Namespaces
namespace	detail

Classes
struct	BondWedgingParameters

struct	StereoInfo

class	WedgeInfoAtropisomer

class	WedgeInfoBase

class	WedgeInfoChiral

Enumerations
enum class	StereoType { Unspecified , Atom_Tetrahedral , Atom_SquarePlanar , Atom_TrigonalBipyramidal , Atom_Octahedral , Bond_Double , Bond_Cumulene_Even , Bond_Atropisomer }

enum class	StereoDescriptor { None , Tet_CW , Tet_CCW , Bond_Cis , Bond_Trans , Bond_AtropCW , Bond_AtropCCW }

enum class	StereoSpecified { Unspecified , Specified , Unknown }

enum class	WedgeInfoType { WedgeInfoTypeChiral , WedgeInfoTypeAtropisomer }

Functions
RDKIT_GRAPHMOL_EXPORT void	setAllowNontetrahedralChirality (bool val)

RDKIT_GRAPHMOL_EXPORT bool	getAllowNontetrahedralChirality ()

RDKIT_GRAPHMOL_EXPORT void	setUseLegacyStereoPerception (bool val)

RDKIT_GRAPHMOL_EXPORT bool	getUseLegacyStereoPerception ()

RDKIT_GRAPHMOL_EXPORT void	removeNonExplicit3DChirality (ROMol &mol)

RDKIT_GRAPHMOL_EXPORT std::vector< StereoInfo >	findPotentialStereo (ROMol &mol, bool cleanIt, bool flagPossible=true)
	identifies potential stereoatoms and stereobonds in a molecule

RDKIT_GRAPHMOL_EXPORT std::vector< StereoInfo >	findPotentialStereo (const ROMol &mol)
	overload

RDKIT_GRAPHMOL_EXPORT void	cleanupStereoGroups (ROMol &mol)
	removes atoms without specified chirality from stereo groups

RDKIT_GRAPHMOL_EXPORT void	assignLegacyCIPLabels (ROMol &mol, bool flagPossibleStereoCenters=false)
	calls the approximate legacy code for assigning CIP labels

RDKIT_GRAPHMOL_EXPORT INT_VECT	findStereoAtoms (const Bond *bond)

RDKIT_GRAPHMOL_EXPORT std::ostream &	operator<< (std::ostream &oss, const StereoSpecified &s)

RDKIT_GRAPHMOL_EXPORT std::ostream &	operator<< (std::ostream &oss, const StereoType &s)

RDKIT_GRAPHMOL_EXPORT std::map< int, std::unique_ptr< Chirality::WedgeInfoBase > >	pickBondsToWedge (const ROMol &mol, const BondWedgingParameters *params=nullptr)

RDKIT_GRAPHMOL_EXPORT std::map< int, std::unique_ptr< Chirality::WedgeInfoBase > >	pickBondsToWedge (const ROMol &mol, const BondWedgingParameters params, const Conformer conf)

RDKIT_GRAPHMOL_EXPORT void	wedgeMolBonds (ROMol &mol, const Conformer conf=nullptr, const BondWedgingParameters params=nullptr)

RDKIT_GRAPHMOL_EXPORT void	wedgeBond (Bond bond, unsigned int fromAtomIdx, const Conformer conf)

RDKIT_GRAPHMOL_EXPORT bool	shouldBeACrossedBond (const Bond *bond)
	Returns true for double bonds which should be shown as a crossed bonds.

RDKIT_GRAPHMOL_EXPORT void	reapplyMolBlockWedging (ROMol &mol, bool allBondTypes=true)
	Clears existing bond wedging and forces use of atom wedging from MolBlock.

RDKIT_GRAPHMOL_EXPORT void	clearMolBlockWedgingInfo (ROMol &mol)
	Remove MolBlock bond wedging information from molecule.

RDKIT_GRAPHMOL_EXPORT void	invertMolBlockWedgingInfo (ROMol &mol)
	Invert bond wedging information read from a mol block (if present).

RDKIT_GRAPHMOL_EXPORT void	GetMolFileBondStereoInfo (const Bond bond, const std::map< int, std::unique_ptr< RDKit::Chirality::WedgeInfoBase > > &wedgeBonds, const Conformer conf, int &dirCode, bool &reverse)
	gets stereo info for a bond

RDKIT_GRAPHMOL_EXPORT void	GetMolFileBondStereoInfo (const Bond bond, const std::map< int, std::unique_ptr< RDKit::Chirality::WedgeInfoBase > > &wedgeBonds, const Conformer conf, Bond::BondDir &dir, bool &reverse)

RDKIT_GRAPHMOL_EXPORT void	addStereoAnnotations (ROMol &mol, std::string absLabel="abs ({cip})", std::string orLabel="or{id}", std::string andLabel="and{id}", std::string cipLabel="({cip})", std::string bondLabel="({cip})")
	add R/S, relative stereo, and E/Z annotations to atoms and bonds

RDKIT_GRAPHMOL_EXPORT void	simplifyEnhancedStereo (ROMol &mol, bool removeAffectedStereoGroups=true)

RDKIT_GRAPHMOL_EXPORT std::vector< std::pair< unsigned int, unsigned int > >	findMesoCenters (const ROMol &mol, bool includeIsotopes=true, bool includeAtomMaps=false)
	returns the meso centers in a molecule (if any)

Non-tetrahedral stereochemistry
RDKIT_GRAPHMOL_EXPORT bool	hasNonTetrahedralStereo (const Atom *center)

RDKIT_GRAPHMOL_EXPORT Bond *	getChiralAcrossBond (const Atom center, const Bond qry)

RDKIT_GRAPHMOL_EXPORT Bond *	getChiralAcrossBond (const Atom center, const Atom qry)

RDKIT_GRAPHMOL_EXPORT Atom *	getChiralAcrossAtom (const Atom center, const Bond qry)

RDKIT_GRAPHMOL_EXPORT Atom *	getChiralAcrossAtom (const Atom center, const Atom qry)

RDKIT_GRAPHMOL_EXPORT Bond *	getTrigonalBipyramidalAxialBond (const Atom *center, int which=0)

RDKIT_GRAPHMOL_EXPORT Atom *	getTrigonalBipyramidalAxialAtom (const Atom *center, int which=0)

RDKIT_GRAPHMOL_EXPORT int	isTrigonalBipyramidalAxialBond (const Atom center, const Bond qry)

RDKIT_GRAPHMOL_EXPORT int	isTrigonalBipyramidalAxialAtom (const Atom center, const Atom qry)

RDKIT_GRAPHMOL_EXPORT double	getIdealAngleBetweenLigands (const Atom center, const Atom lig1, const Atom *lig2)

RDKIT_GRAPHMOL_EXPORT unsigned int	getMaxNbors (const Atom::ChiralType tag)

RDKIT_GRAPHMOL_EXPORT unsigned int	getChiralPermutation (const Atom *center, const INT_LIST &probe, bool inverse=false)

Variables
constexpr unsigned int	minRingSizeForDoubleBondStereo = 8
	double bond stereo will be ignored/removed for rings smaller than this:

constexpr auto	nonTetrahedralStereoEnvVar = "RDK_ENABLE_NONTETRAHEDRAL_STEREO"

constexpr auto	useLegacyStereoEnvVar = "RDK_USE_LEGACY_STEREO_PERCEPTION"

constexpr bool	nonTetrahedralStereoDefaultVal
	whether or not nontetrahedral stereo is perceived by default

constexpr bool	useLegacyStereoDefaultVal

RDKIT_GRAPHMOL_EXPORT bool	useLegacyStereoPerception

Enumeration Type Documentation

◆ StereoDescriptor

enum class RDKit::Chirality::StereoDescriptor

strong

Enumerator
None
Tet_CW
Tet_CCW
Bond_Cis
Bond_Trans
Bond_AtropCW
Bond_AtropCCW

Definition at line 101 of file Chirality.h.

◆ StereoSpecified

enum class RDKit::Chirality::StereoSpecified

strong

Enumerator
Unspecified
Specified
Unknown

Definition at line 111 of file Chirality.h.

◆ StereoType

enum class RDKit::Chirality::StereoType

strong

Enumerator
Unspecified
Atom_Tetrahedral
Atom_SquarePlanar
Atom_TrigonalBipyramidal
Atom_Octahedral
Bond_Double
Bond_Cumulene_Even
Bond_Atropisomer

Definition at line 90 of file Chirality.h.

◆ WedgeInfoType

enum class RDKit::Chirality::WedgeInfoType

strong

Enumerator
WedgeInfoTypeChiral
WedgeInfoTypeAtropisomer

Definition at line 240 of file Chirality.h.

Function Documentation

◆ addStereoAnnotations()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::addStereoAnnotations	(	ROMol &	mol,
		std::string	absLabel = `"abs ({cip})"`,
		std::string	orLabel = `"or{id}"`,
		std::string	andLabel = `"and{id}"`,
		std::string	cipLabel = `"({cip})"`,
		std::string	bondLabel = `"({cip})"`
	)

add R/S, relative stereo, and E/Z annotations to atoms and bonds

Parameters

mol	molecule to modify
absLabel	label for atoms in an ABS stereo group
orLabel	label for atoms in an OR stereo group
andLabel	label for atoms in an AND stereo group
cipLabel	label for chiral atoms that aren't in a stereo group.
bondLabel	label for CIP stereochemistry on bonds

If any label is empty, the corresponding annotations will not be added.

The labels can contain the following placeholders: {id} - the stereo group's index {cip} - the atom or bond's CIP stereochemistry

Note that CIP labels will only be added if CIP stereochemistry has been assigned to the molecule.

◆ assignLegacyCIPLabels()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::assignLegacyCIPLabels	(	ROMol &	mol,
		bool	flagPossibleStereoCenters = `false`
	)

calls the approximate legacy code for assigning CIP labels

◆ cleanupStereoGroups()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::cleanupStereoGroups ( ROMol & mol )

removes atoms without specified chirality from stereo groups

◆ clearMolBlockWedgingInfo()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::clearMolBlockWedgingInfo ( ROMol & mol )

Remove MolBlock bond wedging information from molecule.

Parameters

mol	molecule to modify

◆ findMesoCenters()

RDKIT_GRAPHMOL_EXPORT std::vector< std::pair< unsigned int, unsigned int > > RDKit::Chirality::findMesoCenters	(	const ROMol &	mol,
		bool	includeIsotopes = `true`,
		bool	includeAtomMaps = `false`
	)

returns the meso centers in a molecule (if any)

Parameters

mol	molecule to work with

◆ findPotentialStereo() [1/2]

RDKIT_GRAPHMOL_EXPORT std::vector< StereoInfo > RDKit::Chirality::findPotentialStereo ( const ROMol & mol )

overload

◆ findPotentialStereo() [2/2]

RDKIT_GRAPHMOL_EXPORT std::vector< StereoInfo > RDKit::Chirality::findPotentialStereo	(	ROMol &	mol,
		bool	cleanIt,
		bool	flagPossible = `true`
	)

identifies potential stereoatoms and stereobonds in a molecule

Note that this function is still somewhat experimental and the API and results may change in a future release.

Parameters

mol	the molecule to look for stereo in
cleanIt	remove chirality/stereo specifications from atoms/bonds that cannot be chiral/stereo

◆ findStereoAtoms()

RDKIT_GRAPHMOL_EXPORT INT_VECT RDKit::Chirality::findStereoAtoms ( const Bond * bond )

◆ getAllowNontetrahedralChirality()

RDKIT_GRAPHMOL_EXPORT bool RDKit::Chirality::getAllowNontetrahedralChirality ( )

extern

◆ getChiralAcrossAtom() [1/2]

RDKIT_GRAPHMOL_EXPORT Atom * RDKit::Chirality::getChiralAcrossAtom	(	const Atom *	center,
		const Atom *	qry
	)

◆ getChiralAcrossAtom() [2/2]

RDKIT_GRAPHMOL_EXPORT Atom * RDKit::Chirality::getChiralAcrossAtom	(	const Atom *	center,
		const Bond *	qry
	)

◆ getChiralAcrossBond() [1/2]

RDKIT_GRAPHMOL_EXPORT Bond * RDKit::Chirality::getChiralAcrossBond	(	const Atom *	center,
		const Atom *	qry
	)

◆ getChiralAcrossBond() [2/2]

RDKIT_GRAPHMOL_EXPORT Bond * RDKit::Chirality::getChiralAcrossBond	(	const Atom *	center,
		const Bond *	qry
	)

◆ getChiralPermutation()

RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::Chirality::getChiralPermutation	(	const Atom *	center,
		const INT_LIST &	probe,
		bool	inverse = `false`
	)

◆ getIdealAngleBetweenLigands()

RDKIT_GRAPHMOL_EXPORT double RDKit::Chirality::getIdealAngleBetweenLigands	(	const Atom *	center,
		const Atom *	lig1,
		const Atom *	lig2
	)

◆ getMaxNbors()

RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::Chirality::getMaxNbors ( const Atom::ChiralType tag )

◆ GetMolFileBondStereoInfo() [1/2]

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::GetMolFileBondStereoInfo	(	const Bond *	bond,
		const std::map< int, std::unique_ptr< RDKit::Chirality::WedgeInfoBase > > &	wedgeBonds,
		const Conformer *	conf,
		Bond::BondDir &	dir,
		bool &	reverse
	)

◆ GetMolFileBondStereoInfo() [2/2]

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::GetMolFileBondStereoInfo	(	const Bond *	bond,
		const std::map< int, std::unique_ptr< RDKit::Chirality::WedgeInfoBase > > &	wedgeBonds,
		const Conformer *	conf,
		int &	dirCode,
		bool &	reverse
	)

gets stereo info for a bond

Parameters

bond	bond to check
wedgeBonds	- the list of bonds to have wedges
conf	- Conformer to use
dirCode	- receives the dircode for the bond
reverse	- receives the reverse flag only returned if it was exlicility set witha wiggle bond

◆ getTrigonalBipyramidalAxialAtom()

RDKIT_GRAPHMOL_EXPORT Atom * RDKit::Chirality::getTrigonalBipyramidalAxialAtom	(	const Atom *	center,
		int	which = `0`
	)

◆ getTrigonalBipyramidalAxialBond()

RDKIT_GRAPHMOL_EXPORT Bond * RDKit::Chirality::getTrigonalBipyramidalAxialBond	(	const Atom *	center,
		int	which = `0`
	)

Parameters

which if this is -1 then the second axial bond will be returned, otherwise the first

◆ getUseLegacyStereoPerception()

RDKIT_GRAPHMOL_EXPORT bool RDKit::Chirality::getUseLegacyStereoPerception ( )

extern

◆ hasNonTetrahedralStereo()

RDKIT_GRAPHMOL_EXPORT bool RDKit::Chirality::hasNonTetrahedralStereo ( const Atom * center )

◆ invertMolBlockWedgingInfo()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::invertMolBlockWedgingInfo ( ROMol & mol )

Invert bond wedging information read from a mol block (if present).

Parameters

mol	molecule to modify

◆ isTrigonalBipyramidalAxialAtom()

RDKIT_GRAPHMOL_EXPORT int RDKit::Chirality::isTrigonalBipyramidalAxialAtom	(	const Atom *	center,
		const Atom *	qry
	)

◆ isTrigonalBipyramidalAxialBond()

RDKIT_GRAPHMOL_EXPORT int RDKit::Chirality::isTrigonalBipyramidalAxialBond	(	const Atom *	center,
		const Bond *	qry
	)

Returns: 1 if it's the first axial atom, -1 if it's the second

◆ operator<<() [1/2]

RDKIT_GRAPHMOL_EXPORT std::ostream & RDKit::Chirality::operator<<	(	std::ostream &	oss,
		const StereoSpecified &	s
	)

◆ operator<<() [2/2]

RDKIT_GRAPHMOL_EXPORT std::ostream & RDKit::Chirality::operator<<	(	std::ostream &	oss,
		const StereoType &	s
	)

◆ pickBondsToWedge() [1/2]

RDKIT_GRAPHMOL_EXPORT std::map< int, std::unique_ptr< Chirality::WedgeInfoBase > > RDKit::Chirality::pickBondsToWedge	(	const ROMol &	mol,
		const BondWedgingParameters *	params,
		const Conformer *	conf
	)

◆ pickBondsToWedge() [2/2]

RDKIT_GRAPHMOL_EXPORT std::map< int, std::unique_ptr< Chirality::WedgeInfoBase > > RDKit::Chirality::pickBondsToWedge	(	const ROMol &	mol,
		const BondWedgingParameters *	params = `nullptr`
	)

picks the bonds which should be wedged returns a map from bond idx -> controlling atom idx

◆ reapplyMolBlockWedging()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::reapplyMolBlockWedging	(	ROMol &	mol,
		bool	allBondTypes = `true`
	)

Clears existing bond wedging and forces use of atom wedging from MolBlock.

Parameters

mol	molecule to have its wedges altered
allBondTypes	reapply the wedging also on bonds other than single and aromatic ones

◆ removeNonExplicit3DChirality()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::removeNonExplicit3DChirality ( ROMol & mol )

◆ setAllowNontetrahedralChirality()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::setAllowNontetrahedralChirality ( bool val )

extern

◆ setUseLegacyStereoPerception()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::setUseLegacyStereoPerception ( bool val )

extern

◆ shouldBeACrossedBond()

RDKIT_GRAPHMOL_EXPORT bool RDKit::Chirality::shouldBeACrossedBond ( const Bond * bond )

Returns true for double bonds which should be shown as a crossed bonds.

◆ simplifyEnhancedStereo()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::simplifyEnhancedStereo	(	ROMol &	mol,
		bool	removeAffectedStereoGroups = `true`
	)

simplifies the stereochemical representation of a molecule where all specified stereocenters are in the same StereoGroup

Parameters

mol	molecule to modify
removeAffectedStereoGroups	if set then the affected StereoGroups will be removed

If all specified stereocenters are in the same AND or OR stereogroup, a moleculeNote property will be set on the molecule with the value "AND enantiomer" or "OR enantiomer". CIP labels, if present, are removed.

◆ wedgeBond()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::wedgeBond	(	Bond *	bond,
		unsigned int	fromAtomIdx,
		const Conformer *	conf
	)

◆ wedgeMolBonds()

RDKIT_GRAPHMOL_EXPORT void RDKit::Chirality::wedgeMolBonds	(	ROMol &	mol,
		const Conformer *	conf = `nullptr`,
		const BondWedgingParameters *	params = `nullptr`
	)

Variable Documentation

◆ minRingSizeForDoubleBondStereo

constexpr unsigned int RDKit::Chirality::minRingSizeForDoubleBondStereo = 8

constexpr

double bond stereo will be ignored/removed for rings smaller than this:

Definition at line 31 of file Chirality.h.

◆ nonTetrahedralStereoDefaultVal

constexpr bool RDKit::Chirality::nonTetrahedralStereoDefaultVal

constexpr

Initial value:

=

true

whether or not nontetrahedral stereo is perceived by default

Definition at line 35 of file Chirality.h.

◆ nonTetrahedralStereoEnvVar

constexpr auto RDKit::Chirality::nonTetrahedralStereoEnvVar = "RDK_ENABLE_NONTETRAHEDRAL_STEREO"

constexpr

Definition at line 33 of file Chirality.h.

◆ useLegacyStereoDefaultVal

constexpr bool RDKit::Chirality::useLegacyStereoDefaultVal

constexpr

Initial value:

=

true

whether or not the legacy stereo perception code is used by default

Definition at line 37 of file Chirality.h.

◆ useLegacyStereoEnvVar

constexpr auto RDKit::Chirality::useLegacyStereoEnvVar = "RDK_USE_LEGACY_STEREO_PERCEPTION"

constexpr

Definition at line 34 of file Chirality.h.

◆ useLegacyStereoPerception

RDKIT_GRAPHMOL_EXPORT bool RDKit::Chirality::useLegacyStereoPerception

extern

Toggle usage of the legacy stereo perception code

Definition at line 54 of file Chirality.h.

Namespaces

Classes

Enumerations

Functions

Variables

Enumeration Type Documentation

◆ StereoDescriptor

◆ StereoSpecified

◆ StereoType

◆ WedgeInfoType

Function Documentation

◆ addStereoAnnotations()

◆ assignLegacyCIPLabels()

◆ cleanupStereoGroups()

◆ clearMolBlockWedgingInfo()

◆ findMesoCenters()

◆ findPotentialStereo() [1/2]

◆ findPotentialStereo() [2/2]

◆ findStereoAtoms()

◆ getAllowNontetrahedralChirality()

◆ getChiralAcrossAtom() [1/2]

◆ getChiralAcrossAtom() [2/2]

◆ getChiralAcrossBond() [1/2]

◆ getChiralAcrossBond() [2/2]

◆ getChiralPermutation()

◆ getIdealAngleBetweenLigands()

◆ getMaxNbors()

◆ GetMolFileBondStereoInfo() [1/2]

◆ GetMolFileBondStereoInfo() [2/2]

◆ getTrigonalBipyramidalAxialAtom()

◆ getTrigonalBipyramidalAxialBond()

◆ getUseLegacyStereoPerception()

◆ hasNonTetrahedralStereo()

◆ invertMolBlockWedgingInfo()

◆ isTrigonalBipyramidalAxialAtom()

◆ isTrigonalBipyramidalAxialBond()

◆ operator<<() [1/2]

◆ operator<<() [2/2]

◆ pickBondsToWedge() [1/2]

◆ pickBondsToWedge() [2/2]

◆ reapplyMolBlockWedging()

◆ removeNonExplicit3DChirality()

◆ setAllowNontetrahedralChirality()

◆ setUseLegacyStereoPerception()

◆ shouldBeACrossedBond()

◆ simplifyEnhancedStereo()

◆ wedgeBond()

◆ wedgeMolBonds()

Variable Documentation

◆ minRingSizeForDoubleBondStereo

◆ nonTetrahedralStereoDefaultVal

◆ nonTetrahedralStereoEnvVar

◆ useLegacyStereoDefaultVal

◆ useLegacyStereoEnvVar

◆ useLegacyStereoPerception