MolOps.h File Reference

#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 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
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 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 (those on non-sp3 centers):
RDKIT_GRAPHMOL_EXPORT void	RDKit::MolOps::cleanupAtropisomers (RWMol &)
RDKIT_GRAPHMOL_EXPORT void	RDKit::MolOps::cleanupAtropisomers (RWMol &mol, Hybridizations &hybridizations)
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

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_CLEANUP_ORGANOMETALLICS = 0x400 ,   RDKit::MolOps::SANITIZE_CLEANUPATROPISOMERS = 0x800 , 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"
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.
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.
RDKIT_GRAPHMOL_EXPORT int	RDKit::MolOps::setAromaticity (RWMol &mol, AromaticityModel model=AROMATICITY_DEFAULT, int(*func)(RWMol &)=nullptr)
	Sets up the aromaticity for a molecule.
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.
RDKIT_GRAPHMOL_EXPORT void	RDKit::MolOps::adjustHs (RWMol &mol)
	adjust the number of implicit and explicit Hs for special cases
RDKIT_GRAPHMOL_EXPORT void	RDKit::MolOps::Kekulize (RWMol &mol, bool markAtomsBonds=true, unsigned int maxBackTracks=100)
	Kekulizes the molecule.
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
RDKIT_GRAPHMOL_EXPORT void	RDKit::MolOps::setHybridization (ROMol &mol)
	calculates and sets the hybridization of all a molecule's Stoms

Variable Documentation

ci_LOCAL_INF

RDKIT_GRAPHMOL_EXPORT const int ci_LOCAL_INF

extern