v0.5.2: multiple small improvements

This release accumulates improvements over the past two weeks:

Better CIFs and better output names, bugfix for multiple ligands, lower memory consumption by default, arbitrary number of diffusion samples;

What's Changed

• CLI command to merge a3ms in a directory by @wukevin in #229
• low-memory regime by @arogozhnikov in #172
• Rewrite CIF saving logic by @arogozhnikov in #233
• Handle covalent bond leaving atoms by @wukevin in #234
• SMILES naming fix and associated tests by @wukevin in #236
• Covalent ligand example + bugfix by @wukevin in #244
• Fix cif writing logic for multiple ligands by @wukevin in #247
• Fix colliding ligand entity IDs by @wukevin in #249
• auto-detect same entity for non-ligands by @arogozhnikov in #251
• arbitrary num_diffn_samples + use ds to enumerate diffusion samples by @arogozhnikov in #260
• Update asym chain names to be A, B, C, D, ... by @wukevin in #262

Minor:

• Bump version to 0.5.1 by @jackdent in #223
• Bump version 0.5.1 > 0.5.2 by @wukevin in #243
• reorder commands to have hatch while checking for version by @arogozhnikov in #263
• check version before deployment by @arogozhnikov in #256
• • fix typo by @arogozhnikov in #230

Full Changelog: v0.5.1...v0.5.2

v0.5.1: fixes for glycan parsing

What's Changed

• Minor fixes to glycan parsing by @wukevin in #219
• Additional fixes for glycans by @wukevin in #221

(tag and release were updated because previous did not deploy correctly to pypi)

Full Changelog: v0.5.0...v0.5.1

v0.5.0: Covalent bonds, glycans, and improved MSA pairing

What's Changed

Major changes

• Support for specifying covalent bonds and glycans by @wukevin in #205
• Improve colabfold MSAs to include unpaired MSA hits by @wukevin in #213

Minor changes

• Don't warn on missing MSAs for non-protein entities. by @wukevin in #209
• Helper to sort StructureCandidates object by @wukevin in #208
• Fix case where empty list is passed to colabfold MSA generation by @wukevin in #212
• Add test for ion charge by @wukevin in #214

Full Changelog: v0.4.4...v0.5.0

v0.4.4: Update command line interface

What's Changed

Major

• Add CLI option to set colabfold server url by @danpf in #199. N.B. this is a breaking change to CLI: the msa_server command line argument has been renamed to use_msa_server

Minor

• Sleeping messages should be info, not error by @wukevin in #198
• Update CLI docs by @jackdent in #197

New Contributors

• @danpf made their first contribution in #199

Full Changelog: v0.4.3...v0.4.4

v0.4.3: Command line interface

What's Changed

Major

• Easy command line interface by @wukevin in #190

Minor

• Update LICENSE link in README by @jackdent in #188
• Cleanup cif code; properly write ligands as HETATM by @wukevin in #189
• Clarify license by @jackdent in #193

Full Changelog: v0.4.2...v0.4.3

v0.4.2: Apache 2.0 license (commercial use)

Corrects license file in project root

What's Changed

• Update LICENSE.md by @joshim5 in #186
• Move LICENSE and bump version by @jackdent in #187

Full Changelog: v0.4.1...v0.4.2

v0.4.1: Apache 2.0 license (commercial use)

Re-release of release v0.4.0 with one bug fix

What's Changed

• Fix case for homomers resulting in errors by @wukevin in #183

Full Changelog: v0.4.0...v0.4.1

v0.4.0: Apache 2.0 license (commercial use)

What's Changed

Major changes

• Update license to Apache 2.0 by @jackdent in #179
• Example MSA generation script by @jackdent in #181

Minor changes

• Use Python 3.10 in development by @jackdent in #167

Full Changelog: v0.3.1...v0.4.0

v0.3.1: Python 3.10.0 compatibility

What's Changed

• Update README.md with link to restraints documentation by @joshim5 in #158
• Fix assert_never import for Python 3.10 by @jackdent in #163
• Bump version to 0.3.1 by @jackdent in #165

New Contributors

• @joshim5 made their first contribution in #158

Full Changelog: v0.3.0...v0.3.1

v0.3.0: Chai-1r - support for restraints

What's Changed

We provide tools to prompt the model with prior structural information

PRs:

• Support for user-specified restraints by @wukevin in #148
• Specify restraints with 1-based indexing for residues by @wukevin in #154
• Updates for restraints documentation by @wukevin in #156

Full Changelog: v0.2.1...v0.3.0