Thank you very much!
On Wed, Apr 22, 2015 at 5:41 AM, Greg Landrum <greg.land...@gmail.com> wrote:
> 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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