def _highlightSmilesFragment(data, smarts, size, legend, computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True, atomMapNumber=False, kekulize=True, force=False): mols = _parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize) matches = _getMatches(mols, smarts, force) return _mols2imageString(mols, size, legend, 'PNG', atomMapNumber, computeCoords, matches, kekulize=kekulize)
def _smiles2svg(data, size, legend, computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True, kekulize=True, wedgeBonds=True, fitImage=True, atomMapNumber=False): return _mols2svg(_parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize), size, legend, kekulize=kekulize, wedgeBonds=wedgeBonds, fitImage=fitImage, atomMapNumber=atomMapNumber, computeCoords=computeCoords)
def _highlightSmilesFragmentSVG(data, smarts, size, legend, computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True, kekulize=True, wedgeBonds=True, fitImage=True, atomMapNumber=False, force=False): mols = _parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize) matches = _getMatches(mols, smarts, force) return _mols2svg(mols, size, legend, kekulize=kekulize, wedgeBonds=wedgeBonds, fitImage=fitImage, atomMapNumber=atomMapNumber, computeCoords=computeCoords, highlightAtomLists=matches)
def _canonicalize_smiles(data, computeCoords=False, in_delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True, out_delimiter=' ', nameHeader='Name', includeHeader=True, isomericSmiles=False, kekuleSmiles=False): return _getSMILESString(_parseSMILESData(data, computeCoords=computeCoords, delimiter=in_delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize), delimiter=out_delimiter, nameHeader=nameHeader, includeHeader=includeHeader, isomericSmiles=isomericSmiles, kekuleSmiles=kekuleSmiles)
def _smiles2ctab(data, computeCoords=True, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True): return _getSDFString( _parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize))
def _smiles2inchi(data, computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True): return '\n'.join( _apply( _parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize), Chem.MolToInchi))
def _smiles2json(data, size, legend, computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True): return _mols2json( _parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize), size, legend)
def _smiles23D(data, multi, mmff, computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True): mols = _parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize) optimisedMols = _apply(mols, _2D23D, multi, mmff) return _getSDFString(optimisedMols)
def _smiles2image(data, size, legend, computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True, atomMapNumber=False): return _mols2imageString( _parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize), size, legend, 'PNG', atomMapNumber, computeCoords)
def _smiles2SimilarityMap(data, width=500, height=500, radius=2, fingerprint='morgan', computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True, format='png'): return _similarityMap(_parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize), width=width, height=height, radius=radius, fingerprint=fingerprint, format=format)
def _smiles2ctab(data): return _getSDFString(_parseSMILESData(data, True))
def _canonicalize_smiles(data): return _getSMILESString(_parseSMILESData(data))
def _smiles2image(data, size, legend, computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True, atomMapNumber=False): return _mols2imageString(_parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize), size, legend, 'PNG', atomMapNumber, computeCoords)
def _smiles2SimilarityMap(data, params): return _similarityMap(_parseSMILESData(data, True), params)
def _smiles2SimilarityMap(data, width=100, height=100, radius=2, fingerprint = 'morgan', computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True): return _similarityMap(_parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize), width=width, height=height, radius=radius, fingerprint = fingerprint)
def _smiles23D(data, multi, mmff): mols = _parseSMILESData(data) optimisedMols = _apply(mols, _2D23D, multi, mmff) return _getSDFString(optimisedMols)
def _smiles2inchi(data, computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True): return '\n'.join(_apply(_parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize), Chem.MolToInchi))
def _smiles2json(data, size, legend): return _mols2json(_parseSMILESData(data), size, legend)
def _smiles2image(data, size, legend): return _mols2imageString(_parseSMILESData(data), size, legend, 'PNG')
def _smiles2svg(data,size,legend): return _mols2svg(_parseSMILESData(data), size, legend)
def _smiles2ctab(data, computeCoords=True, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True): return _getSDFString(_parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize))
def _smiles2SimilarityMap(data,params): return _similarityMap(_parseSMILESData(data, True), params)
def _smiles2image(data,size,legend): return _mols2imageString(_parseSMILESData(data), size, legend, 'PNG', recalc=recalc)
def _smiles2json(data, size, legend, computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True, sanitize=True): return _mols2json(_parseSMILESData(data, computeCoords=computeCoords, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine, sanitize=sanitize), size,legend)