Pdb Loading Fix #666
Merged
Pdb Loading Fix #666
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Previously, an error would be raised when attempting to find bonds in a PDB file that lacked bond information and contained multiple chain identifiers. Now, the atoms are first loaded and then connected.
|
Thanks for this! Are you able to add a test case with some example data that would fail on the old method but now succeeds with this fix? |
|
No problem. I just added a new test that loads a pdb called "no_bonds.pdb" very similar to the one I posted on #658 and checks the position and bond types (which are none). When executing it without the fix the test fails. |
|
I tweaked it to add back in the attempt to import with bond information. People like to abuse the heck out of the PDB format, so they could have all sorts of weird and wonderful bond information. I'd rather try and get the bonds first, then if that fails fall back on finding via residue names. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Previously, an error would be raised when attempting to find bonds in a PDB file that lacked bond information and contained multiple chain identifiers. Now, the atoms are first loaded and then connected. This is mainly an issue about how biotite handles getting the structure from the pdb.
More information can be found on #658.