Recent Releases of haddock3

haddock3 - 2025.8.0

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

- Python
Published by VGPReys 10 months ago

haddock3 - HADDOCK3 2025.5.0

What's Changed

Bump httpx from 0.27.2 to 0.28.0 by @dependabot in https://github.com/haddocking/haddock3/pull/1164
Bump hypothesis from 6.119.3 to 6.122.0 by @dependabot in https://github.com/haddocking/haddock3/pull/1162
Bump coverage from 7.6.7 to 7.6.8 by @dependabot in https://github.com/haddocking/haddock3/pull/1163
[caprieval] comparisons against multiple references by @VGPReys in https://github.com/haddocking/haddock3/pull/1136
Remove tox and adjust markdown files by @mgiulini in https://github.com/haddocking/haddock3/pull/1159
Increased parameters in various CNS files for max path length by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1170
back to kaleido 0.2.1 until they fix it by @VGPReys in https://github.com/haddocking/haddock3/pull/1175
refactored check for chain combinations by @mgiulini in https://github.com/haddocking/haddock3/pull/1176
added flat tar extraction by @mgiulini in https://github.com/haddocking/haddock3/pull/1180
modify way of getting the ncores by @VGPReys in https://github.com/haddocking/haddock3/pull/1172
back to basics for macos users when detecting number of cores by @VGPReys in https://github.com/haddocking/haddock3/pull/1183
allow for digit fluctuation in mdscoring integration tests by @VGPReys in https://github.com/haddocking/haddock3/pull/1185
quick fix openm install and 8.2 version by @VGPReys in https://github.com/haddocking/haddock3/pull/1145
Handle reference issue when multiple conformation provided in [caprieval] by @VGPReys in https://github.com/haddocking/haddock3/pull/1133
Bump httpx from 0.28.0 to 0.28.1 by @dependabot in https://github.com/haddocking/haddock3/pull/1189
Bump coverage from 7.6.8 to 7.6.10 by @dependabot in https://github.com/haddocking/haddock3/pull/1188
Bump fastapi from 0.115.5 to 0.115.6 by @dependabot in https://github.com/haddocking/haddock3/pull/1186
Bump hypothesis from 6.122.0 to 6.123.2 by @dependabot in https://github.com/haddocking/haddock3/pull/1187
Bump pytest from 8.3.3 to 8.3.4 by @dependabot in https://github.com/haddocking/haddock3/pull/1190
Added CNS troubleshooting instructions (issue #1191) by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1197
Bump hypothesis from 6.123.2 to 6.124.7 by @dependabot in https://github.com/haddocking/haddock3/pull/1194
Bump fastapi from 0.115.6 to 0.115.8 by @dependabot in https://github.com/haddocking/haddock3/pull/1196
removed debug log calls by @mgiulini in https://github.com/haddocking/haddock3/pull/1199
Upgrade plotly by @mgiulini in https://github.com/haddocking/haddock3/pull/1200
Add radius passive from active by @mgiulini in https://github.com/haddocking/haddock3/pull/1206
add python3.13 to automatic pipelines by @rvhonorato in https://github.com/haddocking/haddock3/pull/1209
Bump coverage from 7.6.10 to 7.6.12 by @dependabot in https://github.com/haddocking/haddock3/pull/1211
Bump fastapi from 0.115.8 to 0.115.11 by @dependabot in https://github.com/haddocking/haddock3/pull/1218
Bump mpi4py from 4.0.1 to 4.0.3 by @dependabot in https://github.com/haddocking/haddock3/pull/1213
Bump hypothesis from 6.124.7 to 6.127.4 by @dependabot in https://github.com/haddocking/haddock3/pull/1217
modified alascan by @mgiulini in https://github.com/haddocking/haddock3/pull/1219
Adding rank to filenames in [contactmap] module by @VGPReys in https://github.com/haddocking/haddock3/pull/1228
Bump plotly from 6.0.0 to 6.0.1 by @dependabot in https://github.com/haddocking/haddock3/pull/1237
Increase number of supported molecules with common co-factors by @VGPReys in https://github.com/haddocking/haddock3/pull/1233
Bump fastapi from 0.115.11 to 0.115.12 by @dependabot in https://github.com/haddocking/haddock3/pull/1238
Bump pytest from 8.3.4 to 8.3.5 by @dependabot in https://github.com/haddocking/haddock3/pull/1236
Update README.md by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1245
Bump coverage from 7.6.12 to 7.8.0 by @dependabot in https://github.com/haddocking/haddock3/pull/1234
Bump hypothesis from 6.127.4 to 6.130.6 by @dependabot in https://github.com/haddocking/haddock3/pull/1235
[prodigyligand] and [prodigyprotein] scoring modules by @VGPReys in https://github.com/haddocking/haddock3/pull/1069
Updating Pull Request template checklist by @VGPReys in https://github.com/haddocking/haddock3/pull/1230
Returning unequilibrated structure in openmm by @VGPReys in https://github.com/haddocking/haddock3/pull/1243
pin prodigy-prot version by @rvhonorato in https://github.com/haddocking/haddock3/pull/1250
add schedule to ci.yml by @rvhonorato in https://github.com/haddocking/haddock3/pull/1253
Fine tuning for web app purpose by @VGPReys in https://github.com/haddocking/haddock3/pull/1126
fix inconsistent use of top_cluster parameter by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1222
Added link to BioExcel 2025 survey by @AnnaKravchenko in https://github.com/haddocking/haddock3/pull/1254
added nanobody example data by @mgiulini in https://github.com/haddocking/haddock3/pull/1207
Bump prodigy-prot version + small ugrades on prodigy modules by @VGPReys in https://github.com/haddocking/haddock3/pull/1252
Adding new filtering module [filter] by @VGPReys in https://github.com/haddocking/haddock3/pull/1226
fix path in CONTRIBUTING.md by @VGPReys in https://github.com/haddocking/haddock3/pull/1256
Active passive to ambig exception by @mgiulini in https://github.com/haddocking/haddock3/pull/1258
Bump hypothesis from 6.130.6 to 6.131.9 by @dependabot in https://github.com/haddocking/haddock3/pull/1261
Bump pytest-cov from 6.0.0 to 6.1.1 by @dependabot in https://github.com/haddocking/haddock3/pull/1260
removed verbose log call from seletopclusts by @mgiulini in https://github.com/haddocking/haddock3/pull/1263
added biorxiv ref by @mgiulini in https://github.com/haddocking/haddock3/pull/1265
changed version by @mgiulini in https://github.com/haddocking/haddock3/pull/1266

Full Changelog: https://github.com/haddocking/haddock3/compare/2024.12.0b7...2025.5.0

- Python
Published by mgiulini about 1 year ago

haddock3 - 2024.12.0b7

What's Changed

Workaround plotly / kaleido static figure generation by @VGPReys in https://github.com/haddocking/haddock3/pull/1086
Remove self.params["debug"] logic in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/1088
numpy upgrade by @mgiulini in https://github.com/haddocking/haddock3/pull/1091
Bump mpi4py from 4.0.0 to 4.0.1 by @dependabot in https://github.com/haddocking/haddock3/pull/1093
Bump hypothesis from 6.112.2 to 6.115.0 by @dependabot in https://github.com/haddocking/haddock3/pull/1094
Bump pytest-cov from 4.0.0 to 5.0.0 by @dependabot in https://github.com/haddocking/haddock3/pull/1097
Bump fastapi from 0.115.0 to 0.115.2 by @dependabot in https://github.com/haddocking/haddock3/pull/1095
Bump httpx from 0.27.0 to 0.27.2 by @dependabot in https://github.com/haddocking/haddock3/pull/1096
Fix z restraints examples by @VGPReys in https://github.com/haddocking/haddock3/pull/1101
Remove dead cli_bm by @rvhonorato in https://github.com/haddocking/haddock3/pull/1102
sasascore module by @mgiulini in https://github.com/haddocking/haddock3/pull/862
Remove adaptative sleep logic in libhpc by @rvhonorato in https://github.com/haddocking/haddock3/pull/1103
Bump coverage from 7.6.1 to 7.6.4 by @dependabot in https://github.com/haddocking/haddock3/pull/1110
Bump hypothesis from 6.115.0 to 6.115.3 by @dependabot in https://github.com/haddocking/haddock3/pull/1111
Bump fastapi from 0.115.2 to 0.115.4 by @dependabot in https://github.com/haddocking/haddock3/pull/1118
Bump hypothesis from 6.115.3 to 6.115.5 by @dependabot in https://github.com/haddocking/haddock3/pull/1117
Correct auto documentation by @mgiulini in https://github.com/haddocking/haddock3/pull/1109
Fix tests by @mgiulini in https://github.com/haddocking/haddock3/pull/1123
Solves issue #1119 related to MPI execution with mpirun or run by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1127
fix random error by @mgiulini in https://github.com/haddocking/haddock3/pull/1129
Bump hypothesis from 6.115.5 to 6.116.0 by @dependabot in https://github.com/haddocking/haddock3/pull/1130
Bump pytest-cov from 5.0.0 to 6.0.0 by @dependabot in https://github.com/haddocking/haddock3/pull/1131
Analysis not capri by @mgiulini in https://github.com/haddocking/haddock3/pull/1120
Bump hypothesis from 6.116.0 to 6.118.7 by @dependabot in https://github.com/haddocking/haddock3/pull/1137
fixed analysis on cleaned, downloaded runs by @mgiulini in https://github.com/haddocking/haddock3/pull/1124
caught CNS exception in scoring modules by @mgiulini in https://github.com/haddocking/haddock3/pull/1138
Per interface scoring for dimers by @mgiulini in https://github.com/haddocking/haddock3/pull/1143
Reducing number of steps in openmm examples by @VGPReys in https://github.com/haddocking/haddock3/pull/1142
Bump hypothesis from 6.118.7 to 6.119.3 by @dependabot in https://github.com/haddocking/haddock3/pull/1151
Bump coverage from 7.6.4 to 7.6.7 by @dependabot in https://github.com/haddocking/haddock3/pull/1148
Bump fastapi from 0.115.4 to 0.115.5 by @dependabot in https://github.com/haddocking/haddock3/pull/1150
add new glycans by @mgiulini in https://github.com/haddocking/haddock3/pull/1134
Update README.md by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1146
Bump kaleido from 0.2.1 to 0.4.1 by @dependabot in https://github.com/haddocking/haddock3/pull/1149
Create validate_citation.yml by @mgiulini in https://github.com/haddocking/haddock3/pull/1156
adding bioexcel forum by @VGPReys in https://github.com/haddocking/haddock3/pull/1161

Full Changelog: https://github.com/haddocking/haddock3/compare/2024.10.0b6...2024.12.0b7

- Python
Published by mgiulini over 1 year ago

haddock3 - 2024.10.0b6

What's Changed

Openmm by @VGPReys in https://github.com/haddocking/haddock3/pull/654
Interactive rescoring reviewed by @VGPReys in https://github.com/haddocking/haddock3/pull/778
added chain ID by @mgiulini in https://github.com/haddocking/haddock3/pull/793
Interactive rescoring and reclustering by @mgiulini in https://github.com/haddocking/haddock3/pull/769
Zip structures by @mgiulini in https://github.com/haddocking/haddock3/pull/794
Create action.yml by @amjjbonvin in https://github.com/haddocking/haddock3/pull/797
Adding mirror pushing to the Castiel EuroHPC GitLab repo by @amjjbonvin in https://github.com/haddocking/haddock3/pull/798
Add conditional execution for integration job by @rvhonorato in https://github.com/haddocking/haddock3/pull/801
changed capri columns by @mgiulini in https://github.com/haddocking/haddock3/pull/805
Side by side2 by @sverhoeven in https://github.com/haddocking/haddock3/pull/799
Round other cluster + dont add score which was not there before by @sverhoeven in https://github.com/haddocking/haddock3/pull/810
update codehub sync by @rvhonorato in https://github.com/haddocking/haddock3/pull/812
Show top 10 ranked clusters + Other cluster by @sverhoeven in https://github.com/haddocking/haddock3/pull/813
Improve docs by @mgiulini in https://github.com/haddocking/haddock3/pull/803
Validate example workflows by @mgiulini in https://github.com/haddocking/haddock3/pull/816
Low level docs by @mgiulini in https://github.com/haddocking/haddock3/pull/815
Fine tuning Contact map module by @VGPReys in https://github.com/haddocking/haddock3/pull/749
Mapping TIMEOUT output to failure in libhpc by @VGPReys in https://github.com/haddocking/haddock3/pull/727
corrected parameter handling for cli-score by @mgiulini in https://github.com/haddocking/haddock3/pull/807
Calc accessibility by @mgiulini in https://github.com/haddocking/haddock3/pull/820
Work arround chain matching in IL-RMSDMatrix by @VGPReys in https://github.com/haddocking/haddock3/pull/828
ordered traceback by @mgiulini in https://github.com/haddocking/haddock3/pull/831
Fast rmsd by @mgiulini in https://github.com/haddocking/haddock3/pull/809
Resolves issue #845 - adding missing parameters by @amjjbonvin in https://github.com/haddocking/haddock3/pull/847
Interactivity fixes by @mgiulini in https://github.com/haddocking/haddock3/pull/823
Graphical representation of clusters by @VGPReys in https://github.com/haddocking/haddock3/pull/772
added traceback plot and sum of ranks file by @mgiulini in https://github.com/haddocking/haddock3/pull/850
Offline mode by @VGPReys in https://github.com/haddocking/haddock3/pull/825
Fix offlinemode by @VGPReys in https://github.com/haddocking/haddock3/pull/854
Upgrade contact heatmap by @VGPReys in https://github.com/haddocking/haddock3/pull/855
changing header info in contact map tsv files by @VGPReys in https://github.com/haddocking/haddock3/pull/856
Fixing error in caprieval using shapes by @VGPReys in https://github.com/haddocking/haddock3/pull/851
Fix auto analysis by @mgiulini in https://github.com/haddocking/haddock3/pull/853
Improved seletopclusts by @VGPReys in https://github.com/haddocking/haddock3/pull/819
Chain match coords load issue by @VGPReys in https://github.com/haddocking/haddock3/pull/864
added groups data by @VGPReys in https://github.com/haddocking/haddock3/pull/872
create new CNSScoringModule class by @VGPReys in https://github.com/haddocking/haddock3/pull/870
Fair by @VGPReys in https://github.com/haddocking/haddock3/pull/868
Added alascan modules to tests execution and comparison by @amjjbonvin in https://github.com/haddocking/haddock3/pull/876
Add prefix to model names from input ensemble by @VGPReys in https://github.com/haddocking/haddock3/pull/878
Save outputs in case of faulty tolerance by @VGPReys in https://github.com/haddocking/haddock3/pull/880
Heavy atoms RMSD calculation in caprieval by @VGPReys in https://github.com/haddocking/haddock3/pull/837
Add codacy/codacy-coverage-reporter-action action to tests.yml by @rvhonorato in https://github.com/haddocking/haddock3/pull/875
Remove faulty outputs before saving io.json by @VGPReys in https://github.com/haddocking/haddock3/pull/883
Define contact distance cutoff parameter in ilrmsdmatrix by @VGPReys in https://github.com/haddocking/haddock3/pull/881
corrected absolute path in seletopclusts by @mgiulini in https://github.com/haddocking/haddock3/pull/888
Improve alascan output by @mgiulini in https://github.com/haddocking/haddock3/pull/889
Reclusts matrixplot by @VGPReys in https://github.com/haddocking/haddock3/pull/859
check that file exists before renaming by @VGPReys in https://github.com/haddocking/haddock3/pull/893
Update CONTRIBUTING.md by @AnnaKravchenko in https://github.com/haddocking/haddock3/pull/890
Per interface scoring by @amjjbonvin in https://github.com/haddocking/haddock3/pull/896
updating to latest main version by @amjjbonvin in https://github.com/haddocking/haddock3/pull/899
Add option to keep the existing b-factor in the input PDB by @amjjbonvin in https://github.com/haddocking/haddock3/pull/898
Updated CNS installation instructions by @amjjbonvin in https://github.com/haddocking/haddock3/pull/895
Merge of main branch into the score branch by @amjjbonvin in https://github.com/haddocking/haddock3/pull/902
Adds the HADDOCK score to the PDB headers - issue #901 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/903
only run codacy-coverage-reporter-action for same repo by @rvhonorato in https://github.com/haddocking/haddock3/pull/904
Inverted chains by @mgiulini in https://github.com/haddocking/haddock3/pull/905
added code of conduct by @mgiulini in https://github.com/haddocking/haddock3/pull/910
improved postprocessing scaling by @mgiulini in https://github.com/haddocking/haddock3/pull/874
remove deprecation warnings by @mgiulini in https://github.com/haddocking/haddock3/pull/907
Reduce number of files in mode = "local" by @rvhonorato in https://github.com/haddocking/haddock3/pull/918
add more good byes by @rvhonorato in https://github.com/haddocking/haddock3/pull/929
Avoid generating .seed files by @rvhonorato in https://github.com/haddocking/haddock3/pull/924
Makes haddock3 restraints subcommands available as web service by @sverhoeven in https://github.com/haddocking/haddock3/pull/841
Refactor rigidbody module to allow the preparation of cns_input to be done in parallel by @rvhonorato in https://github.com/haddocking/haddock3/pull/933
Use less_io parameter in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/928
increased max sampling_factor by @mgiulini in https://github.com/haddocking/haddock3/pull/939
removed duplicated w_air parameter by @amjjbonvin in https://github.com/haddocking/haddock3/pull/946
Add MPI execution tests by @rvhonorato in https://github.com/haddocking/haddock3/pull/942
Update repository templates by @rvhonorato in https://github.com/haddocking/haddock3/pull/951
lazy load MPI module and COMM variable by @rvhonorato in https://github.com/haddocking/haddock3/pull/953
Refactor capri.extract_data_from_capri_class to propagate the model's energy terms by @rvhonorato in https://github.com/haddocking/haddock3/pull/950
changed min and max clust_cutoff by @mgiulini in https://github.com/haddocking/haddock3/pull/954
Use prepare_cns_input_sequential when mode is not local by @rvhonorato in https://github.com/haddocking/haddock3/pull/943
better description for some modules by @VGPReys in https://github.com/haddocking/haddock3/pull/947
added ilrmsd to capri clt by @mgiulini in https://github.com/haddocking/haddock3/pull/957
update caprieval integration tests by @rvhonorato in https://github.com/haddocking/haddock3/pull/958
Handle exceptions in Worker.run by @rvhonorato in https://github.com/haddocking/haddock3/pull/962
Clean intermediate files in batch mode by @VGPReys in https://github.com/haddocking/haddock3/pull/937
change log level of exceptions in the Worker's run method by @rvhonorato in https://github.com/haddocking/haddock3/pull/966
Update caprieval integration tests with new score values by @rvhonorato in https://github.com/haddocking/haddock3/pull/964
Fix rescore by @mgiulini in https://github.com/haddocking/haddock3/pull/972
Add logic to check for incompatible parameters by @rvhonorato in https://github.com/haddocking/haddock3/pull/935
Propagate cluster related properties in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/978
Ilrmsd onechain clarified by @mgiulini in https://github.com/haddocking/haddock3/pull/922
Update README.md by @rvhonorato in https://github.com/haddocking/haddock3/pull/976
Change the naming of the phoshpate oxygens to OP1/OP2 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/985
links to feedbacks by @VGPReys in https://github.com/haddocking/haddock3/pull/997
Single chain caprieval by @VGPReys in https://github.com/haddocking/haddock3/pull/994
remove dead code related to DNA in cm_restraints.cns by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1001
modifying ambscale and unambscale parameter names by @VGPReys in https://github.com/haddocking/haddock3/pull/983
avoid fileexist on empty strings by @amjjbonvin in https://github.com/haddocking/haddock3/pull/995
Fileexist issue update by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1010
Set tolerance to 5 for non-topoaa modules by @sverhoeven in https://github.com/haddocking/haddock3/pull/1004
ordering by size in clustrmsd by @mgiulini in https://github.com/haddocking/haddock3/pull/974
added integration tests for scoring modules by @mgiulini in https://github.com/haddocking/haddock3/pull/968
adding test to checks for duplicated parameters in defaults.yaml by @VGPReys in https://github.com/haddocking/haddock3/pull/913
exposes cyclisation distance cutoffs by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1003
Add all global parameters description by @VGPReys in https://github.com/haddocking/haddock3/pull/1009
make sure hbond restraints are read under a separate class by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1015
update pull_request_template.md by @rvhonorato in https://github.com/haddocking/haddock3/pull/1017
refactor clustfcc and it's tests to use the proper path by @rvhonorato in https://github.com/haddocking/haddock3/pull/1016
Enhance flexible definition in config files / defaults.yaml by @amjjbonvin in https://github.com/haddocking/haddock3/pull/969
create libfcc.py by @rvhonorato in https://github.com/haddocking/haddock3/pull/1019
Automatically reduce the tadfactor to 4 when fully flexible segments are defined by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1020
lower expertise level of ligands params by @VGPReys in https://github.com/haddocking/haddock3/pull/1023
Integration tests by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1014
validate ncs parameters by @VGPReys in https://github.com/haddocking/haddock3/pull/1026
Added DISCLAIMER statement by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1031
Detection of known CNS errors when failed run by @VGPReys in https://github.com/haddocking/haddock3/pull/1018
re-work haddock3 installation by @rvhonorato in https://github.com/haddocking/haddock3/pull/1013
less_io to debug by @VGPReys in https://github.com/haddocking/haddock3/pull/1035
Update pages.yml by @rvhonorato in https://github.com/haddocking/haddock3/pull/1036
Simplify definition of counted parameters by computing them on the fly from definition. by @VGPReys in https://github.com/haddocking/haddock3/pull/975
Update main cli description by @VGPReys in https://github.com/haddocking/haddock3/pull/1043
Update installation instructions by @rvhonorato in https://github.com/haddocking/haddock3/pull/1039
add development instructions by @rvhonorato in https://github.com/haddocking/haddock3/pull/988
Fixing some examples workflow configuration files by @VGPReys in https://github.com/haddocking/haddock3/pull/1045
Cleaning of the random AIRs CNS code by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1050
removed NCS from rigidbody by @VGPReys in https://github.com/haddocking/haddock3/pull/1048
Updating DNA examples to match parameters in tutorial by @VGPReys in https://github.com/haddocking/haddock3/pull/1055
z-surface restraints scripts by @VGPReys in https://github.com/haddocking/haddock3/pull/839
Refactor tempfile usage in tests by @rvhonorato in https://github.com/haddocking/haddock3/pull/1058
update cyclic peptides examples by @VGPReys in https://github.com/haddocking/haddock3/pull/1057
Make project compatible with recent python versions by @rvhonorato in https://github.com/haddocking/haddock3/pull/1042
Update pandas requirement from ==1.* to ==2.* by @dependabot in https://github.com/haddocking/haddock3/pull/1065
Bump mpi4py from 3.1.6 to 4.0.0 by @dependabot in https://github.com/haddocking/haddock3/pull/1064
Bump pytest from 7.3.1 to 8.3.3 by @dependabot in https://github.com/haddocking/haddock3/pull/1066
Bump hypothesis from 6.75.1 to 6.112.2 by @dependabot in https://github.com/haddocking/haddock3/pull/1067
Parameter incompatibilities: Increase flexibility in incompatibilities handles. by @VGPReys in https://github.com/haddocking/haddock3/pull/991
Corrected incompatibility values for the debug parameter by @amjjbonvin in https://github.com/haddocking/haddock3/pull/1071
Import plotly offline mode by @VGPReys in https://github.com/haddocking/haddock3/pull/1041
Replace haddock3-analysis-components with haddock3-ui package by @sverhoeven in https://github.com/haddocking/haddock3/pull/1025
Add OpenMM module by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/482
Bump plotly from 5.11.0 to 5.24.1 by @dependabot in https://github.com/haddocking/haddock3/pull/1080
Bump coverage from 7.2.5 to 7.6.1 by @dependabot in https://github.com/haddocking/haddock3/pull/1076
Bump fastapi from 0.110.1 to 0.115.0 by @dependabot in https://github.com/haddocking/haddock3/pull/1077
Bump pytest-mock from 3.12.0 to 3.14.0 by @dependabot in https://github.com/haddocking/haddock3/pull/1079
Use YYYY.MM.PATCH for versioning by @rvhonorato in https://github.com/haddocking/haddock3/pull/1083
limiting cpu usage in [openmm] by @VGPReys in https://github.com/haddocking/haddock3/pull/1075
Add pipeline to publish image to ghcr.io by @rvhonorato in https://github.com/haddocking/haddock3/pull/1085
add pipeline to automatically publish package in pypi on every release by @rvhonorato in https://github.com/haddocking/haddock3/pull/1087

New Contributors

@AnnaKravchenko made their first contribution in https://github.com/haddocking/haddock3/pull/890

Full Changelog: https://github.com/haddocking/haddock3/compare/v3.0.0-beta.5...2024.10.0b6

- Python
Published by rvhonorato over 1 year ago

haddock3 - v3.0.0-beta.5

haddock3 beta 5 release

What's Changed

Clean and postprocess true by @mgiulini in https://github.com/haddocking/haddock3/pull/712
Glycan example by @mgiulini in https://github.com/haddocking/haddock3/pull/711
Tweak CI by @rvhonorato in https://github.com/haddocking/haddock3/pull/717
Add topoaa integration test stub by @rvhonorato in https://github.com/haddocking/haddock3/pull/716
Glycan 1 6 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/714
add function and variable annotations by @alchemistcai in https://github.com/haddocking/haddock3/pull/645
added symmetry energy to output by @mgiulini in https://github.com/haddocking/haddock3/pull/723
Integration tweak by @rvhonorato in https://github.com/haddocking/haddock3/pull/726
Implement type annotations by @rvhonorato in https://github.com/haddocking/haddock3/pull/724
commented workdir parameter by @mgiulini in https://github.com/haddocking/haddock3/pull/708
Randomisation of starting orientations at flexref by @amjjbonvin in https://github.com/haddocking/haddock3/pull/729
Haddock3 restraints by @mgiulini in https://github.com/haddocking/haddock3/pull/732
removed xaxis sharing in report by @mgiulini in https://github.com/haddocking/haddock3/pull/736
alascan module by @mgiulini in https://github.com/haddocking/haddock3/pull/690
added bsa box plot by @mgiulini in https://github.com/haddocking/haddock3/pull/737
added fnat - energy scatter plots by @mgiulini in https://github.com/haddocking/haddock3/pull/725
Add missing parameters and update compare_runs.py by @amjjbonvin in https://github.com/haddocking/haddock3/pull/743
contact map analysis module by @VGPReys in https://github.com/haddocking/haddock3/pull/731
Updated color scheme of chord chart by @amjjbonvin in https://github.com/haddocking/haddock3/pull/745
updated freesasa by @mgiulini in https://github.com/haddocking/haddock3/pull/748
short description in haddock3-cfg CLI by @mgiulini in https://github.com/haddocking/haddock3/pull/753
Bugfix traceback contactmap by @mgiulini in https://github.com/haddocking/haddock3/pull/751
added description to analysis modules by @mgiulini in https://github.com/haddocking/haddock3/pull/688
show gzipped structures in analysis report by @mgiulini in https://github.com/haddocking/haddock3/pull/758
modif float comparisons in contact map tests by @VGPReys in https://github.com/haddocking/haddock3/pull/764
Deep CNS scripts checking and example cleaning by @amjjbonvin in https://github.com/haddocking/haddock3/pull/763
update protein-peptide examples/ files by @amjjbonvin in https://github.com/haddocking/haddock3/pull/768
update key deletion logic in topoaa by @VGPReys in https://github.com/haddocking/haddock3/pull/766
corrected crossbar values by @mgiulini in https://github.com/haddocking/haddock3/pull/771
ilrmsdmatrix module by @mgiulini in https://github.com/haddocking/haddock3/pull/685
Cli score fix by @mgiulini in https://github.com/haddocking/haddock3/pull/783
uniform running modes by @mgiulini in https://github.com/haddocking/haddock3/pull/775
Solves issue #785 about unstable energies when changing the param file by @amjjbonvin in https://github.com/haddocking/haddock3/pull/787
Add topo/params for covalent docking Serine (SEC) - issue #757 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/788
Fix prot segid by @mgiulini in https://github.com/haddocking/haddock3/pull/780

New Contributors

@alchemistcai made their first contribution in https://github.com/haddocking/haddock3/pull/645

Full Changelog: https://github.com/haddocking/haddock3/compare/v3.0.0-beta.4...v3.0.0-beta.5

- Python
Published by mgiulini over 2 years ago

haddock3 - v3.0.0-beta.4

What's Changed

solve unicode problem in restarting and copying runs by @mgiulini in https://github.com/haddocking/haddock3/pull/610
change log handler by @rvhonorato in https://github.com/haddocking/haddock3/pull/616
added score components to capri_clt by @mgiulini in https://github.com/haddocking/haddock3/pull/618
Update pullrequesttemplate.md by @rvhonorato in https://github.com/haddocking/haddock3/pull/620
added packages to std envs by @mgiulini in https://github.com/haddocking/haddock3/pull/622
added postprocess option to workflow by @mgiulini in https://github.com/haddocking/haddock3/pull/619
Test cli analyse and remove matplotlib plots by @mgiulini in https://github.com/haddocking/haddock3/pull/627
Remove duplicated key in src/haddock/modules/refinement/flexref/defaults.yaml by @rvhonorato in https://github.com/haddocking/haddock3/pull/630
correct model-cluster-ranking by @mgiulini in https://github.com/haddocking/haddock3/pull/626
updated paths in capriss clianalyse by @mgiulini in https://github.com/haddocking/haddock3/pull/615
Postprocess example workflows by @mgiulini in https://github.com/haddocking/haddock3/pull/634
removed other_params from call to postprocess by @mgiulini in https://github.com/haddocking/haddock3/pull/636
Adjust clustrmsd by @mgiulini in https://github.com/haddocking/haddock3/pull/632
haddock3-analyse: create report html page based on individual plots by @SarahAlidoost in https://github.com/haddocking/haddock3/pull/611
Add support for new carbohydrate linkages in line with 2.4 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/640
bugfix for when nemsteps=0 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/646
correct existing linting errors by @mgiulini in https://github.com/haddocking/haddock3/pull/649
changed exported file names by @mgiulini in https://github.com/haddocking/haddock3/pull/650
Update INSTALL.md sementic on various haddock3 by @VGPReys in https://github.com/haddocking/haddock3/pull/652
change codecov failciif_error by @rvhonorato in https://github.com/haddocking/haddock3/pull/656
Fixes b16 glycan linkage issue #659 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/660
Add structure viewer to the analysis report by @SarahAlidoost in https://github.com/haddocking/haddock3/pull/639
Increased dihedral restraints array size - in line with haddock2.4/5 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/664
Add caprieval_rank to hover text in scatter and box plots by @SarahAlidoost in https://github.com/haddocking/haddock3/pull/666
score-sorted scoring files by @mgiulini in https://github.com/haddocking/haddock3/pull/669
Bump scipy from 1.8.0 to 1.10.0 by @dependabot in https://github.com/haddocking/haddock3/pull/671
fixes issue #662 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/672
Hide install deprecation warnings by @VGPReys in https://github.com/haddocking/haddock3/pull/661
modify location of SetuptoolsDeprecationWarning by @VGPReys in https://github.com/haddocking/haddock3/pull/674
Make the table sortable(Use a React component in libplots) by @SarahAlidoost in https://github.com/haddocking/haddock3/pull/667
fix maxmoleculesallowed formatting by @VGPReys in https://github.com/haddocking/haddock3/pull/678
haddock3-traceback by @mgiulini in https://github.com/haddocking/haddock3/pull/668
Issuefixes by @VGPReys in https://github.com/haddocking/haddock3/pull/658
Pin versions of react libraries by @SarahAlidoost in https://github.com/haddocking/haddock3/pull/682
Chain matching and multibody capri by @mgiulini in https://github.com/haddocking/haddock3/pull/675
update CI by @rvhonorato in https://github.com/haddocking/haddock3/pull/693
handled max sampling_factor by @mgiulini in https://github.com/haddocking/haddock3/pull/691
Access long description of module parameters by @VGPReys in https://github.com/haddocking/haddock3/pull/695
Use ngl component by @SarahAlidoost in https://github.com/haddocking/haddock3/pull/683
no traceback on pure analysis runs by @mgiulini in https://github.com/haddocking/haddock3/pull/702
Fixing issues running examples by @VGPReys in https://github.com/haddocking/haddock3/pull/703
Input to json by @mgiulini in https://github.com/haddocking/haddock3/pull/705

New Contributors

@SarahAlidoost made their first contribution in https://github.com/haddocking/haddock3/pull/611
@dependabot made their first contribution in https://github.com/haddocking/haddock3/pull/671

Full Changelog: https://github.com/haddocking/haddock3/compare/v3.0.0-beta.3...v3.0.0-beta.4

- Python
Published by mgiulini over 2 years ago

haddock3 - v3.0.0-beta.3

What's Changed

Added new antibody-antigen example using epitope definition from NMR by @amjjbonvin in https://github.com/haddocking/haddock3/pull/491
Improve two titles in documentation by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/490
Added exit module by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/494
Improve running topoaa as an intermediate step in the workflow by @mgiulini in https://github.com/haddocking/haddock3/pull/498
Update pdb-tools version. by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/493
Add documentation to the limit parameter in topoaa by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/499
Correct function selection in topoaa when order=0 and limit is used (or not) by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/500
Add missing parameter in run_tests.py after #494 by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/501
PDB pre-processing by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/144
Added shape.top to the supported residues by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/508
implemented check_chains by @mgiulini in https://github.com/haddocking/haddock3/pull/507
Add documentation paragraph to rigidbody module description by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/511
add missing init file by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/512
Added a brief intro do HADDOCK3 by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/514
Correct typo in documentation by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/513
Removes --verbosity in isort lint check by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/521
Add action to deploy pages by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/525
changed to py39 in GA for pages by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/526
Updates docs theme to Karma theme by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/524
Uses action to deploy pages by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/527
add nojekyll file to GA generating pages by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/530
Corrects minor lint issues by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/523
Update guidelines to contribute to documentation by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/531
Add template to write new modules by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/520
Added support for 3-hydroxyproline (HY3) by @amjjbonvin in https://github.com/haddocking/haddock3/pull/533
Update the --restart option to cope with subfolders in steps. by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/522
Rank capri_ss.tsv by score and sort by sortkey by @rvhonorato in https://github.com/haddocking/haddock3/pull/537
Add full support to toml by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/539
changed retrieve_models logic by @mgiulini in https://github.com/haddocking/haddock3/pull/543
Create haddock3-score CLI by @rvhonorato in https://github.com/haddocking/haddock3/pull/510
Update the docs badge to match the pages.yml file. by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/540
Revert "changed retrieve_models logic" by @mgiulini in https://github.com/haddocking/haddock3/pull/553
removed sampling parameter by @mgiulini in https://github.com/haddocking/haddock3/pull/552
Add missing transfor_to_list in molecules when reading config by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/554
addressed bug in haddock3-copy cli by @mgiulini in https://github.com/haddocking/haddock3/pull/560
Unclustered structures by @mgiulini in https://github.com/haddocking/haddock3/pull/556
Handle single chains caprieval by @mgiulini in https://github.com/haddocking/haddock3/pull/548
removed absolute paths in topoaa by @mgiulini in https://github.com/haddocking/haddock3/pull/562
fixed dockq calculation by @mgiulini in https://github.com/haddocking/haddock3/pull/572
Fault tolerant caprieval by @mgiulini in https://github.com/haddocking/haddock3/pull/574
Add --ncores param to clean clients by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/579
Top cluster integer by @mgiulini in https://github.com/haddocking/haddock3/pull/576
Fix clt order by @mgiulini in https://github.com/haddocking/haddock3/pull/582
removed cluster file from tests and prettified code by @mgiulini in https://github.com/haddocking/haddock3/pull/583
Add CNS installation instructions by @cvnoort in https://github.com/haddocking/haddock3/pull/469
Multiple ambig files by @mgiulini in https://github.com/haddocking/haddock3/pull/563
Adding the varia directory containing the CNS and lmod code by @amjjbonvin in https://github.com/haddocking/haddock3/pull/571
Updates haddock3-cfg for toml compatibility - bool variables by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/591
Changed in yaml files some boeleans to use lowercase for consistency by @amjjbonvin in https://github.com/haddocking/haddock3/pull/592
Update INSTALL.md to add an optional MPI dependency by @amjjbonvin in https://github.com/haddocking/haddock3/pull/577
fixed handling of restr_fname in refinement modules by @mgiulini in https://github.com/haddocking/haddock3/pull/590
Compress .inp, .out, and .seed in CNS Jobs on the fly by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/594
Implement option to use MAX CPUs and bypass the N-1 rule for local mode. by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/597
add w+ to data dir by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/599
Related to issue #598 - now compatible with OSX as well by @amjjbonvin in https://github.com/haddocking/haddock3/pull/600
implement haddock3 postprocessing by @mgiulini in https://github.com/haddocking/haddock3/pull/567
minor: correct test for #597 by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/602
Correct rmsds by @mgiulini in https://github.com/haddocking/haddock3/pull/604
Capri memory error by @mgiulini in https://github.com/haddocking/haddock3/pull/585
Changed max_cpus to true as default (and its description) by @amjjbonvin in https://github.com/haddocking/haddock3/pull/605
added png option by @mgiulini in https://github.com/haddocking/haddock3/pull/606
increased tolerance for MD modules by @mgiulini in https://github.com/haddocking/haddock3/pull/609
text/typo edits in the documentation by @bvreede in https://github.com/haddocking/haddock3/pull/607

New Contributors

@cvnoort made their first contribution in https://github.com/haddocking/haddock3/pull/469
@bvreede made their first contribution in https://github.com/haddocking/haddock3/pull/607

Full Changelog: https://github.com/haddocking/haddock3/compare/v3.0.0-beta.2...v3.0.0-beta.3

- Python
Published by rvhonorato over 3 years ago

haddock3 - v3.0.0-beta.2

What's Changed since v3.0.0-beta.1

Refactor caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/441
Generate .rst documentation page for .yaml default configuration files by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/436
Add user documentation on configuration files by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/445
Update MANIFEST.in by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/455
Enhance clustering protocols by @rvhonorato in https://github.com/haddocking/haddock3/pull/454
amended clt_threshold behavior by @mgiulini in https://github.com/haddocking/haddock3/pull/460
Add md5 property to libontology by @rvhonorato in https://github.com/haddocking/haddock3/pull/459
Populate mol_ expandable parameters when using --extend-run by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/450
Allows single entries in molecules parameter by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/439
add cluster name to seletopclusts.txt by @rvhonorato in https://github.com/haddocking/haddock3/pull/462
add tests to topoaa by @rvhonorato in https://github.com/haddocking/haddock3/pull/461
add haddock3-docs to .gitignore by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/463
remove duplicated entry in clustfcc.txt by @rvhonorato in https://github.com/haddocking/haddock3/pull/465
Corrects bug in --restart option by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/467
Add missing header to seletopclusts.txt by @rvhonorato in https://github.com/haddocking/haddock3/pull/471
Implements clean output - compress/archive output files by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/468
Corrects check modules names in config on startup by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/477
Update CI workflows by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/478
Improve reading md5 from REMARK lines by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/475
Allows topoaa to run in different parts of the workflow by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/474
Adds parameter validation to general parameters by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/479
Improves mandatory parameter check by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/481
added chain-matching AlignError by @mgiulini in https://github.com/haddocking/haddock3/pull/483
added single linkage as clustrmsd default by @mgiulini in https://github.com/haddocking/haddock3/pull/486
added check on tolerance in clustrmsd by @mgiulini in https://github.com/haddocking/haddock3/pull/489
run analysis modules after topoaa by @mgiulini in https://github.com/haddocking/haddock3/pull/484
Add general parameters to haddock3-cfg client by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/476

Full Changelog: https://github.com/haddocking/haddock3/compare/v3.0.0-beta.1...v3.0.0-beta.2

- Python
Published by joaomcteixeira almost 4 years ago

haddock3 - v3.0.0-beta.1

What's Changed

activate exports by @SSchott in https://github.com/haddocking/haddock3/pull/18
LightDock sampling by @brianjimenez in https://github.com/haddocking/haddock3/pull/20
Drop class name analogies favoring technical names by @rvhonorato in https://github.com/haddocking/haddock3/pull/21
Clarifies main branch status by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/23
data_path not being found by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/24
renames flavour to mode missing files by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/26
Update installation instructions by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/25
Transforms haddock3 into a python package by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/28
Reduces code repetition in pdbutil when checking for new files by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/31
Correct ln command typo and updates CNS_EXE path to bin/cns by @rvhonorato in https://github.com/haddocking/haddock3/pull/34
Example cleaning by @rvhonorato in https://github.com/haddocking/haddock3/pull/36
Refactor scoring pipeline by @rvhonorato in https://github.com/haddocking/haddock3/pull/38
corrects ln typo by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/46
Re-implement rigid body docking by @rvhonorato in https://github.com/haddocking/haddock3/pull/41
Implement the semi flexible refinement module (flexref) by @rvhonorato in https://github.com/haddocking/haddock3/pull/50
Implement water refinement (waterref) module by @rvhonorato in https://github.com/haddocking/haddock3/pull/51
Add emref module by @rvhonorato in https://github.com/haddocking/haddock3/pull/56
Rename waterref to mdref by @rvhonorato in https://github.com/haddocking/haddock3/pull/58
Example fix by @rvhonorato in https://github.com/haddocking/haddock3/pull/60
Remove input layer from configuration file by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/62
New modules structure and names by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/59
Removing stage key as a requirement for the configuration file by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/63
Moves and adjusts greeting messages by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/65
Implement clustfcc module by @rvhonorato in https://github.com/haddocking/haddock3/pull/67
Update readme and minor path after #67 by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/70
Move examples data to its own folder by @rvhonorato in https://github.com/haddocking/haddock3/pull/73
Add third-party module gdock by @rvhonorato in https://github.com/haddocking/haddock3/pull/72
Handling defaults by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/64
Corrects path to example/data in lightdock.toml file by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/79
Add seletop module by @rvhonorato in https://github.com/haddocking/haddock3/pull/77
reviewing subprocesses by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/66
Ensures misspelled keys in config files do not pass silently by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/83
adds setup only option by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/84
Modularizes cli.py by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/85
Updates clusterfcc to #66 - missing by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/87
moves mathutil to libmath by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/86
Reactivates --restart option by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/88
ReOrganizes some files, folder, and code by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/89
Inspect dependencies are installed for thirdparty libraries by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/93
Make weights configurable parameters by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/91
Implements dedicated configuration reader by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/81
Removes the need for activate_haddock global variables setup by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/104
Corrects for the rare case of number of CPUs = 0 by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/107
Removes remaining toml dependency after #81 by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/109
Implements CI for python modules by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/110
remove py310 action and env by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/111
Updates the logging system by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/106
Improves Scheduler ctrl+c handling by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/105
Corrects var names critical errors by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/112
Codecoving by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/114
Lints the code so far by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/113
removed py310 from tox by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/115
Clean the CNS part of the rigidbody docking module by @amjjbonvin in https://github.com/haddocking/haddock3/pull/124
Further cleaning of the topoaa, rigidbody and flexref modules by @amjjbonvin in https://github.com/haddocking/haddock3/pull/127
Models start 1-index by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/129
Implement caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/130
Update caprieval defaults.cfg by @rvhonorato in https://github.com/haddocking/haddock3/pull/135
Correct enumerate syntax by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/137
Adds support for global variables for CNS by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/136
Cleaned emref module and adapted other to new env variables by @amjjbonvin in https://github.com/haddocking/haddock3/pull/140
Added example, some cns module corrections/additions by @amjjbonvin in https://github.com/haddocking/haddock3/pull/145
Bugfix caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/147
Solves missing repeated modules during prepare_run by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/150
Fixes arrays being overwritten in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/155
Implement ensemble support for docking in CNS-based modules by @rvhonorato in https://github.com/haddocking/haddock3/pull/152
Add support for ligands and DNA and refactor mdref module by @amjjbonvin in https://github.com/haddocking/haddock3/pull/156
Add homotrimer docking example with C3 symmetry by @amjjbonvin in https://github.com/haddocking/haddock3/pull/161
None variables are NOT written to CNS by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/163
improves on #163 by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/167
empty strings are written to CNS by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/168
input params in topoaa/defaults.cfg now with proper behaviour by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/169
Added protein-ligand-shape example by @amjjbonvin in https://github.com/haddocking/haddock3/pull/170
Improves regex for scientific notation in config reader by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/174
Added check to make sure the seed file is present before reading. by @amjjbonvin in https://github.com/haddocking/haddock3/pull/175
Add scores to caprieval output by @rvhonorato in https://github.com/haddocking/haddock3/pull/180
Add .vscode to gitignore by @rvhonorato in https://github.com/haddocking/haddock3/pull/181
Add option to "sortby" in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/182
Revert "Merge pull request #182 from haddocking/153" by @rvhonorato in https://github.com/haddocking/haddock3/pull/184
Change log statements by @rvhonorato in https://github.com/haddocking/haddock3/pull/159
Benchmarking system and configuration. by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/116
Add option to sort-by in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/185
Tweak logs by @rvhonorato in https://github.com/haddocking/haddock3/pull/188
Refactor code to allow for Refinement by @rvhonorato in https://github.com/haddocking/haddock3/pull/187
Add sampling_factor parameter to refinement modules by @rvhonorato in https://github.com/haddocking/haddock3/pull/189
Implement HPC execution by @rvhonorato in https://github.com/haddocking/haddock3/pull/192
Fix HPC completed percentage by @rvhonorato in https://github.com/haddocking/haddock3/pull/193
Sort tasks while initializing libparallel by @rvhonorato in https://github.com/haddocking/haddock3/pull/197
Small tweaks to the benchmark scripts by @rvhonorato in https://github.com/haddocking/haddock3/pull/195
Fix sorting of paralel jobs by @rvhonorato in https://github.com/haddocking/haddock3/pull/202
Updates clarifies install instructions by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/203
Refactor code to allow for scoring by @rvhonorato in https://github.com/haddocking/haddock3/pull/199
Use MODDIR instead of MODRUN rigidbody.cns by @amjjbonvin in https://github.com/haddocking/haddock3/pull/207
Do not delete the run dir. by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/191
Add queue parameter to libhpc by @rvhonorato in https://github.com/haddocking/haddock3/pull/205
Fix libparallel to correctly use ncores by @rvhonorato in https://github.com/haddocking/haddock3/pull/211
Export environment variables to a file per module. by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/214
remove prints / asserts by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/215
Starts using flake8-print by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/218
Implement rank column in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/213
Solves issue 220 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/223
Add support for DNA/Ligands in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/224
Edit libhpc with new variable scheme by @rvhonorato in https://github.com/haddocking/haddock3/pull/226
Make caprieval automatically match numbering and identify atoms by @rvhonorato in https://github.com/haddocking/haddock3/pull/230
Sort models from previous module by score in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/234
fix caprieval reading from the wrong reslist when assembling the numbering reference by @rvhonorato in https://github.com/haddocking/haddock3/pull/237
Use data dir to store input data and point relative paths by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/219
Implement unit tests for caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/239
Update clustfcc by @rvhonorato in https://github.com/haddocking/haddock3/pull/241
Validates module's name by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/246
Add cluster information in PDBobject by @rvhonorato in https://github.com/haddocking/haddock3/pull/247
gdock update by @rvhonorato in https://github.com/haddocking/haddock3/pull/252
add run examples scripts by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/238
corrects dictionary to tuple of tuples in run_examples.py by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/256
Add ori_names to PDBobject by @rvhonorato in https://github.com/haddocking/haddock3/pull/250
Fixes issue #257 by @amjjbonvin in https://github.com/haddocking/haddock3/pull/258
Implement automatic threshold in clustfcc by @rvhonorato in https://github.com/haddocking/haddock3/pull/255
No limit of 20 molecules for topoaa by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/261
Implement fault tolerance by @rvhonorato in https://github.com/haddocking/haddock3/pull/260
tolerancy should be tolerance by @rvhonorato in https://github.com/haddocking/haddock3/pull/264
Update libhpc by @rvhonorato in https://github.com/haddocking/haddock3/pull/263
Implement lt, gt and eq operators to PDBFile by @rvhonorato in https://github.com/haddocking/haddock3/pull/266
Update seletopclusts with the newest changes by @rvhonorato in https://github.com/haddocking/haddock3/pull/248
Implemented JobInputFirst by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/267
Refactored the parameter flow by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/268
Changes to make caprieval work on the homotrimer example by @amjjbonvin in https://github.com/haddocking/haddock3/pull/279
Add support for mixed-systems and modified aminoacids in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/281
Implement expandable parameter groups, clean default parameters, refactor CNS scripts, and tweak examples by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/280
Switched to cdie for emref and mdref (to match 2.4 settings) by @amjjbonvin in https://github.com/haddocking/haddock3/pull/283
Add option to select all clusters in seletopclusts by @rvhonorato in https://github.com/haddocking/haddock3/pull/286
Add dockq metric to caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/287
Add cluster information to caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/288
Restrict characters accepted in strings and paths by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/277
Added full sampling -full.cfg and create test scenarios -test.cfg config files by @amjjbonvin in https://github.com/haddocking/haddock3/pull/291
Solves issue #292 - adds test/full cfg files for protein-peptide by @amjjbonvin in https://github.com/haddocking/haddock3/pull/293
Update modules to pass the correct variable to ModuleIO by @rvhonorato in https://github.com/haddocking/haddock3/pull/295
Remove input layer in topoaa module. by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/300
Add documentation about whitespaces in run_test.py by @rvhonorato in https://github.com/haddocking/haddock3/pull/299
[REDO] Set tolerance of modules in the workflow integration tests to 20% by @rvhonorato in https://github.com/haddocking/haddock3/pull/298
Correct libhpc.HPCScheduler defaults by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/301
Convert default.cfg to YAML files by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/274
Correct explevels by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/306
Added description to topoaa default.yaml file by @amjjbonvin in https://github.com/haddocking/haddock3/pull/308
update pdbtools dependencies by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/310
Update deps versions - forcing exact numbers by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/311
Updated install instructions by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/314
Remove missing PDBs from ModuleIO by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/313
Add hierarchy to the categories by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/316
Corrects explevels in haddock3-cfg choices by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/315
Add unittests to cns_paths lib by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/319
Add YAML for mandatory parameters by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/318
Adds some comments and testing for the main CLI by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/320
ignores explvl = hidden by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/322
Corrects #322 by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/324
Rigidbody yaml by @amjjbonvin in https://github.com/haddocking/haddock3/pull/325
corrects explvl by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/326
Emref yaml documentation and script cleaning by @amjjbonvin in https://github.com/haddocking/haddock3/pull/330
deafult.yaml additional tests by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/331
Reviews and updates CONTRIBUTING by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/328
Removing prot_segid_* from yaml configs by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/323
Mdref yaml documentation and CNS scripts updates by @amjjbonvin in https://github.com/haddocking/haddock3/pull/332
Add elapsed time to modules and to the whole run by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/335
Implement libmpi by @rvhonorato in https://github.com/haddocking/haddock3/pull/336
Add new rule for expandable parameters by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/338
Flexref yaml documentation by @amjjbonvin in https://github.com/haddocking/haddock3/pull/341
Further improves CONTRIBUTING by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/334
Added documentation to emscoring yaml file by @amjjbonvin in https://github.com/haddocking/haddock3/pull/343
Added new MD refinement module by @amjjbonvin in https://github.com/haddocking/haddock3/pull/344
Consider cluster centers in clustfcc by @rvhonorato in https://github.com/haddocking/haddock3/pull/346
Cleaning expandable parameters logic by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/340
Verbosity by @amjjbonvin in https://github.com/haddocking/haddock3/pull/347
Remove hardcoded top_n value in clustfcc by @rvhonorato in https://github.com/haddocking/haddock3/pull/348
update PR template by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/351
make topoaa.molX and mol_ parameter expandable by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/350
Impelement cluster-based output in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/353
Updates examples by @amjjbonvin in https://github.com/haddocking/haddock3/pull/359
Fix % display in libhpc by @rvhonorato in https://github.com/haddocking/haddock3/pull/360
tile in topoaa.defaults.mol1 should be title by @sverhoeven in https://github.com/haddocking/haddock3/pull/361
Improves defaults.yaml tests by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/362
Googleform by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/363
Install fcc over https by @sverhoeven in https://github.com/haddocking/haddock3/pull/368
Read yaml should return always a dictionary by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/374
removes requirement of docstrings in tests by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/377
lifts ModuleIO export to baseclass by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/375
Max number of molecules defined in a single place - the config by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/379
Zerofill by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/378
Faster fuzzy matching on user supplied parameters and paths by @douweschulte in https://github.com/haddocking/haddock3/pull/381
Corrects edge case in zero filling modules folder names by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/383
Lifts zero fill logic to gear by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/391
Improve docs and tests for a part of the setup_run function by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/390
modules prefix to defaults by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/389
Caprieval parallel by @mgiulini in https://github.com/haddocking/haddock3/pull/385
Ignore WAT residues in caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/399
Remove solvent molecules from the output of mdscoring by @amjjbonvin in https://github.com/haddocking/haddock3/pull/401
Bugfix for numbering reference between model and receptor by @rvhonorato in https://github.com/haddocking/haddock3/pull/404
Correct small (future) bug in reading self_contained parameter by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/410
added input output dictionary in scoring modules by @mgiulini in https://github.com/haddocking/haddock3/pull/397
Updates manual integration tests with documentation by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/396
added missing os by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/412
Modules output params.cfg by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/409
Add documentation file structure and CI by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/413
amend threshold behavior in clustfcc by @mgiulini in https://github.com/haddocking/haddock3/pull/415
updates CI to flake8-print v5 by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/419
Additional unit tests and newline improvements in config_writer by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/418
Correct minor typo by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/420
Reduce pytest verbosity by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/423
update pdb-tools version to 2.4.5 by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/424
Implement RMSD clustering and matrix analysis modules by @mgiulini in https://github.com/haddocking/haddock3/pull/414
Improves method to find step folders in a run directory by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/427
Corrects bug in --restart by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/428
Documentation for "continuing" runs functionalities by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/392
Implements --start-from-copy option defined in #392 by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/425
Test module clustfcc by @mgiulini in https://github.com/haddocking/haddock3/pull/430
rename --start-from-copy to --extend-run by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/429
Geometry library by @mgiulini in https://github.com/haddocking/haddock3/pull/431
Changed some parameters to hidden by @amjjbonvin in https://github.com/haddocking/haddock3/pull/434
Update README file for Beta version by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/435
Corrects README.md heading numbers by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/440

New Contributors

@SSchott made their first contribution in https://github.com/haddocking/haddock3/pull/18
@joaomcteixeira made their first contribution in https://github.com/haddocking/haddock3/pull/23
@sverhoeven made their first contribution in https://github.com/haddocking/haddock3/pull/361
@douweschulte made their first contribution in https://github.com/haddocking/haddock3/pull/381
@mgiulini made their first contribution in https://github.com/haddocking/haddock3/pull/385

Full Changelog: https://github.com/haddocking/haddock3/compare/v3.0.alpha2...v3.0.0-beta.1

- Python
Published by joaomcteixeira about 4 years ago

haddock3 - Haddock3.0.alpha2

Setup/execute in a single command (haddock3.py)
Scoring workflow refactoring to correctly implement third-party software
Scoring scripts updated to the latest version (as per Haddock2.4)
Add CNS compilation patches
Implemented benchmarking tools
New routine to re-submit failed jobs by changing the random seed

- Python
Published by rvhonorato about 6 years ago

haddock3 - Alpha 1

First version of the skeleton code, Simple protein-protein with ambiguious restraints Scoring of an ensamble of models (clustering included)

- Python
Published by rvhonorato over 6 years ago

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