def _highlightSmilesFragmentSVG(data,
smarts,
size,
computeCoords=False,
delimiter=' ',
smilesColumn=0,
nameColumn=1,
titleLine=True,
sanitize=True,
kekulize=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,
kekulize=kekulize,
atomMapNumber=atomMapNumber,
computeCoords=computeCoords,
highlightAtomLists=matches)
def _smiles22D(data,
computeCoords=False,
delimiter=' ',
smilesColumn=0,
nameColumn=1,
titleLine=True,
sanitize=False):
mols = _parseSMILESData(data,
computeCoords=computeCoords,
delimiter=delimiter,
smilesColumn=smilesColumn,
nameColumn=nameColumn,
titleLine=titleLine,
sanitize=sanitize)
optimisedMols = _apply(mols, _2D22D)
return _getSDFString(optimisedMols)
def _smiles2svg(data,
size,
computeCoords=False,
delimiter=' ',
smilesColumn=0,
nameColumn=1,
titleLine=True,
sanitize=True,
kekulize=True,
atomMapNumber=False):
return _mols2svg(_parseSMILESData(data,
computeCoords=computeCoords,
delimiter=delimiter,
smilesColumn=smilesColumn,
nameColumn=nameColumn,
titleLine=titleLine,
sanitize=sanitize),
size,
kekulize=kekulize,
atomMapNumber=atomMapNumber,
computeCoords=computeCoords)
def _smiles2SimilarityMapSVG(data,
width=500,
height=500,
radius=2,
fingerprint='morgan',
computeCoords=False,
delimiter=' ',
smilesColumn=0,
nameColumn=1,
titleLine=True,
sanitize=True,
format='svg'):
return _similarityMapSVG(_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 _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 _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 _canonicalize_smiles(data, computeCoords=False, in_delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True,
sanitize=True, out_delimiter=' ', nameHeader='Name', includeHeader=True):
return _getSMILESString(_parseSMILESData(data, computeCoords=computeCoords, delimiter=in_delimiter,
smilesColumn=smilesColumn, nameColumn=nameColumn, titleLine=titleLine,
sanitize=sanitize),
delimiter=out_delimiter, nameHeader=nameHeader, includeHeader=includeHeader)