alphafold3-pytorch

What's Changed

• Fix return type in cluster_pdb_mmcifs.py by @amorehead in https://github.com/lucidrains/alphafold3-pytorch/pull/83

Full Changelog: https://github.com/lucidrains/alphafold3-pytorch/compare/0.1.125...0.1.126

Full Changelog: https://github.com/lucidrains/alphafold3-pytorch/compare/0.1.124...0.1.125

Full Changelog: https://github.com/lucidrains/alphafold3-pytorch/compare/0.1.123...0.1.124

Full Changelog: https://github.com/lucidrains/alphafold3-pytorch/compare/0.1.122...0.1.123

Full Changelog: https://github.com/lucidrains/alphafold3-pytorch/compare/0.1.121...0.1.122

Full Changelog: https://github.com/lucidrains/alphafold3-pytorch/compare/0.1.120...0.1.121

Full Changelog: https://github.com/lucidrains/alphafold3-pytorch/compare/0.1.118...0.1.120

Full Changelog: https://github.com/lucidrains/alphafold3-pytorch/compare/0.1.117...0.1.118

What's Changed

• Fix a new source of crashes in cluster_pdb_mmcifs.py by @amorehead in https://github.com/lucidrains/alphafold3-pytorch/pull/76
• Upload all SMILES strings contained in the PDB's Chemical Component Dictionary (CCD) by @amorehead in https://github.com/lucidrains/alphafold3-pytorch/pull/75
• Add compact_atom mappings for each molecule type, and add OneDrive PDB dataset download link by @amorehead in https://github.com/lucidrains/alphafold3-pytorch/pull/77
• Ensure all residue constants and atom mappings match ligand residue templates in the PDB by @amorehead in https://github.com/lucidrains/alphafold3-pytorch/pull/78
• Upload all 28 template residue mmCIF files from the PDB, and parse them into Chem.Mols by @amorehead in https://github.com/lucidrains/alphafold3-pytorch/pull/79
• Add standardized (template) SMILES strings for each residue by @amorehead in https://github.com/lucidrains/alphafold3-pytorch/pull/80

Full Changelog: https://github.com/lucidrains/alphafold3-pytorch/compare/0.1.116...0.1.117

What's Changed

• Take a step towards loading, training, and sampling with mmCIF files by @amorehead in https://github.com/lucidrains/alphafold3-pytorch/pull/74

Full Changelog: https://github.com/lucidrains/alphafold3-pytorch/compare/0.1.115...0.1.116

What's Changed

• Default to downloading the PDB from its 20240101 AWS snapshot by @amorehead in https://github.com/lucidrains/alphafold3-pytorch/pull/70
• Add parsing steps described in second paragraph of AF3 supplement Section 2.1 by @amorehead in https://github.com/lucidrains/alphafold3-pytorch/pull/71
• Generalize CovalentBond to Bond to prepare for bond featurization during model training by @amorehead in https://github.com/lucidrains/alphafold3-pytorch/pull/72

Full Changelog: https://github.com/lucidrains/alphafold3-pytorch/compare/0.1.114...0.1.115