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 <[email protected]> wrote: > 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
