That's where I was looking at, but I wasn't sure.
I think the all-axial groups are the result of trying to configure as many bonds as trans
as possible.
I've fiddled with RdKit for a while, and their geometry building method is extremely fast,
thanks to all the lookup they do, I guess.
By looking at the current code, it seems implementing the new DG method wouldn't be
incompatible with the perception of higher-order bond geometries.
Although, following up on the old discussion started by Noel, I'm suspecting that specific
section of the code could benefit by being rewritten to use SMARTS (i.e., generic
topologies of 5-bonded atoms), and remove all the "if" statements.
Thanks for the reply, Geoff.
S
On 07/26/2017 01:57 PM, Geoffrey Hutchison wrote:
I've tried looking into it to propose a possible solution, but I couldn't pin
exactly
where this happens in the code.
...
I suspect the problem might be in builder.cpp, where the math for the bond
angles is
computed, but where exactly I have no idea.
It's most likely here in GetNewBondVector()
https://github.com/openbabel/openbabel/blob/master/src/builder.cpp#L150
I suspect that the code that attempts to place alkyl chains correctly is the
culprit -
can't find the exact line.
I've been playing with the DG and knowledge-based DG methods in RDKit more and
would love
to have an OB equivalent. Greg's code is definitely better for 3D structure
generation of
organics. (Not sure if they've handled all the square planar, octahedral, etc.
cases that
are in OB, though.)
-Geoff
--
Stefano Forli, PhD
Assistant Professor
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
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