#include <RDGeneral/types.h>#include <boost/tuple/tuple.hpp>#include <boost/smart_ptr.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) | |
Functions | |
| int | RDKit::MolOps::countAtomElec (const Atom *at) |
| return the number of electrons available on an atom to donate for aromaticity | |
| int | RDKit::MolOps::getFormalCharge (const ROMol &mol) |
| sums up all atomic formal charges and returns the result | |
| bool | RDKit::MolOps::atomHasConjugatedBond (const Atom *at) |
| returns whether or not the given Atom is involved in a conjugated bond | |
| 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) | |
| std::vector< boost::shared_ptr < ROMol > > | RDKit::MolOps::getMolFrags (const ROMol &mol, bool sanitizeFrags=true, INT_VECT *frags=0) |
| splits a molecule into its component fragments | |
| 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, unsigned int nb, unsigned 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 | |
Dealing with hydrogens | |
| 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) |
Sanitization | |
| void | RDKit::MolOps::sanitizeMol (RWMol &mol) |
| carries out a collection of tasks for cleaning up a molecule and ensuring that it makes "chemical sense" | |
| 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 | |
| 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 | |
| void | RDKit::MolOps::setHybridization (ROMol &mol) |
| calculates and sets the hybridization of all a molecule's Stoms | |
Ring finding and SSSR | |
| 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 | |
| int | RDKit::MolOps::symmetrizeSSSR (ROMol &mol) |
Shortest paths and other matrices | |
| 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. | |
Canonicalization | |
| void | RDKit::MolOps::rankAtoms (const ROMol &mol, INT_VECT &ranks, bool breakTies=true, VECT_INT_VECT *rankHistory=0) |
| assign a canonical ordering to a molecule's atoms | |
Stereochemistry | |
| void | RDKit::MolOps::cleanupChirality (RWMol &mol) |
| removes bogus chirality markers (those on non-sp3 centers): | |
| void | RDKit::MolOps::assignChiralTypesFrom3D (ROMol &mol, int confId=-1, bool replaceExistingTags=true) |
| Uses a conformer to assign ChiralType to a molecule's atoms. | |
| void | RDKit::MolOps::assignStereochemistry (ROMol &mol, bool cleanIt=false, bool force=false) |
| Assign stereochemistry tags to atoms (i.e. R/S) and bonds (i.e. Z/E). | |
| void | RDKit::MolOps::removeStereochemistry (ROMol &mol) |
| Removes all stereochemistry information from atoms (i.e. R/S) and bonds (i.e. Z/E). | |
| static void | RDKit::MolOps::assignAtomChiralCodes (ROMol &mol, bool cleanIt=false, bool force=false) |
| static void | RDKit::MolOps::assignBondStereoCodes (ROMol &mol, bool cleanIt=false, bool force=false) |
| 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 | |
Variables | |
| const int | ci_LOCAL_INF |
| const int ci_LOCAL_INF |
1.5.6