RDCode: MolOps.h File Reference

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# MolOps.h File Reference

`#include <RDGeneral/types.h>`
`#include <boost/tuple/tuple.hpp>`

Go to the source code of this file.

## Namespaces
namespace | RDKit
namespace | RDKit::MolOps
## Typedefs
typedef std::vector < double > | RDKit::INVAR_VECT
typedef INVAR_VECT::iterator | RDKit::INVAR_VECT_I
typedef INVAR_VECT::const_iterator | RDKit::INVAR_VECT_CI
typedef boost::tuples::tuple < double, double, double > | RDKit::DiscrimTuple
| used to return atomic discriminators (three doubles)
## Enumerations
enum | RDKit::AtomInvariantType { RDKit::ComprehensiveInvariants, RDKit::ChiralSearchInvariants }
| used to request particular types of atom invariants More...
## Functions
unsigned int | RDKit::MolOps::getMolFrags (const ROMol &mol, INT_VECT &mapping)
| find fragments (disconnected components of the molecular graph)
unsigned int | RDKit::MolOps::getMolFrags (const ROMol &mol, VECT_INT_VECT &frags)
| find fragments (disconnected components of the molecular graph)
ROMol * | RDKit::MolOps::addHs (const ROMol &mol, bool explicitOnly=false, bool addCoords=false)
| returns a copy of a molecule with hydrogens added in as explicit Atoms
ROMol * | RDKit::MolOps::removeHs (const ROMol &mol, bool implicitOnly=false, bool updateExplicitCount=false, bool sanitize=true)
| returns a copy of a molecule with hydrogens removed
ROMol * | RDKit::MolOps::mergeQueryHs (const ROMol &mol)
int | RDKit::MolOps::countAtomElec (const Atom *at)
| return the number of electrons available on an atom to donate for aromaticity
int | RDKit::MolOps::setAromaticity (RWMol &mol)
| Sets up the aromaticity for a molecule.
void | RDKit::MolOps::cleanUp (RWMol &mol)
| Designed to be called by the sanitizer to handle special cases before anything is done.
void | RDKit::MolOps::adjustHs (RWMol &mol)
| adjust the number of implicit and explicit Hs for special cases
int | RDKit::MolOps::findSSSR (const ROMol &mol, VECT_INT_VECT &res)
| finds a molecule's Smallest Set of Smallest Rings
int | RDKit::MolOps::findSSSR (const ROMol &mol, VECT_INT_VECT *res=0)
int | RDKit::MolOps::symmetrizeSSSR (ROMol &mol, VECT_INT_VECT &res)
| symmetrize the molecule's Smallest Set of Smallest Rings
void | RDKit::MolOps::Kekulize (RWMol &mol, bool markAtomsBonds=true, unsigned int maxBackTracks=100)
| Kekulizes the molecule.
void | RDKit::MolOps::setConjugation (ROMol &mol)
| flags the molecule's conjugated bonds
bool | RDKit::MolOps::atomHasConjugatedBond (const Atom *at)
| returns whether or not the given Atom is involved in a conjugated bond
void | RDKit::MolOps::setHybridization (ROMol &mol)
| calculates and sets the hybridization of all a molecule's Stoms
void | RDKit::MolOps::sanitizeMol (RWMol &mol)
| carries out a collection of tasks for cleaning up a molecule and ensuring that it makes "chemical sense"
double * | RDKit::MolOps::getAdjacencyMatrix (const ROMol &mol, bool useBO=false, int emptyVal=0, bool force=false, const char *propNamePrefix=0)
| returns a molecule's adjacency matrix
double * | RDKit::MolOps::getDistanceMat (const ROMol &mol, bool useBO=false, bool useAtomWts=false, bool force=false, const char *propNamePrefix=0)
| Computes the molecule's topological distance matrix.
double * | RDKit::MolOps::getDistanceMat (const ROMol &mol, const std::vector< int > &activeAtoms, const std::vector< const Bond * > &bonds, bool useBO=false, bool useAtomWts=false)
| Computes the molecule's topological distance matrix.
INT_LIST | RDKit::MolOps::getShortestPath (const ROMol &mol, int aid1, int aid2)
| Find the shortest path between two atoms.
DiscrimTuple | RDKit::MolOps::computeDiscriminators (const ROMol &mol, bool useBO=true, bool force=false)
| calculates a set of molecular discriminators from the distance matrix
DiscrimTuple | RDKit::MolOps::computeDiscriminators (double *distMat, int nb, int na)
| Same as MolOps::computeDiscriminators(const ROMol &mol), except that this directly uses the user-supplied distance matrix.
double | RDKit::MolOps::computeBalabanJ (const ROMol &mol, bool useBO=true, bool force=false, const std::vector< int > *bondPath=0, bool cacheIt=true)
| calculates Balaban's J index for the molecule
void | RDKit::MolOps::findSpanningTree (const ROMol &mol, INT_VECT &mst)
| finds a molecule's minimium spanning tree (MST)
void | RDKit::MolOps::rankAtoms (const ROMol &mol, INT_VECT &ranks, AtomInvariantType invariantType=ComprehensiveInvariants, bool breakTies=true, VECT_INT_VECT *rankHistory=0, bool includeChirality=false)
| assign a canonical ordering to a molecule's atoms
void | RDKit::MolOps::buildAtomInvariants (const ROMol &mol, INVAR_VECT &res, bool includeChirality=false)
| calculates a set of atom invariants
void | RDKit::MolOps::buildChiralAtomInvariants (const ROMol &mol, INVAR_VECT &res)
| calculates a set of chiral atom invariants
void | RDKit::MolOps::assignAtomChiralCodes (ROMol &mol, bool cleanIt=false, bool force=false)
| calculate CIP (R/S) codes for a molecule's chiral centers
void | RDKit::MolOps::assignBondStereoCodes (ROMol &mol, bool cleanIt=false, bool force=false)
| calculate CIP (Z/E) codes for a molecule's double bonds
void | RDKit::MolOps::findPotentialStereoBonds (ROMol &mol, bool cleanIt=false)
| finds bonds that could be cis/trans in a molecule and mark them as Bond::STEREONONE
int | RDKit::MolOps::getFormalCharge (const ROMol &mol)
| sums up all atomic formal charges and returns the result
void | RDKit::MolOps::cleanupChirality (RWMol &mol)
| removes bogus chirality markers (those on non-sp3 centers):
## Variables
const int | ci_LOCAL_INF

## Variable Documentation

const int ci_LOCAL_INF