v1.0.2

1.0.2 (2025-09-18)

Bug Fixes

• update homepage and documentation URLs in pyproject.toml (4591c98)

v1.0.1

Includes:

• Bug fixes to support RF3 inference
• More complex AtomSelection syntax
• Refactoring of datasets

Migration notes:

• We have moved some of the ml.common and io.common into a single common file
• StructuralDatasetWrapper now requires a name attribute; however, we are deprecating StructuralDatasetWrapper in favor of a simple PandasDataset or equivalent and will remove the class entirely in a later release

v1.0.0

1.0.0 (2025-08-18)

• BREAKING CHANGE: update to cifutils 2.0 (#50) (77dd6fd)

Bug Fixes

• 3to1 (ab6b4b2)
• adapt naming of regression tests to match new names (c44b387)
• add 'overwrite' option to view_pymol to avoid updating existing structures (#64) (ac0f12d)
• add make to apptainer (7cba23e)
• add back readme (#1) (831bc23)
• add back stacking msas by recycle (#2) (fbe0c32)
• add conda init (2e0a0c2)
• add current data to fail log for ease of analysis (da4bdf7)
• add links to the ccd & pdb mirrors (430ae71)
• add missing default (4f020cf)
• add missing test files for local test (68f2e0a)
• add missing transforms in AF3 pipeline (39a465d)
• add new logo and changes of urls to public url (b753e57)
• add test (80b6113)
• add test cases (11dbb61)
• add test coverage bit (57166f5)
• add testpypi setup: (7ded1bf)
• add tests for fix_formal_charge, ruff (0a4072d)
• adding badges (4588955)
• address minor pipeline issues in af3 (3943cd7)
• adjust error type on transform history tracking (a468233)
• af3 parsing (#130) (37c6791)
• allow remove_unsupported_chain_types to work without specified query_pn_unit_iids. Implement functional API while we're at it. (126b846)
• allow AddRFTemplates to proceed when no pdb_id given (c63f10e)
• Allow compatibility with newer rdkit version. (#122) (e6ecbac)
• allow more general covalent bonds (1ef9858)
• allow parsing entries with multiple methods (e.g. 5e5j) (28ad455)
• allow passing on boolean annotations, allowing distogram bins to be a list (9253102)
• allow processing to continue in the case of covalent bonds between... (88036e4)
• allow saving of failed examples to error, default to a user-based failures path on scratch (c3160de)
• allow unknown users for CI (fa14dda)
• apptainer creation to expose /net (24b8be4)
• apptainer spec (a0c3294)
• arg_fixing: swap coordinates of nh1/nh2 instead of renaming when resolving ARG naming ambiguity, since otherwise charges & bond order are inconsistent (NH2 carries positive charge & double bond by convention) (#41) (8d4b0a6)
• argument error (9c5daba)
• atom level embeddings (#159) (ebaaf51)
• automorphisms (#36) (7cd6ad2)
• avoid building covalent bonds with water or crystallization aids (951a12c)
• bad ligands, new test dataset (0234fab)
• bonds (#125) (2b1a714)
• bug fixes for inference (#46) (e5254d9)
• bug in initializing chain info (7c89186)
• bugfix when using get_residue_starts and general annot_start_stop_idxs, which incorrectly used len() instead of .array_length() to determine the size of an AtomArrayStack (#65) (9b2cc83)
• Bugfixes in get_within_group_res_idx and get_within_poly_res_idx (#121) (4955d19)
• bugs in tests (6b72a3f)
• bugs in using MSAs for inference, supporting MSAs with # headers (f7c2c44)
• build apptainer (ce3c4d6)
• build assembly arguments (905e6b9)
• by default cast aromatic bonds to same order when comparing atom arrays for graph hashes (4587d10)
• cached conformers with chirals (#149) (cec9f83)
• calculate rf2aa chirals off af3 centers (so they are correct) (#114) (64bfca9)
• categories: keep residues not in the CCD instead of converting to UNL (#47) (6a9b0a1)
• chain type miss (0099133)
• chain_id to _iid in Frank's hotfix (9fe6186)
• chains with all resolved tokens (886ffc3)
• changing chain_iid to pn_unit_iid in AF3 features (181467e)
• changing inference ligand residue names to use non-conflicting characters (641f1e6)
• charges (d730b8a)
• chirals ([#105](https://github.com/R...