Hi Patrik,
On Fri, Nov 26, 2010 at 12:08 PM, <p...@farma.ku.dk> wrote:
> Is there any way to perceive if atoms around a double bond are in cis or
> trans position to each other without generating 2D coordinates?
I do not think reading of \/ or \\ information from SMILES is
currently implemented in the CDK, nor that anyone is working on that.
> Since the information is in the SMILES string I assume this should be
> possible in some way.
Yes, it is merely a fact of lack of resources.
(Seriously, the CDK project needs some source of money, so that we can
hire a programmer to do maintenance stuff, and implementation of
functional additions like this. We have the infrastructure to do this,
but we lack a community who is actively donating money to the project.
(Or contracting support...)
I (and Chris, and others) are working hard on securing funding from
which CDK development can be supported, but there is a role the CDK
community can (and should) play here...)
But, that does not solve your problem...
The hooks for processing the information can be found around line 500
in the SmilesParser:
} else if (mychar == '/' || mychar == '\\') {
logger.warn("Ignoring stereo information for double bond");
position++;
}
But processing this information is non-trivial, due to e.g. ring
closures... interesting use cases have recently be described by Noel:
http://baoilleach.blogspot.com/2010/09/are-you-on-my-side-or-not-its-ez-part.html
I hope this helps,
Egon
--
Dr E.L. Willighagen
Postdoctoral Research Associate
University of Cambridge
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
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