RDKit
Open-source cheminformatics and machine learning.
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
 Structure Check Options. More...
 
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::Bond::BondType convertBondType (AABondType bt)
 
AABondType convertBondType (RDKit::Bond::BondType rdbt)
 
unsigned getAtomicNumber (const std::string symbol)
 
bool AtomSymbolMatch (const std::string symbol, const std::string pattern)
 
bool LigandMatches (const Atom &a, const Bond &b, const Ligand &l, bool use_charge=false)
 
bool isBondTypeMatch (const RDKit::Bond &b, AABondType lbt)
 
bool RecMatch (const ROMol &mol, unsigned atomIdx, const AugmentedAtom &aa, const std::vector< Neighbourhood > &nbp, bool verbose)
 
bool AAMatch (const ROMol &mol, unsigned i, const AugmentedAtom &aa, const std::vector< unsigned > &atom_ring_status, const std::vector< Neighbourhood > &nbp, bool verbose)
 
bool TransformAugmentedAtoms (RWMol &mol, const std::vector< std::pair< AugmentedAtom, AugmentedAtom > > &aapair, bool verbose)
 
bool CheckAtoms (const ROMol &mol, const std::vector< AugmentedAtom > &good_atoms, bool verbose)
 
int TotalCharge (const ROMol &mol)
 
static int INVERT_PARITY (int p)
 
int DubiousStereochemistry (RWMol &mol)
 
int FixDubious3DMolecule (RWMol &mol)
 
void RemoveDubiousStereochemistry (RWMol &mol)
 
bool CheckStereo (const ROMol &mol)
 
bool AtomClash (RWMol &mol, double clash_limit)
 
int AtomParity (const ROMol &mol, unsigned iatom, const Neighbourhood &nbp)
 
int CisTransPerception (const ROMol &mol, const std::vector< RDGeom::Point3D > &points, const std::vector< unsigned > &numbering, std::vector< unsigned > &bondColor)
 
bool StripSmallFragments (RWMol &mol, bool verbose=false)
 
void AddMWMF (RWMol &mol, bool pre)
 
bool parseOptionsJSON (const std::string &json, StructCheckerOptions &op)
 
bool loadOptionsFromFiles (StructCheckerOptions &op, const std::string &augmentedAtomTranslationsFile="", const std::string &patternFile="", const std::string &rotatePatternFile="", const std::string &stereoPatternFile="", const std::string &tautomerFile="")
 
void SetupNeighbourhood (const ROMol &mol, std::vector< Neighbourhood > &neighbour_array)
 
bool getMolAtomPoints (const ROMol &mol, std::vector< RDGeom::Point3D > &atomPoint, bool twod=false)
 
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

Enumerator
BT_NONE 
SINGLE 
DOUBLE 
TRIPLE 
AROMATIC 
SINGLE_DOUBLE 
SINGLE_AROMATIC 
DOUBLE_AROMATIC 
ANY_BOND 
ALL_BOND_TYPES 

Definition at line 43 of file StructChecker.h.

Enumerator
TP_NONE 
RING 
CHAIN 

Definition at line 56 of file StructChecker.h.

Enumerator
RT_NONE 
SINGLET 
DOUBLET 
TRIPLET 
ANY_RADICAL 

Definition at line 35 of file StructChecker.h.

Function Documentation

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 
)
void RDKit::StructureCheck::AddMWMF ( RWMol mol,
bool  pre 
)
bool RDKit::StructureCheck::AtomClash ( RWMol mol,
double  clash_limit 
)
int RDKit::StructureCheck::AtomParity ( const ROMol mol,
unsigned  iatom,
const Neighbourhood nbp 
)
bool RDKit::StructureCheck::AtomSymbolMatch ( const std::string  symbol,
const std::string  pattern 
)
bool RDKit::StructureCheck::CheckAtoms ( const ROMol mol,
const std::vector< AugmentedAtom > &  good_atoms,
bool  verbose 
)
bool RDKit::StructureCheck::CheckStereo ( const ROMol mol)
int RDKit::StructureCheck::CisTransPerception ( const ROMol mol,
const std::vector< RDGeom::Point3D > &  points,
const std::vector< unsigned > &  numbering,
std::vector< unsigned > &  bondColor 
)
RDKit::Bond::BondType RDKit::StructureCheck::convertBondType ( AABondType  bt)
AABondType RDKit::StructureCheck::convertBondType ( RDKit::Bond::BondType  rdbt)
int RDKit::StructureCheck::DubiousStereochemistry ( RWMol mol)
int RDKit::StructureCheck::FixDubious3DMolecule ( RWMol mol)
unsigned RDKit::StructureCheck::getAtomicNumber ( const std::string  symbol)
bool RDKit::StructureCheck::getMolAtomPoints ( const ROMol mol,
std::vector< RDGeom::Point3D > &  atomPoint,
bool  twod = false 
)
static int RDKit::StructureCheck::INVERT_PARITY ( int  p)
inlinestatic

Definition at line 27 of file Stereo.h.

bool RDKit::StructureCheck::isBondTypeMatch ( const RDKit::Bond b,
AABondType  lbt 
)
bool RDKit::StructureCheck::LigandMatches ( const Atom a,
const Bond b,
const Ligand l,
bool  use_charge = false 
)
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 = "" 
)
std::string RDKit::StructureCheck::LogNeighbourhood ( const ROMol mol,
unsigned int  idx,
const std::vector< Neighbourhood > &  bneighbour_array 
)
bool RDKit::StructureCheck::parseOptionsJSON ( const std::string &  json,
StructCheckerOptions op 
)
bool RDKit::StructureCheck::RecMatch ( const ROMol mol,
unsigned  atomIdx,
const AugmentedAtom aa,
const std::vector< Neighbourhood > &  nbp,
bool  verbose 
)
void RDKit::StructureCheck::RemoveDubiousStereochemistry ( RWMol mol)
void RDKit::StructureCheck::SetupNeighbourhood ( const ROMol mol,
std::vector< Neighbourhood > &  neighbour_array 
)
bool RDKit::StructureCheck::StripSmallFragments ( RWMol mol,
bool  verbose = false 
)
int RDKit::StructureCheck::TotalCharge ( const ROMol mol)
bool RDKit::StructureCheck::TransformAugmentedAtoms ( RWMol mol,
const std::vector< std::pair< AugmentedAtom, AugmentedAtom > > &  aapair,
bool  verbose 
)

Variable Documentation

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

Definition at line 22 of file Stereo.h.

const int RDKit::StructureCheck::ANY_CHARGE = 8
static

Definition at line 34 of file StructChecker.h.

const int RDKit::StructureCheck::CIS = 1
static

Definition at line 30 of file Stereo.h.

const int RDKit::StructureCheck::CONVERTED_TO_2D = 8
static

Definition at line 37 of file Stereo.h.

const int RDKit::StructureCheck::EITHER_BOND_FOUND = 1
static

Definition at line 34 of file Stereo.h.

const int RDKit::StructureCheck::EVEN = 2
static

Definition at line 19 of file Stereo.h.

const int RDKit::StructureCheck::EVEN_PARITY = 2
static

Definition at line 26 of file Stereo.h.

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

Definition at line 23 of file Stereo.h.

const int RDKit::StructureCheck::ODD = 1
static

Definition at line 18 of file Stereo.h.

const int RDKit::StructureCheck::ODD_PARITY = 1
static

Definition at line 25 of file Stereo.h.

const int RDKit::StructureCheck::STEREO_BOND_AT_NON_STEREO_ATOM = 2
static

Definition at line 35 of file Stereo.h.

const int RDKit::StructureCheck::TRANS = 2
static

Definition at line 31 of file Stereo.h.

const int RDKit::StructureCheck::UNDEFINED_PARITY = 0
static

Definition at line 24 of file Stereo.h.

const int RDKit::StructureCheck::UNMARKED = 3
static

Definition at line 20 of file Stereo.h.

const int RDKit::StructureCheck::ZEROED_Z_COORDINATES = 4
static

Definition at line 36 of file Stereo.h.