cdk-jchempaint

[Cdk-jchempaint] Internal consistency of molecule IDs

[James <jea...@gm...>]

I've noticed when using latest JChemPaint that when processing reactions 
into CML that there is a situation where the ID strings assigned to the 
individual entities are not comparable within a scheme due to the random 
element of the generation. I notice that there is an IDCreator available 
that can provide more consistent forms which I'm using now, but wondered 
if this was something that would be considered for taking upstream (I 
have unified diffs here, one for the CDK library to change the ID 
creator, and one for JChemPaint itself that adds IDCreator support to 
the labelling.

Re: [Cdk-jchempaint] Internal consistency of molecule IDs

[Egon W. <ego...@gm...>]

On Fri, Feb 3, 2012 at 2:36 PM, James <jea...@gm...> wrote:
> I've noticed when using latest JChemPaint that when processing reactions
> into CML that there is a situation where the ID strings assigned to the
> individual entities are not comparable within a scheme due to the random
> element of the generation. I notice that there is an IDCreator available
> that can provide more consistent forms which I'm using now, but wondered
> if this was something that would be considered for taking upstream (I
> have unified diffs here, one for the CDK library to change the ID
> creator, and one for JChemPaint itself that adds IDCreator support to
> the labelling.

The 'normal' way is to make git patches... which I can do for you, if
you provide a full name and email address, and a commit message...
this patch would be then be proposed for review...

I sounds interesting, in fact, and I'm happy people are using the IDCreator :)

Mapping molecules, atoms, bonds in reactions is not always easy, and
the SMSD corner works in this area too... I'm looking forward to the
code changes you suggest!

Egon


-- 
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers