RDKit
Open-source cheminformatics and machine learning.
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#include <MolStandardize.h>
Public Member Functions | |
CleanupParameters () | |
Public Attributes | |
std::string | rdbase = rdbase_cstr != nullptr ? rdbase_cstr : "" |
std::string | normalizations |
std::string | acidbaseFile |
std::string | fragmentFile |
std::string | tautomerTransforms |
int | maxRestarts {200} |
bool | preferOrganic {false} |
bool | doCanonical {true} |
int | maxTautomers {1000} |
int | maxTransforms {1000} |
bool | tautomerRemoveSp3Stereo |
bool | tautomerRemoveBondStereo |
bool | tautomerRemoveIsotopicHs |
bool | tautomerReassignStereo |
bool | largestFragmentChooserUseAtomCount |
bool | largestFragmentChooserCountHeavyAtomsOnly |
std::vector< std::pair< std::string, std::string > > | normalizationData |
std::vector< std::pair< std::string, std::string > > | fragmentData |
std::vector< std::tuple< std::string, std::string, std::string > > | acidbaseData |
std::vector< std::tuple< std::string, std::string, std::string, std::string > > | tautomerTransformData |
The CleanupParameters structure defines the default parameters for the cleanup process and also allows the user to customize the process by changing the parameters.
Notes:
Definition at line 41 of file MolStandardize.h.
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inline |
Definition at line 85 of file MolStandardize.h.
std::vector<std::tuple<std::string, std::string, std::string> > RDKit::MolStandardize::CleanupParameters::acidbaseData |
Definition at line 82 of file MolStandardize.h.
Referenced by RDKit::MolStandardize::reionizerFromParams().
std::string RDKit::MolStandardize::CleanupParameters::acidbaseFile |
Definition at line 49 of file MolStandardize.h.
Referenced by RDKit::MolStandardize::reionizerFromParams().
Whether to apply normalizations in a canonical order
Definition at line 56 of file MolStandardize.h.
std::vector<std::pair<std::string, std::string> > RDKit::MolStandardize::CleanupParameters::fragmentData |
Definition at line 81 of file MolStandardize.h.
Referenced by RDKit::MolStandardize::fragmentRemoverFromParams().
std::string RDKit::MolStandardize::CleanupParameters::fragmentFile |
Definition at line 50 of file MolStandardize.h.
Referenced by RDKit::MolStandardize::fragmentRemoverFromParams().
bool RDKit::MolStandardize::CleanupParameters::largestFragmentChooserCountHeavyAtomsOnly |
Whether LargestFragmentChooser should only count heavy atoms (defaults to false)
Definition at line 77 of file MolStandardize.h.
bool RDKit::MolStandardize::CleanupParameters::largestFragmentChooserUseAtomCount |
Whether LargestFragmentChooser should use atom count as main criterion before MW (defaults to true)
Definition at line 74 of file MolStandardize.h.
int RDKit::MolStandardize::CleanupParameters::maxRestarts {200} |
The maximum number of times to attempt to apply the series of normalizations (default 200).
Definition at line 52 of file MolStandardize.h.
Referenced by RDKit::MolStandardize::normalizerFromParams().
int RDKit::MolStandardize::CleanupParameters::maxTautomers {1000} |
The maximum number of tautomers to enumerate (default 1000).
Definition at line 58 of file MolStandardize.h.
int RDKit::MolStandardize::CleanupParameters::maxTransforms {1000} |
The maximum number of tautomer transformations to apply (default 1000).
Definition at line 60 of file MolStandardize.h.
std::vector<std::pair<std::string, std::string> > RDKit::MolStandardize::CleanupParameters::normalizationData |
Definition at line 80 of file MolStandardize.h.
Referenced by RDKit::MolStandardize::normalizerFromParams().
std::string RDKit::MolStandardize::CleanupParameters::normalizations |
Definition at line 48 of file MolStandardize.h.
Referenced by RDKit::MolStandardize::normalizerFromParams().
Whether to prioritize organic fragments when choosing fragment parent (default False).
Definition at line 54 of file MolStandardize.h.
std::string RDKit::MolStandardize::CleanupParameters::rdbase = rdbase_cstr != nullptr ? rdbase_cstr : "" |
Definition at line 47 of file MolStandardize.h.
bool RDKit::MolStandardize::CleanupParameters::tautomerReassignStereo |
Whether enumerate() should call assignStereochemistry on all generated tautomers (defaults to true)
Definition at line 71 of file MolStandardize.h.
bool RDKit::MolStandardize::CleanupParameters::tautomerRemoveBondStereo |
Whether to remove stereochemistry from double bonds involved in tautomerism (defaults to true)
Definition at line 65 of file MolStandardize.h.
bool RDKit::MolStandardize::CleanupParameters::tautomerRemoveIsotopicHs |
Whether to remove isotopic Hs from centers involved in tautomerism (defaults to true)
Definition at line 68 of file MolStandardize.h.
bool RDKit::MolStandardize::CleanupParameters::tautomerRemoveSp3Stereo |
Whether to remove stereochemistry from sp3 centers involved in tautomerism (defaults to true)
Definition at line 62 of file MolStandardize.h.
std::vector<std::tuple<std::string, std::string, std::string, std::string> > RDKit::MolStandardize::CleanupParameters::tautomerTransformData |
Definition at line 84 of file MolStandardize.h.
std::string RDKit::MolStandardize::CleanupParameters::tautomerTransforms |
Definition at line 51 of file MolStandardize.h.