Allow restraints w.r.t. entity name-based subchains; fix parsing with empty comments#379
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Allow restraints w.r.t. entity name-based subchains; fix parsing with empty comments#379
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wukevin
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Pull Request Overview
This PR enables using entity names as subchain identifiers for restraints and fixes handling of empty comment fields during restraint parsing.
- Introduces
entity_name_as_subchainflag throughout raw input loading, chain creation, and feature context pipelines - Updates
_parse_rowto default empty comments to""instead ofNaN - Adds tests covering manual chain naming and subchain ID assignment
Reviewed Changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| tests/test_restraints.py | Expanded imports and added test_restraints_with_manual_chain_names to verify restraint loading |
| tests/test_inference_dataset.py | Added test_entity_names_as_subchain to check subchain IDs with/without entity_name_as_subchain |
| chai_lab/data/parsing/restraints.py | Changed parsing in _parse_row to map NaN comments to empty strings |
| chai_lab/data/dataset/inference_dataset.py | Added entity_name_as_subchain parameter to raw_inputs_to_entitites_data and load_chains_from_raw |
| chai_lab/chai1.py | Propagated entity_name_as_subchain flag into make_all_atom_feature_context and chain loading |
Comments suppressed due to low confidence (4)
chai_lab/data/dataset/inference_dataset.py:94
- Update the docstring to document the new
entity_name_as_subchainparameter and its effect onsource_pdb_chain_idandsubchain_id.
def raw_inputs_to_entitites_data(
chai_lab/data/dataset/inference_dataset.py:180
- Extend the docstring to explain the
entity_name_as_subchainflag and how it alters chain IDs when loading raw inputs.
def load_chains_from_raw(
chai_lab/chai1.py:339
- Add documentation for the new
entity_name_as_subchainargument in the function signature, describing its behavior.
def make_all_atom_feature_context(
tests/test_restraints.py:44
- Add a unit test to verify that
parse_pairwise_tablecorrectly setscommentto an empty string when the CSV comment cell isNaN.
def test_restraints_with_manual_chain_names(entity_name_as_subchain: bool):
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Description
Allow restraints to be specified w.r.t. fasta-based chain naming.
Motivation
Like in #378 this allows for more consistent and predictable chain naming behavior, streamlining post hoc analysis.
Test plan
Added tests to ensure that fasta and restraint parsing have expected compatibility combinations (e.g., if they are mismatched they shouldn't load, if they are matched they should load).