ()
	get an AtomIterator pointing at our first hetero Atom
ConstHeteroatomIterator	beginHeteros () const
HeteroatomIterator	endHeteros ()
	get an AtomIterator pointing at the end of our Atoms
ConstHeteroatomIterator	endHeteros () const
QueryAtomIterator	beginQueryAtoms (QueryAtom const *query)
	get an AtomIterator pointing at our first Atom that matches `query`
ConstQueryAtomIterator	beginQueryAtoms (QueryAtom const *) const
QueryAtomIterator	endQueryAtoms ()
	gte an AtomIterator pointing at the end of our Atoms
ConstQueryAtomIterator	endQueryAtoms () const
ConformerIterator	beginConformers ()
ConformerIterator	endConformers ()
ConstConformerIterator	beginConformers () const
ConstConformerIterator	endConformers () const
Properties

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 char *key, T val, bool computed=false) const
	sets a `property` value
template<typename T >
void	setProp (const std::string key, T val, bool computed=false) const
template<typename T >
void	getProp (const char *key, T &res) const
	allows retrieval of a particular property value
template<typename T >
void	getProp (const std::string key, T &res) const
bool	hasProp (const char *key) const
	returns whether or not we have a `property` with name `key`
bool	hasProp (const std::string key) const
void	clearProp (const char *key) const
	clears the value of a `property`
void	clearProp (const std::string key) const
void	clearComputedProps (bool includeRings=true) const
	clears all of our `computed` `properties`
void	updatePropertyCache (bool strict=true)
	calculates any of our lazy `properties`
Misc

void	debugMol (std::ostream &str) const
	sends some debugging info to a stream
Friends
class	MolPickler
class	RWMol

Detailed Description

ROMol is a molecule class that is intended to have a fixed topology.

This is the primary class for most molecule operations.

If you need to be manipulating the molecule (e.g. adding or deleting atoms or bonds, use an RWMol instead.

Notes:

each ROMol maintains a Dict of properties:
- Each property is keyed by name and can store an arbitrary type.
- Properties can be marked as calculated, in which case they will be cleared when the clearComputedProps() method is called.
- Because they have no impact upon chemistry, all property operations are const, this allows extra flexibility for clients who need to store extra data on ROMol objects.

each ROMol has collections of bookmarks for Atoms and Bonds:
- the Atom bookmarks and Bond bookmarks are stored separately from each other
- each bookmark, an integer, can map to more than one Atom or Bond
- these are currently used in molecule construction, but could also be useful for reaction mapping and the like

information about rings (SSSR and the like) is stored in the molecule's RingInfo pointer.

Definition at line 102 of file ROMol.h.

Constructor & Destructor Documentation

RDKit::ROMol::ROMol ( ) [inline]

Definition at line 172 of file ROMol.h.

RDKit::ROMol::ROMol	(	const ROMol &	other,
		bool	quickCopy = `false`
	)			`[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).

Definition at line 181 of file ROMol.h.

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

construct a molecule from a pickle string

virtual RDKit::ROMol::~ROMol ( ) [inline, virtual]

Definition at line 185 of file ROMol.h.

Member Function Documentation

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 the conformation if true otherwise it is assumed that the conformation already has an (unique) ID set

AromaticAtomIterator RDKit::ROMol::beginAromaticAtoms ( )

get an AtomIterator pointing at our first aromatic Atom

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.

AtomIterator RDKit::ROMol::beginAtoms ( )

get an AtomIterator pointing at our first Atom

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.

BondIterator RDKit::ROMol::beginBonds ( )

get a BondIterator pointing at our first Bond

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.

ConformerIterator RDKit::ROMol::beginConformers ( ) [inline]

Definition at line 463 of file ROMol.h.

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

Definition at line 471 of file ROMol.h.

HeteroatomIterator RDKit::ROMol::beginHeteros ( )

get an AtomIterator pointing at our first hetero Atom

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.

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

get an AtomIterator pointing at our first Atom that matches query

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.

void RDKit::ROMol::clearAllAtomBookmarks ( ) [inline]

blows out all atomic bookmarks

Definition at line 237 of file ROMol.h.

void RDKit::ROMol::clearAllBondBookmarks ( ) [inline]

blows out all bond bookmarks

Definition at line 258 of file ROMol.h.

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

removes a particular Atom from the list associated with the bookmark

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

removes a bookmark from our collection

void RDKit::ROMol::clearAtomBookmark	(	const int	mark,
		ATOM_SPTR	atom
	)			`[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 235 of file ROMol.h.

References clearAtomBookmark().

Referenced by clearAtomBookmark().

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

removes a particular Bond from the list associated with the bookmark

void RDKit::ROMol::clearBondBookmark	(	int	mark,
		BOND_SPTR	bond
	)			`[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 256 of file ROMol.h.

References clearBondBookmark().

Referenced by clearBondBookmark().

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

removes a bookmark from our collection

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

clears all of our computed properties

void RDKit::ROMol::clearConformers ( ) [inline]

Clear all the conformations on the molecule.

Definition at line 282 of file ROMol.h.

void RDKit::ROMol::clearProp ( const std::string key ) 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 584 of file ROMol.h.

References RDKit::Dict::clearVal(), getProp(), and RDKit::Dict::setVal().

void RDKit::ROMol::clearProp ( const char * key ) const [inline]

clears the value of a property

Notes:

if no property with name key exists, a KeyErrorException will be thrown.
if the property is marked as computed, it will also be removed from our list of computedProperties

Definition at line 579 of file ROMol.h.

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

sends some debugging info to a stream

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.

AromaticAtomIterator RDKit::ROMol::endAromaticAtoms ( )

get an AtomIterator pointing at the end of our Atoms

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.

AtomIterator RDKit::ROMol::endAtoms ( )

get an AtomIterator pointing at the end of our Atoms

BondIterator RDKit::ROMol::endBonds ( )

get a BondIterator pointing at the end of our Bonds

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.

ConformerIterator RDKit::ROMol::endConformers ( ) [inline]

Definition at line 467 of file ROMol.h.

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

Definition at line 475 of file ROMol.h.

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.

HeteroatomIterator RDKit::ROMol::endHeteros ( )

get an AtomIterator pointing at the end of our Atoms

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.

QueryAtomIterator RDKit::ROMol::endQueryAtoms ( )

gte an AtomIterator pointing at the end of our Atoms

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

returns all Atoms associated with the bookmark provided

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

returns all bonds associated with the bookmark provided

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

        ... molPtr is a const ROMol * ...
        ... atomPtr is a const Atom * ...
        ROMol::OEDGE_ITER beg,end;
        boost::tie(beg,end) = molPtr->getAtomBonds(atomPtr);
        while(beg!=end){
          const BOND_SPTR bond=(*molPtr)[*beg];
          ... do something with the Bond ...
          ++beg;
        }

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

        ... molPtr is a ROMol * ...
        ... atomPtr is a const Atom * ...
        ROMol::OEDGE_ITER beg,end;
        boost::tie(beg,end) = molPtr->getAtomBonds(atomPtr);
        while(beg!=end){
          BOND_SPTR bond=(*molPtr)[*beg];
          ... do something with the Bond ...
          ++beg;
        }

Referenced by RDKit::queryAtomRingBondCount().

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

returns a pointer to all of our atom bookmarks

Definition at line 241 of file ROMol.h.

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

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

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

        ... molPtr is a const ROMol & ...
        ... atomPtr is a const Atom * ...
        ROMol::ADJ_ITER nbrIdx,endNbrs;
        boost::tie(nbrIdx,endNbrs) = molPtr.getAtomNeighbors(atomPtr);
        while(nbrIdx!=endNbrs){
          const ATOM_SPTR at=molPtr[*nbrIdx];
          ... do something with the Atom ...
          ++nbrIdx;
        }

ADJ_ITER_PAIR RDKit::ROMol::getAtomNeighbors ( ATOM_SPTR at ) const

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

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

returns the first Atom associated with the bookmark provided

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

returns a pointer to a particular Atom

Referenced by RDKit::RWMol::getLastAtom().

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.

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

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

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.

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

returns a pointer to all of our bond bookmarks

Definition at line 262 of file ROMol.h.

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

returns the first Bond associated with the bookmark provided

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.

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

returns a pointer to a particular Bond

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

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

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;
        }

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.

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

returns our number of Atoms

Referenced by RDKit::RWMol::getLastAtom(), and RDKit::MolChemicalFeatureDef::setWeights().

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

returns our number of Bonds

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

Definition at line 293 of file ROMol.h.

template<typename T >

void RDKit::ROMol::getProp	(	const char *	key,
		T &	res
	)			const `[inline]`

allows retrieval of a particular property value

Parameters:

	key	the name under which the `property` should be stored. If a `property` is already stored under this name, it will be replaced.
	res	a reference to the storage location for the value.

Notes:

if no property with name key exists, a KeyErrorException will be thrown.
the boost::lexical_cast machinery is used to attempt type conversions. If this fails, a boost::bad_lexical_cast exception will be thrown.

Definition at line 549 of file ROMol.h.

References RDKit::Dict::getVal().

Referenced by clearProp(), getPropList(), and setProp().

template<typename T >

void RDKit::ROMol::getProp	(	const std::string	key,
		T &	res
	)			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 554 of file ROMol.h.

References RDKit::Dict::getVal().

STR_VECT RDKit::ROMol::getPropList	(	bool	includePrivate = `true`,
		bool	includeComputed = `true`
	)			const `[inline]`

returns a list with the names of our properties

Definition at line 485 of file ROMol.h.

References getProp(), hasProp(), and RDKit::Dict::keys().

RingInfo* RDKit::ROMol::getRingInfo ( ) const [inline]

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

Definition at line 305 of file ROMol.h.

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

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 412 of file ROMol.h.

Referenced by RDKit::queryAtomRingBondCount().

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;
        }

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.

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

queries whether or not any atoms are associated with a bookmark

Definition at line 239 of file ROMol.h.

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

queries whether or not any bonds are associated with a bookmark

Definition at line 260 of file ROMol.h.

bool RDKit::ROMol::hasProp ( const std::string key ) 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 565 of file ROMol.h.

References RDKit::Dict::hasVal().

bool RDKit::ROMol::hasProp ( const char * key ) const [inline]

returns whether or not we have a property with name key

Definition at line 560 of file ROMol.h.

References RDKit::Dict::hasVal().

Referenced by getPropList().

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

Definition at line 616 of file ROMol.h.

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

Definition at line 619 of file ROMol.h.

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

Definition at line 615 of file ROMol.h.

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

Definition at line 618 of file ROMol.h.

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

Delete the conformation with the specified ID.

void RDKit::ROMol::setAtomBookmark	(	ATOM_SPTR	at,
		int	mark
	)			`[inline]`

associates an Atom pointer with a bookmark

Definition at line 223 of file ROMol.h.

void RDKit::ROMol::setAtomBookmark	(	Atom *	at,
		int	mark
	)			`[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 225 of file ROMol.h.

void RDKit::ROMol::setBondBookmark	(	BOND_SPTR	bond,
		int	mark
	)			`[inline]`

associates a Bond pointer with a bookmark

Definition at line 244 of file ROMol.h.

void RDKit::ROMol::setBondBookmark	(	Bond *	bond,
		int	mark
	)			`[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 246 of file ROMol.h.

template<typename T >

void RDKit::ROMol::setProp	(	const char *	key,
		T	val,
		bool	computed = `false`
	)			const `[inline]`

sets a property value

Parameters:

	key	the name under which the `property` should be stored. If a `property` is already stored under this name, it will be replaced.
	val	the value to be stored
	computed	(optional) allows the `property` to be flagged `computed`.

Definition at line 516 of file ROMol.h.

template<typename T >

void RDKit::ROMol::setProp	(	const std::string	key,
		T	val,
		bool	computed = `false`
	)			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 522 of file ROMol.h.

References getProp(), and RDKit::Dict::setVal().

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 Function Documentation

friend class MolPickler [friend]

Definition at line 104 of file ROMol.h.

friend class RWMol [friend]

Definition at line 105 of file ROMol.h.

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

ROMol.h

RDKit::ROMol Class Reference

Public Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation