I like the idea of multiple CONECT with bond orders.
I second David van der Spoel's analysis: if we don't know about any major
programs that would fail/crash, with multiple CONECT per bond, then we should
go for it.
Even if that's the case, though, it could be easily addressed by having a flag
that disables the feature for sake of compatibility with the PDB standard
('strict=true', or something).
S
On 7/29/19 1:11 PM, Geoffrey Hutchison wrote:
> David Koes has contributed a pull request that fixes a bunch of file handling
> errors via round-trip testing.
>
> One thing he's implemented is to bring back writing PDB files with multiple
> bond orders via repeated CONECT records.
>
> Before I consider the rest of the patch, I want to know opinions on this.
> It's been a few years since OB reverted to "standard" PDB output and omitted
> only one CONECT per bond connection. This matches the practice of the PDB
> itself, although the "bond order" practice is fairly wide-spread.
>
> David feels strongly that OB should default to write files with bond order
> information.
>
> I can't find the threads of previous discussion, which suggests some of it
> was in the SourceForge bug tracker - I can't find anything pro or con from
> that discussion, only that it was eventually decided to stick with one CONECT
> per bond.
> - Do you favor single CONECT records?
> - Do you favor bond order information?
> - What do you feel are pro or cons?
>
> I'd like an open discussion. If it's possible, I know many people expect PDB
> files to support bond orders.
>
> -Geoff
>
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>
--
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: [email protected]
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