Re: [Cdk-devel] partial 2D coordinate generation

[Christoph S. <c.s...@un...>]

The StructureDiagramGenerator gradually builds coordinates by first=20
laying out ring systems and then doing chain by chain with decreasing=20
length.
There are a couple of methods to do those single tasks and it should be=20
possible already to perform a lot of the layouts for fragments added to=20
an existing system.
A writeup on how to do these things would be nice of course and I guess=20
that would be my task.
We should start with a couple of explicit problems (start with=20
constitution X with coordinates and added fragment Y and Z, then do the=20
layout). Then we could see how to automate this stuff.

Cheers,

Chris

--=20
Dr. Christoph Steinbeck (e-mail: c.s...@un...)
Groupleader Junior Research Group for Applied Bioinformatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..


Peter Murray-Rust wrote:
> At 18:09 18/07/2003 +0200, E.L. Willighagen (Egon) wrote:
>=20
>> > I assume that what you want is to clean up a structure in which an=20
>> author
>> > has added or moved some atoms. That doesn't seem to be completely
>> > automatic.
>>
>> Right. What I actually want is this: JCP now has to option to add=20
>> hydrogens,
>> and but the now get the 2D coordinates of the atom to which they are=20
>> added.
>> Only for the new H atoms, I want to calculate 2D coordinates...
>=20
>=20
> That should be straightforward. I'm busy this week but if you look at=20
> the 3D H generator I posted to CDK that should be easily tweaked to do=20
> 2D - there are fewer options and they should be easier.
>=20
>> > If the new atoms are in a substituent then that could be laid out
>> > separately and oriented/joined on the current 2D vector.
>>
>> Haven't thought of that... just making a new AtomContainer with the ne=
w
>> atoms, and then do a layout...
>=20
>=20
> That would be worth doing.
>=20
>> > That would be
>> > relatively easy though might overlap with current structure. If the =
new
>> > atoms alter a ring nucleus then I can't see an alternative to=20
>> recomputing
>> > the whole nucleus and probably the whole structure. As a simple=20
>> example,
>> > join the 1,6 atoms of cyclodecane with a 1 atom bridge. Do you just=20
>> want to
>> > layout the bridge?
>>
>> Maybe... a future option I want to add to JCP too, is the relayout of =
the
>> selected atoms... and that might involve a situation like to one you=20
>> gave as
>> an example...
>=20
>=20
> I would restrict it to chains and complete ring nuclei - then it will b=
e=20
> fairly simple and robust. It will also be useful if you ever have to=20
> expand (say) Bz to a methylene and a benzene ring.