16 #ifndef __RD_MOLSTANDARDIZE_H__
17 #define __RD_MOLSTANDARDIZE_H__
26 namespace MolStandardize {
43 const char *rdbase_cstr = std::getenv(
"RDBASE");
46 std::string rdbase = rdbase_cstr !=
nullptr ? rdbase_cstr :
"";
55 bool preferOrganic{
false};
57 bool doCanonical{
true};
59 int maxTautomers{1000};
61 int maxTransforms{1000};
63 bool tautomerRemoveSp3Stereo{
66 bool tautomerRemoveBondStereo{
69 bool tautomerRemoveIsotopicHs{
72 bool tautomerReassignStereo{
78 normalizations(rdbase +
"/Data/MolStandardize/normalizations.txt"),
79 acidbaseFile(rdbase +
"/Data/MolStandardize/acid_base_pairs.txt"),
80 fragmentFile(rdbase +
"/Data/MolStandardize/fragmentPatterns.txt"),
82 tautomerTransforms(rdbase +
83 "/Data/MolStandardize/tautomerTransforms.in")
107 bool skip_standardize =
false);
123 bool skip_standardize =
false);
142 const std::string &smiles);
146 const std::string &smiles,
pulls in the core RDKit functionality
RWMol is a molecule class that is intended to be edited.
#define RDKIT_MOLSTANDARDIZE_EXPORT
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * cleanup(const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters)
The cleanup function is equivalent to the.
RDKIT_MOLSTANDARDIZE_EXPORT void stereoParent(RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters)
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::string > enumerateTautomerSmiles(const std::string &smiles, const CleanupParameters ¶ms=defaultCleanupParameters)
TODO.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * fragmentParent(const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters, bool skip_standardize=false)
Returns the fragment parent of a given molecule. The fragment parent is the.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * reionize(const RWMol *mol, const CleanupParameters ¶ms=defaultCleanupParameters)
Works the same as Reionizer().reionize(mol)
RDKIT_MOLSTANDARDIZE_EXPORT void tautomerParent(RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters)
TODO not yet finished!
RDKIT_MOLSTANDARDIZE_EXPORT void isotopeParent(RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters)
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * chargeParent(const RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters, bool skip_standardize=false)
RDKIT_MOLSTANDARDIZE_EXPORT void superParent(RWMol &mol, const CleanupParameters ¶ms=defaultCleanupParameters)
RDKIT_MOLSTANDARDIZE_EXPORT const CleanupParameters defaultCleanupParameters
RDKIT_MOLSTANDARDIZE_EXPORT std::string standardizeSmiles(const std::string &smiles)
Convenience function for quickly standardizing a single SMILES string.
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * normalize(const RWMol *mol, const CleanupParameters ¶ms=defaultCleanupParameters)
Works the same as Normalizer().normalize(mol)
The CleanupParameters structure defines the default parameters for the.
std::string normalizations
std::string tautomerTransforms