Re: [Rdkit-discuss] FeatureRequest: Properties of Mol to be written out to SDF by SDWriter

[JP <jea...@in...>]

Thanks Greg for this -- I must be doing something silly in my code
because your example works fine...
I'll have a look.

<:( - embarrassed>

Jean-Paul Ebejer
Early Stage Researcher




On 2 August 2011 16:33, Greg Landrum <gre...@gm...> wrote:
> Dear JP,
>
> On Tue, Aug 2, 2011 at 11:36 AM, JP <jea...@in...> wrote:
>> I would just like to re-iterate how useful and nice (and expected
>> behaviour)  it would be if when I have a mol instance with properties
>> (which I painstakingly computed) and the .write() method in SDWriter
>> actually writes them to file.
>> I know there is a SetProps method ... but why do I have to do this
>> everytime?  Can it be a default? Or an optional parameter in the
>> SDWriter constructor e.g. "writeProps=True" ?
>
> By default an SDWriter should write out all properties of a molecule
> that have not been flagged as "computed" when you call mol.SetProp().
> Here's an example:
>
> [1]>>> from rdkit import Chem
>
> [2]>>> m = Chem.MolFromSmiles('c1ccccc1')
>
> [3]>>> m.SetProp('_Name','benzene')
>
> [4]>>> m.SetProp('Prop1','4')
>
> [9]>>> m2 = Chem.MolFromSmiles('c1ccccc1C')
>
> [10]>>> m2.SetProp('_Name','toluene')
>
> [11]>>> m2.SetProp('Prop2','5')
>
> [12]>>> w = Chem.SDWriter('test.sdf')
>
> [13]>>> w.write(m)
>
> [14]>>> w.write(m2)
>
> [15]>>> w.close()
>
> [16]>>> !cat test.sdf
> benzene
>     RDKit
>
>  6  6  0  0  0  0  0  0  0  0999 V2000
>    0.0000    0.0000    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    0.0000    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    0.0000    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
>  1  2  2  0
>  2  3  1  0
>  3  4  2  0
>  4  5  1  0
>  5  6  2  0
>  6  1  1  0
> M  END
>>  <Prop1>  (1)
> 4
>
> $$$$
> toluene
>     RDKit
>
>  7  7  0  0  0  0  0  0  0  0999 V2000
>    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>  1  2  2  0
>  2  3  1  0
>  3  4  2  0
>  4  5  1  0
>  5  6  2  0
>  6  7  1  0
>  6  1  1  0
> M  END
>>  <Prop2>  (2)
> 5
>
> $$$$
>
> [17]>>>
>
> If you're seeing different behavior, and you are using SetProp without
> the optional third argument set to True, then I'd love to see some
> sample code, because it's a bug.
>
>> Related discussion:
>> http://www.mail-archive.com/rdk...@li.../msg01712.html
>
> That was a different request: the question was how to write a
> compressed SD file from the RDKit without first generating a standard
> SD file.
>
> -greg
>