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RDKit
Open-source cheminformatics and machine learning.
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#include <RDGeneral/export.h>
#include <vector>
#include <map>
#include <list>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/smart_ptr.hpp>
#include <boost/dynamic_bitset.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <RDGeneral/types.h>
#include "SanitException.h"
#include <RDGeneral/FileParseException.h>
Go to the source code of this file.
Classes | |
struct | RDKit::MolOps::RemoveHsParameters |
struct | RDKit::MolOps::AdjustQueryParameters |
Parameters controlling the behavior of MolOps::adjustQueryProperties. More... | |
class | RDKit::MolOps::Hybridizations |
Namespaces | |
namespace | RDKit |
Std stuff. | |
namespace | RDKit::MolOps |
Groups a variety of molecular query and transformation operations. | |
namespace | RDKit::MolOps::details |
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 | |
RDKIT_GRAPHMOL_EXPORT int | RDKit::MolOps::countAtomElec (const Atom *at) |
RDKIT_GRAPHMOL_EXPORT int | RDKit::MolOps::getFormalCharge (const ROMol &mol) |
sums up all atomic formal charges and returns the result | |
RDKIT_GRAPHMOL_EXPORT bool | RDKit::MolOps::atomHasConjugatedBond (const Atom *at) |
returns whether or not the given Atom is involved in a conjugated bond | |
RDKIT_GRAPHMOL_EXPORT unsigned int | RDKit::MolOps::getMolFrags (const ROMol &mol, std::vector< int > &mapping) |
find fragments (disconnected components of the molecular graph) | |
RDKIT_GRAPHMOL_EXPORT unsigned int | RDKit::MolOps::getMolFrags (const ROMol &mol, std::vector< std::vector< int > > &frags) |
find fragments (disconnected components of the molecular graph) | |
RDKIT_GRAPHMOL_EXPORT unsigned int | RDKit::MolOps::getMolFrags (const ROMol &mol, std::vector< std::unique_ptr< ROMol > > &molFrags, bool sanitizeFrags=true, std::vector< int > *frags=nullptr, std::vector< std::vector< int > > *fragsMolAtomMapping=nullptr, bool copyConformers=true) |
RDKIT_GRAPHMOL_EXPORT std::vector< boost::shared_ptr< ROMol > > | RDKit::MolOps::getMolFrags (const ROMol &mol, bool sanitizeFrags=true, std::vector< int > *frags=nullptr, std::vector< std::vector< int > > *fragsMolAtomMapping=nullptr, bool copyConformers=true) |
template<typename T > | |
RDKIT_GRAPHMOL_EXPORT 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=nullptr, bool negateList=false) |
splits a molecule into pieces based on labels assigned using a query | |
template<typename T > | |
RDKIT_GRAPHMOL_EXPORT unsigned int | RDKit::MolOps::getMolFragsWithQuery (const ROMol &mol, T(*query)(const ROMol &, const Atom *), std::map< T, std::unique_ptr< ROMol > > &molFrags, bool sanitizeFrags=true, const std::vector< T > *whiteList=nullptr, bool negateList=false) |
RDKIT_GRAPHMOL_EXPORT unsigned | RDKit::MolOps::getNumAtomsWithDistinctProperty (const ROMol &mol, std::string prop) |
returns the number of atoms which have a particular property set | |
RDKIT_GRAPHMOL_EXPORT bool | RDKit::MolOps::needsHs (const ROMol &mol) |
returns whether or not a molecule needs to have Hs added to it. | |
RDKIT_GRAPHMOL_EXPORT ROMol * | RDKit::MolOps::hapticBondsToDative (const ROMol &mol) |
Replaces haptic bond with explicit dative bonds. | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::hapticBondsToDative (RWMol &mol) |
RDKIT_GRAPHMOL_EXPORT ROMol * | RDKit::MolOps::dativeBondsToHaptic (const ROMol &mol) |
Replaces explicit dative bonds with haptic. | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::dativeBondsToHaptic (RWMol &mol) |
RDKIT_GRAPHMOL_EXPORT double | RDKit::MolOps::getAvgMolWt (const ROMol &mol, bool onlyHeavy=false) |
RDKIT_GRAPHMOL_EXPORT double | RDKit::MolOps::getExactMolWt (const ROMol &mol, bool onlyHeavy=false) |
RDKIT_GRAPHMOL_EXPORT std::string | RDKit::MolOps::getMolFormula (const ROMol &mol, bool separateIsotopes=false, bool abbreviateHIsotopes=true) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::details::KekulizeFragment (RWMol &mol, const boost::dynamic_bitset<> &atomsToUse, boost::dynamic_bitset<> bondsToUse, bool markAtomsBonds=true, unsigned int maxBackTracks=100) |
not recommended for use in other code | |
RDKIT_GRAPHMOL_EXPORT std::vector< int > | RDKit::MolOps::details::hapticBondEndpoints (const Bond *bond) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::expandAttachmentPoints (RWMol &mol, bool addAsQueries=true, bool addCoords=true) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::collapseAttachmentPoints (RWMol &mol, bool markedOnly=true) |
RDKIT_GRAPHMOL_EXPORT unsigned int | RDKit::MolOps::details::addExplicitAttachmentPoint (RWMol &mol, unsigned int atomIdx, unsigned int val, bool addAsQuery=true, bool addCoords=true) |
RDKIT_GRAPHMOL_EXPORT bool | RDKit::MolOps::details::isAttachmentPoint (const Atom *atom, bool markedOnly=true) |
returns whether or not an atom is an attachment point | |
Ring finding and SSSR | |
RDKIT_GRAPHMOL_EXPORT int | RDKit::MolOps::findSSSR (const ROMol &mol, std::vector< std::vector< int > > &res, bool includeDativeBonds=false) |
finds a molecule's Smallest Set of Smallest Rings | |
RDKIT_GRAPHMOL_EXPORT int | RDKit::MolOps::findSSSR (const ROMol &mol, std::vector< std::vector< int > > *res=nullptr, bool includeDativeBonds=false) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::fastFindRings (const ROMol &mol) |
use a DFS algorithm to identify ring bonds and atoms in a molecule | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::findRingFamilies (const ROMol &mol) |
RDKIT_GRAPHMOL_EXPORT int | RDKit::MolOps::symmetrizeSSSR (ROMol &mol, std::vector< std::vector< int > > &res, bool includeDativeBonds=false) |
symmetrize the molecule's Smallest Set of Smallest Rings | |
RDKIT_GRAPHMOL_EXPORT int | RDKit::MolOps::symmetrizeSSSR (ROMol &mol, bool includeDativeBonds=false) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
Shortest paths and other matrices | |
RDKIT_GRAPHMOL_EXPORT double * | RDKit::MolOps::getAdjacencyMatrix (const ROMol &mol, bool useBO=false, int emptyVal=0, bool force=false, const char *propNamePrefix=nullptr, const boost::dynamic_bitset<> *bondsToUse=nullptr) |
returns a molecule's adjacency matrix | |
RDKIT_GRAPHMOL_EXPORT double * | RDKit::MolOps::getDistanceMat (const ROMol &mol, bool useBO=false, bool useAtomWts=false, bool force=false, const char *propNamePrefix=nullptr) |
Computes the molecule's topological distance matrix. | |
RDKIT_GRAPHMOL_EXPORT 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. | |
RDKIT_GRAPHMOL_EXPORT double * | RDKit::MolOps::get3DDistanceMat (const ROMol &mol, int confId=-1, bool useAtomWts=false, bool force=false, const char *propNamePrefix=nullptr) |
Computes the molecule's 3D distance matrix. | |
RDKIT_GRAPHMOL_EXPORT std::list< int > | RDKit::MolOps::getShortestPath (const ROMol &mol, int aid1, int aid2) |
Find the shortest path between two atoms. | |
Stereochemistry | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::cleanupChirality (RWMol &mol) |
removes bogus chirality markers (e.g. tetrahedral flags on non-sp3 centers): | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::cleanupAtropisomers (RWMol &mol, Hybridizations &hybridizations) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::cleanupAtropisomers (RWMol &) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::assignChiralTypesFrom3D (ROMol &mol, int confId=-1, bool replaceExistingTags=true) |
Uses a conformer to assign ChiralTypes to a molecule's atoms. | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::assignStereochemistryFrom3D (ROMol &mol, int confId=-1, bool replaceExistingTags=true) |
Uses a conformer to assign ChiralTypes to a molecule's atoms and stereo flags to its bonds. | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::assignChiralTypesFromBondDirs (ROMol &mol, int confId=-1, bool replaceExistingTags=true) |
Use bond directions to assign ChiralTypes to a molecule's atoms and stereo flags to its bonds. | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::detectBondStereochemistry (ROMol &mol, int confId=-1) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::setDoubleBondNeighborDirections (ROMol &mol, const Conformer *conf=nullptr) |
Sets bond directions based on double bond stereochemistry. | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::clearSingleBondDirFlags (ROMol &mol, bool onlyWedgeFlags=false) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::clearAllBondDirFlags (ROMol &mol) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::clearDirFlags (ROMol &mol, bool onlyWedgeFlags=false) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::setBondStereoFromDirections (ROMol &mol) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::assignStereochemistry (ROMol &mol, bool cleanIt=false, bool force=false, bool flagPossibleStereoCenters=false) |
Assign stereochemistry tags to atoms and bonds. | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::removeStereochemistry (ROMol &mol) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::findPotentialStereoBonds (ROMol &mol, bool cleanIt=false) |
finds bonds that could be cis/trans in a molecule and mark them as Bond::STEREOANY. | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::assignChiralTypesFromMolParity (ROMol &mol, bool replaceExistingTags=true) |
Uses the molParity atom property to assign ChiralType to a molecule's atoms. | |
Variables | |
RDKIT_GRAPHMOL_EXPORT const int | ci_LOCAL_INF |
Dealing with hydrogens | |
enum | RDKit::MolOps::AdjustQueryWhichFlags { RDKit::MolOps::ADJUST_IGNORENONE = 0x0 , RDKit::MolOps::ADJUST_IGNORECHAINS = 0x1 , RDKit::MolOps::ADJUST_IGNORERINGS = 0x4 , RDKit::MolOps::ADJUST_IGNOREDUMMIES = 0x2 , RDKit::MolOps::ADJUST_IGNORENONDUMMIES = 0x8 , RDKit::MolOps::ADJUST_IGNOREMAPPED = 0x10 , RDKit::MolOps::ADJUST_IGNOREALL = 0xFFFFFFF } |
RDKIT_GRAPHMOL_EXPORT ROMol * | RDKit::MolOps::addHs (const ROMol &mol, bool explicitOnly=false, bool addCoords=false, const UINT_VECT *onlyOnAtoms=nullptr, bool addResidueInfo=false) |
returns a copy of a molecule with hydrogens added in as explicit Atoms | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::addHs (RWMol &mol, bool explicitOnly=false, bool addCoords=false, const UINT_VECT *onlyOnAtoms=nullptr, bool addResidueInfo=false) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::setTerminalAtomCoords (ROMol &mol, unsigned int idx, unsigned int otherIdx) |
RDKIT_GRAPHMOL_EXPORT 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 | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::removeHs (RWMol &mol, bool implicitOnly=false, bool updateExplicitCount=false, bool sanitize=true) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::removeHs (RWMol &mol, const RemoveHsParameters &ps, bool sanitize=true) |
RDKIT_GRAPHMOL_EXPORT ROMol * | RDKit::MolOps::removeHs (const ROMol &mol, const RemoveHsParameters &ps, bool sanitize=true) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::removeAllHs (RWMol &mol, bool sanitize=true) |
removes all Hs from a molecule | |
RDKIT_GRAPHMOL_EXPORT ROMol * | RDKit::MolOps::removeAllHs (const ROMol &mol, bool sanitize=true) |
RDKIT_GRAPHMOL_EXPORT ROMol * | RDKit::MolOps::mergeQueryHs (const ROMol &mol, bool mergeUnmappedOnly=false, bool mergeIsotopes=false) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::mergeQueryHs (RWMol &mol, bool mergeUnmappedOnly=false, bool mergeIsotopes=false) |
RDKIT_GRAPHMOL_EXPORT std::pair< bool, bool > | RDKit::MolOps::hasQueryHs (const ROMol &mol) |
returns a pair of booleans (hasQueryHs, hasUnmergaebleQueryHs) | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::parseAdjustQueryParametersFromJSON (MolOps::AdjustQueryParameters &p, const std::string &json) |
updates an AdjustQueryParameters object from a JSON string | |
RDKIT_GRAPHMOL_EXPORT ROMol * | RDKit::MolOps::adjustQueryProperties (const ROMol &mol, const AdjustQueryParameters *params=nullptr) |
returns a copy of a molecule with query properties adjusted | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::adjustQueryProperties (RWMol &mol, const AdjustQueryParameters *params=nullptr) |
RDKIT_GRAPHMOL_EXPORT ROMol * | RDKit::MolOps::renumberAtoms (const ROMol &mol, const std::vector< unsigned int > &newOrder) |
returns a copy of a molecule with the atoms renumbered | |
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