HADDOCK3 - modular integrative modelling software

Haddock3 v.2025.8.0 - Hot summer stable release

What's Changed

• adding random removal in haddock3-restraint cli by @VGPReys in https://github.com/haddocking/haddock3/pull/1232
• correction to alascan mutants by @mgiulini in https://github.com/haddocking/haddock3/pull/1275
• Update README with url to user manual by @VGPReys in https://github.com/haddocking/haddock3/pull/1278
• fix path to access matrix in tests cli re clustrmsd by @VGPReys in https://github.com/haddocking/haddock3/pull/1280
• Bump plotly from 6.0.1 to 6.1.2 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1287
• Bump pytest-mock from 3.14.0 to 3.14.1 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1285
• Bump coverage from 7.8.0 to 7.8.2 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1286
• Bump hypothesis from 6.131.9 to 6.132.0 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1284
• Selection of Nter, Cter and 5'end states at topology generation by @VGPReys in https://github.com/haddocking/haddock3/pull/1273
• Update CHANGELOG.md by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1295
• Added support for pyroglutamic acid - issue #1228 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1290
• make deepcopy of molecule params so they can be used multiple times by @VGPReys in https://github.com/haddocking/haddock3/pull/1297
• fix url to user manual in readme by @VGPReys in https://github.com/haddocking/haddock3/pull/1303
• Restrain ligand by @VGPReys in https://github.com/haddocking/haddock3/pull/1301
• update readme with link to publication by @VGPReys in https://github.com/haddocking/haddock3/pull/1306
• adding citruline parameters/topology definition by @VGPReys in https://github.com/haddocking/haddock3/pull/1304
• add permissions to actions by @rvhonorato in https://github.com/haddocking/haddock3/pull/1308
• Added separate mpi install option by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1294
• Bump hypothesis from 6.133.2 to 6.135.20 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1311
• Bump coverage from 7.8.2 to 7.9.1 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1313
• Bump pytest-cov from 6.1.1 to 6.2.1 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1310
• Bump plotly from 6.1.2 to 6.2.0 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1314
• Bump mpi4py from 4.0.3 to 4.1.0 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1312
• Fix restrain lig test by @VGPReys in https://github.com/haddocking/haddock3/pull/1316
• Alascan parallel tests by @AnnaKravchenko in https://github.com/haddocking/haddock3/pull/1322
• Implements feature #1323 - adding bonded energies to the PDB headers by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1330
• allow zero steps of energy minimization by @sjdv1982 in https://github.com/haddocking/haddock3/pull/1331
• computing std dev in alascan by @VGPReys in https://github.com/haddocking/haddock3/pull/1334
• version incrementation by @VGPReys in https://github.com/haddocking/haddock3/pull/1335
• Per-residue parallelization in alasan by @AnnaKravchenko in https://github.com/haddocking/haddock3/pull/1317
• Bump pytest-random-order from 1.1.1 to 1.2.0 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1342
• Bump kaleido from 0.2.1 to 1.0.0 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1341
• Bump coverage from 7.9.1 to 7.10.1 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1340
• Bump hypothesis from 6.135.20 to 6.136.6 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1339
• Bump pytest from 8.3.5 to 8.4.1 by @dependabot[bot] in https://github.com/haddocking/haddock3/pull/1338
• adding support for HETATM in caprieval by @VGPReys in https://github.com/haddocking/haddock3/pull/1279
• Increase parallelism in alascan by @VGPReys in https://github.com/haddocking/haddock3/pull/1337
• add no-restraints guardrail in rigidbody module by @VGPReys in https://github.com/haddocking/haddock3/pull/1346
• Allow clustering of single model in clustfcc by @VGPReys in https://github.com/haddocking/haddock3/pull/1348
• August package bumps by @VGPReys in https://github.com/haddocking/haddock3/pull/1344
• haddock3 v.2025.08.0 stable release by @VGPReys in https://github.com/haddocking/haddock3/pull/1347

New Contributors

• @sjdv1982 made their first contribution in https://github.com/haddocking/haddock3/pull/1331

Full Changelog: https://github.com/haddocking/haddock3/compare/2025.5.0...2025.8.0