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//
// Copyright (C) 2018 Susan H. Leung
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
/*! \file MolStandardize.h
\brief Defines the CleanupParameters and some convenience functions.
*/
#include <RDGeneral/export.h>
#ifndef __RD_MOLSTANDARDIZE_H__
#define __RD_MOLSTANDARDIZE_H__
#include <string>
#include <GraphMol/RDKitBase.h>
namespace RDKit {
class RWMol;
class ROMol;
namespace MolStandardize {
//! The CleanupParameters structure defines the default parameters for the
// cleanup process and also allows the user to customize the process by changing
// the parameters.
/*!
<b>Notes:</b>
- 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)
*/
struct RDKIT_MOLSTANDARDIZE_EXPORT CleanupParameters {
// TODO reveal all parameters
private:
const char *rdbase_cstr = std::getenv("RDBASE");
public:
std::string rdbase = rdbase_cstr != nullptr ? rdbase_cstr : "";
std::string normalizations;
std::string acidbaseFile;
std::string fragmentFile;
// std::vector<std::string> chargeCorrections;
std::string tautomerTransforms;
// std::vector<std::string> TautomerScores;
int maxRestarts{200}; //! The maximum number of times to attempt to apply the
//! series of normalizations (default 200).
bool preferOrganic{false}; //! Whether to prioritize organic fragments when
//! choosing fragment parent (default False).
bool doCanonical{true}; //! Whether to apply normalizations in a
//! canonical order
int maxTautomers{1000}; //! The maximum number of tautomers to enumerate
//! (default 1000).
int maxTransforms{1000}; //! The maximum number of tautomer transformations
//! to apply (default 1000).
bool tautomerRemoveSp3Stereo{
true}; //! Whether to remove stereochemistry from sp3
//! centers involved in tautomerism (defaults to true)
bool tautomerRemoveBondStereo{
true}; //! Whether to remove stereochemistry from double
//! bonds involved in tautomerism (defaults to true)
bool tautomerRemoveIsotopicHs{
true}; //! Whether to remove isotopic Hs from centers
//! involved in tautomerism (defaults to true)
bool tautomerReassignStereo{
true}; //! Whether enumerate() should call assignStereochemistry
//! on all generated tautomers (defaults to true)
CleanupParameters()
: // TODO
// normalizations(""),//this->DEFAULT_TRANSFORMS),
normalizations(rdbase + "/Data/MolStandardize/normalizations.txt"),
acidbaseFile(rdbase + "/Data/MolStandardize/acid_base_pairs.txt"),
fragmentFile(rdbase + "/Data/MolStandardize/fragmentPatterns.txt"),
// chargeCorrections()
tautomerTransforms(rdbase +
"/Data/MolStandardize/tautomerTransforms.in")
{}
};
RDKIT_MOLSTANDARDIZE_EXPORT extern const CleanupParameters
defaultCleanupParameters;
//! The cleanup function is equivalent to the
// molvs.Standardizer().standardize(mol) function. It calls the same steps,
// namely: RemoveHs, RDKit SanitizeMol, MetalDisconnector, Normalizer,
// Reionizer, RDKit AssignStereochemistry.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol *cleanup(
const RWMol &mol,
const CleanupParameters ¶ms = defaultCleanupParameters);
//! TODO not yet finished!
RDKIT_MOLSTANDARDIZE_EXPORT void tautomerParent(
RWMol &mol, const CleanupParameters ¶ms = defaultCleanupParameters);
//! Returns the fragment parent of a given molecule. The fragment parent is the
// largest organic covalent unit in the molecule.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol *fragmentParent(
const RWMol &mol,
const CleanupParameters ¶ms = defaultCleanupParameters,
bool skip_standardize = false);
// TODO
RDKIT_MOLSTANDARDIZE_EXPORT void stereoParent(
RWMol &mol, const CleanupParameters ¶ms = defaultCleanupParameters);
// TODO
RDKIT_MOLSTANDARDIZE_EXPORT void isotopeParent(
RWMol &mol, const CleanupParameters ¶ms = defaultCleanupParameters);
//! Returns the charge parent of a given molecule. The charge parent is the
//! uncharged
// version of the fragment parent.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol *chargeParent(
const RWMol &mol,
const CleanupParameters ¶ms = defaultCleanupParameters,
bool skip_standardize = false);
// TODO Need to do tautomers first
RDKIT_MOLSTANDARDIZE_EXPORT void superParent(
RWMol &mol, const CleanupParameters ¶ms = defaultCleanupParameters);
//! Works the same as Normalizer().normalize(mol)
RDKIT_MOLSTANDARDIZE_EXPORT RWMol *normalize(
const RWMol *mol,
const CleanupParameters ¶ms = defaultCleanupParameters);
//! Works the same as Reionizer().reionize(mol)
RDKIT_MOLSTANDARDIZE_EXPORT RWMol *reionize(
const RWMol *mol,
const CleanupParameters ¶ms = defaultCleanupParameters);
//! Convenience function for quickly standardizing a single SMILES string.
// Returns a standardized canonical SMILES string given a SMILES string.
RDKIT_MOLSTANDARDIZE_EXPORT std::string standardizeSmiles(
const std::string &smiles);
//! TODO
RDKIT_MOLSTANDARDIZE_EXPORT std::vector<std::string> enumerateTautomerSmiles(
const std::string &smiles,
const CleanupParameters ¶ms = defaultCleanupParameters);
}; // namespace MolStandardize
} // namespace RDKit
#endif
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