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

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 )

◆ AddMWMF()

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

◆ AtomClash()

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

◆ AtomParity()

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

◆ AtomSymbolMatch()

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

◆ CheckAtoms()

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

◆ CheckStereo()

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

◆ 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 )

◆ convertBondType() [1/2]

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

◆ convertBondType() [2/2]

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

◆ DubiousStereochemistry()

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

◆ FixDubious3DMolecule()

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

◆ getAtomicNumber()

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

◆ getMolAtomPoints()

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

◆ 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 )

◆ LigandMatches()

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

◆ 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 = "" )

◆ LogNeighbourhood()

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

◆ parseOptionsJSON()

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

◆ RecMatch()

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

◆ RemoveDubiousStereochemistry()

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

◆ SetupNeighbourhood()

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

◆ StringToAugmentedAtom()

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

◆ StripSmallFragments()

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

◆ 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 )

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.