RDKit: MolStandardize.h File Reference

| RDKit Open-source cheminformatics and machine learning.

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MolStandardize.h File Reference

Defines the CleanupParameters and some convenience functions. More...

`#include <RDGeneral/export.h>`
`#include <string>`
`#include <GraphMol/RDKitBase.h>`
`#include <GraphMol/MolStandardize/Metal.h>`

Go to the source code of this file.

## Classes
struct | RDKit::MolStandardize::CleanupParameters

## Namespaces
namespace | RDKit
| Std stuff.
namespace | RDKit::MolStandardize

## Functions
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::updateCleanupParamsFromJSON (CleanupParameters &params, const std::string &json)
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | RDKit::MolStandardize::cleanup (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
RWMol * | RDKit::MolStandardize::cleanup (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::cleanupInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
| Works the same as cleanup(mol)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::cleanupInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters)
| Operates on multiple molecules.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | RDKit::MolStandardize::normalize (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
| Works the same as Normalizer().normalize(mol)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::normalizeInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
| Works the same as Normalizer().normalizeInPlace(mol)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::normalizeInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters)
| Operates on multiple molecules.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | RDKit::MolStandardize::reionize (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
| Works the same as Reionizer().reionize(mol)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::reionizeInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
| Works the same as Reionizer().reionizeInPlace(mol)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::reionizeInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters)
| Operates on multiple molecules.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | RDKit::MolStandardize::removeFragments (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
| Works the same as FragmentRemover().remove(mol)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::removeFragmentsInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
| Works the same as FragmentRemover().removeInPlace(mol)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::removeFragmentsInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters)
| Operates on multiple molecules.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | RDKit::MolStandardize::canonicalTautomer (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
| Works the same as TautomerEnumerator().canonicalize(mol)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::canonicalTautomerInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | RDKit::MolStandardize::tautomerParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skipStandardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::tautomerParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skipStandardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::tautomerParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skipStandardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | RDKit::MolStandardize::fragmentParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::fragmentParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::fragmentParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | RDKit::MolStandardize::stereoParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
| calls removeStereochemistry() on the given molecule
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::stereoParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::stereoParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | RDKit::MolStandardize::isotopeParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
| removes all isotopes specifications from the given molecule
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::isotopeParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::isotopeParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | RDKit::MolStandardize::chargeParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::chargeParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::chargeParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
| operates on multiple molecules
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * | RDKit::MolStandardize::superParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::superParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::superParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT std::string | RDKit::MolStandardize::standardizeSmiles (const std::string &smiles)
RDKIT_MOLSTANDARDIZE_EXPORT void | RDKit::MolStandardize::disconnectOrganometallics (RWMol &mol, RDKit::MolStandardize::MetalDisconnectorOptions mdo={ true, true, false, true})
RDKIT_MOLSTANDARDIZE_EXPORT ROMol * | RDKit::MolStandardize::disconnectOrganometallics (const ROMol &mol, RDKit::MolStandardize::MetalDisconnectorOptions mdo={ true, true, false, true})
| As above, but returns new disconnected molecule.
void | RDKit::MolStandardize::disconnectOrganometallicsInPlace (RWMol &mol, RDKit::MolStandardize::MetalDisconnectorOptions mdo={ true, true, false, true})
| As above, included for API consistency.
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::string > | RDKit::MolStandardize::enumerateTautomerSmiles (const std::string &smiles, const CleanupParameters &params=defaultCleanupParameters)
| TODO.

## Detailed Description

Defines the CleanupParameters and some convenience functions.

Definition in file MolStandardize.h.