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RDKit
Open-source cheminformatics and machine learning.
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ROMol is a molecule class that is intended to have a fixed topology. More...
#include <ROMol.h>
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... | |
Atom * | getAtomWithIdx (unsigned int idx) |
returns a pointer to a particular Atom More... | |
const Atom * | getAtomWithIdx (unsigned int idx) const |
template<class U > | |
Atom * | getAtomWithIdx (const U idx) |
template<class U > | |
const Atom * | getAtomWithIdx (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... | |
Bond * | getBondWithIdx (unsigned int idx) |
returns a pointer to a particular Bond More... | |
const Bond * | getBondWithIdx (unsigned int idx) const |
template<class U > | |
Bond * | getBondWithIdx (const U idx) |
template<class U > | |
const Bond * | getBondWithIdx (const U idx) const |
Bond * | getBondBetweenAtoms (unsigned int idx1, unsigned int idx2) |
returns a pointer to the bond between two atoms, Null on failure More... | |
const Bond * | getBondBetweenAtoms (unsigned int idx1, unsigned int idx2) const |
template<class U , class V > | |
Bond * | getBondBetweenAtoms (const U idx1, const V idx2) |
template<class U , class V > | |
const Bond * | getBondBetweenAtoms (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) |
Atom * | getAtomWithBookmark (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) |
Bond * | getBondWithBookmark (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 Conformer & | getConformer (int id=-1) const |
Conformer & | getConformer (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 | |
RingInfo * | getRingInfo () 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... | |
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RDProps () | |
RDProps (const RDProps &rhs) | |
RDProps & | operator= (const RDProps &rhs) |
void | clear () |
const Dict & | getDict () const |
gets the underlying Dictionary More... | |
Dict & | getDict () |
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 > | |
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... | |
void | updateProps (const RDProps &source, bool preserveExisting=false) |
update the properties from another More... | |
Protected Attributes | |
unsigned int | numBonds |
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Dict | dp_props |
Friends | |
class | MolPickler |
class | RWMol |
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:
properties:
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.property
operations are const
, this allows extra flexibility for clients who need to store extra data on ROMol objects.bookmarks
for Atoms and Bonds:
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copy constructor with a twist
other | the molecule to be copied |
quickCopy | (optional) if this is true, the resulting ROMol will not copy any of the properties or bookmarks and conformers from other . This can make the copy substantially faster (thus the name). |
confId | (optional) if this is >=0, the resulting ROMol will contain only the specified conformer from other . |
RDKit::ROMol::ROMol | ( | const std::string & | binStr | ) |
construct a molecule from a pickle string
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Definition at line 200 of file ROMol.h.
References getAtomWithIdx(), getNumAtoms(), and getNumHeavyAtoms().
unsigned int RDKit::ROMol::addConformer | ( | Conformer * | conf, |
bool | assignId = false |
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) |
Add a new conformation to the molecule.
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.
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Definition at line 544 of file ROMol.h.
Referenced by RDKit::MMFF::MMFFOptimizeMolecule(), RDKit::MMFF::MMFFOptimizeMoleculeConfs(), RDKit::UFF::UFFOptimizeMolecule(), and RDKit::UFF::UFFOptimizeMoleculeConfs().
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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.
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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
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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 298 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
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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 325 of file ROMol.h.
References clearBondBookmark().
void RDKit::ROMol::clearComputedProps | ( | bool | includeRings = true | ) | const |
clears all of our computed
properties
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Clear all the conformations on the molecule.
Definition at line 352 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.
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Definition at line 546 of file ROMol.h.
Referenced by RDKit::MMFF::MMFFOptimizeMolecule(), RDKit::MMFF::MMFFOptimizeMoleculeConfs(), RDKit::UFF::UFFOptimizeMolecule(), and RDKit::UFF::UFFOptimizeMoleculeConfs().
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Definition at line 552 of file ROMol.h.
References RDKit::RDProps::clearComputedProps(), debugMol(), needsUpdatePropertyCache(), and updatePropertyCache().
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
at | the atom whose neighbors we are looking for |
Usage
or, if you need a non-const Bond *:
Referenced by RDKit::Drawing::DrawMol(), getRingInfo(), RDKit::queryAtomHasRingBond(), and RDKit::queryAtomRingBondCount().
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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
at | the atom whose neighbors we are looking for |
Usage
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.
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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 216 of file ROMol.h.
References getAtomWithIdx().
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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 221 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.
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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 255 of file ROMol.h.
References getBondBetweenAtoms().
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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 261 of file ROMol.h.
References getBondBetweenAtoms().
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returns a pointer to all of our bond bookmarks
Definition at line 333 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 | ) |
returns a pointer to a particular Bond
Referenced by RDKit::FMCS::RingMatchTableSet::computeRingMatchTable(), getAtomWithIdx(), and getBondWithIdx().
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.
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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 241 of file ROMol.h.
References getBondWithIdx().
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
Definition at line 246 of file ROMol.h.
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
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::getNumAtoms | ( | bool | onlyExplicit = 1 | ) | const |
returns our number of atoms
Referenced by RDKit::Canon::BreakTies(), RDKit::Drawing::DrawMol(), RDKit::RWMol::getLastAtom(), RDKit::FMCS::TargetMatch::init(), RDKit::MMFF::MMFFOptimizeMolecule(), RDKit::MMFF::MMFFOptimizeMoleculeConfs(), RDKit::Canon::RefinePartitions(), RDKit::MolChemicalFeatureDef::setWeights(), RDKit::UFF::UFFOptimizeMolecule(), and ~ROMol().
unsigned int RDKit::ROMol::getNumBonds | ( | bool | onlyHeavy = 1 | ) | const |
returns our number of Bonds
Referenced by RDKit::FMCS::RingMatchTableSet::addTargetBondRingsIndeces(), getAtomWithIdx(), RDKit::FragCatalogEntry::getOrder(), RDKit::FMCS::TargetMatch::init(), and RDKit::FMCS::RingMatchTableSet::init().
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Definition at line 366 of file ROMol.h.
Referenced by RDKit::MMFF::MMFFOptimizeMoleculeConfs(), RDKit::Drawing::MolToDrawing(), and RDKit::UFF::UFFOptimizeMoleculeConfs().
unsigned int RDKit::ROMol::getNumHeavyAtoms | ( | ) | const |
returns our number of heavy atoms (atomic number > 1)
Referenced by ~ROMol().
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returns a pointer to our RingInfo structure Note: the client should not delete this.
Definition at line 377 of file ROMol.h.
References getAtomBonds(), getAtomNeighbors(), getEdges(), and getVertices().
Referenced by RDKit::FMCS::RingMatchTableSet::addTargetBondRingsIndeces(), RDKit::FMCS::RingMatchTableSet::computeRingMatchTable(), RDKit::Drawing::DrawMol(), RDKit::FMCS::RingMatchTableSet::init(), RDKit::queryAtomHasRingBond(), RDKit::queryAtomIsInRingOfSize(), RDKit::queryAtomMinRingSize(), RDKit::queryAtomRingBondCount(), RDKit::queryAtomRingMembership(), RDKit::queryBondIsInRingOfSize(), RDKit::queryBondMinRingSize(), RDKit::queryIsAtomInNRings(), RDKit::queryIsAtomInRing(), RDKit::queryIsBondInNRings(), and RDKit::queryIsBondInRing().
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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:
Definition at line 484 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
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.
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bool RDKit::ROMol::needsUpdatePropertyCache | ( | ) | const |
Referenced by endConformers().
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void RDKit::ROMol::removeConformer | ( | unsigned int | id | ) |
Delete the conformation with the specified ID.
Referenced by getBondBookmarks().
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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 285 of file ROMol.h.
References clearAtomBookmark(), getAllAtomsWithBookmark(), and getAtomWithBookmark().
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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 313 of file ROMol.h.
References clearBondBookmark(), getAllBondsWithBookmark(), and getBondWithBookmark().
void RDKit::ROMol::updatePropertyCache | ( | bool | strict = true | ) |
calculates any of our lazy properties
Notes:
updatePropertyCache()
on each of our Atoms and Bonds Referenced by endConformers(), and RDKit::CachedTrustedSmilesMolHolder::getMol().
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friend |
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protected |
Definition at line 598 of file ROMol.h.
Referenced by RDKit::RWMol::clear(), and ROMol().