This is read in from a PDB file containing a normal PRO residue extracted from
a larger protein. Going through the bond list iterator ?produces this:
---BONDS---
CA --- N
N --- CD
CD --- HD2
CD --- HD3
CB --- CG
HG3--- CG
CG --- HG2
HB3--- CB
CA --- CB
CB --- HB2
HA --- CA
CA --- C
C --- O ?
________________________________
From: Geoffrey Hutchison <geoff.hutchi...@gmail.com>
Sent: Thursday, January 19, 2017 7:56 PM
To: Browning Nicholas John
Cc: OpenBabel-Devel@lists.sourceforge.net
Subject: Re: [OpenBabel-Devel] Proline Bond Lists
Sorry, small error in the loop variable labels. Here is the correct version:
I think my bigger question is "how are you getting here?" That is, are you
reading a PDB file and the bonds aren't created correctly? Or are you reading
in an XYZ file and perhaps bond perception and residue perception gets confused?
I can see you have workaround code, but it's not clear what the state of the
molecule is prior to your problem. Normally bonds in residues are assigned
through data/resdata.txt which does have the CD-CG bond:
RES PRO
ATOM CA C3 3
...
BOND CD CG 1
...
Thanks,
-Geoff
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