|
| RWMol () |
|
| RWMol (const ROMol &other, bool quickCopy=false, int confId=-1) |
| copy constructor with a twist More...
|
|
| RWMol (const RWMol &other) |
|
RWMol & | operator= (const RWMol &) |
|
void | insertMol (const ROMol &other) |
| insert the atoms and bonds from other into this molecule More...
|
|
|
unsigned int | addAtom (bool updateLabel=true) |
| adds an empty Atom to our collection More...
|
|
unsigned int | addAtom (Atom *atom, bool updateLabel=true, bool takeOwnership=false) |
| adds an Atom to our collection More...
|
|
void | replaceAtom (unsigned int idx, Atom *atom, bool updateLabel=false, bool preserveProps=false) |
| adds an Atom to our collection More...
|
|
Atom * | getLastAtom () |
| returns a pointer to the highest-numbered Atom More...
|
|
Atom * | getActiveAtom () |
| returns a pointer to the "active" Atom More...
|
|
void | setActiveAtom (Atom *atom) |
| sets our activeAtom More...
|
|
void | setActiveAtom (unsigned int idx) |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
|
|
void | removeAtom (unsigned int idx) |
| removes an Atom from the molecule More...
|
|
void | removeAtom (Atom *atom) |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
|
|
|
unsigned int | addBond (unsigned int beginAtomIdx, unsigned int endAtomIdx, Bond::BondType order=Bond::UNSPECIFIED) |
| adds a Bond between the indicated Atoms More...
|
|
unsigned int | addBond (Atom *beginAtom, Atom *endAtom, Bond::BondType order=Bond::UNSPECIFIED) |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
|
|
unsigned int | addBond (Bond *bond, bool takeOwnership=false) |
| adds a Bond to our collection More...
|
|
Bond * | createPartialBond (unsigned int beginAtomIdx, Bond::BondType order=Bond::UNSPECIFIED) |
| starts a Bond and sets its beginAtomIdx More...
|
|
unsigned int | finishPartialBond (unsigned int endAtomIdx, int bondBookmark, Bond::BondType order=Bond::UNSPECIFIED) |
| finishes a partially constructed bond More...
|
|
void | removeBond (unsigned int beginAtomIdx, unsigned int endAtomIdx) |
| removes a bond from the molecule More...
|
|
void | replaceBond (unsigned int idx, Bond *bond, bool preserveProps=false, bool keepSGroups=true) |
| replaces a particular Bond More...
|
|
void | setStereoGroups (std::vector< StereoGroup > &&stereo_groups) |
| Sets groups of atoms with relative stereochemistry. More...
|
|
void | clear () |
| removes all atoms, bonds, properties, bookmarks, etc. More...
|
|
void | beginBatchEdit () |
|
void | rollbackBatchEdit () |
|
void | commitBatchEdit () |
|
CXXAtomIterator< MolGraph, Atom * > | atoms () |
| C++11 Range iterator. More...
|
|
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 More...
|
|
| ROMol (const std::string &binStr) |
| construct a molecule from a pickle string More...
|
|
| ROMol (const std::string &binStr, unsigned int propertyFlags) |
| construct a molecule from a pickle string More...
|
|
virtual | ~ROMol () |
|
unsigned int | getNumAtoms () const |
| returns our number of atoms More...
|
|
unsigned int | getNumAtoms (bool onlyExplicit) const |
|
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 |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
|
|
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. More...
|
|
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. More...
|
|
unsigned int | getAtomDegree (const Atom *at) const |
| returns the degree (number of neighbors) of an Atom in the graph More...
|
|
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 |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
|
|
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. More...
|
|
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. More...
|
|
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 |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
|
|
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. More...
|
|
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. More...
|
|
void | setAtomBookmark (Atom *at, int mark) |
| associates an Atom pointer with a bookmark More...
|
|
void | replaceAtomBookmark (Atom *at, int mark) |
| associates an Atom pointer with a bookmark More...
|
|
Atom * | getAtomWithBookmark (int mark) |
| returns the first Atom associated with the bookmark provided More...
|
|
Atom * | getUniqueAtomWithBookmark (int mark) |
|
ATOM_PTR_LIST & | getAllAtomsWithBookmark (int mark) |
| returns all Atoms associated with the bookmark provided More...
|
|
void | clearAtomBookmark (int mark) |
| removes a bookmark from our collection More...
|
|
void | clearAtomBookmark (int mark, const Atom *atom) |
| removes a particular Atom from the list associated with the bookmark More...
|
|
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 *bond, int mark) |
| associates a Bond pointer with a bookmark More...
|
|
Bond * | getBondWithBookmark (int mark) |
| returns the first Bond associated with the bookmark provided More...
|
|
Bond * | getUniqueBondWithBookmark (int mark) |
|
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 | 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...
|
|
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 |
|
RingInfo * | getRingInfo () const |
|
ADJ_ITER_PAIR | getAtomNeighbors (Atom const *at) const |
| provides access to all neighbors around an Atom More...
|
|
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 |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
|
|
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. More...
|
|
MolGraph const & | getTopology () const |
| brief returns a pointer to our underlying BGL object More...
|
|
AtomIterator | beginAtoms () |
| get an AtomIterator pointing at our first Atom More...
|
|
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. More...
|
|
AtomIterator | endAtoms () |
| get an AtomIterator pointing at the end of our Atoms More...
|
|
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. More...
|
|
BondIterator | beginBonds () |
| get a BondIterator pointing at our first Bond More...
|
|
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. More...
|
|
BondIterator | endBonds () |
| get a BondIterator pointing at the end of our Bonds More...
|
|
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. More...
|
|
AromaticAtomIterator | beginAromaticAtoms () |
| get an AtomIterator pointing at our first aromatic Atom More...
|
|
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. More...
|
|
AromaticAtomIterator | endAromaticAtoms () |
| get an AtomIterator pointing at the end of our Atoms More...
|
|
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. More...
|
|
HeteroatomIterator | beginHeteros () |
| get an AtomIterator pointing at our first hetero Atom More...
|
|
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. More...
|
|
HeteroatomIterator | endHeteros () |
| get an AtomIterator pointing at the end of our Atoms More...
|
|
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. More...
|
|
QueryAtomIterator | beginQueryAtoms (QueryAtom const *query) |
| get an AtomIterator pointing at our first Atom that matches query More...
|
|
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. More...
|
|
QueryAtomIterator | endQueryAtoms () |
| get an AtomIterator pointing at the end of our Atoms More...
|
|
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. More...
|
|
MatchingAtomIterator | beginMatchingAtoms (bool(*query)(Atom *)) |
| get an AtomIterator pointing at our first Atom that matches query More...
|
|
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. More...
|
|
MatchingAtomIterator | endMatchingAtoms () |
| get an AtomIterator pointing at the end of our Atoms More...
|
|
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. More...
|
|
ConformerIterator | beginConformers () |
|
ConformerIterator | endConformers () |
|
ConstConformerIterator | beginConformers () const |
|
ConstConformerIterator | endConformers () const |
|
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 |
|
void | debugMol (std::ostream &str) const |
| sends some debugging info to a stream More...
|
|
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. More...
|
|
| 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 |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
|
|
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. More...
|
|
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...
|
|