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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"
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... | |
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 More... | |
RDKIT_GRAPHMOL_EXPORT bool | RDKit::MolOps::atomHasConjugatedBond (const Atom *at) |
returns whether or not the given Atom is involved in a conjugated bond More... | |
RDKIT_GRAPHMOL_EXPORT unsigned int | RDKit::MolOps::getMolFrags (const ROMol &mol, std::vector< int > &mapping) |
find fragments (disconnected components of the molecular graph) More... | |
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) More... | |
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 More... | |
RDKIT_GRAPHMOL_EXPORT unsigned | RDKit::MolOps::getNumAtomsWithDistinctProperty (const ROMol &mol, std::string prop) |
returns the number of atoms which have a particular property set More... | |
RDKIT_GRAPHMOL_EXPORT bool | RDKit::MolOps::needsHs (const ROMol &mol) |
returns whether or not a molecule needs to have Hs added to it. More... | |
RDKIT_GRAPHMOL_EXPORT ROMol * | RDKit::MolOps::hapticBondsToDative (const ROMol &mol) |
Replaces haptic bond with explicit dative bonds. More... | |
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. More... | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::dativeBondsToHaptic (RWMol &mol) |
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 More... | |
RDKIT_GRAPHMOL_EXPORT std::vector< int > | RDKit::MolOps::details::hapticBondEndpoints (const Bond *bond) |
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 More... | |
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. More... | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::fastFindRings (const ROMol &mol) |
use a DFS algorithm to identify ring bonds and atoms in a molecule More... | |
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 More... | |
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. More... | |
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 More... | |
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. More... | |
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. More... | |
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. More... | |
RDKIT_GRAPHMOL_EXPORT std::list< int > | RDKit::MolOps::getShortestPath (const ROMol &mol, int aid1, int aid2) |
Find the shortest path between two atoms. More... | |
Stereochemistry | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::cleanupChirality (RWMol &mol) |
removes bogus chirality markers (those on non-sp3 centers): More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::clearSingleBondDirFlags (ROMol &mol) |
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 (i.e. R/S) and bonds (i.e. Z/E) More... | |
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. More... | |
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. More... | |
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 More... | |
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 More... | |
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 More... | |
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 void | RDKit::MolOps::parseAdjustQueryParametersFromJSON (MolOps::AdjustQueryParameters &p, const std::string &json) |
updates an AdjustQueryParameters object from a JSON string More... | |
RDKIT_GRAPHMOL_EXPORT ROMol * | RDKit::MolOps::adjustQueryProperties (const ROMol &mol, const AdjustQueryParameters *params=nullptr) |
returns a copy of a molecule with query properties adjusted More... | |
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 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 } |
enum | RDKit::MolOps::AromaticityModel { RDKit::MolOps::AROMATICITY_DEFAULT = 0x0 , RDKit::MolOps::AROMATICITY_RDKIT = 0x1 , RDKit::MolOps::AROMATICITY_SIMPLE = 0x2 , RDKit::MolOps::AROMATICITY_MDL = 0x4 , RDKit::MolOps::AROMATICITY_CUSTOM = 0xFFFFFFF } |
Possible aromaticity models. More... | |
RDKIT_GRAPHMOL_EXPORT 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 ensuring that it makes "chemical sense" More... | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::sanitizeMol (RWMol &mol) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More... | |
RDKIT_GRAPHMOL_EXPORT std::vector< std::unique_ptr< MolSanitizeException > > | RDKit::MolOps::detectChemistryProblems (const ROMol &mol, unsigned int sanitizeOps=SANITIZE_ALL) |
Identifies chemistry problems (things that don't make chemical sense) in a molecule. More... | |
RDKIT_GRAPHMOL_EXPORT int | RDKit::MolOps::setAromaticity (RWMol &mol, AromaticityModel model=AROMATICITY_DEFAULT, int(*func)(RWMol &)=nullptr) |
Sets up the aromaticity for a molecule. More... | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::cleanUp (RWMol &mol) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::cleanUpOrganometallics (RWMol &mol) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::assignRadicals (RWMol &mol) |
Called by the sanitizer to assign radical counts to atoms. More... | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::adjustHs (RWMol &mol) |
adjust the number of implicit and explicit Hs for special cases More... | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::Kekulize (RWMol &mol, bool markAtomsBonds=true, unsigned int maxBackTracks=100) |
Kekulizes the molecule. More... | |
RDKIT_GRAPHMOL_EXPORT bool | RDKit::MolOps::KekulizeIfPossible (RWMol &mol, bool markAtomsBonds=true, unsigned int maxBackTracks=100) |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::setConjugation (ROMol &mol) |
flags the molecule's conjugated bonds More... | |
RDKIT_GRAPHMOL_EXPORT void | RDKit::MolOps::setHybridization (ROMol &mol) |
calculates and sets the hybridization of all a molecule's Stoms More... | |
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