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RDKit
Open-source cheminformatics and machine learning.
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#include <ROMol.h>
Public Member Functions | |
CXXAtomIterator< MolGraph, Atom * > | atoms () |
C++11 Range iterator. | |
CXXAtomIterator< const MolGraph, Atom *const > | atoms () const |
CXXAtomIterator< const MolGraph, Atom *const, MolGraph::adjacency_iterator > | atomNeighbors (Atom const *at) const |
CXXAtomIterator< MolGraph, Atom *, MolGraph::adjacency_iterator > | atomNeighbors (Atom const *at) |
CXXBondIterator< const MolGraph, Bond *const, MolGraph::out_edge_iterator > | atomBonds (Atom const *at) const |
CXXBondIterator< MolGraph, Bond *, MolGraph::out_edge_iterator > | atomBonds (Atom const *at) |
CXXBondIterator< MolGraph, Bond * > | bonds () |
CXXBondIterator< const MolGraph, Bond *const > | bonds () const |
ROMol () | |
ROMol (const ROMol &other, bool quickCopy=false, int confId=-1) | |
copy constructor with a twist | |
ROMol (const std::string &binStr) | |
construct a molecule from a pickle string | |
ROMol (const std::string &binStr, unsigned int propertyFlags) | |
construct a molecule from a pickle string | |
ROMol (ROMol &&o) noexcept | |
ROMol & | operator= (ROMol &&o) noexcept |
ROMol & | operator= (const ROMol &)=delete |
virtual | ~ROMol () |
Atom * | operator[] (const vertex_descriptor &v) |
const Atom * | operator[] (const vertex_descriptor &v) const |
Bond * | operator[] (const edge_descriptor &e) |
const Bond * | operator[] (const edge_descriptor &e) const |
const std::vector< StereoGroup > & | getStereoGroups () const |
Gets a reference to the groups of atoms with relative stereochemistry. | |
void | setStereoGroups (std::vector< StereoGroup > stereo_groups) |
Sets groups of atoms with relative stereochemistry. | |
Atoms | |
unsigned int | getNumAtoms () const |
returns our number of atoms | |
unsigned int | getNumAtoms (bool onlyExplicit) const |
unsigned int | getNumHeavyAtoms () const |
returns our number of heavy atoms (atomic number > 1) | |
Atom * | getAtomWithIdx (unsigned int idx) |
returns a pointer to a particular Atom | |
const Atom * | 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 * | getAtomWithIdx (const U idx) |
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 > | |
const Atom * | getAtomWithIdx (const U idx) 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 | getAtomDegree (const Atom *at) const |
returns the degree (number of neighbors) of an Atom in the graph | |
Bonds | |
unsigned int | getNumBonds (bool onlyHeavy=1) const |
returns our number of Bonds | |
Bond * | getBondWithIdx (unsigned int idx) |
returns a pointer to a particular Bond | |
const Bond * | getBondWithIdx (unsigned int idx) const |
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 * | getBondWithIdx (const U idx) |
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 > | |
const Bond * | getBondWithIdx (const U idx) const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
Bond * | getBondBetweenAtoms (unsigned int idx1, unsigned int idx2) |
returns a pointer to the bond between two atoms, Null on failure | |
const Bond * | getBondBetweenAtoms (unsigned int idx1, unsigned int idx2) const |
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 * | getBondBetweenAtoms (const U idx1, const V idx2) |
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 > | |
const Bond * | getBondBetweenAtoms (const U idx1, const V idx2) const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
Bookmarks | |
void | setAtomBookmark (Atom *at, int mark) |
associates an Atom pointer with a bookmark | |
void | replaceAtomBookmark (Atom *at, int mark) |
associates an Atom pointer with a bookmark | |
Atom * | getAtomWithBookmark (int mark) |
returns the first Atom associated with the bookmark provided | |
Atom * | getUniqueAtomWithBookmark (int mark) |
ATOM_PTR_LIST & | getAllAtomsWithBookmark (int mark) |
returns all Atoms associated with the bookmark provided | |
void | clearAtomBookmark (int mark) |
removes a bookmark from our collection | |
void | clearAtomBookmark (int mark, const Atom *atom) |
removes a particular Atom from the list associated with the bookmark | |
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 *bond, int mark) |
associates a Bond pointer with a bookmark | |
Bond * | getBondWithBookmark (int mark) |
returns the first Bond associated with the bookmark provided | |
Bond * | getUniqueBondWithBookmark (int mark) |
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 | clearAllBondBookmarks () |
blows out all bond bookmarks | |
bool | hasBondBookmark (int mark) const |
queries whether or not any bonds are associated with a bookmark | |
BOND_BOOKMARK_MAP * | getBondBookmarks () |
returns a pointer to all of our bond bookmarks | |
Conformers | |
const Conformer & | getConformer (int id=-1) const |
Conformer & | getConformer (int id=-1) |
void | removeConformer (unsigned int id) |
Delete the conformation with the specified ID. | |
void | clearConformers () |
Clear all the conformations on the molecule. | |
unsigned int | addConformer (Conformer *conf, bool assignId=false) |
Add a new conformation to the molecule. | |
unsigned int | getNumConformers () const |
Topology | |
RingInfo * | getRingInfo () const |
ADJ_ITER_PAIR | getAtomNeighbors (Atom const *at) const |
provides access to all neighbors around an Atom | |
OBOND_ITER_PAIR | getAtomBonds (Atom const *at) const |
provides access to all Bond objects connected to an Atom | |
ATOM_ITER_PAIR | getVertices () |
returns an iterator pair for looping over all Atoms | |
BOND_ITER_PAIR | getEdges () |
returns an iterator pair for looping over all Bonds | |
ATOM_ITER_PAIR | getVertices () const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
BOND_ITER_PAIR | getEdges () const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
MolGraph const & | getTopology () const |
brief returns a pointer to our underlying BGL object | |
Iterators | |
AtomIterator | beginAtoms () |
get an AtomIterator pointing at our first Atom | |
ConstAtomIterator | beginAtoms () const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
AtomIterator | endAtoms () |
get an AtomIterator pointing at the end of our Atoms | |
ConstAtomIterator | 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 | beginBonds () |
get a BondIterator pointing at our first Bond | |
ConstBondIterator | beginBonds () const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
BondIterator | endBonds () |
get a BondIterator pointing at the end of our Bonds | |
ConstBondIterator | endBonds () const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
AromaticAtomIterator | beginAromaticAtoms () |
get an AtomIterator pointing at our first aromatic Atom | |
ConstAromaticAtomIterator | beginAromaticAtoms () const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
AromaticAtomIterator | endAromaticAtoms () |
get an AtomIterator pointing at the end of our Atoms | |
ConstAromaticAtomIterator | endAromaticAtoms () const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
HeteroatomIterator | beginHeteros () |
get an AtomIterator pointing at our first hetero Atom | |
ConstHeteroatomIterator | beginHeteros () const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
HeteroatomIterator | endHeteros () |
get an AtomIterator pointing at the end of our Atoms | |
ConstHeteroatomIterator | endHeteros () const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
bool | hasQuery () const |
if the Mol has any Query atoms or bonds | |
QueryAtomIterator | beginQueryAtoms (QueryAtom const *query) |
get an AtomIterator pointing at our first Atom that matches query | |
ConstQueryAtomIterator | 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. | |
QueryAtomIterator | endQueryAtoms () |
get an AtomIterator pointing at the end of our Atoms | |
ConstQueryAtomIterator | endQueryAtoms () const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
MatchingAtomIterator | beginMatchingAtoms (bool(*query)(Atom *)) |
get an AtomIterator pointing at our first Atom that matches query | |
ConstMatchingAtomIterator | beginMatchingAtoms (bool(*query)(const Atom *)) const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
MatchingAtomIterator | endMatchingAtoms () |
get an AtomIterator pointing at the end of our Atoms | |
ConstMatchingAtomIterator | endMatchingAtoms () const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
ConformerIterator | beginConformers () |
ConformerIterator | endConformers () |
ConstConformerIterator | beginConformers () const |
ConstConformerIterator | endConformers () const |
Properties | |
void | clearComputedProps (bool includeRings=true) const |
clears all of our computed properties | |
void | updatePropertyCache (bool strict=true) |
calculates any of our lazy properties | |
bool | needsUpdatePropertyCache () const |
Misc | |
sends some debugging info to a stream | |
void | debugMol (std::ostream &str) const |
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RDProps () | |
RDProps (const RDProps &rhs) | |
RDProps & | operator= (const RDProps &rhs) |
RDProps (RDProps &&o) noexcept=default | |
RDProps & | operator= (RDProps &&rhs) noexcept=default |
void | clear () |
const Dict & | getDict () const |
gets the underlying Dictionary | |
Dict & | getDict () |
STR_VECT | getPropList (bool includePrivate=true, bool includeComputed=true) const |
returns a list with the names of our properties | |
template<typename T > | |
void | setProp (const std::string &key, T val, bool computed=false) const |
sets a property value | |
template<typename T > | |
void | getProp (const std::string &key, T &res) const |
allows retrieval of a particular property value | |
template<typename T > | |
T | getProp (const std::string &key) const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
template<typename T > | |
bool | getPropIfPresent (const std::string &key, T &res) const |
bool | hasProp (const std::string &key) const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
void | clearProp (const std::string &key) const |
clears the value of a property | |
void | clearComputedProps () const |
clears all of our computed properties | |
void | updateProps (const RDProps &source, bool preserveExisting=false) |
update the properties from another | |
Protected Attributes | |
unsigned int | numBonds {0} |
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Dict | d_props |
Friends | |
class | MolPickler |
class | RWMol |
RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & | getSubstanceGroups (ROMol &mol) |
RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > & | getSubstanceGroups (const ROMol &mol) |
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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 . |
Definition at line 335 of file ROMol.h.
References rdcast.
RDKit::ROMol::ROMol | ( | const std::string & | binStr | ) |
construct a molecule from a pickle string
RDKit::ROMol::ROMol | ( | const std::string & | binStr, |
unsigned int | propertyFlags ) |
construct a molecule from a pickle string
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Definition at line 346 of file ROMol.h.
References RDKit::RDProps::clear().
unsigned int RDKit::ROMol::addConformer | ( | Conformer * | conf, |
bool | assignId = false ) |
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 conformation if true otherwise it is assumed that the conformation already has an (unique) ID set |
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C++11 Range iterator.
Usage
Definition at line 277 of file ROMol.h.
Referenced by RDKit::MolDraw2D_detail::addAtomIndices(), and RDKit::FileParserUtils::getAtomPropertyList().
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AromaticAtomIterator RDKit::ROMol::beginAromaticAtoms | ( | ) |
get an AtomIterator pointing at our first aromatic Atom
ConstAromaticAtomIterator RDKit::ROMol::beginAromaticAtoms | ( | ) | const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
AtomIterator RDKit::ROMol::beginAtoms | ( | ) |
get an AtomIterator pointing at our first Atom
ConstAtomIterator RDKit::ROMol::beginAtoms | ( | ) | const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
BondIterator RDKit::ROMol::beginBonds | ( | ) |
get a BondIterator pointing at our first Bond
ConstBondIterator RDKit::ROMol::beginBonds | ( | ) | const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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Definition at line 743 of file ROMol.h.
Referenced by RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST().
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HeteroatomIterator RDKit::ROMol::beginHeteros | ( | ) |
get an AtomIterator pointing at our first hetero Atom
ConstHeteroatomIterator RDKit::ROMol::beginHeteros | ( | ) | const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
MatchingAtomIterator RDKit::ROMol::beginMatchingAtoms | ( | bool(* | query )(Atom *) | ) |
get an AtomIterator pointing at our first Atom that matches query
ConstMatchingAtomIterator RDKit::ROMol::beginMatchingAtoms | ( | bool(* | query )(const Atom *) | ) | const |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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.
QueryAtomIterator RDKit::ROMol::beginQueryAtoms | ( | QueryAtom const * | query | ) |
get an AtomIterator pointing at our first Atom that matches query
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Usage
Definition at line 316 of file ROMol.h.
Referenced by RDKit::MolDraw2D_detail::addBondIndices().
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void RDKit::ROMol::clearAtomBookmark | ( | int | mark | ) |
removes a bookmark
from our collection
void RDKit::ROMol::clearAtomBookmark | ( | int | mark, |
const Atom * | atom ) |
removes a particular Atom from the list associated with the bookmark
void RDKit::ROMol::clearBondBookmark | ( | int | mark | ) |
removes a bookmark
from our collection
void RDKit::ROMol::clearBondBookmark | ( | int | mark, |
const Bond * | bond ) |
removes a particular Bond from the list associated with the bookmark
void RDKit::ROMol::clearComputedProps | ( | bool | includeRings = true | ) | const |
clears all of our computed
properties
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void RDKit::ROMol::debugMol | ( | std::ostream & | str | ) | const |
AromaticAtomIterator RDKit::ROMol::endAromaticAtoms | ( | ) |
get an AtomIterator pointing at the end of our Atoms
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
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
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 745 of file ROMol.h.
Referenced by RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST().
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HeteroatomIterator RDKit::ROMol::endHeteros | ( | ) |
get an AtomIterator pointing at the end of our Atoms
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
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
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
BOND_PTR_LIST & RDKit::ROMol::getAllBondsWithBookmark | ( | int | mark | ) |
returns all bonds associated with the bookmark
provided
OBOND_ITER_PAIR RDKit::ROMol::getAtomBonds | ( | Atom const * | at | ) | const |
provides access to all Bond objects connected to an Atom
at | the atom whose neighbors we are looking for |
Usage
or, if you need a non-const Bond *:
Referenced by RDKit::queryAtomHasRingBond(), and RDKit::queryAtomRingBondCount().
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returns a pointer to all of our atom bookmarks
Definition at line 512 of file ROMol.h.
Referenced by RDKit::SLNParse::addBranchToMol().
unsigned int RDKit::ROMol::getAtomDegree | ( | const Atom * | at | ) | const |
returns the degree (number of neighbors) of an Atom in the graph
ADJ_ITER_PAIR RDKit::ROMol::getAtomNeighbors | ( | Atom const * | at | ) | const |
provides access to all neighbors around an Atom
at | the atom whose neighbors we are looking for |
Usage
Referenced by RDKit::queryAtomHasAliphaticHeteroatomNbrs(), RDKit::queryAtomHasHeteroatomNbrs(), RDKit::queryAtomHeavyAtomDegree(), RDKit::queryAtomNonHydrogenDegree(), RDKit::queryAtomNumAliphaticHeteroatomNbrs(), and RDKit::queryAtomNumHeteroatomNbrs().
Atom * RDKit::ROMol::getAtomWithBookmark | ( | int | mark | ) |
returns the first Atom associated with the bookmark
provided
Referenced by RDKit::SLNParse::closeRingBond().
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Atom * RDKit::ROMol::getAtomWithIdx | ( | unsigned int | idx | ) |
returns a pointer to a particular Atom
Referenced by RDKit::SLNParse::addBranchToMol(), and RDKit::FileParserUtils::applyMolListPropToAtoms().
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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Bond * RDKit::ROMol::getBondBetweenAtoms | ( | unsigned int | idx1, |
unsigned int | idx2 ) |
returns a pointer to the bond between two atoms, Null on failure
Referenced by RDKit::MolEnumerator::utils::getMolLinkNodes(), 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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returns a pointer to all of our bond bookmarks
Definition at line 535 of file ROMol.h.
Referenced by RDKit::SLNParse::addBranchToMol().
Bond * RDKit::ROMol::getBondWithBookmark | ( | int | mark | ) |
returns the first Bond associated with the bookmark
provided
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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.
Conformer & RDKit::ROMol::getConformer | ( | int | id = -1 | ) |
return the conformer with a specified ID if the ID is negative the first conformation will be returned
const Conformer & RDKit::ROMol::getConformer | ( | int | id = -1 | ) | const |
return the conformer with a specified ID if the ID is negative the first conformation will be returned
Referenced by RDKit::ForceFieldsHelper::createEmptyForceFieldForMol().
BOND_ITER_PAIR RDKit::ROMol::getEdges | ( | ) |
returns an iterator pair for looping over all Bonds
Usage
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.
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returns our number of atoms
Definition at line 421 of file ROMol.h.
References rdcast.
Referenced by RDKit::SLNParse::addBranchToMol(), RDKit::FileParserUtils::applyMolListPropToAtoms(), RDKit::Canon::BreakTies(), RDKit::FMCS::TargetMatch::init(), RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST(), and RDKit::Canon::RefinePartitions().
unsigned int RDKit::ROMol::getNumAtoms | ( | bool | onlyExplicit | ) | const |
unsigned int RDKit::ROMol::getNumBonds | ( | bool | onlyHeavy = 1 | ) | const |
returns our number of Bonds
Referenced by RDKit::FileParserUtils::getV3000CTAB(), and RDKit::FMCS::TargetMatch::init().
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Definition at line 568 of file ROMol.h.
References rdcast.
Referenced by RDKit::MMFF::MMFFOptimizeMoleculeConfs(), RDKit::ForceFieldsHelper::OptimizeMoleculeConfs(), and RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST().
unsigned int RDKit::ROMol::getNumHeavyAtoms | ( | ) | const |
returns our number of heavy atoms (atomic number > 1)
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returns a pointer to our RingInfo structure Note: the client should not delete this.
Definition at line 577 of file ROMol.h.
Referenced by RDKit::queryAtomHasRingBond(), RDKit::queryAtomIsInRingOfSize(), RDKit::queryAtomMinRingSize(), RDKit::queryAtomRingBondCount(), 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 680 of file ROMol.h.
Referenced by RDKit::queryAtomHasRingBond(), and RDKit::queryAtomRingBondCount().
Atom * RDKit::ROMol::getUniqueAtomWithBookmark | ( | int | mark | ) |
returns the Atom associated with the bookmark
provided a check is made to ensure it is the only atom with that bookmark
Bond * RDKit::ROMol::getUniqueBondWithBookmark | ( | int | mark | ) |
returns the Bond associated with the bookmark
provided a check is made to ensure it is the only bond with that bookmark
ATOM_ITER_PAIR RDKit::ROMol::getVertices | ( | ) |
returns an iterator pair for looping over all Atoms
Usage
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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queries whether or not any atoms are associated with a bookmark
Definition at line 510 of file ROMol.h.
Referenced by RDKit::SLNParse::addBranchToMol(), and RDKit::SLNParse::closeRingBond().
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queries whether or not any bonds are associated with a bookmark
Definition at line 533 of file ROMol.h.
Referenced by RDKit::SLNParse::addBranchToMol().
bool RDKit::ROMol::hasQuery | ( | ) | const |
if the Mol has any Query atoms or bonds
bool RDKit::ROMol::needsUpdatePropertyCache | ( | ) | const |
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void RDKit::ROMol::removeConformer | ( | unsigned int | id | ) |
Delete the conformation with the specified ID.
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associates an Atom pointer with a bookmark
Definition at line 487 of file ROMol.h.
Referenced by RDKit::SLNParse::addBranchToMol().
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associates a Bond pointer with a bookmark
Definition at line 515 of file ROMol.h.
Referenced by RDKit::SLNParse::addBranchToMol(), and RDKit::SLNParse::closeRingBond().
void RDKit::ROMol::setStereoGroups | ( | std::vector< StereoGroup > | stereo_groups | ) |
Sets groups of atoms with relative stereochemistry.
stereo_groups | the new set of stereo groups. All will be replaced. |
Stereo groups are also called enhanced stereochemistry in the SDF/Mol3000 file format. stereo_groups should be std::move()ed into this function.
void RDKit::ROMol::updatePropertyCache | ( | bool | strict = true | ) |
calculates any of our lazy properties
Notes:
updatePropertyCache()
on each of our Atoms and Bonds
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