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
>
>
> ------------------------------------------------------------------------------
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live
> exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
> event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
