Dear JP,
If you want to write a compressed SD file that includes molecular
properties, you can use a function like this:
#----------
def MolToSDFBlock(mol):
res=[Chem.MolToMolBlock(mol)]
for pn in mol.GetPropNames():
pv = mol.GetProp(pn)
res.append('> <%s>\n%s\n'%(pn,pv))
res.append('$$$$\n')
return '\n'.join(res)
#----------
A little demonstration of using it:
>>> ms = [x for x in Chem.SDMolSupplier('hERG_inhibition_dataset.sdf') if x is
>>> not None]
>>> from cStringIO import StringIO
>>> sio = StringIO()
>>> for m in ms: sio.write(util.MolToSDFBlock(m))
...
>>> suppl2 = Chem.SDMolSupplier()
>>> suppl2.SetData(txt)
>>> ms2 = [x for x in suppl2]
>>> len(ms)==len(ms2)
True
I hope this helps,
-greg
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