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RDKit
Open-source cheminformatics and machine learning.
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Classes | |
class | AcidBaseCatalogEntry |
class | AcidBaseCatalogParams |
class | AllowedAtomsValidation |
struct | ChargeCorrection |
struct | CleanupParameters |
The CleanupParameters structure defines the default parameters for the. More... | |
class | DisallowedAtomsValidation |
class | FragmentCatalogEntry |
class | FragmentCatalogParams |
class | FragmentRemover |
class | FragmentValidation |
The FragmentValidation class logs if certain fragments are present. More... | |
class | IsotopeValidation |
The IsotopeValidation class logs if molecule contains isotopes. More... | |
class | LargestFragmentChooser |
class | MetalDisconnector |
class | MolVSValidation |
The MolVSValidation class can be used to perform all MolVSValidions. More... | |
class | MolVSValidations |
The MolVSValidations class includes most of the same validations as. More... | |
class | NeutralValidation |
The NeutralValidation class logs if not an overall neutral system. More... | |
class | NoAtomValidation |
The NoAtomValidation class throws an error if no atoms are present in the. More... | |
class | Normalizer |
The Normalizer class for applying Normalization transforms. More... | |
class | RDKitValidation |
The RDKitValidation class throws an error when there are no atoms in the. More... | |
class | Reionizer |
The reionizer class to fix charges and reionize a molecule such that the. More... | |
class | TautomerCanonicalizer |
class | TautomerCatalogEntry |
class | TautomerCatalogParams |
class | TautomerEnumerator |
class | TautomerTransform |
class | TransformCatalogEntry |
class | TransformCatalogParams |
class | Uncharger |
The Uncharger class for neutralizing ionized acids and bases. More... | |
class | ValidationErrorInfo |
The ValidationErrorInfo class is used to store the information returned by a. More... | |
class | ValidationMethod |
The ValidationMethod class is the abstract base class upon which all the. More... | |
Typedefs | |
typedef RDCatalog::HierarchCatalog< AcidBaseCatalogEntry, AcidBaseCatalogParams, int > | AcidBaseCatalog |
typedef RDCatalog::HierarchCatalog< FragmentCatalogEntry, FragmentCatalogParams, int > | FragmentCatalog |
typedef RDCatalog::HierarchCatalog< TransformCatalogEntry, TransformCatalogParams, int > | TransformCatalog |
typedef RDCatalog::HierarchCatalog< TautomerCatalogEntry, TautomerCatalogParams, int > | TautomerCatalog |
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::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 RWMol * | cleanup (const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters) |
The cleanup function is equivalent to the. More... | |
RDKIT_MOLSTANDARDIZE_EXPORT void | tautomerParent (RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters) |
TODO not yet finished! More... | |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | fragmentParent (const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters, bool skip_standardize=false) |
Returns the fragment parent of a given molecule. The fragment parent is the. More... | |
RDKIT_MOLSTANDARDIZE_EXPORT void | stereoParent (RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters) |
RDKIT_MOLSTANDARDIZE_EXPORT void | isotopeParent (RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters) |
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | chargeParent (const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters, bool skip_standardize=false) |
RDKIT_MOLSTANDARDIZE_EXPORT void | superParent (RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters) |
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 std::string | standardizeSmiles (const std::string &smiles) |
Convenience function for quickly standardizing a single SMILES string. More... | |
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::string > | enumerateTautomerSmiles (const std::string &smiles, const CleanupParameters ¶ms=defaultCleanupParameters) |
TODO. More... | |
std::vector< std::pair< unsigned int, unsigned int > > | pairwise (const std::vector< int > vect) |
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< 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< ValidationErrorInfo > | validateSmiles (const std::string &smiles) |
A convenience function for quickly validating a single SMILES string. More... | |
Variables | |
const RDKIT_MOLSTANDARDIZE_EXPORT 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 RDCatalog::HierarchCatalog<TautomerCatalogEntry, TautomerCatalogParams, int> RDKit::MolStandardize::TautomerCatalog |
Definition at line 27 of file MolStandardize/Tautomer.h.
typedef RDCatalog::HierarchCatalog<TransformCatalogEntry, TransformCatalogParams, int> RDKit::MolStandardize::TransformCatalog |
Definition at line 34 of file Normalize.h.
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
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.
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.
RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::isotopeParent | ( | RWMol & | mol, |
const CleanupParameters & | params = defaultCleanupParameters |
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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)
std::vector<std::pair<unsigned int, unsigned int> > RDKit::MolStandardize::pairwise | ( | const std::vector< int > | vect | ) |
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 | ( | 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 | ( | 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 | ( | 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)
RDKIT_MOLSTANDARDIZE_EXPORT std::string RDKit::MolStandardize::standardizeSmiles | ( | const std::string & | smiles | ) |
Convenience function for quickly standardizing a single SMILES string.
RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::stereoParent | ( | RWMol & | mol, |
const CleanupParameters & | params = defaultCleanupParameters |
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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 void RDKit::MolStandardize::superParent | ( | RWMol & | mol, |
const CleanupParameters & | params = defaultCleanupParameters |
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RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::tautomerParent | ( | RWMol & | mol, |
const CleanupParameters & | params = defaultCleanupParameters |
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TODO not yet finished!
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<ValidationErrorInfo> RDKit::MolStandardize::validateSmiles | ( | const std::string & | smiles | ) |
A convenience function for quickly validating a single SMILES string.
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<ChargeCorrection> RDKit::MolStandardize::CHARGE_CORRECTIONS |
const RDKIT_MOLSTANDARDIZE_EXPORT CleanupParameters RDKit::MolStandardize::defaultCleanupParameters |
Definition at line 25 of file Fragment.h.