def _standardise(data, sanitize=True, removeHs=True, strictParsing=True):
mols = _parseMolData(data,
sanitize=sanitize,
removeHs=removeHs,
strictParsing=strictParsing)
res = _apply(mols, standardise)
return _getSDFString(res)
def _sanitize(data, sanitizeOps=SANITIZE_ALL):
mols = _parseMolData(data, sanitize=False, removeHs=False, strictParsing=False)
try:
_apply(mols, Chem.SanitizeMol, sanitizeOps=sanitizeOps)
except:
pass
return _getSDFString(mols)
def _break_bonds(data, sanitize=True, removeHs=True, strictParsing=True):
mols = _parseMolData(data,
sanitize=sanitize,
removeHs=removeHs,
strictParsing=strictParsing)
res = _apply(mols, break_bonds)
return _getSDFString(res)
def _kekulize(data, sanitize=True, removeHs=True, strictParsing=True):
mols = _parseMolData(data,
sanitize=sanitize,
removeHs=removeHs,
strictParsing=strictParsing)
_apply(mols, Chem.Kekulize)
return _getSDFString(mols)
def _unsalt(data, sanitize=True, removeHs=True, strictParsing=True):
mols = _parseMolData(data,
sanitize=sanitize,
removeHs=removeHs,
strictParsing=strictParsing)
res = _apply(mols, unsalt)
return _getSDFString(res)
def _standardise(data):
mols = _parseMolData(data)
res = _apply(mols, standardise)
return _getSDFString(res)
#-----------------------------------------------------------------------------------------------------------------------
def _removeHs(data, implicitOnly=False):
mols = _parseMolData(data,
sanitize=False,
removeHs=False,
strictParsing=True)
mols = _apply(mols, Chem.RemoveHs, implicitOnly=implicitOnly)
return _getSDFString(mols)
def _addHs(data, explicitOnly=False, addCoords=False):
mols = _parseMolData(data,
sanitize=True,
removeHs=False,
strictParsing=True)
mols = _apply(mols,
Chem.AddHs,
explicitOnly=explicitOnly,
addCoords=addCoords)
return _getSDFString(mols)
def _sanitize(data, sanitizeOps=SANITIZE_ALL):
mols = _parseMolData(data,
sanitize=False,
removeHs=False,
strictParsing=False)
try:
_apply(mols, Chem.SanitizeMol, sanitizeOps=sanitizeOps)
except:
pass
return _getSDFString(mols)
def _neutralise(data,
balance,
sanitize=True,
removeHs=True,
strictParsing=True):
mols = _parseMolData(data,
sanitize=sanitize,
removeHs=removeHs,
strictParsing=strictParsing)
res = _apply(mols, neutralise, balance)
return _getSDFString(res)
def _align(data, template, force=False):
mols = _parseMolData(data)
if template:
pattern = _parseMolData(template)
else:
pattern = [mols[0]]
mols = mols[1:]
if not pattern or not mols or len(pattern) != 1:
return 'Wrong arguments'
aligned_mols = ct._align(mols, pattern[0], force)
if aligned_mols:
return _getSDFString(aligned_mols)
def _ctab23D(data,
multi,
mmff,
sanitize=True,
removeHs=True,
strictParsing=True):
mols = _parseMolData(data,
sanitize=sanitize,
removeHs=removeHs,
strictParsing=strictParsing)
optimisedMols = _apply(mols, _2D23D, multi, mmff)
return _getSDFString(optimisedMols)
def _align(data, template, force=False):
mols = _parseMolData(data)
if template:
pattern = _parseMolData(template)
else:
pattern = [mols[0]]
mols = mols[1:]
if not pattern or not mols or len(pattern) != 1:
return 'Wrong arguments'
aligned_mols = ct._align(mols, pattern[0], force)
if aligned_mols:
return _getSDFString(aligned_mols)
def _smarts2ctab(data, computeCoords=True, delimiter=' ', sanitize=True):
mols = []
for line in data.splitlines():
if not line:
continue
for chunk in line.strip().split(delimiter):
if not chunk:
continue
mols.append(_molFromSmarts(chunk))
if computeCoords:
_apply(mols, _computeCoords, True)
if sanitize:
_apply(mols, _sanitize)
return _getSDFString(mols)
def _smarts2ctab(data, computeCoords=True, delimiter=' ', sanitize=True):
mols = []
for line in data.splitlines():
if not line:
continue
for chunk in line.strip().split(delimiter):
if not chunk:
continue
mols.append(_molFromSmarts(chunk))
if computeCoords:
_apply(mols, _computeCoords, True)
if sanitize:
_apply(mols, _sanitize)
return _getSDFString(mols)
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 _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 _smiles2ctab(data):
return _getSDFString(_parseSMILESData(data, True))
def _standardise(data):
mols = _parseMolData(data)
res = _apply(mols, standardise)
return _getSDFString(res)
#-----------------------------------------------------------------------------------------------------------------------
def _unsalt(data):
mols = _parseMolData(data)
res = _apply(mols, unsalt)
return _getSDFString(res)
def _ctab23D(data, multi, mmff):
mols = _parseMolData(data)
optimisedMols = _apply(mols, _2D23D, multi, mmff)
return _getSDFString(optimisedMols)
def _ctab23D(data, multi, mmff):
mols = _parseMolData(data)
optimisedMols = _apply(mols, _2D23D, multi, mmff)
return _getSDFString(optimisedMols)
def _addHs(data, explicitOnly=False, addCoords=False):
mols = _parseMolData(data, sanitize=True, removeHs=False, strictParsing=True)
mols = _apply(mols, Chem.AddHs, explicitOnly=explicitOnly, addCoords=addCoords)
return _getSDFString(mols)
def _smiles23D(data, multi, mmff):
mols = _parseSMILESData(data)
optimisedMols = _apply(mols, _2D23D, multi, mmff)
return _getSDFString(optimisedMols)
def _unsalt(data):
mols = _parseMolData(data)
res = _apply(mols, unsalt)
return _getSDFString(res)
def _neutralise(data, balance):
mols = _parseMolData(data)
res = _apply(mols, neutralise, balance)
return _getSDFString(res)
def _kekulize(data):
mols = _parseMolData(data)
_apply(mols, Chem.Kekulize)
return _getSDFString(mols)
def _ctab23D(data, multi, mmff, sanitize=True, removeHs=True, strictParsing=True):
mols = _parseMolData(data, sanitize=sanitize, removeHs=removeHs, strictParsing=strictParsing)
optimisedMols = _apply(mols, _2D23D, multi, mmff)
return _getSDFString(optimisedMols)
def _smiles2ctab(data):
return _getSDFString(_parseSMILESData(data, True))
def _inchi2ctab(inchis):
mols = _apply(inchis.split(), Chem.MolFromInchi)
_apply(mols, _computeCoords)
return _getSDFString(mols)
def _removeHs(data, implicitOnly=False):
mols = _parseMolData(data, sanitize=False, removeHs=False, strictParsing=True)
mols = _apply(mols, Chem.RemoveHs, implicitOnly=implicitOnly)
return _getSDFString(mols)
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 _break_bonds(data):
mols = _parseMolData(data)
res = _apply(mols, break_bonds)
return _getSDFString(res)
def _inchi2ctab(inchis):
mols = _apply(inchis.split(),Chem.MolFromInchi)
_apply(mols, _computeCoords)
return _getSDFString(mols)
def _neutralise(data, balance):
mols = _parseMolData(data)
res = _apply(mols, neutralise, balance)
return _getSDFString(res)
def _smiles23D(data, multi, mmff):
mols = _parseSMILESData(data)
optimisedMols = _apply(mols, _2D23D, multi, mmff)
return _getSDFString(optimisedMols)
def _rules(data):
mols = _parseMolData(data)
res = _apply(mols, rules)
return _getSDFString(res)
def _break_bonds(data, sanitize=True, removeHs=True, strictParsing=True):
mols = _parseMolData(data, sanitize=sanitize, removeHs=removeHs, strictParsing=strictParsing)
res = _apply(mols, break_bonds)
return _getSDFString(res)
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 _unsalt(data, sanitize=True, removeHs=True, strictParsing=True):
mols = _parseMolData(data, sanitize=sanitize, removeHs=removeHs, strictParsing=strictParsing)
res = _apply(mols, unsalt)
return _getSDFString(res)
def _rules(data):
mols = _parseMolData(data)
res = _apply(mols, rules)
return _getSDFString(res)
def _neutralise(data, balance, sanitize=True, removeHs=True, strictParsing=True):
mols = _parseMolData(data, sanitize=sanitize, removeHs=removeHs, strictParsing=strictParsing)
res = _apply(mols, neutralise, balance)
return _getSDFString(res)
def _kekulize(data, sanitize=True, removeHs=True, strictParsing=True):
mols = _parseMolData(data, sanitize=sanitize, removeHs=removeHs, strictParsing=strictParsing)
_apply(mols, Chem.Kekulize)
return _getSDFString(mols)
def _standardise(data, sanitize=True, removeHs=True, strictParsing=True):
mols = _parseMolData(data, sanitize=sanitize, removeHs=removeHs, strictParsing=strictParsing)
res = _apply(mols, standardise)
return _getSDFString(res)
def _break_bonds(data):
mols = _parseMolData(data)
res = _apply(mols, break_bonds)
return _getSDFString(res)