Classes
struct	AugmentedAtom

class	ChargeFix

struct	IncEntry

struct	Ligand

struct	Neighbourhood

struct	PathEntry

class	StructChecker
	Class for performing structure validation and cleanup. More...

struct	StructCheckerOptions

class	StructCheckTautomer

Enumerations
enum	RadicalType { RT_NONE = 0 , SINGLET = 1 , DOUBLET = 2 , TRIPLET = 3 , ANY_RADICAL = 0xFF }

enum	AABondType { BT_NONE = 0 , SINGLE = 1 , DOUBLE = 2 , TRIPLE = 3 , AROMATIC = 4 , SINGLE_DOUBLE = 5 , SINGLE_AROMATIC = 6 , DOUBLE_AROMATIC = 7 , ANY_BOND = 8 , ALL_BOND_TYPES = 0xF }

enum	AATopology { TP_NONE = 0 , RING = 1 , CHAIN = 2 }

Functions
RDKIT_STRUCTCHECKER_EXPORT RDKit::Bond::BondType	convertBondType (AABondType bt)

RDKIT_STRUCTCHECKER_EXPORT AABondType	convertBondType (RDKit::Bond::BondType rdbt)

RDKIT_STRUCTCHECKER_EXPORT unsigned	getAtomicNumber (const std::string symbol)

RDKIT_STRUCTCHECKER_EXPORT bool	AtomSymbolMatch (const std::string symbol, const std::string pattern)

RDKIT_STRUCTCHECKER_EXPORT bool	LigandMatches (const Atom &a, const Bond &b, const Ligand &l, bool use_charge=false)

RDKIT_STRUCTCHECKER_EXPORT bool	isBondTypeMatch (const RDKit::Bond &b, AABondType lbt)

RDKIT_STRUCTCHECKER_EXPORT bool	RecMatch (const ROMol &mol, unsigned atomIdx, const AugmentedAtom &aa, const std::vector< Neighbourhood > &nbp, bool verbose)

RDKIT_STRUCTCHECKER_EXPORT bool	AAMatch (const ROMol &mol, unsigned i, const AugmentedAtom &aa, const std::vector< unsigned > &atom_ring_status, const std::vector< Neighbourhood > &nbp, bool verbose)

RDKIT_STRUCTCHECKER_EXPORT bool	TransformAugmentedAtoms (RWMol &mol, const std::vector< std::pair< AugmentedAtom, AugmentedAtom > > &aapair, bool verbose)

RDKIT_STRUCTCHECKER_EXPORT bool	CheckAtoms (const ROMol &mol, const std::vector< AugmentedAtom > &good_atoms, bool verbose)

int	TotalCharge (const ROMol &mol)

static int	INVERT_PARITY (int p)

RDKIT_STRUCTCHECKER_EXPORT int	DubiousStereochemistry (RWMol &mol)

RDKIT_STRUCTCHECKER_EXPORT int	FixDubious3DMolecule (RWMol &mol)

RDKIT_STRUCTCHECKER_EXPORT void	RemoveDubiousStereochemistry (RWMol &mol)

RDKIT_STRUCTCHECKER_EXPORT bool	CheckStereo (const ROMol &mol)

RDKIT_STRUCTCHECKER_EXPORT bool	AtomClash (RWMol &mol, double clash_limit)

RDKIT_STRUCTCHECKER_EXPORT int	AtomParity (const ROMol &mol, unsigned iatom, const Neighbourhood &nbp)

RDKIT_STRUCTCHECKER_EXPORT int	CisTransPerception (const ROMol &mol, const std::vector< RDGeom::Point3D > &points, const std::vector< unsigned > &numbering, std::vector< unsigned > &bondColor)

RDKIT_STRUCTCHECKER_EXPORT bool	StripSmallFragments (RWMol &mol, bool verbose=false)

RDKIT_STRUCTCHECKER_EXPORT void	AddMWMF (RWMol &mol, bool pre)

RDKIT_STRUCTCHECKER_EXPORT bool	parseOptionsJSON (const std::string &json, StructCheckerOptions &op)

RDKIT_STRUCTCHECKER_EXPORT bool	loadOptionsFromFiles (StructCheckerOptions &op, const std::string &augmentedAtomTranslationsFile="", const std::string &patternFile="", const std::string &rotatePatternFile="", const std::string &stereoPatternFile="", const std::string &tautomerFile="")

RDKIT_STRUCTCHECKER_EXPORT bool	StringToAugmentedAtom (const char *str, AugmentedAtom &aa)

RDKIT_STRUCTCHECKER_EXPORT void	SetupNeighbourhood (const ROMol &mol, std::vector< Neighbourhood > &neighbour_array)

RDKIT_STRUCTCHECKER_EXPORT bool	getMolAtomPoints (const ROMol &mol, std::vector< RDGeom::Point3D > &atomPoint, bool twod=false)

RDKIT_STRUCTCHECKER_EXPORT std::string	LogNeighbourhood (const ROMol &mol, unsigned int idx, const std::vector< Neighbourhood > &bneighbour_array)

Variables
static const int	ODD = 1

static const int	EVEN = 2

static const int	UNMARKED = 3

static const int	ALLENE_PARITY = -2

static const int	ILLEGAL_REPRESENTATION = -1

static const int	UNDEFINED_PARITY = 0

static const int	ODD_PARITY = 1

static const int	EVEN_PARITY = 2

static const int	CIS = 1

static const int	TRANS = 2

static const int	EITHER_BOND_FOUND = 1

static const int	STEREO_BOND_AT_NON_STEREO_ATOM = 2

static const int	ZEROED_Z_COORDINATES = 4

static const int	CONVERTED_TO_2D = 8

static const int	ANY_CHARGE = 8

Enumeration Type Documentation

◆ AABondType

enum RDKit::StructureCheck::AABondType

Enumerator
BT_NONE
SINGLE
DOUBLE
TRIPLE
AROMATIC
SINGLE_DOUBLE
SINGLE_AROMATIC
DOUBLE_AROMATIC
ANY_BOND
ALL_BOND_TYPES

Definition at line 44 of file StructChecker.h.

◆ AATopology

enum RDKit::StructureCheck::AATopology

Enumerator
TP_NONE
RING
CHAIN

Definition at line 57 of file StructChecker.h.

◆ RadicalType

enum RDKit::StructureCheck::RadicalType

Enumerator
RT_NONE
SINGLET
DOUBLET
TRIPLET
ANY_RADICAL

Definition at line 36 of file StructChecker.h.

Function Documentation

◆ AAMatch()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::AAMatch	(	const ROMol &	mol,
		unsigned	i,
		const AugmentedAtom &	aa,
		const std::vector< unsigned > &	atom_ring_status,
		const std::vector< Neighbourhood > &	nbp,
		bool	verbose )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ AddMWMF()

RDKIT_STRUCTCHECKER_EXPORT void RDKit::StructureCheck::AddMWMF	(	RWMol &	mol,
		bool	pre )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ AtomClash()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::AtomClash	(	RWMol &	mol,
		double	clash_limit )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ AtomParity()

RDKIT_STRUCTCHECKER_EXPORT int RDKit::StructureCheck::AtomParity	(	const ROMol &	mol,
		unsigned	iatom,
		const Neighbourhood &	nbp )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ AtomSymbolMatch()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::AtomSymbolMatch	(	const std::string	symbol,
		const std::string	pattern )

References RDKIT_STRUCTCHECKER_EXPORT, and symbol.

◆ CheckAtoms()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::CheckAtoms	(	const ROMol &	mol,
		const std::vector< AugmentedAtom > &	good_atoms,
		bool	verbose )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ CheckStereo()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::CheckStereo ( const ROMol & mol )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ CisTransPerception()

RDKIT_STRUCTCHECKER_EXPORT int RDKit::StructureCheck::CisTransPerception	(	const ROMol &	mol,
		const std::vector< RDGeom::Point3D > &	points,
		const std::vector< unsigned > &	numbering,
		std::vector< unsigned > &	bondColor )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ convertBondType() [1/2]

RDKIT_STRUCTCHECKER_EXPORT RDKit::Bond::BondType RDKit::StructureCheck::convertBondType ( AABondType bt )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ convertBondType() [2/2]

RDKIT_STRUCTCHECKER_EXPORT AABondType RDKit::StructureCheck::convertBondType ( RDKit::Bond::BondType rdbt )

◆ DubiousStereochemistry()

RDKIT_STRUCTCHECKER_EXPORT int RDKit::StructureCheck::DubiousStereochemistry ( RWMol & mol )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ FixDubious3DMolecule()

RDKIT_STRUCTCHECKER_EXPORT int RDKit::StructureCheck::FixDubious3DMolecule ( RWMol & mol )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ getAtomicNumber()

RDKIT_STRUCTCHECKER_EXPORT unsigned RDKit::StructureCheck::getAtomicNumber ( const std::string symbol )

References RDKIT_STRUCTCHECKER_EXPORT, and symbol.

◆ getMolAtomPoints()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::getMolAtomPoints	(	const ROMol &	mol,
		std::vector< RDGeom::Point3D > &	atomPoint,
		bool	twod = false )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ INVERT_PARITY()

static int RDKit::StructureCheck::INVERT_PARITY ( int p )

inlinestatic

Definition at line 28 of file Stereo.h.

◆ isBondTypeMatch()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::isBondTypeMatch	(	const RDKit::Bond &	b,
		AABondType	lbt )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ LigandMatches()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::LigandMatches	(	const Atom &	a,
		const Bond &	b,
		const Ligand &	l,
		bool	use_charge = false )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ loadOptionsFromFiles()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::loadOptionsFromFiles	(	StructCheckerOptions &	op,
		const std::string &	augmentedAtomTranslationsFile = "",
		const std::string &	patternFile = "",
		const std::string &	rotatePatternFile = "",
		const std::string &	stereoPatternFile = "",
		const std::string &	tautomerFile = "" )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ LogNeighbourhood()

RDKIT_STRUCTCHECKER_EXPORT std::string RDKit::StructureCheck::LogNeighbourhood	(	const ROMol &	mol,
		unsigned int	idx,
		const std::vector< Neighbourhood > &	bneighbour_array )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ parseOptionsJSON()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::parseOptionsJSON	(	const std::string &	json,
		StructCheckerOptions &	op )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ RecMatch()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::RecMatch	(	const ROMol &	mol,
		unsigned	atomIdx,
		const AugmentedAtom &	aa,
		const std::vector< Neighbourhood > &	nbp,
		bool	verbose )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ RemoveDubiousStereochemistry()

RDKIT_STRUCTCHECKER_EXPORT void RDKit::StructureCheck::RemoveDubiousStereochemistry ( RWMol & mol )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ SetupNeighbourhood()

RDKIT_STRUCTCHECKER_EXPORT void RDKit::StructureCheck::SetupNeighbourhood	(	const ROMol &	mol,
		std::vector< Neighbourhood > &	neighbour_array )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ StringToAugmentedAtom()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::StringToAugmentedAtom	(	const char *	str,
		AugmentedAtom &	aa )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ StripSmallFragments()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::StripSmallFragments	(	RWMol &	mol,
		bool	verbose = false )

References RDKIT_STRUCTCHECKER_EXPORT.

◆ TotalCharge()

int RDKit::StructureCheck::TotalCharge ( const ROMol & mol )

◆ TransformAugmentedAtoms()

RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::TransformAugmentedAtoms	(	RWMol &	mol,
		const std::vector< std::pair< AugmentedAtom, AugmentedAtom > > &	aapair,
		bool	verbose )

References RDKIT_STRUCTCHECKER_EXPORT.

Variable Documentation

◆ ALLENE_PARITY

const int RDKit::StructureCheck::ALLENE_PARITY = -2

static

Definition at line 23 of file Stereo.h.

◆ ANY_CHARGE

const int RDKit::StructureCheck::ANY_CHARGE = 8

static

Definition at line 35 of file StructChecker.h.

Referenced by RDKit::StructureCheck::AugmentedAtom::AugmentedAtom(), and RDKit::StructureCheck::Ligand::Ligand().

◆ CIS

const int RDKit::StructureCheck::CIS = 1

static

Definition at line 31 of file Stereo.h.

◆ CONVERTED_TO_2D

const int RDKit::StructureCheck::CONVERTED_TO_2D = 8

static

Definition at line 38 of file Stereo.h.

◆ EITHER_BOND_FOUND

const int RDKit::StructureCheck::EITHER_BOND_FOUND = 1

static

Definition at line 35 of file Stereo.h.

◆ EVEN

const int RDKit::StructureCheck::EVEN = 2

static

Definition at line 20 of file Stereo.h.

◆ EVEN_PARITY

const int RDKit::StructureCheck::EVEN_PARITY = 2

static

Definition at line 27 of file Stereo.h.

◆ ILLEGAL_REPRESENTATION

const int RDKit::StructureCheck::ILLEGAL_REPRESENTATION = -1

static

Definition at line 24 of file Stereo.h.

◆ ODD

const int RDKit::StructureCheck::ODD = 1

static

Definition at line 19 of file Stereo.h.

◆ ODD_PARITY

const int RDKit::StructureCheck::ODD_PARITY = 1

static

Definition at line 26 of file Stereo.h.

◆ STEREO_BOND_AT_NON_STEREO_ATOM

const int RDKit::StructureCheck::STEREO_BOND_AT_NON_STEREO_ATOM = 2

static

Definition at line 36 of file Stereo.h.

◆ TRANS

const int RDKit::StructureCheck::TRANS = 2

static

Definition at line 32 of file Stereo.h.

◆ UNDEFINED_PARITY

const int RDKit::StructureCheck::UNDEFINED_PARITY = 0

static

Definition at line 25 of file Stereo.h.

◆ UNMARKED

const int RDKit::StructureCheck::UNMARKED = 3

static

Definition at line 21 of file Stereo.h.

◆ ZEROED_Z_COORDINATES

const int RDKit::StructureCheck::ZEROED_Z_COORDINATES = 4

static

Definition at line 37 of file Stereo.h.

Classes

Enumerations

Functions

Variables

Enumeration Type Documentation

◆ AABondType

◆ AATopology

◆ RadicalType

Function Documentation

◆ AAMatch()

◆ AddMWMF()

◆ AtomClash()

◆ AtomParity()

◆ AtomSymbolMatch()

◆ CheckAtoms()

◆ CheckStereo()

◆ CisTransPerception()

◆ convertBondType() [1/2]

◆ convertBondType() [2/2]

◆ DubiousStereochemistry()

◆ FixDubious3DMolecule()

◆ getAtomicNumber()

◆ getMolAtomPoints()

◆ INVERT_PARITY()

◆ isBondTypeMatch()

◆ LigandMatches()

◆ loadOptionsFromFiles()

◆ LogNeighbourhood()

◆ parseOptionsJSON()

◆ RecMatch()

◆ RemoveDubiousStereochemistry()

◆ SetupNeighbourhood()

◆ StringToAugmentedAtom()

◆ StripSmallFragments()

◆ TotalCharge()

◆ TransformAugmentedAtoms()

Variable Documentation

◆ ALLENE_PARITY

◆ ANY_CHARGE

◆ CIS

◆ CONVERTED_TO_2D

◆ EITHER_BOND_FOUND

◆ EVEN

◆ EVEN_PARITY

◆ ILLEGAL_REPRESENTATION

◆ ODD

◆ ODD_PARITY

◆ STEREO_BOND_AT_NON_STEREO_ATOM

◆ TRANS

◆ UNDEFINED_PARITY

◆ UNMARKED

◆ ZEROED_Z_COORDINATES