RDKit
Open-source cheminformatics and machine learning.
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RDKit::Chirality Namespace Reference

Classes

struct  StereoInfo
 

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
}
 
enum class  StereoSpecified { Unspecified , Specified , Unknown }
 

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 std::vector< StereoInfo > findPotentialStereo (ROMol &mol, bool cleanIt, bool flagPossible=true)
 identifies potential stereoatoms and stereobonds in a molecule More...
 
RDKIT_GRAPHMOL_EXPORT std::vector< StereoInfo > findPotentialStereo (const ROMol &mol)
 overload More...
 
RDKIT_GRAPHMOL_EXPORT void cleanupStereoGroups (ROMol &mol)
 removes atoms without specified chirality from stereo groups More...
 
RDKIT_GRAPHMOL_EXPORT void assignLegacyCIPLabels (ROMol &mol, bool flagPossibleStereoCenters=false)
 calls the approximate legacy code for assigning CIP labels More...
 
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)
 
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 getChiralPermutation (const Atom *center, const INT_LIST &probe)
 

Variables

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

Definition at line 97 of file Chirality.h.

◆ StereoSpecified

enum class RDKit::Chirality::StereoSpecified
strong
Enumerator
Unspecified 
Specified 
Unknown 

Definition at line 99 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 86 of file Chirality.h.

Function Documentation

◆ 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

◆ 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
molthe molecule to look for stereo in
cleanItremove 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 ( )

◆ 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 
)

◆ getIdealAngleBetweenLigands()

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

◆ 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
whichif this is -1 then the second axial bond will be returned, otherwise the first

◆ getUseLegacyStereoPerception()

RDKIT_GRAPHMOL_EXPORT bool RDKit::Chirality::getUseLegacyStereoPerception ( )

◆ hasNonTetrahedralStereo()

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

◆ 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 
)

◆ setAllowNontetrahedralChirality()

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

◆ setUseLegacyStereoPerception()

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

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 29 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 33 of file Chirality.h.

◆ nonTetrahedralStereoEnvVar

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

Definition at line 31 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 35 of file Chirality.h.

◆ useLegacyStereoEnvVar

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

Definition at line 32 of file Chirality.h.

◆ useLegacyStereoPerception

RDKIT_GRAPHMOL_EXPORT bool RDKit::Chirality::useLegacyStereoPerception
extern

Toggle usage of the legacy stereo perception code

Definition at line 50 of file Chirality.h.