ExcitedStates/qfit-3.0: 2024.3

What's Changed

The main change for this version is an improvement in ligand multiconformer modeling. Additionally, we have some code improvements in protein.

• Allow qFit to run with multiple backbone inputs by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/382
• add find_close_residues.py to setup.py by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/396
• fix argparse error in qfit_ligand.py by @jessicaflowers in https://github.com/ExcitedStates/qfit-3.0/pull/398
• 404 qfit residue is missing by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/407
• update for CVXPY citation by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/408
• Add p flag by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/409
• Add em to README.md example by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/411
• re-implementing conda & M1 instructions by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/412
• Add calc rscc to setup.py by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/413
• update default labels by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/417
• split QP into 3000 conformers by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/419
• update to be compatible with mac os for tests by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/422
• re-write em refinement by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/418
• Update README.md by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/421
• install using enviornment.yml by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/423
• Fix Complete Residue by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/424
• update order of readme by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/425
• Implement maxpool sampling by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/420
• Update em example by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/430
• Use deposited conformers if clashes by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/429
• set ci to use macos-13 by @dhogan-io in https://github.com/ExcitedStates/qfit-3.0/pull/431
• Edit test to fix macOS issues by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/427
• New qfit ligand by @jessicaflowers in https://github.com/ExcitedStates/qfit-3.0/pull/426
• Update ligand test by @jessicaflowers in https://github.com/ExcitedStates/qfit-3.0/pull/432
• Ligand additions by @jessicaflowers in https://github.com/ExcitedStates/qfit-3.0/pull/452
• formatting README by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/454
• Replacing 3K0N as the example, adding 1G8A by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/457
• Edit _zero_out_most_similar_conformer() to add the optional ability to add the occupancy of the conformer by @jessicaflowers in https://github.com/ExcitedStates/qfit-3.0/pull/459
• Update Refinement Phenix 2024 by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/458
• update ligand refine to remove low occ conformers by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/460
• Update lig_occ.py by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/461
• Maxpool fix by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/462
• remove duplicate rotamer sampling by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/463
• Restraint creation file in loop by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/466
• change qfit protein test by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/464
• add to ligand examples folder and scripts README by @jessicaflowers in https://github.com/ExcitedStates/qfit-3.0/pull/467
• correct comp omit for ligand by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/469
• Add bdc scaling for PanDDA models into ligand final refine script by @jessicaflowers in https://github.com/ExcitedStates/qfit-3.0/pull/471
• blackening all files by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/472
• fix calc_coord function by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/473
• Creating qFit version 2024.3 by @stephaniewankowicz in https://github.com/ExcitedStates/qfit-3.0/pull/475

Full Changelog: https://github.com/ExcitedStates/qfit-3.0/compare/2024.2...2024.3