Den 2019-07-29 kl. 22:11, skrev Geoffrey Hutchison:
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.
What would be the drawback? Will other programs crash when they read a
pdb file where the same CONECT is stated twice?
I would love to have accurate bond orders in .sdf files (and also
location of charged groups) but do not know what the status is. I
mention these things since last time I checked (4 years ago) determining
border was not very accurate (10% error rate).
-Geoff
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