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RDKit
Open-source cheminformatics and machine learning.
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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_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 |
Enumerator | |
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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.
Enumerator | |
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TP_NONE | |
RING | |
CHAIN |
Definition at line 57 of file StructChecker.h.
Enumerator | |
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RT_NONE | |
SINGLET | |
DOUBLET | |
TRIPLET | |
ANY_RADICAL |
Definition at line 36 of file StructChecker.h.
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 | ||
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RDKIT_STRUCTCHECKER_EXPORT void RDKit::StructureCheck::AddMWMF | ( | RWMol & | mol, |
bool | pre | ||
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RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::AtomClash | ( | RWMol & | mol, |
double | clash_limit | ||
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RDKIT_STRUCTCHECKER_EXPORT int RDKit::StructureCheck::AtomParity | ( | const ROMol & | mol, |
unsigned | iatom, | ||
const Neighbourhood & | nbp | ||
) |
RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::AtomSymbolMatch | ( | const std::string | symbol, |
const std::string | pattern | ||
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RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::CheckAtoms | ( | const ROMol & | mol, |
const std::vector< AugmentedAtom > & | good_atoms, | ||
bool | verbose | ||
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RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::CheckStereo | ( | const ROMol & | mol | ) |
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 | ||
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RDKIT_STRUCTCHECKER_EXPORT RDKit::Bond::BondType RDKit::StructureCheck::convertBondType | ( | AABondType | bt | ) |
RDKIT_STRUCTCHECKER_EXPORT AABondType RDKit::StructureCheck::convertBondType | ( | RDKit::Bond::BondType | rdbt | ) |
RDKIT_STRUCTCHECKER_EXPORT int RDKit::StructureCheck::DubiousStereochemistry | ( | RWMol & | mol | ) |
RDKIT_STRUCTCHECKER_EXPORT int RDKit::StructureCheck::FixDubious3DMolecule | ( | RWMol & | mol | ) |
RDKIT_STRUCTCHECKER_EXPORT unsigned RDKit::StructureCheck::getAtomicNumber | ( | const std::string | symbol | ) |
Referenced by RDKit::PeriodicTable::getAtomicNumber().
RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::getMolAtomPoints | ( | const ROMol & | mol, |
std::vector< RDGeom::Point3D > & | atomPoint, | ||
bool | twod = false |
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inlinestatic |
RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::isBondTypeMatch | ( | const RDKit::Bond & | b, |
AABondType | lbt | ||
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RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::LigandMatches | ( | const Atom & | a, |
const Bond & | b, | ||
const Ligand & | l, | ||
bool | use_charge = false |
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RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::loadOptionsFromFiles | ( | StructCheckerOptions & | op, |
const std::string & | augmentedAtomTranslationsFile = "" , |
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const std::string & | patternFile = "" , |
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const std::string & | rotatePatternFile = "" , |
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const std::string & | stereoPatternFile = "" , |
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const std::string & | tautomerFile = "" |
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Referenced by RDKit::StructureCheck::StructCheckerOptions::clear().
RDKIT_STRUCTCHECKER_EXPORT std::string RDKit::StructureCheck::LogNeighbourhood | ( | const ROMol & | mol, |
unsigned int | idx, | ||
const std::vector< Neighbourhood > & | bneighbour_array | ||
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RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::parseOptionsJSON | ( | const std::string & | json, |
StructCheckerOptions & | op | ||
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Referenced by RDKit::StructureCheck::StructCheckerOptions::clear().
RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::RecMatch | ( | const ROMol & | mol, |
unsigned | atomIdx, | ||
const AugmentedAtom & | aa, | ||
const std::vector< Neighbourhood > & | nbp, | ||
bool | verbose | ||
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RDKIT_STRUCTCHECKER_EXPORT void RDKit::StructureCheck::RemoveDubiousStereochemistry | ( | RWMol & | mol | ) |
RDKIT_STRUCTCHECKER_EXPORT void RDKit::StructureCheck::SetupNeighbourhood | ( | const ROMol & | mol, |
std::vector< Neighbourhood > & | neighbour_array | ||
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RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::StringToAugmentedAtom | ( | const char * | str, |
AugmentedAtom & | aa | ||
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RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::StripSmallFragments | ( | RWMol & | mol, |
bool | verbose = false |
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int RDKit::StructureCheck::TotalCharge | ( | const ROMol & | mol | ) |
RDKIT_STRUCTCHECKER_EXPORT bool RDKit::StructureCheck::TransformAugmentedAtoms | ( | RWMol & | mol, |
const std::vector< std::pair< AugmentedAtom, AugmentedAtom > > & | aapair, | ||
bool | verbose | ||
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Definition at line 35 of file StructChecker.h.
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