Dear JP,
On Tue, Aug 2, 2011 at 11:36 AM, JP <[email protected]> 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/[email protected]/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
------------------------------------------------------------------------------
BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
The must-attend event for mobile developers. Connect with experts.
Get tools for creating Super Apps. See the latest technologies.
Sessions, hands-on labs, demos & much more. Register early & save!
http://p.sf.net/sfu/rim-blackberry-1
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
