Den 2018-06-15 kl. 01:20, skrev Geoffrey Hutchison:
Hi,
One of the GSoC projects this summer is an improved fragment-based coordinate
generation method. While that's going, I've been reading a lot of papers on 3D
coordinate generation.
As near as I can tell, no other program attempts to do a conformer search as
part of the 3D generation. Everyone just generates one 3D geometry and then
lets people do conformer searching on top if they choose.
Some of the papers (e.g. Pierre Baldi) compare to Open Babel and then say that
babel is slow - but that's because a lot more work is performed.
I'd like to change --gen3d to default to creating a geometry. Optionally,
geometry optimization can be performed, but the conformer searching will be
separate:
--gen3d # default: will only create a geometry
--gen3d=opt # will perform MMFF or UFF optimization on the geometry
I think for many uses, this will provide much faster performance.
From your description above it is the conformer searching that makes it
slow, so why not make that optional rather than the optimization?
In addition it would be nice if the 3D generation would not crash every
once in a while (at least it does in Avogadro). I guess due to numerical
issues.
Thoughts? Concerns?
-Geoff
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