RDKit::ROMol

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 Types

typedef
boost::property_map
< MolGraph,
vertex_atom_t > GRAPH_MOL_ATOM_PMAP

typedef
boost::property_map
< MolGraph,
edge_bond_t > GRAPH_MOL_BOND_PMAP

typedef
boost::graph_traits
< MolGraph > GRAPH_MOL_TRAITS

typedef
GRAPH_MOL_TRAITS::edge_iterator EDGE_ITER

typedef
GRAPH_MOL_TRAITS::out_edge_iterator OEDGE_ITER

typedef
GRAPH_MOL_TRAITS::vertex_iterator VERTEX_ITER

typedef
GRAPH_MOL_TRAITS::adjacency_iterator ADJ_ITER

typedef std::pair
< EDGE_ITER,
EDGE_ITER > BOND_ITER_PAIR

typedef std::pair
< OEDGE_ITER,
OEDGE_ITER > OBOND_ITER_PAIR

typedef std::pair
< VERTEX_ITER,
VERTEX_ITER > ATOM_ITER_PAIR

typedef std::pair
< ADJ_ITER, ADJ_ITER > ADJ_ITER_PAIR

typedef std::vector
< ATOM_SPTR > ATOM_SPTR_VECT

typedef
ATOM_SPTR_VECT::iterator ATOM_SPTR_VECT_I

typedef
ATOM_SPTR_VECT::const_iterator ATOM_SPTR_VECT_CI

typedef std::vector
< BOND_SPTR > BOND_SPTR_VECT

typedef
BOND_SPTR_VECT::iterator BOND_SPTR_VECT_I

typedef
BOND_SPTR_VECT::const_iterator BOND_SPTR_VECT_CI

typedef std::vector
< Atom * > ATOM_PTR_VECT

typedef
ATOM_PTR_VECT::iterator ATOM_PTR_VECT_I

typedef
ATOM_PTR_VECT::const_iterator ATOM_PTR_VECT_CI

typedef std::vector
< Bond * > BOND_PTR_VECT

typedef
BOND_PTR_VECT::iterator BOND_PTR_VECT_I

typedef
BOND_PTR_VECT::const_iterator BOND_PTR_VECT_CI

typedef std::list
< Atom * > ATOM_PTR_LIST

typedef
ATOM_PTR_LIST::iterator ATOM_PTR_LIST_I

typedef
ATOM_PTR_LIST::const_iterator ATOM_PTR_LIST_CI

typedef std::list
< Bond * > BOND_PTR_LIST

typedef
BOND_PTR_LIST::iterator BOND_PTR_LIST_I

typedef
BOND_PTR_LIST::const_iterator BOND_PTR_LIST_CI

typedef std::list
< CONFORMER_SPTR > CONF_SPTR_LIST

typedef
CONF_SPTR_LIST::iterator CONF_SPTR_LIST_I

typedef
CONF_SPTR_LIST::const_iterator CONF_SPTR_LIST_CI

typedef std::pair
< CONF_SPTR_LIST_I,
CONF_SPTR_LIST_I > CONFS_I_PAIR

typedef Atom * GRAPH_NODE_TYPE

typedef Bond * GRAPH_EDGE_TYPE

typedef Atom const * GRAPH_NODE_CONST_TYPE

typedef Bond const * GRAPH_EDGE_CONST_TYPE

typedef std::map
< int, ATOM_PTR_LIST > ATOM_BOOKMARK_MAP

typedef std::map
< int, BOND_PTR_LIST > BOND_BOOKMARK_MAP

typedef class
AtomIterator_< Atom,
ROMol,
GRAPH_MOL_ATOM_PMAP::type > AtomIterator

typedef class
AtomIterator_< const
Atom, const ROMol,
GRAPH_MOL_ATOM_PMAP::const_type > ConstAtomIterator

typedef class
AromaticAtomIterator_
< Atom, ROMol,
GRAPH_MOL_ATOM_PMAP::type > AromaticAtomIterator

typedef class
AromaticAtomIterator_
< const Atom, const
ROMol,
GRAPH_MOL_ATOM_PMAP::const_type > ConstAromaticAtomIterator

typedef class
HeteroatomIterator_
< Atom, ROMol,
GRAPH_MOL_ATOM_PMAP::type > HeteroatomIterator

typedef class
HeteroatomIterator_
< const Atom, const
ROMol,
GRAPH_MOL_ATOM_PMAP::const_type > ConstHeteroatomIterator

typedef class
QueryAtomIterator_
< Atom, ROMol,
GRAPH_MOL_ATOM_PMAP::type > QueryAtomIterator

typedef class
QueryAtomIterator_
< const Atom, const
ROMol,
GRAPH_MOL_ATOM_PMAP::const_type > ConstQueryAtomIterator

typedef class
BondIterator_ BondIterator

typedef class
ConstBondIterator_ ConstBondIterator

typedef CONF_SPTR_LIST_I ConformerIterator

typedef CONF_SPTR_LIST_CI ConstConformerIterator

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 ()

unsigned int getNumAtoms (bool onlyHeavy=1) const

returns our number of Atoms

GRAPH_NODE_TYPE getAtomWithIdx (unsigned int idx)

returns a pointer to a particular Atom

GRAPH_NODE_CONST_TYPE 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

unsigned int getNumBonds (bool onlyHeavy=1) const

returns our number of Bonds

GRAPH_EDGE_TYPE getBondWithIdx (unsigned int idx)

returns a pointer to a particular Bond

GRAPH_EDGE_CONST_TYPE getBondWithIdx (unsigned int idx) const

GRAPH_EDGE_TYPE getBondBetweenAtoms (unsigned int idx1, unsigned int idx2)

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

GRAPH_EDGE_CONST_TYPE getBondBetweenAtoms (unsigned int idx1, unsigned int idx2) const

void setAtomBookmark (ATOM_SPTR at, int mark)

associates an Atom pointer with a bookmark

void setAtomBookmark (Atom *at, int mark)

GRAPH_NODE_TYPE 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)

GRAPH_EDGE_TYPE 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)

queries whether or not any bonds are associated with a bookmark

BOND_BOOKMARK_MAP * getBondBookmarks ()

returns a pointer to all of our bond bookmarks

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

GRAPH_MOL_ATOM_PMAP::type getAtomPMap ()

returns the atom PMap

GRAPH_MOL_BOND_PMAP::type getBondPMap ()

returns the bond PMap (required to use Bond iterators)

GRAPH_MOL_ATOM_PMAP::const_type getAtomPMap () const

GRAPH_MOL_BOND_PMAP::const_type getBondPMap () const

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

void debugMol (std::ostream &str) const

sends some debugging info to a stream

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

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

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

STR_VECT getPropList () 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

RingInfo * getRingInfo () const

returns a pointer to our RingInfo structure

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

return a reference to the list of conformers

ConformerIterator beginConformers ()

ConformerIterator endConformers ()

ConstConformerIterator beginConformers () const

ConstConformerIterator endConformers () const

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 93 of file ROMol.h.

Member Typedef Documentation

typedef boost::property_map<MolGraph,vertex_atom_t> RDKit::ROMol::GRAPH_MOL_ATOM_PMAP

Definition at line 99 of file ROMol.h.

typedef boost::property_map<MolGraph,edge_bond_t> RDKit::ROMol::GRAPH_MOL_BOND_PMAP

Definition at line 100 of file ROMol.h.

typedef boost::graph_traits<MolGraph> RDKit::ROMol::GRAPH_MOL_TRAITS

Definition at line 101 of file ROMol.h.

typedef GRAPH_MOL_TRAITS::edge_iterator RDKit::ROMol::EDGE_ITER

Definition at line 102 of file ROMol.h.

typedef GRAPH_MOL_TRAITS::out_edge_iterator RDKit::ROMol::OEDGE_ITER

Definition at line 103 of file ROMol.h.

typedef GRAPH_MOL_TRAITS::vertex_iterator RDKit::ROMol::VERTEX_ITER

Definition at line 104 of file ROMol.h.

typedef GRAPH_MOL_TRAITS::adjacency_iterator RDKit::ROMol::ADJ_ITER

Definition at line 105 of file ROMol.h.

typedef std::pair<EDGE_ITER,EDGE_ITER> RDKit::ROMol::BOND_ITER_PAIR

Definition at line 106 of file ROMol.h.

typedef std::pair<OEDGE_ITER,OEDGE_ITER> RDKit::ROMol::OBOND_ITER_PAIR

Definition at line 107 of file ROMol.h.

typedef std::pair<VERTEX_ITER,VERTEX_ITER> RDKit::ROMol::ATOM_ITER_PAIR

Definition at line 108 of file ROMol.h.

typedef std::pair<ADJ_ITER,ADJ_ITER> RDKit::ROMol::ADJ_ITER_PAIR

Definition at line 109 of file ROMol.h.

typedef std::vector<ATOM_SPTR> RDKit::ROMol::ATOM_SPTR_VECT

Definition at line 111 of file ROMol.h.

typedef ATOM_SPTR_VECT::iterator RDKit::ROMol::ATOM_SPTR_VECT_I

Definition at line 112 of file ROMol.h.

typedef ATOM_SPTR_VECT::const_iterator RDKit::ROMol::ATOM_SPTR_VECT_CI

Definition at line 113 of file ROMol.h.

typedef std::vector<BOND_SPTR> RDKit::ROMol::BOND_SPTR_VECT

Definition at line 114 of file ROMol.h.

typedef BOND_SPTR_VECT::iterator RDKit::ROMol::BOND_SPTR_VECT_I

Definition at line 115 of file ROMol.h.

typedef BOND_SPTR_VECT::const_iterator RDKit::ROMol::BOND_SPTR_VECT_CI

Definition at line 116 of file ROMol.h.

typedef std::vector<Atom *> RDKit::ROMol::ATOM_PTR_VECT

Definition at line 118 of file ROMol.h.

typedef ATOM_PTR_VECT::iterator RDKit::ROMol::ATOM_PTR_VECT_I

Definition at line 119 of file ROMol.h.

typedef ATOM_PTR_VECT::const_iterator RDKit::ROMol::ATOM_PTR_VECT_CI

Definition at line 120 of file ROMol.h.

typedef std::vector<Bond *> RDKit::ROMol::BOND_PTR_VECT

Definition at line 121 of file ROMol.h.

typedef BOND_PTR_VECT::iterator RDKit::ROMol::BOND_PTR_VECT_I

Definition at line 122 of file ROMol.h.

typedef BOND_PTR_VECT::const_iterator RDKit::ROMol::BOND_PTR_VECT_CI

Definition at line 123 of file ROMol.h.

typedef std::list<Atom *> RDKit::ROMol::ATOM_PTR_LIST

Definition at line 125 of file ROMol.h.

typedef ATOM_PTR_LIST::iterator RDKit::ROMol::ATOM_PTR_LIST_I

Definition at line 126 of file ROMol.h.

typedef ATOM_PTR_LIST::const_iterator RDKit::ROMol::ATOM_PTR_LIST_CI

Definition at line 127 of file ROMol.h.

typedef std::list<Bond *> RDKit::ROMol::BOND_PTR_LIST

Definition at line 128 of file ROMol.h.

typedef BOND_PTR_LIST::iterator RDKit::ROMol::BOND_PTR_LIST_I

Definition at line 129 of file ROMol.h.

typedef BOND_PTR_LIST::const_iterator RDKit::ROMol::BOND_PTR_LIST_CI

Definition at line 130 of file ROMol.h.

typedef std::list<CONFORMER_SPTR> RDKit::ROMol::CONF_SPTR_LIST

Definition at line 133 of file ROMol.h.

typedef CONF_SPTR_LIST::iterator RDKit::ROMol::CONF_SPTR_LIST_I

Definition at line 134 of file ROMol.h.

typedef CONF_SPTR_LIST::const_iterator RDKit::ROMol::CONF_SPTR_LIST_CI

Definition at line 135 of file ROMol.h.

typedef std::pair<CONF_SPTR_LIST_I, CONF_SPTR_LIST_I> RDKit::ROMol::CONFS_I_PAIR

Definition at line 136 of file ROMol.h.

typedef Atom* RDKit::ROMol::GRAPH_NODE_TYPE

Definition at line 139 of file ROMol.h.

typedef Bond* RDKit::ROMol::GRAPH_EDGE_TYPE

Definition at line 140 of file ROMol.h.

typedef Atom const* RDKit::ROMol::GRAPH_NODE_CONST_TYPE

Definition at line 141 of file ROMol.h.

typedef Bond const* RDKit::ROMol::GRAPH_EDGE_CONST_TYPE

Definition at line 142 of file ROMol.h.

typedef std::map<int,ATOM_PTR_LIST> RDKit::ROMol::ATOM_BOOKMARK_MAP

Definition at line 143 of file ROMol.h.

typedef std::map<int,BOND_PTR_LIST> RDKit::ROMol::BOND_BOOKMARK_MAP

Definition at line 144 of file ROMol.h.

typedef class AtomIterator_< Atom, ROMol, GRAPH_MOL_ATOM_PMAP::type > RDKit::ROMol::AtomIterator

Definition at line 146 of file ROMol.h.

typedef class AtomIterator_< const Atom, const ROMol, GRAPH_MOL_ATOM_PMAP::const_type > RDKit::ROMol::ConstAtomIterator

Definition at line 147 of file ROMol.h.

typedef class AromaticAtomIterator_< Atom, ROMol, GRAPH_MOL_ATOM_PMAP::type > RDKit::ROMol::AromaticAtomIterator

Definition at line 148 of file ROMol.h.

typedef class AromaticAtomIterator_< const Atom, const ROMol, GRAPH_MOL_ATOM_PMAP::const_type > RDKit::ROMol::ConstAromaticAtomIterator

Definition at line 149 of file ROMol.h.

typedef class HeteroatomIterator_< Atom, ROMol, GRAPH_MOL_ATOM_PMAP::type > RDKit::ROMol::HeteroatomIterator

Definition at line 150 of file ROMol.h.

typedef class HeteroatomIterator_< const Atom, const ROMol, GRAPH_MOL_ATOM_PMAP::const_type > RDKit::ROMol::ConstHeteroatomIterator

Definition at line 151 of file ROMol.h.

typedef class QueryAtomIterator_< Atom, ROMol, GRAPH_MOL_ATOM_PMAP::type > RDKit::ROMol::QueryAtomIterator

Definition at line 152 of file ROMol.h.

typedef class QueryAtomIterator_< const Atom, const ROMol, GRAPH_MOL_ATOM_PMAP::const_type > RDKit::ROMol::ConstQueryAtomIterator

Definition at line 153 of file ROMol.h.

typedef class BondIterator_ RDKit::ROMol::BondIterator

Definition at line 154 of file ROMol.h.

typedef class ConstBondIterator_ RDKit::ROMol::ConstBondIterator

Definition at line 155 of file ROMol.h.

typedef CONF_SPTR_LIST_I RDKit::ROMol::ConformerIterator

Definition at line 157 of file ROMol.h.

typedef CONF_SPTR_LIST_CI RDKit::ROMol::ConstConformerIterator

Definition at line 158 of file ROMol.h.

Constructor & Destructor Documentation

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

Definition at line 160 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 169 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 173 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().

GRAPH_NODE_TYPE RDKit::ROMol::getAtomWithIdx ( unsigned int idx )

returns a pointer to a particular Atom

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

GRAPH_NODE_CONST_TYPE 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().

GRAPH_EDGE_TYPE RDKit::ROMol::getBondWithIdx ( unsigned int idx )

returns a pointer to a particular Bond

GRAPH_EDGE_CONST_TYPE RDKit::ROMol::getBondWithIdx ( unsigned int idx ) const

GRAPH_EDGE_TYPE RDKit::ROMol::getBondBetweenAtoms	(	unsigned int	idx1,
		unsigned int	idx2
	)

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

GRAPH_EDGE_CONST_TYPE 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 218 of file ROMol.h.

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

Definition at line 220 of file ROMol.h.

GRAPH_NODE_TYPE 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 230 of file ROMol.h.

References clearAtomBookmark().

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

blows out all atomic bookmarks

Definition at line 232 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 234 of file ROMol.h.

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

returns a pointer to all of our atom bookmarks

Definition at line 236 of file ROMol.h.

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

associates a Bond pointer with a bookmark

Definition at line 239 of file ROMol.h.

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

Definition at line 241 of file ROMol.h.

GRAPH_EDGE_TYPE 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 251 of file ROMol.h.

References clearBondBookmark().

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

blows out all bond bookmarks

Definition at line 253 of file ROMol.h.

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

queries whether or not any bonds are associated with a bookmark

Definition at line 255 of file ROMol.h.

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

returns a pointer to all of our bond bookmarks

Definition at line 257 of file ROMol.h.

ADJ_ITER_PAIR RDKit::ROMol::getAtomNeighbors ( Atom const * at ) const

provides access to all neighbors around an Atom

Parameters:

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 *at=molPtr->getAtomWithIdx(*nbrIdx);
          ... do something with the Atom ...
          nbrIdx++;
        }

Notes:

technically, we're probably suppposed to be using the atom pmap here (accessible using ROMol::getAtomPMap()), but that's not actually required.

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:

the atom whose neighbors we are looking for

Usage

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

Referenced by RDKit::queryAtomRingBondCount().

GRAPH_MOL_ATOM_PMAP::type RDKit::ROMol::getAtomPMap ( )

returns the atom PMap

GRAPH_MOL_BOND_PMAP::type RDKit::ROMol::getBondPMap ( )

returns the bond PMap (required to use Bond iterators)

Referenced by RDKit::queryAtomRingBondCount().

GRAPH_MOL_ATOM_PMAP::const_type RDKit::ROMol::getAtomPMap ( ) const

GRAPH_MOL_BOND_PMAP::const_type RDKit::ROMol::getBondPMap ( ) const

ATOM_ITER_PAIR RDKit::ROMol::getVertices ( )

returns an iterator pair for looping over all Atoms

Usage

        ... molPtr is an ROMol * ...
        ROMol::GRAPH_MOL_ATOM_PMAP::type atomMap = molPtr->getAtomPMap();
        ROMol::VERTEX_ITER atBegin,atEnd;
        boost::tie(atBegin,atEnd) = mol.getVertices();  
        while(atBegin!=atEnd){
          Atom *at2=atomMap[*atBegin];
          ... do something with the Atom ...
          atBegin++;
        }

BOND_ITER_PAIR RDKit::ROMol::getEdges ( )

returns an iterator pair for looping over all Bonds

Usage

        ... molPtr is a ROMol * ...
        ROMol::EDGE_ITER firstB,lastB;
        boost::tie(firstB,lastB) = mol.getEdges();
        ROMol::GRAPH_MOL_BOND_PMAP::type bondMap = mol.getBondPMap();
        while(firstB!=lastB){
          Bond *bond = bondMap[*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 387 of file ROMol.h.

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

sends some debugging info to a stream

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

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

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

STR_VECT RDKit::ROMol::getPropList ( ) const [inline]

returns a list with the names of our properties

Definition at line 450 of file ROMol.h.

References 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 464 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 470 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 497 of file ROMol.h.

References RDKit::Dict::getVal().

Referenced by clearProp(), and setProp().

template<typename T>

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

Definition at line 502 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 508 of file ROMol.h.

References RDKit::Dict::hasVal().

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

Definition at line 513 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 527 of file ROMol.h.

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

Definition at line 532 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

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

returns a pointer to our RingInfo structure

Definition at line 554 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().

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 568 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]

return a reference to the list of conformers

Definition at line 589 of file ROMol.h.

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

Definition at line 593 of file ROMol.h.

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

Definition at line 597 of file ROMol.h.

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

Definition at line 601 of file ROMol.h.

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

Definition at line 605 of file ROMol.h.

Friends And Related Function Documentation

friend class MolPickler [friend]

Definition at line 95 of file ROMol.h.

friend class RWMol [friend]

Definition at line 96 of file ROMol.h.

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

ROMol.h

Generated on Sat May 24 08:36:34 2008 for RDCode by

1.5.3


Public Types
typedef boost::property_map < MolGraph, vertex_atom_t >	GRAPH_MOL_ATOM_PMAP
typedef boost::property_map < MolGraph, edge_bond_t >	GRAPH_MOL_BOND_PMAP
typedef boost::graph_traits < MolGraph >	GRAPH_MOL_TRAITS
typedef GRAPH_MOL_TRAITS::edge_iterator	EDGE_ITER
typedef GRAPH_MOL_TRAITS::out_edge_iterator	OEDGE_ITER
typedef GRAPH_MOL_TRAITS::vertex_iterator	VERTEX_ITER
typedef GRAPH_MOL_TRAITS::adjacency_iterator	ADJ_ITER
typedef std::pair < EDGE_ITER, EDGE_ITER >	BOND_ITER_PAIR
typedef std::pair < OEDGE_ITER, OEDGE_ITER >	OBOND_ITER_PAIR
typedef std::pair < VERTEX_ITER, VERTEX_ITER >	ATOM_ITER_PAIR
typedef std::pair < ADJ_ITER, ADJ_ITER >	ADJ_ITER_PAIR
typedef std::vector < ATOM_SPTR >	ATOM_SPTR_VECT
typedef ATOM_SPTR_VECT::iterator	ATOM_SPTR_VECT_I
typedef ATOM_SPTR_VECT::const_iterator	ATOM_SPTR_VECT_CI
typedef std::vector < BOND_SPTR >	BOND_SPTR_VECT
typedef BOND_SPTR_VECT::iterator	BOND_SPTR_VECT_I
typedef BOND_SPTR_VECT::const_iterator	BOND_SPTR_VECT_CI
typedef std::vector < Atom * >	ATOM_PTR_VECT
typedef ATOM_PTR_VECT::iterator	ATOM_PTR_VECT_I
typedef ATOM_PTR_VECT::const_iterator	ATOM_PTR_VECT_CI
typedef std::vector < Bond * >	BOND_PTR_VECT
typedef BOND_PTR_VECT::iterator	BOND_PTR_VECT_I
typedef BOND_PTR_VECT::const_iterator	BOND_PTR_VECT_CI
typedef std::list < Atom * >	ATOM_PTR_LIST
typedef ATOM_PTR_LIST::iterator	ATOM_PTR_LIST_I
typedef ATOM_PTR_LIST::const_iterator	ATOM_PTR_LIST_CI
typedef std::list < Bond * >	BOND_PTR_LIST
typedef BOND_PTR_LIST::iterator	BOND_PTR_LIST_I
typedef BOND_PTR_LIST::const_iterator	BOND_PTR_LIST_CI
typedef std::list < CONFORMER_SPTR >	CONF_SPTR_LIST
typedef CONF_SPTR_LIST::iterator	CONF_SPTR_LIST_I
typedef CONF_SPTR_LIST::const_iterator	CONF_SPTR_LIST_CI
typedef std::pair < CONF_SPTR_LIST_I, CONF_SPTR_LIST_I >	CONFS_I_PAIR
typedef Atom *	GRAPH_NODE_TYPE
typedef Bond *	GRAPH_EDGE_TYPE
typedef Atom const *	GRAPH_NODE_CONST_TYPE
typedef Bond const *	GRAPH_EDGE_CONST_TYPE
typedef std::map < int, ATOM_PTR_LIST >	ATOM_BOOKMARK_MAP
typedef std::map < int, BOND_PTR_LIST >	BOND_BOOKMARK_MAP
typedef class AtomIterator_< Atom, ROMol, GRAPH_MOL_ATOM_PMAP::type >	AtomIterator
typedef class AtomIterator_< const Atom, const ROMol, GRAPH_MOL_ATOM_PMAP::const_type >	ConstAtomIterator
typedef class AromaticAtomIterator_ < Atom, ROMol, GRAPH_MOL_ATOM_PMAP::type >	AromaticAtomIterator
typedef class AromaticAtomIterator_ < const Atom, const ROMol, GRAPH_MOL_ATOM_PMAP::const_type >	ConstAromaticAtomIterator
typedef class HeteroatomIterator_ < Atom, ROMol, GRAPH_MOL_ATOM_PMAP::type >	HeteroatomIterator
typedef class HeteroatomIterator_ < const Atom, const ROMol, GRAPH_MOL_ATOM_PMAP::const_type >	ConstHeteroatomIterator
typedef class QueryAtomIterator_ < Atom, ROMol, GRAPH_MOL_ATOM_PMAP::type >	QueryAtomIterator
typedef class QueryAtomIterator_ < const Atom, const ROMol, GRAPH_MOL_ATOM_PMAP::const_type >	ConstQueryAtomIterator
typedef class BondIterator_	BondIterator
typedef class ConstBondIterator_	ConstBondIterator
typedef CONF_SPTR_LIST_I	ConformerIterator
typedef CONF_SPTR_LIST_CI	ConstConformerIterator
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 ()
unsigned int	getNumAtoms (bool onlyHeavy=1) const
	returns our number of Atoms
GRAPH_NODE_TYPE	getAtomWithIdx (unsigned int idx)
	returns a pointer to a particular Atom
GRAPH_NODE_CONST_TYPE	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
unsigned int	getNumBonds (bool onlyHeavy=1) const
	returns our number of Bonds
GRAPH_EDGE_TYPE	getBondWithIdx (unsigned int idx)
	returns a pointer to a particular Bond
GRAPH_EDGE_CONST_TYPE	getBondWithIdx (unsigned int idx) const
GRAPH_EDGE_TYPE	getBondBetweenAtoms (unsigned int idx1, unsigned int idx2)
	returns a pointer to the bond between two atoms, Null on failure
GRAPH_EDGE_CONST_TYPE	getBondBetweenAtoms (unsigned int idx1, unsigned int idx2) const
void	setAtomBookmark (ATOM_SPTR at, int mark)
	associates an Atom pointer with a bookmark
void	setAtomBookmark (Atom *at, int mark)
GRAPH_NODE_TYPE	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)
GRAPH_EDGE_TYPE	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)
	queries whether or not any bonds are associated with a `bookmark`
BOND_BOOKMARK_MAP *	getBondBookmarks ()
	returns a pointer to all of our bond `bookmarks`
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
GRAPH_MOL_ATOM_PMAP::type	getAtomPMap ()
	returns the atom PMap
GRAPH_MOL_BOND_PMAP::type	getBondPMap ()
	returns the bond PMap (required to use Bond iterators)
GRAPH_MOL_ATOM_PMAP::const_type	getAtomPMap () const
GRAPH_MOL_BOND_PMAP::const_type	getBondPMap () const
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
void	debugMol (std::ostream &str) const
	sends some debugging info to a stream
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
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
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
STR_VECT	getPropList () 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`
RingInfo *	getRingInfo () const
	returns a pointer to our RingInfo structure
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
	return a reference to the list of conformers
ConformerIterator	beginConformers ()
ConformerIterator	endConformers ()
ConstConformerIterator	beginConformers () const
ConstConformerIterator	endConformers () const
Friends
class	MolPickler
class	RWMol