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RDKit
Open-source cheminformatics and machine learning.
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Namespaces | |
defaults | |
TautomerScoringFunctions | |
Typedefs | |
typedef RDCatalog::HierarchCatalog< AcidBaseCatalogEntry, AcidBaseCatalogParams, int > | AcidBaseCatalog |
typedef RDCatalog::HierarchCatalog< FragmentCatalogEntry, FragmentCatalogParams, int > | FragmentCatalog |
typedef RDCatalog::HierarchCatalog< TransformCatalogEntry, TransformCatalogParams, int > | TransformCatalog |
typedef std::pair< std::string, ROMOL_SPTR > | SmilesMolPair |
typedef RDCatalog::HierarchCatalog< TautomerCatalogEntry, TautomerCatalogParams, int > | TautomerCatalog |
typedef std::map< std::string, Tautomer > | SmilesTautomerMap |
typedef std::pair< std::string, Tautomer > | SmilesTautomerPair |
using | TautomerTransformDefs = std::vector< std::tuple< std::string, std::string, std::string, std::string > > |
Enumerations | |
enum class | TautomerEnumeratorStatus { Completed = 0 , MaxTautomersReached , MaxTransformsReached , Canceled } |
Functions | |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > | readPairs (std::string fileName) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > | readPairs (std::istream &inStream, int nToRead=-1) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > | readPairs (const std::vector< std::tuple< std::string, std::string, std::string >> &data) |
Reionizer * | reionizerFromParams (const CleanupParameters ¶ms) |
FragmentRemover * | fragmentRemoverFromParams (const CleanupParameters ¶ms, bool leave_last=true, bool skip_if_all_match=false) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ROMol > > | readFuncGroups (std::string fileName) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ROMol > > | readFuncGroups (std::istream &inStream, int nToRead=-1) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ROMol > > | readFuncGroups (const std::vector< std::pair< std::string, std::string >> &data) |
RDKIT_MOLSTANDARDIZE_EXPORT void | updateCleanupParamsFromJSON (CleanupParameters ¶ms, const std::string &json) |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | cleanup (const RWMol *mol, const CleanupParameters ¶ms=defaultCleanupParameters) |
RWMol * | cleanup (const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More... | |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | normalize (const RWMol *mol, const CleanupParameters ¶ms=defaultCleanupParameters) |
Works the same as Normalizer().normalize(mol) More... | |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | reionize (const RWMol *mol, const CleanupParameters ¶ms=defaultCleanupParameters) |
Works the same as Reionizer().reionize(mol) More... | |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | removeFragments (const RWMol *mol, const CleanupParameters ¶ms=defaultCleanupParameters) |
Works the same as FragmentRemover().remove(mol) More... | |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | canonicalTautomer (const RWMol *mol, const CleanupParameters ¶ms=defaultCleanupParameters) |
Works the same as TautomerEnumerator().canonicalize(mol) More... | |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | tautomerParent (const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters, bool skipStandardize=false) |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | fragmentParent (const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters, bool skip_standardize=false) |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | stereoParent (const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters, bool skip_standardize=false) |
calls removeStereochemistry() on the given molecule More... | |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | isotopeParent (const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters, bool skip_standardize=false) |
removes all isotopes specifications from the given molecule More... | |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | chargeParent (const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters, bool skip_standardize=false) |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | superParent (const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters, bool skip_standardize=false) |
RDKIT_MOLSTANDARDIZE_EXPORT std::string | standardizeSmiles (const std::string &smiles) |
RDKIT_MOLSTANDARDIZE_EXPORT void | disconnectOrganometallics (RWMol &mol, RDKit::MolStandardize::MetalDisconnectorOptions mdo={ true, true, false, true}) |
RDKIT_MOLSTANDARDIZE_EXPORT ROMol * | disconnectOrganometallics (const ROMol &mol, RDKit::MolStandardize::MetalDisconnectorOptions mdo={ true, true, false, true}) |
As above, but returns new disconnected molecule. More... | |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::string > | enumerateTautomerSmiles (const std::string &smiles, const CleanupParameters ¶ms=defaultCleanupParameters) |
TODO. More... | |
Normalizer * | normalizerFromParams (const CleanupParameters ¶ms) |
TautomerEnumerator * | tautomerEnumeratorFromParams (const CleanupParameters ¶ms) |
TautomerEnumerator * | getV1TautomerEnumerator () |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< Bond::BondType > | stringToBondType (std::string bond_str) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< int > | stringToCharge (std::string charge_str) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< TautomerTransform > | readTautomers (std::string fileName) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< TautomerTransform > | readTautomers (std::istream &inStream, int nToRead=-1) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< TautomerTransform > | readTautomers (const std::vector< std::tuple< std::string, std::string, std::string, std::string >> &data) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ChemicalReaction > > | readTransformations (std::string fileName) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ChemicalReaction > > | readTransformations (std::istream &inStream, int nToRead=-1) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ChemicalReaction > > | readTransformations (const std::vector< std::pair< std::string, std::string >> &data) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< ValidationErrorInfo > | validateSmiles (const std::string &smiles) |
A convenience function for quickly validating a single SMILES string. More... | |
Variables | |
RDKIT_MOLSTANDARDIZE_EXPORT const CleanupParameters | defaultCleanupParameters |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< ChargeCorrection > | CHARGE_CORRECTIONS |
typedef RDCatalog::HierarchCatalog<FragmentCatalogEntry, FragmentCatalogParams, int> RDKit::MolStandardize::FragmentCatalog |
Definition at line 29 of file Fragment.h.
typedef std::pair<std::string, ROMOL_SPTR> RDKit::MolStandardize::SmilesMolPair |
Definition at line 35 of file Normalize.h.
typedef std::map<std::string, Tautomer> RDKit::MolStandardize::SmilesTautomerMap |
Definition at line 74 of file MolStandardize/Tautomer.h.
typedef std::pair<std::string, Tautomer> RDKit::MolStandardize::SmilesTautomerPair |
Definition at line 75 of file MolStandardize/Tautomer.h.
typedef RDCatalog::HierarchCatalog<TautomerCatalogEntry, TautomerCatalogParams, int> RDKit::MolStandardize::TautomerCatalog |
Definition at line 33 of file MolStandardize/Tautomer.h.
using RDKit::MolStandardize::TautomerTransformDefs = typedef std::vector<std::tuple<std::string, std::string, std::string, std::string> > |
Definition at line 27 of file TautomerCatalogParams.h.
typedef RDCatalog::HierarchCatalog<TransformCatalogEntry, TransformCatalogParams, int> RDKit::MolStandardize::TransformCatalog |
Definition at line 34 of file Normalize.h.
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Enumerator | |
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Completed | |
MaxTautomersReached | |
MaxTransformsReached | |
Canceled |
Definition at line 47 of file MolStandardize/Tautomer.h.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol* RDKit::MolStandardize::canonicalTautomer | ( | const RWMol * | mol, |
const CleanupParameters & | params = defaultCleanupParameters |
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Works the same as TautomerEnumerator().canonicalize(mol)
RDKIT_MOLSTANDARDIZE_EXPORT RWMol* RDKit::MolStandardize::chargeParent | ( | const RWMol & | mol, |
const CleanupParameters & | params = defaultCleanupParameters , |
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bool | skip_standardize = false |
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Returns the charge parent of a given molecule. The charge parent is the uncharged version of the fragment parent.
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
Definition at line 102 of file MolStandardize.h.
References cleanup().
RDKIT_MOLSTANDARDIZE_EXPORT RWMol* RDKit::MolStandardize::cleanup | ( | const RWMol * | mol, |
const CleanupParameters & | params = defaultCleanupParameters |
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The cleanup function is equivalent to the molvs.Standardizer().standardize(mol) function. It calls the same steps, namely: RemoveHs, RDKit SanitizeMol, MetalDisconnector, Normalizer, Reionizer, RDKit AssignStereochemistry.
Referenced by cleanup().
RDKIT_MOLSTANDARDIZE_EXPORT ROMol* RDKit::MolStandardize::disconnectOrganometallics | ( | const ROMol & | mol, |
RDKit::MolStandardize::MetalDisconnectorOptions | mdo = { true, true, false, true} |
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As above, but returns new disconnected molecule.
RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::disconnectOrganometallics | ( | RWMol & | mol, |
RDKit::MolStandardize::MetalDisconnectorOptions | mdo = { true, true, false, true} |
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Do a disconnection of an organometallic complex according to rules preferred by Syngenta. All bonds to metals are broken, including covalent bonds to Group I/II metals (so including Grignards, lithium complexes etc.). The ligands are left in the charge states they came in with. If there are haptic bonds defined by a dummy atom bonded to a metal by a bond that has a _MolFileBondEndPts (which will contain the indices of the atoms involved in the haptic bond) then the dummy atom is removed also. Do the disconnection in place. The options are splitGrignards, splitAromaticC, adjustCharges and removeHapticDummies. Roll on C++20 and designated initializers!
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<std::string> RDKit::MolStandardize::enumerateTautomerSmiles | ( | const std::string & | smiles, |
const CleanupParameters & | params = defaultCleanupParameters |
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TODO.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol* RDKit::MolStandardize::fragmentParent | ( | const RWMol & | mol, |
const CleanupParameters & | params = defaultCleanupParameters , |
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bool | skip_standardize = false |
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Returns the fragment parent of a given molecule. The fragment parent is the largest organic covalent unit in the molecule.
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Definition at line 61 of file Fragment.h.
References RDKit::MolStandardize::CleanupParameters::fragmentData, and RDKit::MolStandardize::CleanupParameters::fragmentFile.
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Definition at line 419 of file MolStandardize/Tautomer.h.
References RDKit::MolStandardize::defaults::defaultTautomerTransformsv1.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol* RDKit::MolStandardize::isotopeParent | ( | const RWMol & | mol, |
const CleanupParameters & | params = defaultCleanupParameters , |
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bool | skip_standardize = false |
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removes all isotopes specifications from the given molecule
RDKIT_MOLSTANDARDIZE_EXPORT RWMol* RDKit::MolStandardize::normalize | ( | const RWMol * | mol, |
const CleanupParameters & | params = defaultCleanupParameters |
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Works the same as Normalizer().normalize(mol)
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Definition at line 93 of file Normalize.h.
References RDKit::MolStandardize::CleanupParameters::maxRestarts, RDKit::MolStandardize::CleanupParameters::normalizationData, and RDKit::MolStandardize::CleanupParameters::normalizations.
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<std::shared_ptr<ROMol> > RDKit::MolStandardize::readFuncGroups | ( | const std::vector< std::pair< std::string, std::string >> & | data | ) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<std::shared_ptr<ROMol> > RDKit::MolStandardize::readFuncGroups | ( | std::istream & | inStream, |
int | nToRead = -1 |
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RDKIT_MOLSTANDARDIZE_EXPORT std::vector<std::shared_ptr<ROMol> > RDKit::MolStandardize::readFuncGroups | ( | std::string | fileName | ) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> > RDKit::MolStandardize::readPairs | ( | const std::vector< std::tuple< std::string, std::string, std::string >> & | data | ) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> > RDKit::MolStandardize::readPairs | ( | std::istream & | inStream, |
int | nToRead = -1 |
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RDKIT_MOLSTANDARDIZE_EXPORT std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> > RDKit::MolStandardize::readPairs | ( | std::string | fileName | ) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<TautomerTransform> RDKit::MolStandardize::readTautomers | ( | const std::vector< std::tuple< std::string, std::string, std::string, std::string >> & | data | ) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<TautomerTransform> RDKit::MolStandardize::readTautomers | ( | std::istream & | inStream, |
int | nToRead = -1 |
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RDKIT_MOLSTANDARDIZE_EXPORT std::vector<TautomerTransform> RDKit::MolStandardize::readTautomers | ( | std::string | fileName | ) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<std::shared_ptr<ChemicalReaction> > RDKit::MolStandardize::readTransformations | ( | const std::vector< std::pair< std::string, std::string >> & | data | ) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<std::shared_ptr<ChemicalReaction> > RDKit::MolStandardize::readTransformations | ( | std::istream & | inStream, |
int | nToRead = -1 |
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RDKIT_MOLSTANDARDIZE_EXPORT std::vector<std::shared_ptr<ChemicalReaction> > RDKit::MolStandardize::readTransformations | ( | std::string | fileName | ) |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol* RDKit::MolStandardize::reionize | ( | const RWMol * | mol, |
const CleanupParameters & | params = defaultCleanupParameters |
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Works the same as Reionizer().reionize(mol)
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Definition at line 103 of file Charge.h.
References RDKit::MolStandardize::CleanupParameters::acidbaseData, and RDKit::MolStandardize::CleanupParameters::acidbaseFile.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol* RDKit::MolStandardize::removeFragments | ( | const RWMol * | mol, |
const CleanupParameters & | params = defaultCleanupParameters |
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Works the same as FragmentRemover().remove(mol)
RDKIT_MOLSTANDARDIZE_EXPORT std::string RDKit::MolStandardize::standardizeSmiles | ( | const std::string & | smiles | ) |
Convenience function for quickly standardizing a single SMILES string. Returns a standardized canonical SMILES string given a SMILES string. This is the equivalent of calling cleanup() on each of the molecules
RDKIT_MOLSTANDARDIZE_EXPORT RWMol* RDKit::MolStandardize::stereoParent | ( | const RWMol & | mol, |
const CleanupParameters & | params = defaultCleanupParameters , |
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bool | skip_standardize = false |
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calls removeStereochemistry() on the given molecule
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<Bond::BondType> RDKit::MolStandardize::stringToBondType | ( | std::string | bond_str | ) |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<int> RDKit::MolStandardize::stringToCharge | ( | std::string | charge_str | ) |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol* RDKit::MolStandardize::superParent | ( | const RWMol & | mol, |
const CleanupParameters & | params = defaultCleanupParameters , |
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bool | skip_standardize = false |
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Returns the super parent. The super parent is the fragment, charge, isotope, stereo, and tautomer parent of the molecule.
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Definition at line 414 of file MolStandardize/Tautomer.h.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol* RDKit::MolStandardize::tautomerParent | ( | const RWMol & | mol, |
const CleanupParameters & | params = defaultCleanupParameters , |
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bool | skipStandardize = false |
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Returns the tautomer parent of a given molecule. The fragment parent is the standardized canonical tautomer of the molecule
RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::updateCleanupParamsFromJSON | ( | CleanupParameters & | params, |
const std::string & | json | ||
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RDKIT_MOLSTANDARDIZE_EXPORT std::vector<ValidationErrorInfo> RDKit::MolStandardize::validateSmiles | ( | const std::string & | smiles | ) |
A convenience function for quickly validating a single SMILES string.
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Definition at line 25 of file Fragment.h.