rdkit.Chem.rdAbbreviations module

Module containing functions for working with molecular abbreviations

class rdkit.Chem.rdAbbreviations.AbbreviationDefinition((object)self)

Bases: instance

Abbreviation Definition

C++ signature :

void __init__(_object*)

property displayLabel

the label in a drawing when the bond comes from the right

property displayLabelW

the label in a drawing when the bond comes from the west

property label

the label

property mol

the query molecule (should have a dummy as the first atom)

rdkit.Chem.rdAbbreviations.CondenseAbbreviationSubstanceGroups((Mol)mol) → Mol :

Finds and replaces abbreviation (i.e. “SUP”) substance groups in a molecule. The result is not sanitized.

C++ signature :

RDKit::ROMol* CondenseAbbreviationSubstanceGroups(RDKit::ROMol const*)

rdkit.Chem.rdAbbreviations.CondenseMolAbbreviations((Mol)mol, (AtomPairsParameters)abbrevs[, (float)maxCoverage=0.4[, (bool)sanitize=True]]) → Mol :

Finds and replaces abbreviations in a molecule. The result is not sanitized.

C++ signature :

RDKit::ROMol* CondenseMolAbbreviations(RDKit::ROMol const*,boost::python::api::object [,double=0.4 [,bool=True]])

rdkit.Chem.rdAbbreviations.GetDefaultAbbreviations() → _vectN5RDKit13Abbreviations22AbbreviationDefinitionE :

returns a list of the default abbreviation definitions

C++ signature :

std::vector<RDKit::Abbreviations::AbbreviationDefinition, std::allocator<RDKit::Abbreviations::AbbreviationDefinition> > GetDefaultAbbreviations()

rdkit.Chem.rdAbbreviations.GetDefaultLinkers() → _vectN5RDKit13Abbreviations22AbbreviationDefinitionE :

returns a list of the default linker definitions

C++ signature :

std::vector<RDKit::Abbreviations::AbbreviationDefinition, std::allocator<RDKit::Abbreviations::AbbreviationDefinition> > GetDefaultLinkers()

rdkit.Chem.rdAbbreviations.LabelMolAbbreviations((Mol)mol, (AtomPairsParameters)abbrevs[, (float)maxCoverage=0.4]) → Mol :

Finds abbreviations and adds to them to a molecule as “SUP” SubstanceGroups

C++ signature :

RDKit::ROMol* LabelMolAbbreviations(RDKit::ROMol const*,boost::python::api::object [,double=0.4])

rdkit.Chem.rdAbbreviations.ParseAbbreviations((str)text[, (bool)removeExtraDummies=False[, (bool)allowConnectionToDummies=False]]) → _vectN5RDKit13Abbreviations22AbbreviationDefinitionE :

Returns a set of abbreviation definitions from a string. Format of the text data: A series of lines, each of which contains: label SMARTS displayLabel displayLabelW Where label is the label used for the abbreviation, SMARTS is the SMARTS definition of the abbreviation, displayLabel is used in drawings to render the abbreviations and displayLabelW is the display label if a bond comes in from the right. The ‘displayLabel’ and ‘displayLabelW’ fields are optional. Use dummies in the SMARTS to indicate attachment points. The assumption is that the first atom is a dummy (one will be added if this is not true) and that the second atom is the surrogate for the rest of the group.

C++ signature :

std::vector<RDKit::Abbreviations::AbbreviationDefinition, std::allocator<RDKit::Abbreviations::AbbreviationDefinition> > ParseAbbreviations(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > [,bool=False [,bool=False]])

rdkit.Chem.rdAbbreviations.ParseLinkers((str)text) → _vectN5RDKit13Abbreviations22AbbreviationDefinitionE :

Returns a set of linker definitions from a string. Equivalent to calling ParseAbbreviations(text, True True).

C++ signature :

std::vector<RDKit::Abbreviations::AbbreviationDefinition, std::allocator<RDKit::Abbreviations::AbbreviationDefinition> > ParseLinkers(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)