RDKit
Open-source cheminformatics and machine learning.
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:
RDKit::RDProps RDKit::RWMol

Public Member Functions

 ROMol ()
 
 ROMol (const ROMol &other, bool quickCopy=false, int confId=-1)
 copy constructor with a twist More...
 
 ROMol (const std::string &binStr)
 construct a molecule from a pickle string More...
 
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 onlyExplicit=1) const
 returns our number of atoms More...
 
unsigned int getNumHeavyAtoms () const
 returns our number of heavy atoms (atomic number > 1) More...
 
AtomgetAtomWithIdx (unsigned int idx)
 returns a pointer to a particular Atom More...
 
const AtomgetAtomWithIdx (unsigned int idx) const
 
template<class U >
AtomgetAtomWithIdx (const U idx)
 
template<class U >
const AtomgetAtomWithIdx (const U idx) const
 
unsigned int getAtomDegree (const Atom *at) const
 returns the degree (number of neighbors) of an Atom in the graph More...
 
unsigned int getAtomDegree (ATOM_SPTR at) const
 
Bonds
unsigned int getNumBonds (bool onlyHeavy=1) const
 returns our number of Bonds More...
 
BondgetBondWithIdx (unsigned int idx)
 returns a pointer to a particular Bond More...
 
const BondgetBondWithIdx (unsigned int idx) const
 
template<class U >
BondgetBondWithIdx (const U idx)
 
template<class U >
const BondgetBondWithIdx (const U idx) const
 
BondgetBondBetweenAtoms (unsigned int idx1, unsigned int idx2)
 returns a pointer to the bond between two atoms, Null on failure More...
 
const BondgetBondBetweenAtoms (unsigned int idx1, unsigned int idx2) const
 
template<class U , class V >
BondgetBondBetweenAtoms (const U idx1, const V idx2)
 
template<class U , class V >
const BondgetBondBetweenAtoms (const U idx1, const V idx2) const
 
Bookmarks
void setAtomBookmark (ATOM_SPTR at, int mark)
 associates an Atom pointer with a bookmark More...
 
void setAtomBookmark (Atom *at, int mark)
 
void replaceAtomBookmark (ATOM_SPTR at, int mark)
 associates an Atom pointer with a bookmark More...
 
void replaceAtomBookmark (Atom *at, int mark)
 
AtomgetAtomWithBookmark (int mark)
 returns the first Atom associated with the bookmark provided More...
 
ATOM_PTR_LIST & getAllAtomsWithBookmark (int mark)
 returns all Atoms associated with the bookmark provided More...
 
void clearAtomBookmark (const int mark)
 removes a bookmark from our collection More...
 
void clearAtomBookmark (const int mark, const Atom *atom)
 removes a particular Atom from the list associated with the bookmark More...
 
void clearAtomBookmark (const int mark, ATOM_SPTR atom)
 
void clearAllAtomBookmarks ()
 blows out all atomic bookmarks More...
 
bool hasAtomBookmark (int mark) const
 queries whether or not any atoms are associated with a bookmark More...
 
ATOM_BOOKMARK_MAP * getAtomBookmarks ()
 returns a pointer to all of our atom bookmarks More...
 
void setBondBookmark (BOND_SPTR bond, int mark)
 associates a Bond pointer with a bookmark More...
 
void setBondBookmark (Bond *bond, int mark)
 
BondgetBondWithBookmark (int mark)
 returns the first Bond associated with the bookmark provided More...
 
BOND_PTR_LIST & getAllBondsWithBookmark (int mark)
 returns all bonds associated with the bookmark provided More...
 
void clearBondBookmark (int mark)
 removes a bookmark from our collection More...
 
void clearBondBookmark (int mark, const Bond *bond)
 removes a particular Bond from the list associated with the bookmark More...
 
void clearBondBookmark (int mark, BOND_SPTR bond)
 
void clearAllBondBookmarks ()
 blows out all bond bookmarks More...
 
bool hasBondBookmark (int mark) const
 queries whether or not any bonds are associated with a bookmark More...
 
BOND_BOOKMARK_MAP * getBondBookmarks ()
 returns a pointer to all of our bond bookmarks More...
 
Conformers
const ConformergetConformer (int id=-1) const
 
ConformergetConformer (int id=-1)
 
void removeConformer (unsigned int id)
 Delete the conformation with the specified ID. More...
 
void clearConformers ()
 Clear all the conformations on the molecule. More...
 
unsigned int addConformer (Conformer *conf, bool assignId=false)
 Add a new conformation to the molecule. More...
 
unsigned int getNumConformers () const
 
Topology
RingInfogetRingInfo () const
 
ADJ_ITER_PAIR getAtomNeighbors (Atom const *at) const
 provides access to all neighbors around an Atom More...
 
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 More...
 
ATOM_ITER_PAIR getVertices ()
 returns an iterator pair for looping over all Atoms More...
 
BOND_ITER_PAIR getEdges ()
 returns an iterator pair for looping over all Bonds More...
 
ATOM_ITER_PAIR getVertices () const
 
BOND_ITER_PAIR getEdges () const
 
MolGraph const & getTopology () const
 brief returns a pointer to our underlying BGL object More...
 
Iterators
AtomIterator beginAtoms ()
 get an AtomIterator pointing at our first Atom More...
 
ConstAtomIterator beginAtoms () const
 
AtomIterator endAtoms ()
 get an AtomIterator pointing at the end of our Atoms More...
 
ConstAtomIterator endAtoms () const
 
BondIterator beginBonds ()
 get a BondIterator pointing at our first Bond More...
 
ConstBondIterator beginBonds () const
 
BondIterator endBonds ()
 get a BondIterator pointing at the end of our Bonds More...
 
ConstBondIterator endBonds () const
 
AromaticAtomIterator beginAromaticAtoms ()
 get an AtomIterator pointing at our first aromatic Atom More...
 
ConstAromaticAtomIterator beginAromaticAtoms () const
 
AromaticAtomIterator endAromaticAtoms ()
 get an AtomIterator pointing at the end of our Atoms More...
 
ConstAromaticAtomIterator endAromaticAtoms () const
 
HeteroatomIterator beginHeteros ()
 get an AtomIterator pointing at our first hetero Atom More...
 
ConstHeteroatomIterator beginHeteros () const
 
HeteroatomIterator endHeteros ()
 get an AtomIterator pointing at the end of our Atoms More...
 
ConstHeteroatomIterator endHeteros () const
 
QueryAtomIterator beginQueryAtoms (QueryAtom const *query)
 get an AtomIterator pointing at our first Atom that matches query More...
 
ConstQueryAtomIterator beginQueryAtoms (QueryAtom const *) const
 
QueryAtomIterator endQueryAtoms ()
 get an AtomIterator pointing at the end of our Atoms More...
 
ConstQueryAtomIterator endQueryAtoms () const
 
MatchingAtomIterator beginMatchingAtoms (bool(*query)(Atom *))
 get an AtomIterator pointing at our first Atom that matches query More...
 
ConstMatchingAtomIterator beginMatchingAtoms (bool(*query)(const Atom *)) const
 
MatchingAtomIterator endMatchingAtoms ()
 get an AtomIterator pointing at the end of our Atoms More...
 
ConstMatchingAtomIterator endMatchingAtoms () const
 
ConformerIterator beginConformers ()
 
ConformerIterator endConformers ()
 
ConstConformerIterator beginConformers () const
 
ConstConformerIterator endConformers () const
 
Properties
void clearComputedProps (bool includeRings=true) const
 clears all of our computed properties More...
 
void updatePropertyCache (bool strict=true)
 calculates any of our lazy properties More...
 
bool needsUpdatePropertyCache () const
 
Misc
void debugMol (std::ostream &str) const
 sends some debugging info to a stream More...
 
- Public Member Functions inherited from RDKit::RDProps
 RDProps ()
 
 RDProps (const RDProps &rhs)
 
RDPropsoperator= (const RDProps &rhs)
 
void clear ()
 
const DictgetDict () const
 gets the underlying Dictionary More...
 
DictgetDict ()
 
STR_VECT getPropList (bool includePrivate=true, bool includeComputed=true) const
 returns a list with the names of our properties More...
 
template<typename T >
void setProp (const std::string &key, T val, bool computed=false) const
 sets a property value More...
 
template<typename T >
void getProp (const std::string &key, T &res) const
 allows retrieval of a particular property value More...
 
template<typename T >
getProp (const std::string &key) const
 
template<typename T >
bool getPropIfPresent (const std::string &key, T &res) const
 
bool hasProp (const std::string &key) const
 
void clearProp (const std::string &key) const
 clears the value of a property More...
 
void clearComputedProps () const
 clears all of our computed properties More...
 

Protected Attributes

unsigned int numBonds
 
- Protected Attributes inherited from RDKit::RDProps
Dict dp_props
 

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 106 of file ROMol.h.

Constructor & Destructor Documentation

RDKit::ROMol::ROMol ( )
inline

Definition at line 181 of file ROMol.h.

Referenced by ROMol().

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

copy constructor with a twist

Parameters
otherthe molecule to be copied
quickCopy(optional) if this is true, the resulting ROMol will not copy any of the properties or bookmarks and conformers from other. This can make the copy substantially faster (thus the name).
confId(optional) if this is >=0, the resulting ROMol will contain only the specified conformer from other.

Definition at line 194 of file ROMol.h.

References numBonds, and ROMol().

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

construct a molecule from a pickle string

virtual RDKit::ROMol::~ROMol ( )
inlinevirtual

Definition at line 202 of file ROMol.h.

References getAtomWithIdx(), getNumAtoms(), and getNumHeavyAtoms().

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

Referenced by clearConformers().

AromaticAtomIterator RDKit::ROMol::beginAromaticAtoms ( )

get an AtomIterator pointing at our first aromatic Atom

Referenced by getTopology().

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

Referenced by getTopology().

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

Referenced by getTopology().

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

Definition at line 550 of file ROMol.h.

HeteroatomIterator RDKit::ROMol::beginHeteros ( )

get an AtomIterator pointing at our first hetero Atom

Referenced by getTopology().

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.

MatchingAtomIterator RDKit::ROMol::beginMatchingAtoms ( bool(*)(Atom *)  query)

get an AtomIterator pointing at our first Atom that matches query

Referenced by getTopology().

ConstMatchingAtomIterator RDKit::ROMol::beginMatchingAtoms ( bool(*)(const Atom *)  query) const

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

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

get an AtomIterator pointing at our first Atom that matches query

Referenced by getTopology().

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 304 of file ROMol.h.

void RDKit::ROMol::clearAllBondBookmarks ( )
inline

blows out all bond bookmarks

Definition at line 331 of file ROMol.h.

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

removes a bookmark from our collection

Referenced by clearAtomBookmark(), and replaceAtomBookmark().

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

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 300 of file ROMol.h.

References clearAtomBookmark().

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

removes a bookmark from our collection

Referenced by clearBondBookmark(), and setBondBookmark().

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 327 of file ROMol.h.

References clearBondBookmark().

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 354 of file ROMol.h.

References addConformer().

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

sends some debugging info to a stream

Referenced by endConformers().

AromaticAtomIterator RDKit::ROMol::endAromaticAtoms ( )

get an AtomIterator pointing at the end of our Atoms

Referenced by getTopology().

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.

AtomIterator RDKit::ROMol::endAtoms ( )

get an AtomIterator pointing at the end of our Atoms

Referenced by getTopology().

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.

BondIterator RDKit::ROMol::endBonds ( )

get a BondIterator pointing at the end of our Bonds

Referenced by getTopology().

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
ConstConformerIterator RDKit::ROMol::endConformers ( ) const
inline
HeteroatomIterator RDKit::ROMol::endHeteros ( )

get an AtomIterator pointing at the end of our Atoms

Referenced by getTopology().

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.

MatchingAtomIterator RDKit::ROMol::endMatchingAtoms ( )

get an AtomIterator pointing at the end of our Atoms

Referenced by getTopology().

ConstMatchingAtomIterator RDKit::ROMol::endMatchingAtoms ( ) const

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

QueryAtomIterator RDKit::ROMol::endQueryAtoms ( )

get an AtomIterator pointing at the end of our Atoms

Referenced by getTopology().

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.

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

returns all Atoms associated with the bookmark provided

Referenced by replaceAtomBookmark().

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

returns all bonds associated with the bookmark provided

Referenced by setBondBookmark().

OBOND_ITER_PAIR RDKit::ROMol::getAtomBonds ( Atom const *  at) const

provides access to all Bond objects connected to an Atom

Parameters
atthe 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::Drawing::DrawMol(), getRingInfo(), RDKit::queryAtomHasRingBond(), and RDKit::queryAtomRingBondCount().

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

returns a pointer to all of our atom bookmarks

Definition at line 308 of file ROMol.h.

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

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

Referenced by getAtomWithIdx().

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.

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

provides access to all neighbors around an Atom

Parameters
atthe 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;
}

Referenced by getRingInfo().

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

Referenced by replaceAtomBookmark().

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

returns a pointer to a particular Atom

Referenced by RDKit::Drawing::DrawMol(), getAtomWithIdx(), RDKit::RWMol::getLastAtom(), and ~ROMol().

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.

template<class U >
Atom* RDKit::ROMol::getAtomWithIdx ( const U  idx)
inline

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

Definition at line 218 of file ROMol.h.

References getAtomWithIdx().

template<class U >
const Atom* RDKit::ROMol::getAtomWithIdx ( const U  idx) const
inline

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

Definition at line 223 of file ROMol.h.

References getAtomDegree(), getAtomWithIdx(), getBondWithIdx(), and getNumBonds().

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

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

Referenced by getBondBetweenAtoms(), getBondWithIdx(), and RDKit::FMCS::TargetMatch::init().

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.

template<class U , class V >
Bond* RDKit::ROMol::getBondBetweenAtoms ( const U  idx1,
const V  idx2 
)
inline

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

Definition at line 257 of file ROMol.h.

References getBondBetweenAtoms().

template<class U , class V >
const Bond* RDKit::ROMol::getBondBetweenAtoms ( const U  idx1,
const V  idx2 
) const
inline

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

Definition at line 263 of file ROMol.h.

References getBondBetweenAtoms().

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

returns a pointer to all of our bond bookmarks

Definition at line 335 of file ROMol.h.

References getConformer(), and removeConformer().

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

returns the first Bond associated with the bookmark provided

Referenced by setBondBookmark().

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

template<class U >
Bond* RDKit::ROMol::getBondWithIdx ( const U  idx)
inline

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

Definition at line 243 of file ROMol.h.

References getBondWithIdx().

template<class U >
const Bond* RDKit::ROMol::getBondWithIdx ( const U  idx) const
inline

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

Definition at line 248 of file ROMol.h.

References getBondBetweenAtoms(), and getBondWithIdx().

const Conformer& RDKit::ROMol::getConformer ( int  id = -1) const

return the conformer with a specified ID if the ID is negative the first conformation will be returned

Referenced by RDKit::Drawing::DrawMol(), and getBondBookmarks().

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

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;
}

Referenced by getRingInfo().

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

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

Referenced by ~ROMol().

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 486 of file ROMol.h.

References beginAromaticAtoms(), beginAtoms(), beginBonds(), beginHeteros(), beginMatchingAtoms(), beginQueryAtoms(), endAromaticAtoms(), endAtoms(), endBonds(), endHeteros(), endMatchingAtoms(), and endQueryAtoms().

Referenced by RDKit::queryAtomHasRingBond(), and 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;
}

Referenced by RDKit::Drawing::DrawMol(), and getRingInfo().

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 306 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 333 of file ROMol.h.

bool RDKit::ROMol::needsUpdatePropertyCache ( ) const

Referenced by endConformers().

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

Definition at line 580 of file ROMol.h.

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

Definition at line 581 of file ROMol.h.

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

Definition at line 585 of file ROMol.h.

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

Definition at line 586 of file ROMol.h.

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

Delete the conformation with the specified ID.

Referenced by getBondBookmarks().

void RDKit::ROMol::replaceAtomBookmark ( ATOM_SPTR  at,
int  mark 
)
inline

associates an Atom pointer with a bookmark

Definition at line 282 of file ROMol.h.

void RDKit::ROMol::replaceAtomBookmark ( 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 287 of file ROMol.h.

References clearAtomBookmark(), getAllAtomsWithBookmark(), and getAtomWithBookmark().

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

associates an Atom pointer with a bookmark

Definition at line 274 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 278 of file ROMol.h.

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

associates a Bond pointer with a bookmark

Definition at line 311 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 315 of file ROMol.h.

References clearBondBookmark(), getAllBondsWithBookmark(), and getBondWithBookmark().

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

calculates any of our lazy properties

Notes:

Referenced by endConformers().

Friends And Related Function Documentation

friend class MolPickler
friend

Definition at line 108 of file ROMol.h.

friend class RWMol
friend

Definition at line 109 of file ROMol.h.

Member Data Documentation

unsigned int RDKit::ROMol::numBonds
protected

Definition at line 600 of file ROMol.h.

Referenced by ROMol().


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