Got it. The problem is now fixed.
Thanks for reporting it!
-greg
On Tue, Apr 21, 2015 at 5:33 PM, Michał Nowotka <mmm...@gmail.com> wrote:
> Hi Greg,
>
> I would expect to have:
>
> SMILES Name
> c1ccccc1 0
>
>
> instead of
>
> SMILES Name
> c1ccccc1
>
> Note, that for SMILES there is also no place to specify a name but if
> I create a mol object from SMILES I will get the desired output.
>
> On Tue, Apr 21, 2015 at 4:20 PM, Greg Landrum <greg.land...@gmail.com>
> wrote:
> > Michal,
> >
> > What do you expect to get for the molecule from the CTAB? In the example
> > below, it does not have anything in the first line, which is the one
> that's
> > used to populate the _Name attribute.
> >
> > -greg
> >
> >
> > On Tue, Apr 21, 2015 at 4:32 PM, Michał Nowotka <mmm...@gmail.com>
> wrote:
> >>
> >> Hi,
> >>
> >> Imagine I have two rdkit mol objects, one from SD and one from SMILES:
> >>
> >> import os
> >> import StringIO
> >> from rdkit.Chem import SDMolSupplier
> >> from rdkit.Chem import SmilesMolSupplier
> >> from rdkit.Chem import SmilesWriter
> >>
> >> mol = '''
> >> MJ150413
> >>
> >> 6 6 0 0 0 0 0 0 0 0999 V2000
> >> 0.7144 1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> >> 1.4289 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> >> 1.4289 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> >> 0.7144 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> >> 0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> >> 1 2 2 0 0 0 0
> >> 2 3 1 0 0 0 0
> >> 3 4 2 0 0 0 0
> >> 4 5 1 0 0 0 0
> >> 5 6 2 0 0 0 0
> >> 1 6 1 0 0 0 0
> >> M END
> >> '''
> >>
> >> suppl = SDMolSupplier()
> >> suppl.SetData(mol)
> >> fromSD = suppl.next()
> >>
> >> suppl = SmilesMolSupplier()
> >> suppl.SetData('C', titleLine=False)
> >> fromSMILES = suppl.next()
> >>
> >>
> >> Now I want to convert them to SMILES. For the mol from SD, the
> >> identifier is missing:
> >>
> >> sio = StringIO.StringIO()
> >> w = SmilesWriter(sio, delimiter=' ', nameHeader='Name',
> >> includeHeader=True, isomericSmiles=False, kekuleSmiles=False)
> >> w.write(fromSD)
> >> w.flush()
> >> print sio.getvalue()
> >>
> >> >>> SMILES Name
> >> >>> c1ccccc1
> >>
> >> but for mol from SMILES it's fine:
> >>
> >> w.write(fromSMILES)
> >> w.flush()
> >> print sio.getvalue()
> >>
> >> >>> SMILES Name
> >> >>> c1ccccc1
> >> >>> C 1
> >>
> >>
> >> Is that a bug or an expected behavior? Is it possible to get
> >> identifiers for both mols?
> >>
> >>
> >> Kind regards,
> >>
> >> Michał Nowotka
> >>
> >>
> >>
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> >
>
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