RDKit::ROMol Class Reference

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

#include <ROMol.h>

Inheritance diagram for RDKit::ROMol:

List of all members.

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 98 of file ROMol.h.

Constructor & Destructor Documentation

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

Definition at line 168 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 177 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 181 of file ROMol.h.

Member Function Documentation

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

returns our number of Atoms

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

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

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

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

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

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

returns our number of Bonds

Referenced by RDKit::FragCatalogEntry::getOrder().

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

returns a pointer to a particular Bond

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

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

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

associates an Atom pointer with a bookmark

Definition at line 219 of file ROMol.h.

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

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

Definition at line 221 of file ROMol.h.

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

returns the first Atom associated with the bookmark provided

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

returns all Atoms associated with the bookmark provided

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

removes a bookmark from our collection

Referenced by clearAtomBookmark().

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,
		ATOM_SPTR	atom
	)			`[inline]`

Definition at line 231 of file ROMol.h.

References clearAtomBookmark().

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

blows out all atomic bookmarks

Definition at line 233 of file ROMol.h.

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

queries whether or not any atoms are associated with a bookmark

Definition at line 235 of file ROMol.h.

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

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

returns a pointer to all of our atom bookmarks

Definition at line 237 of file ROMol.h.

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

associates a Bond pointer with a bookmark

Definition at line 240 of file ROMol.h.

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

Definition at line 242 of file ROMol.h.

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

returns the first Bond associated with the bookmark provided

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

returns all bonds associated with the bookmark provided

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

removes a bookmark from our collection

Referenced by clearBondBookmark().

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]`

Definition at line 252 of file ROMol.h.

References clearBondBookmark().

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

blows out all bond bookmarks

Definition at line 254 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 256 of file ROMol.h.

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

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

returns a pointer to all of our bond bookmarks

Definition at line 258 of file ROMol.h.

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

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

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

Delete the conformation with the specified ID.

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

Clear all the conformations on the molecule.

Definition at line 278 of file ROMol.h.

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

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

Definition at line 289 of file ROMol.h.

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

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

Definition at line 301 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().

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

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_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;
        }

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;
        }

ATOM_ITER_PAIR RDKit::ROMol::getVertices ( ) const

BOND_ITER_PAIR RDKit::ROMol::getEdges ( ) const

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 408 of file ROMol.h.

Referenced by RDKit::queryAtomRingBondCount().

AtomIterator RDKit::ROMol::beginAtoms ( )

get an AtomIterator pointing at our first Atom

ConstAtomIterator RDKit::ROMol::beginAtoms ( ) const

AtomIterator RDKit::ROMol::endAtoms ( )

get an AtomIterator pointing at the end of our Atoms

ConstAtomIterator RDKit::ROMol::endAtoms ( ) const

BondIterator RDKit::ROMol::beginBonds ( )

get a BondIterator pointing at our first Bond

ConstBondIterator RDKit::ROMol::beginBonds ( ) const

BondIterator RDKit::ROMol::endBonds ( )

get a BondIterator pointing at the end of our Bonds

ConstBondIterator RDKit::ROMol::endBonds ( ) const

AromaticAtomIterator RDKit::ROMol::beginAromaticAtoms ( )

get an AtomIterator pointing at our first aromatic Atom

ConstAromaticAtomIterator RDKit::ROMol::beginAromaticAtoms ( ) const

AromaticAtomIterator RDKit::ROMol::endAromaticAtoms ( )

get an AtomIterator pointing at the end of our Atoms

ConstAromaticAtomIterator RDKit::ROMol::endAromaticAtoms ( ) const

HeteroatomIterator RDKit::ROMol::beginHeteros ( )

get an AtomIterator pointing at our first hetero Atom

ConstHeteroatomIterator RDKit::ROMol::beginHeteros ( ) const

HeteroatomIterator RDKit::ROMol::endHeteros ( )

get an AtomIterator pointing at the end of our Atoms

ConstHeteroatomIterator RDKit::ROMol::endHeteros ( ) const

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

QueryAtomIterator RDKit::ROMol::endQueryAtoms ( )

gte an AtomIterator pointing at the end of our Atoms

ConstQueryAtomIterator RDKit::ROMol::endQueryAtoms ( ) const

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

Definition at line 459 of file ROMol.h.

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

Definition at line 463 of file ROMol.h.

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

Definition at line 467 of file ROMol.h.

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

Definition at line 471 of file ROMol.h.

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 481 of file ROMol.h.

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

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 512 of file ROMol.h.

template<typename T>

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

Definition at line 518 of file ROMol.h.

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

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 545 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]`

Definition at line 550 of file ROMol.h.

References RDKit::Dict::getVal().

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

returns whether or not we have a property with name key

Definition at line 556 of file ROMol.h.

References RDKit::Dict::hasVal().

Referenced by getPropList().

bool RDKit::ROMol::hasProp ( const std::string key ) const [inline]

Definition at line 561 of file ROMol.h.

References RDKit::Dict::hasVal().

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 575 of file ROMol.h.

void RDKit::ROMol::clearProp ( const std::string key ) const [inline]

Definition at line 580 of file ROMol.h.

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

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

clears all of our computed properties

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

calculates any of our lazy properties

Notes:

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

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

sends some debugging info to a stream

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

Definition at line 611 of file ROMol.h.

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

Definition at line 612 of file ROMol.h.

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

Definition at line 614 of file ROMol.h.

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

Definition at line 615 of file ROMol.h.

Friends And Related Function Documentation

friend class MolPickler [friend]

Definition at line 100 of file ROMol.h.

friend class RWMol [friend]

Definition at line 101 of file ROMol.h.

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

ROMol.h


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