Re: [Open Babel] PDB files with multiple bonds via CONECT

2019-07-31 Thread David Koes
Thanks Geoff - I've been meaning to write to the list about this, but haven't made the time. But I'll make the time now since there are other facets of this pull request that deserve discussion. My goal in putting the pull request together was to make it so that openbabel doesn't break molecule

Re: [Open Babel] PDB files with multiple bonds via CONECT

2019-07-30 Thread Geoffrey Hutchison
> Just a note: PDB has stopped accepting X-ray structures in .pdb format a > while back, and is going to stop accepting .pdb NMR structures soon. I.e. > what you are discussing is a dead format essentially. Sadly, as far as users are concerned PDB has become an informal interchange format, so i

Re: [Open Babel] PDB files with multiple bonds via CONECT

2019-07-30 Thread Dimitri Maziuk via OpenBabel-discuss
On 7/29/2019 4:53 PM, Stefano Forli wrote: ... PDB files ... Just a note: PDB has stopped accepting X-ray structures in .pdb format a while back, and is going to stop accepting .pdb NMR structures soon. I.e. what you are discussing is a dead format essentially. Dima ___

Re: [Open Babel] PDB files with multiple bonds via CONECT

2019-07-29 Thread Stefano Forli
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