RDKit
Open-source cheminformatics and machine learning.
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Public Member Functions | Public Attributes | List of all members
RDKit::MolStandardize::CleanupParameters Struct Reference

#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
 

Detailed Description

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:

  • To customize the parameters, the structure must be initialized first. (Another on the TODO list)
    • For this project, not all the parameters have been revealed. (TODO)

Definition at line 41 of file MolStandardize.h.

Constructor & Destructor Documentation

◆ CleanupParameters()

RDKit::MolStandardize::CleanupParameters::CleanupParameters ( )
inline

Definition at line 85 of file MolStandardize.h.

Member Data Documentation

◆ acidbaseData

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().

◆ acidbaseFile

std::string RDKit::MolStandardize::CleanupParameters::acidbaseFile

Definition at line 49 of file MolStandardize.h.

Referenced by RDKit::MolStandardize::reionizerFromParams().

◆ doCanonical

bool RDKit::MolStandardize::CleanupParameters::doCanonical {true}

Whether to apply normalizations in a canonical order

Definition at line 56 of file MolStandardize.h.

◆ fragmentData

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().

◆ fragmentFile

std::string RDKit::MolStandardize::CleanupParameters::fragmentFile

Definition at line 50 of file MolStandardize.h.

Referenced by RDKit::MolStandardize::fragmentRemoverFromParams().

◆ largestFragmentChooserCountHeavyAtomsOnly

bool RDKit::MolStandardize::CleanupParameters::largestFragmentChooserCountHeavyAtomsOnly
Initial value:
{
false}

Whether LargestFragmentChooser should only count heavy atoms (defaults to false)

Definition at line 77 of file MolStandardize.h.

◆ largestFragmentChooserUseAtomCount

bool RDKit::MolStandardize::CleanupParameters::largestFragmentChooserUseAtomCount
Initial value:
{
true}

Whether LargestFragmentChooser should use atom count as main criterion before MW (defaults to true)

Definition at line 74 of file MolStandardize.h.

◆ maxRestarts

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().

◆ maxTautomers

int RDKit::MolStandardize::CleanupParameters::maxTautomers {1000}

The maximum number of tautomers to enumerate (default 1000).

Definition at line 58 of file MolStandardize.h.

◆ maxTransforms

int RDKit::MolStandardize::CleanupParameters::maxTransforms {1000}

The maximum number of tautomer transformations to apply (default 1000).

Definition at line 60 of file MolStandardize.h.

◆ normalizationData

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().

◆ normalizations

std::string RDKit::MolStandardize::CleanupParameters::normalizations

Definition at line 48 of file MolStandardize.h.

Referenced by RDKit::MolStandardize::normalizerFromParams().

◆ preferOrganic

bool RDKit::MolStandardize::CleanupParameters::preferOrganic {false}

Whether to prioritize organic fragments when choosing fragment parent (default False).

Definition at line 54 of file MolStandardize.h.

◆ rdbase

std::string RDKit::MolStandardize::CleanupParameters::rdbase = rdbase_cstr != nullptr ? rdbase_cstr : ""

Definition at line 47 of file MolStandardize.h.

◆ tautomerReassignStereo

bool RDKit::MolStandardize::CleanupParameters::tautomerReassignStereo
Initial value:
{
true}

Whether enumerate() should call assignStereochemistry on all generated tautomers (defaults to true)

Definition at line 71 of file MolStandardize.h.

◆ tautomerRemoveBondStereo

bool RDKit::MolStandardize::CleanupParameters::tautomerRemoveBondStereo
Initial value:
{
true}

Whether to remove stereochemistry from double bonds involved in tautomerism (defaults to true)

Definition at line 65 of file MolStandardize.h.

◆ tautomerRemoveIsotopicHs

bool RDKit::MolStandardize::CleanupParameters::tautomerRemoveIsotopicHs
Initial value:
{
true}

Whether to remove isotopic Hs from centers involved in tautomerism (defaults to true)

Definition at line 68 of file MolStandardize.h.

◆ tautomerRemoveSp3Stereo

bool RDKit::MolStandardize::CleanupParameters::tautomerRemoveSp3Stereo
Initial value:
{
true}

Whether to remove stereochemistry from sp3 centers involved in tautomerism (defaults to true)

Definition at line 62 of file MolStandardize.h.

◆ tautomerTransformData

std::vector<std::tuple<std::string, std::string, std::string, std::string> > RDKit::MolStandardize::CleanupParameters::tautomerTransformData

Definition at line 84 of file MolStandardize.h.

◆ tautomerTransforms

std::string RDKit::MolStandardize::CleanupParameters::tautomerTransforms

Definition at line 51 of file MolStandardize.h.

The documentation for this struct was generated from the following file: