RDKit
Open-source cheminformatics and machine learning.
RDKit::MolStandardize::CleanupParameters Struct Reference

The CleanupParameters structure defines the default parameters for the. More...

#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
 

Detailed Description

The CleanupParameters structure defines the default parameters for the.

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 40 of file MolStandardize.h.

Constructor & Destructor Documentation

◆ CleanupParameters()

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

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

Definition at line 75 of file MolStandardize.h.

Member Data Documentation

◆ acidbaseFile

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

Definition at line 48 of file MolStandardize.h.

◆ doCanonical

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

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

Definition at line 57 of file MolStandardize.h.

◆ fragmentFile

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

Definition at line 49 of file MolStandardize.h.

◆ maxRestarts

int RDKit::MolStandardize::CleanupParameters::maxRestarts {200}

Definition at line 53 of file MolStandardize.h.

◆ maxTautomers

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

Whether to apply normalizations in a canonical order

Definition at line 59 of file MolStandardize.h.

◆ maxTransforms

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

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

Definition at line 61 of file MolStandardize.h.

◆ normalizations

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

Definition at line 47 of file MolStandardize.h.

◆ preferOrganic

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

The maximum number of times to attempt to apply the series of normalizations (default 200).

Definition at line 55 of file MolStandardize.h.

◆ rdbase

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

Definition at line 46 of file MolStandardize.h.

◆ tautomerReassignStereo

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

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

Definition at line 72 of file MolStandardize.h.

◆ tautomerRemoveBondStereo

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

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

Definition at line 66 of file MolStandardize.h.

◆ tautomerRemoveIsotopicHs

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

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

Definition at line 69 of file MolStandardize.h.

◆ tautomerRemoveSp3Stereo

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

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

Definition at line 63 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: