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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