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added 17 commits
February 4, 2026 17:36
…ar to protenix, so not necessary
…flag, and remove abc_config script as this supercedes it
… using mmseqs2, also hopefully have added a fix to the issue in ipsae scoring
… added alphapulldown option to ipsae for shah
…ound ipsae and edited how it's displayed on the output page
added 4 commits
February 27, 2026 15:31
…p for chai and changed use_paired option from OF3 as it was breaking things
hllelli2
reviewed
Mar 6, 2026
| msa = None | ||
| for sequence in json_dict['sequences']: | ||
| protein = sequence.get("protein") | ||
| if protein is not None: |
Collaborator
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I like not nesting too much for readability. Instead of if protein is not None: You can instead do
if protein is None:
continue
Rest of code
This reduces nesting.
Collaborator
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I didn't realise this was
markdown
- --rest of code--
hllelli2
reviewed
Mar 6, 2026
| return yaml_string | ||
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| def add_key_and_value(self, key: str, value: str): | ||
| def add_key_and_value(self, key: str, value): |
Collaborator
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Why was the typing removed from here?
Author
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the value isn't always a string, so it was breaking for bonded pairs iirc
Could potentially replace with Union[str, bool]
hllelli2
reviewed
Mar 6, 2026
| except ValueError: | ||
| logger.error("ValueError when calculating ipSAE score, bypassing ipSAE") | ||
| pass | ||
| ipsae = Ipsae(model, pae_obj) |
hllelli2
reviewed
Mar 6, 2026
| for seed in self.seeds | ||
| } | ||
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| def update_chain_labels(self, cif_file) -> CifFile: |
Collaborator
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Looking good. I think we should add mypy with type-checking to ensure we have all our type-hints in order. Also, what's your local test coverage getting. we have 67% in actions but we don't run the programs here. |
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Updated a few aspects of ABCFold, most notably: