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 _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 _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 _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):
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 _canonicalize_smiles(data):
return _getSMILESString(_parseSMILESData(data))
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 _smiles2ctab(data):
return _getSDFString(_parseSMILESData(data, True))
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):
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 _smiles23D(data, multi, mmff):
mols = _parseSMILESData(data)
optimisedMols = _apply(mols, _2D23D, multi, mmff)
return _getSDFString(optimisedMols)
def _smiles2image(data,size,legend):
return _mols2imageString(_parseSMILESData(data), size, legend, 'PNG', recalc=recalc)
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 _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)
