fix: prevent chain_ids in outer scope from being overridden by loop (#13)

* docs and chore: add examples and consolidate constants (#5)

* clean: remove legacy dependencies, relax various dependency versions, update CI  (#4)

* clean: remove `fire` and `fastparquet` legacy dependencies, relax `biotite`, `hydrid`, `torch` and `einops` versions
* ci: update github actions trigger `digs` workflow manually only.

* clean: clean-up CI (#6)

* ci: restrict workflow permissions (#8)

* clean: clean-up CI

* ci: restrict workflow permissions

* refactor: disentangle CLI form package code and document PDB training example

* refactor: disentangle CLI from package code

* docs: update readme with PDB training example

* docs: further documentation improvements

* Build/numpy version (#10)

* refactor: disentangle CLI from package code

* docs: update readme with PDB training example

* docs: further documentation improvements

* build: enable numpy 2.x, pandas 2.3

* chore: ruff

* docs: fix readme (#11)

* refactor: consolidate `constants` and `common` (#7)

Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com>

* docs: initial examples (#12)

* docs: load and visualize structures

* chore: format

* docs: update README

* docs(readme): improve code block formatting

* docs(readme): fix typos

* Change TOC depth

Just changed the TOC depth from 1 to 2 in the conf.py file to test the GitHub actions workflow.

* Update README.md

Updated the link to the external docs to remove 404 error.

* Update README.md

Changed the documentation link in the contribution section.

* docs(readme): add notice

* clean: remove legacy dependencies, relax various dependency versions, update CI  (#4)

* clean: remove `fire` and `fastparquet` legacy dependencies, relax `biotite`, `hydrid`, `torch` and `einops` versions
* ci: update github actions trigger `digs` workflow manually only.

* clean: clean-up CI (#6)

* ci: restrict workflow permissions (#8)

* clean: clean-up CI

* ci: restrict workflow permissions

* refactor: disentangle CLI form package code and document PDB training example

* refactor: disentangle CLI from package code

* docs: update readme with PDB training example

* docs: further documentation improvements

* Build/numpy version (#10)

* refactor: disentangle CLI from package code

* docs: update readme with PDB training example

* docs: further documentation improvements

* build: enable numpy 2.x, pandas 2.3

* chore: ruff

* docs: fix readme (#11)

* docs: two additional examples for the gallery

---------

Co-authored-by: Nathaniel Corley <nscorley@Nathaniels-MacBook-Pro.local>
Co-authored-by: Buddha7771 <hwlee7771@gmail.com>
Co-authored-by: Rachel Clune <rclune4b@gmail.com>
Co-authored-by: Rachel Clune <rachel.clune@omsf.io>
Co-authored-by: Simon Mathis <simon.mathis@gmail.com>
Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com>

---------

Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com>
Co-authored-by: Nathaniel Corley <nscorley@gmail.com>
Co-authored-by: Nathaniel Corley <nscorley@Nathaniels-MacBook-Pro.local>
Co-authored-by: Buddha7771 <hwlee7771@gmail.com>
Co-authored-by: Rachel Clune <rclune4b@gmail.com>
Co-authored-by: Rachel Clune <rachel.clune@omsf.io>

* fix: prevent chain_ids in outer scope from being overridden by loop

---------

Co-authored-by: Simon Mathis <simon.mathis@gmail.com>
Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com>
Co-authored-by: Nathaniel Corley <nscorley@gmail.com>
Co-authored-by: Nathaniel Corley <nscorley@Nathaniels-MacBook-Pro.local>
Co-authored-by: Buddha7771 <hwlee7771@gmail.com>
Co-authored-by: Rachel Clune <rclune4b@gmail.com>
Co-authored-by: Rachel Clune <rachel.clune@omsf.io>

Author: 7 people

src/atomworks/io/utils/io_utils.py

@@ -421,7 +421,7 @@ def _build_entity_poly(
     entity_poly = {cat: [] for cat in _entity_poly_categories}
     for entity_id in unique_polymer_entity_ids:
         # ... get all relevant chain ids
-        chain_ids = np.unique(chain_ids[entity_ids == entity_id])
+        example_chain_ids = np.unique(chain_ids[entity_ids == entity_id])
 
         # ... get chain type
         chain_type = ChainType.as_enum(chain_types[entity_ids == entity_id][0])
@@ -450,7 +450,7 @@ def _build_entity_poly(
         entity_poly["nstd_monomer"].append("yes" if has_non_standard_monomer else "no")
         entity_poly["pdbx_seq_one_letter_code"].append(processed_entity_non_canonical_sequence)
         entity_poly["pdbx_seq_one_letter_code_can"].append(processed_entity_canonical_sequence)
-        entity_poly["pdbx_strand_id"].append(",".join(chain_ids))
+        entity_poly["pdbx_strand_id"].append(",".join(example_chain_ids))
         entity_poly["pdbx_target_identifier"].append("?")
     return {"entity_poly": entity_poly}