v1.1.0

1.1.0 (2025-11-29)

Bug Fixes

• a couple of Condition updates (#59) (a0f173b)
• add a flag to optionally tolerate the situation of missing or multiple representative/center atoms per token (#67) (896ca38)
• add errors for cases where parsing an AtomArrayPlus is problematic (80d00e3)
• add padding for short residue names in sharding (94abca1)
• add raise_if_not_set to get_msa_dirs_from_env (0f50eb2)
• add raise_if_not_set to get_msa_dirs_from_env (c7bfee6)
• add within poly res idx on-the-fly option (c80104b)
• address code review issues in performance PR (9cda94a)
• allow for deleting 2d annotations from AtomArrayPlus (84e0084)
• allow numpy masks in addition to query syntax in SampleSeed (3468645)
• allow override in add global token id transform (381a743)
• apptainer (37fe7a2)
• apptainer (e3bd135)
• apptainer (0647b20)
• apptainer for CI (670a82a)
• bcif tests (378d03a)
• Be more robust to nulls in a3m files. (a8552a4)
• better messages and assertions for removing design tasks with 0 frequency (9b6391d)
• broken tests (1fcc397)
• bug in default seq cond mask (00484d4)
• change default sequence condition behavior (981d924)
• ci for internal (5096b6c)
• ci workers (f7da3cd)
• circular import (7eafda9)
• claude code review (885eb53)
• condition set mask and terminus conditions changes (56f661c)
• correct cache dir structure and add padding for short IDs (b8645fc)
• correct sharding path construction for cached residue data (79d388b)
• databases: correcting uniontype call bug (8a3e59e)
• databases: correcting uniontype call bug (ebc26db)
• datasets documentation, DSSP path (1565a94)
• docstring formatting (ff296d6)
• documentation (1e5b0d4)
• documentation, formatting (dcdde14)
• downgrade biotite (cab5bcf)
• enable deletion of 2d annotations (1f88391)
• enable spawn multiprocessing (36ac421)
• ensure that parse preserves AtomArrayPlus status, and add a test for this (681fdeb)
• ensure that the Index condition's default annotation respects its mask (#50) (e57be2a)
• Formatting (f6fe986)
• general masks in SampleSeed (53df9a6)
• give more informative error messages for ConditionalRoute or RandomRoute failures (3b72b18)
• Handle non-uniform shard sizes in AseDBDataset (e34eb51)
• infer array type of TokenEncoding where possible (#68) (a6a8fb1)
• informative Route error messages (87b1fbc)
• minor fixes (f45fafb)
• minor fixes for encodings (e043104)
• more informative error messages (7861023)
• parse preserves atom array plus (d1eef92)
• parser defaults (570f3ce)
• reduce logging level in load_atom_array_with_conditions_from_cif (#48) (52f316d)
• remove _spoof (995a260)
• remove ambiguous Greek characters and improve test assertions (bad6dff)
• remove ASE import so we dont introduce a dependency (7e12a8a)
• remove design tasks with zero frequency during sampling instead of erroring (4586fa2)
• remove hardcoded environment-specific default path (24bf03f)
• remove lineprofiler stuff (83fb3c5)
• remove print statements (ecd9e5b)
• residue starts bug with dependent functions. (04da354)
• residue starts bug with dependent functions. (fc252a8)
• rf3: json-level atom selection for bonds argument (a569a7c)
• ruff formatting after merge with dev (71ddb86)
• sasa for empty aa (c2b9302)
• shard cache on structure ID (PDB ID) instead of args hash (e5c29fd)
• Support AtomArrayPlus and AtomArrayPlusStack in parse_atom_array, with some restrictions (#46) (c1e3b00)
• test requirements (4c4c775)
• tests (eb10ba6)
• typing (8d6e39d)
• updates for ame (6530818)
• use warnings.warn instead of print for missing ase (b6f9c7a)

Features

• add as_atom_array_plus_stack (804c854)
• add Claude Hode GitHub workflow (0f4e603)
• add customizable annotation names for SSE validity flag (fd6be37)
• add DSSP secondary structure annotation (f1cc785)
• add molprobity executable? (b87f76b)
• add utomatic msa depth and ext determination (874a1dd)
• adding Conditions, annotator, and io utils (b08c935)
• atom37 with atomization encoding (d35be40)
• atomworks MSA preprocessing (generate, filter, organize) (ef6ac85)
• backbone constants and annotators (de5854c)
• databases: add experimental data database functionality from datahub (f69a499)
• databases: add experimental data database functionality from datahub (8b71614)
• generalize encodings (c886d09)
• generalize encodings (83c8684)
• Make SampleDesignTask handle empty design_tasks gracefully (c9e5900)
• misc fixes for design (71decdf)
• MSA preprocessing (organizing, generating, filtering) (89eb73d)
• MSA preprocessing; zst support (aa3c837)
• paired MSA feature (from Rafi) (805a27a)
• paired MSA feature (from Rafi) (2df1511)
• skip for large structures (6f2f33c)
• update to work with transition metals (6f2a80a)

Performance Improvements

• don't actually check symmetry every time on symmetric conditions since there's just too much overhead (6ae656a)
• improve cache loading and template building performance (c144ec7)
• performance optimizations for parsing (e8faf3e)
• precalculate bond graph for GrowByHoppingAlongBondGraph (fd85178)
• res idx (22703bf)
• res idx optimization (11b5d0d)
• speed up 2d symmetrization check and stop actually checking symmetry every time and make some other stuff faster (5c3127b)
• speed up apply_and_spread (ac612a4)
• speed up bond_graph creation (94f0512)