Topology.from_openmm raises informative error if origin PDB lacks CONECT #357
Conversation
j-wags
commented
Jun 14, 2019
•
j-wags
commented
- Fixes Provide more useful error message if topology.from_openmm has connectivity problems #356
- Adds test to ensure informative error is thrown
j-wags
changed the title
openforcefield/topology/topology.py
Outdated
| msg += 'This would be a very unusual molecule to try and parameterize, ' \ | ||
| 'and it is likely that the data source it was read from does not ' \ | ||
| 'contain connectivity information. If this molecule is coming from ' \ | ||
| 'PDB, please ensure that the file contains CONECT lines.' |
There was a problem hiding this comment.
They're called CONECT "records" or "cards", I believe.
We might also cite the PDB format: https://www.wwpdb.org/documentation/file-format-content/format33/sect10.html
The important part of the PDB format is:
CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table.
That's the key here.
There was a problem hiding this comment.
Added link to the PDB spec. Happy to do my part in the war for the PDB file format :-)
There was a problem hiding this comment.
Also changed wording to "CONECT records"
Codecov Report
@@ Coverage Diff @@
## master #357 +/- ##
==========================================
+ Coverage 75.95% 75.97% +0.01%
==========================================
Files 17 17
Lines 5431 5435 +4
==========================================
+ Hits 4125 4129 +4
Misses 1306 1306
Continue to review full report at Codecov.
|
