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RDKit
Open-source cheminformatics and machine learning.
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RDKit
Open-source cheminformatics and machine learning.
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#include <vector>#include <map>#include <list>#include <boost/smart_ptr.hpp>#include <boost/dynamic_bitset.hpp>#include <RDGeneral/types.h>Go to the source code of this file.
Classes | |
| struct | RDKit::MolOps::AdjustQueryParameters |
Namespaces | |
| RDKit | |
| Includes a bunch of functionality for handling Atom and Bond queries. | |
| RDKit::MolOps | |
| Groups a variety of molecular query and transformation operations. | |
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 |
Functions | |
| int | RDKit::MolOps::countAtomElec (const Atom *at) |
| return the number of electrons available on an atom to donate for More... | |
| int | RDKit::MolOps::getFormalCharge (const ROMol &mol) |
| sums up all atomic formal charges and returns the result More... | |
| bool | RDKit::MolOps::atomHasConjugatedBond (const Atom *at) |
| returns whether or not the given Atom is involved in a conjugated bond More... | |
| unsigned int | RDKit::MolOps::getMolFrags (const ROMol &mol, std::vector< int > &mapping) |
| find fragments (disconnected components of the molecular graph) More... | |
| unsigned int | RDKit::MolOps::getMolFrags (const ROMol &mol, std::vector< std::vector< int > > &frags) |
| find fragments (disconnected components of the molecular graph) More... | |
| std::vector< boost::shared_ptr< ROMol > > | RDKit::MolOps::getMolFrags (const ROMol &mol, bool sanitizeFrags=true, std::vector< int > *frags=0, std::vector< std::vector< int > > *fragsMolAtomMapping=0, bool copyConformers=true) |
| splits a molecule into its component fragments More... | |
| template<typename T > | |
| std::map< T, boost::shared_ptr< ROMol > > | RDKit::MolOps::getMolFragsWithQuery (const ROMol &mol, T(*query)(const ROMol &, const Atom *), bool sanitizeFrags=true, const std::vector< T > *whiteList=0, bool negateList=false) |
| splits a molecule into pieces based on labels assigned using a query More... | |
| 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 More... | |
| double | RDKit::MolOps::computeBalabanJ (double *distMat, int nb, int nAts) |
| unsigned | RDKit::MolOps::getNumAtomsWithDistinctProperty (const ROMol &mol, std::string prop) |
| returns the number of atoms which have a particular property set More... | |
Ring finding and SSSR | |
| int | RDKit::MolOps::findSSSR (const ROMol &mol, std::vector< std::vector< int > > &res) |
| finds a molecule's Smallest Set of Smallest Rings More... | |
| int | RDKit::MolOps::findSSSR (const ROMol &mol, std::vector< std::vector< int > > *res=0) |
| void | RDKit::MolOps::fastFindRings (const ROMol &mol) |
| use a DFS algorithm to identify ring bonds and atoms in a molecule More... | |
| int | RDKit::MolOps::symmetrizeSSSR (ROMol &mol, std::vector< std::vector< int > > &res) |
| symmetrize the molecule's Smallest Set of Smallest Rings More... | |
| 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, const boost::dynamic_bitset<> *bondsToUse=0) |
| returns a molecule's adjacency matrix More... | |
| 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. More... | |
| 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. More... | |
| double * | RDKit::MolOps::get3DDistanceMat (const ROMol &mol, int confId=-1, bool useAtomWts=false, bool force=false, const char *propNamePrefix=0) |
| Computes the molecule's 3D distance matrix. More... | |
| std::list< int > | RDKit::MolOps::getShortestPath (const ROMol &mol, int aid1, int aid2) |
| Find the shortest path between two atoms. More... | |
Stereochemistry | |
| void | RDKit::MolOps::cleanupChirality (RWMol &mol) |
| removes bogus chirality markers (those on non-sp3 centers): More... | |
| void | RDKit::MolOps::assignChiralTypesFrom3D (ROMol &mol, int confId=-1, bool replaceExistingTags=true) |
| Uses a conformer to assign ChiralType to a molecule's atoms. More... | |
| void | RDKit::MolOps::assignStereochemistry (ROMol &mol, bool cleanIt=false, bool force=false, bool flagPossibleStereoCenters=false) |
| Assign stereochemistry tags to atoms (i.e. R/S) and bonds (i.e. Z/E) More... | |
| void | RDKit::MolOps::removeStereochemistry (ROMol &mol) |
| Removes all stereochemistry information from atoms (i.e. R/S) and bonds. More... | |
| 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 More... | |
Variables | |
| const int | ci_LOCAL_INF |
Dealing with hydrogens | |
| enum | RDKit::MolOps::AdjustQueryWhichFlags { RDKit::MolOps::ADJUST_EMPTY = 0x0, RDKit::MolOps::ADJUST_RINGSONLY = 0x1, RDKit::MolOps::ADJUST_IGNOREDUMMIES = 0x2, RDKit::MolOps::ADJUST_SETALL = 0xFFFFFFF } |
| ROMol * | RDKit::MolOps::addHs (const ROMol &mol, bool explicitOnly=false, bool addCoords=false, const UINT_VECT *onlyOnAtoms=NULL) |
| returns a copy of a molecule with hydrogens added in as explicit Atoms More... | |
| void | RDKit::MolOps::addHs (RWMol &mol, bool explicitOnly=false, bool addCoords=false, const UINT_VECT *onlyOnAtoms=NULL) |
| 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 More... | |
| void | RDKit::MolOps::removeHs (RWMol &mol, bool implicitOnly=false, bool updateExplicitCount=false, bool sanitize=true) |
| ROMol * | RDKit::MolOps::mergeQueryHs (const ROMol &mol, bool mergeUnmappedOnly=false) |
| void | RDKit::MolOps::mergeQueryHs (RWMol &mol, bool mergeUnmappedOnly=false) |
| ROMol * | RDKit::MolOps::adjustQueryProperties (const ROMol &mol, const AdjustQueryParameters *params=NULL) |
| returns a copy of a molecule with query properties adjusted More... | |
| void | RDKit::MolOps::adjustQueryProperties (RWMol &mol, const AdjustQueryParameters *params=NULL) |
| ROMol * | RDKit::MolOps::renumberAtoms (const ROMol &mol, const std::vector< unsigned int > &newOrder) |
| returns a copy of a molecule with the atoms renumbered More... | |
Sanitization | |
| enum | RDKit::MolOps::SanitizeFlags { RDKit::MolOps::SANITIZE_NONE = 0x0, RDKit::MolOps::SANITIZE_CLEANUP = 0x1, RDKit::MolOps::SANITIZE_PROPERTIES = 0x2, RDKit::MolOps::SANITIZE_SYMMRINGS = 0x4, RDKit::MolOps::SANITIZE_KEKULIZE = 0x8, RDKit::MolOps::SANITIZE_FINDRADICALS = 0x10, RDKit::MolOps::SANITIZE_SETAROMATICITY = 0x20, RDKit::MolOps::SANITIZE_SETCONJUGATION = 0x40, RDKit::MolOps::SANITIZE_SETHYBRIDIZATION = 0x80, RDKit::MolOps::SANITIZE_CLEANUPCHIRALITY = 0x100, RDKit::MolOps::SANITIZE_ADJUSTHS = 0x200, RDKit::MolOps::SANITIZE_ALL = 0xFFFFFFF } |
| void | RDKit::MolOps::sanitizeMol (RWMol &mol, unsigned int &operationThatFailed, unsigned int sanitizeOps=SANITIZE_ALL) |
| carries out a collection of tasks for cleaning up a molecule and More... | |
| void | RDKit::MolOps::sanitizeMol (RWMol &mol) |
| int | RDKit::MolOps::setAromaticity (RWMol &mol) |
| Sets up the aromaticity for a molecule. More... | |
| void | RDKit::MolOps::cleanUp (RWMol &mol) |
| Designed to be called by the sanitizer to handle special cases before. More... | |
| void | RDKit::MolOps::assignRadicals (RWMol &mol) |
| Called by the sanitizer to assign radical counts to atoms. More... | |
| void | RDKit::MolOps::adjustHs (RWMol &mol) |
| adjust the number of implicit and explicit Hs for special cases More... | |
| void | RDKit::MolOps::Kekulize (RWMol &mol, bool markAtomsBonds=true, unsigned int maxBackTracks=100) |
| Kekulizes the molecule. More... | |
| void | RDKit::MolOps::setConjugation (ROMol &mol) |
| flags the molecule's conjugated bonds More... | |
| void | RDKit::MolOps::setHybridization (ROMol &mol) |
| calculates and sets the hybridization of all a molecule's Stoms More... | |
| const int ci_LOCAL_INF |
1.8.13