def _parseMolData(data):
"""Imports a molfile and verifies if all of the coordinates are set to zeros.
if they are set to zeros then we know there are no real coordinates in the molfile
In this case we allow RDKit to recaculate the positions of the atoms and come up with its own pictorial representation of the molecule
If not we use the molecule as drawn"""
suppl = SDMolSupplier()
suppl.SetData(str(data), sanitize=False)
data = [x for x in suppl if x]
for x in data:
if not x.HasProp("_drawingBondsWedged"):
SanitizeMol(x)
ctab = MolToMolBlock(x)
ctablines = [
item.split("0.0000") for item in ctab.split("\n")
if "0.0000" in item
]
needs_redraw = 0
for line in ctablines:
if len(line) > 3:
needs_redraw += 1
if needs_redraw == len(ctablines):
#check for overlapping molecules in the CTAB
SanitizeMol(x)
Compute2DCoords(x)
return data
def parse_molblock(self, mb):
"""parse molblock and return mol"""
#mol = MolFromMolBlock(mb)
sd = SDMolSupplier()
sd.SetData(mb)
mol = next(sd)
if mol:
return mol
else:
return None
def _parseMolData(data):
suppl = SDMolSupplier()
suppl.SetData(str(data))
return [x for x in suppl if x]