Haddock3 Versions Save

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

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 pull_request_template.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 capri_ss cli_analyse 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 fail_ci_if_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 max_molecules_allowed 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

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

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

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

• 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

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