v3.0.0-beta.5

haddock3 beta 5 release

What's Changed

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

New Contributors

• @alchemistcai made their first contribution in #645

Full Changelog: v3.0.0-beta.4...v3.0.0-beta.5

v3.0.0-beta.4

What's Changed

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

New Contributors

• @SarahAlidoost made their first contribution in #611
• @dependabot made their first contribution in #671

Full Changelog: v3.0.0-beta.3...v3.0.0-beta.4

v3.0.0-beta.3

What's Changed

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

New Contributors

• @cvnoort made their first contribution in #469
• @bvreede made their first contribution in #607

Full Changelog: v3.0.0-beta.2...v3.0.0-beta.3

v3.0.0-beta.2

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

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

Full Changelog: v3.0.0-beta.1...v3.0.0-beta.2

v3.0.0-beta.1

What's Changed

• activate exports by @SSchott in #18
• LightDock sampling by @brianjimenez in #20
• Drop class name analogies favoring technical names by @rvhonorato in #21
• Clarifies main branch status by @joaomcteixeira in #23
• data_path not being found by @joaomcteixeira in #24
• renames flavour to mode missing files by @joaomcteixeira in #26
• Update installation instructions by @joaomcteixeira in #25
• Transforms haddock3 into a python package by @joaomcteixeira in #28
• Reduces code repetition in pdbutil when checking for new files by @joaomcteixeira in #31
• Correct ln command typo and updates CNS_EXE path to bin/cns by @rvhonorato in #34
• Example cleaning by @rvhonorato in #36
• Refactor scoring pipeline by @rvhonorato in #38
• corrects ln typo by @joaomcteixeira in #46
• Re-implement rigid body docking by @rvhonorato in #41
• Implement the semi flexible refinement module (flexref) by @rvhonorato in #50
• Implement water refinement (waterref) module by @rvhonorato in #51
• Add emref module by @rvhonorato in #56
• Rename waterref to mdref by @rvhonorato in #58
• Example fix by @rvhonorato in #60
• Remove input layer from configuration file by @joaomcteixeira in #62
• New modules structure and names by @joaomcteixeira in #59
• Removing stage key as a requirement for the configuration file by @joaomcteixeira in #63
• Moves and adjusts greeting messages by @joaomcteixeira in #65
• Implement clustfcc module by @rvhonorato in #67
• Update readme and minor path after #67 by @joaomcteixeira in #70
• Move examples data to its own folder by @rvhonorato in #73
• Add third-party module gdock by @rvhonorato in #72
• Handling defaults by @joaomcteixeira in #64
• Corrects path to example/data in lightdock.toml file by @joaomcteixeira in #79
• Add seletop module by @rvhonorato in #77
• reviewing subprocesses by @joaomcteixeira in #66
• Ensures misspelled keys in config files do not pass silently by @joaomcteixeira in #83
• adds setup only option by @joaomcteixeira in #84
• Modularizes cli.py by @joaomcteixeira in #85
• Updates clusterfcc to #66 - missing by @joaomcteixeira in #87
• moves mathutil to libmath by @joaomcteixeira in #86
• Reactivates --restart option by @joaomcteixeira in #88
• ReOrganizes some files, folder, and code by @joaomcteixeira in #89
• Inspect dependencies are installed for thirdparty libraries by @joaomcteixeira in #93
• Make weights configurable parameters by @joaomcteixeira in #91
• Implements dedicated configuration reader by @joaomcteixeira in #81
• Removes the need for activate_haddock global variables setup by @joaomcteixeira in #104
• Corrects for the rare case of number of CPUs = 0 by @joaomcteixeira in #107
• Removes remaining toml dependency after #81 by @joaomcteixeira in #109
• Implements CI for python modules by @joaomcteixeira in #110
• remove py310 action and env by @joaomcteixeira in #111
• Updates the logging system by @joaomcteixeira in #106
• Improves Scheduler ctrl+c handling by @joaomcteixeira in #105
• Corrects var names critical errors by @joaomcteixeira in #112
• Codecoving by @joaomcteixeira in #114
• Lints the code so far by @joaomcteixeira in #113
• removed py310 from tox by @joaomcteixeira in #115
• Clean the CNS part of the rigidbody docking module by @amjjbonvin in #124
• Further cleaning of the topoaa, rigidbody and flexref modules by @amjjbonvin in #127
• Models start 1-index by @joaomcteixeira in #129
• Implement caprieval by @rvhonorato in #130
• Update caprieval defaults.cfg by @rvhonorato in #135
• Correct enumerate syntax by @joaomcteixeira in #137
• Adds support for global variables for CNS by @joaomcteixeira in #136
• Cleaned emref module and adapted other to new env variables by @amjjbonvin in #140
• Added example, some cns module corrections/additions by @amjjbonvin in #145
• Bugfix caprieval by @rvhonorato in #147
• Solves missing repeated modules during prepare_run by @joaomcteixeira in #150
• Fixes arrays being overwritten in caprieval by @rvhonorato in #155
• Implement ensemble support for docking in CNS-based modules by @rvhonorato in #152
• Add support for ligands and DNA and refactor mdref module by @amjjbonvin in #156
• Add homotrimer docking example with C3 symmetry by @amjjbonvin in #161
• None variables are NOT written to CNS by @joaomcteixeira in #163
• improves on #163 by @joaomcteixeira in #167
• empty strings are written to CNS by @joaomcteixeira in #168
• input params in topoaa/defaults.cfg now with proper behaviour by @joaomcteixeira in #169
• Added protein-ligand-shape example by @amjjbonvin in #170
• Improves regex for scientific notation in config reader by @joaomcteixeira in #174
• Added check to make sure the seed file is present before reading. by @amjjbonvin in #175
• Add scores to caprieval output by @rvhonorato in #180
• Add .vscode to gitignore by @rvhonorato in #181
• Add option to "sortby" in caprieval by @rvhonorato in #182
• Revert "Merge pull request #182 from haddocking/153" by @rvhonorato in #184
• Change log statements by @rvhonorato in #159
• Benchmarking system and configuration. by @joaomcteixeira in #116
• Add option to sort-by in caprieval by @rvhonorato in #185
• Tweak logs by @rvhonorato in #188
• Refactor code to allow for Refinement by @rvhonorato in #187
• Add sampling_factor parameter to refinement modules by @rvhonorato in #189
• Implement HPC execution by @rvhonorato in #192
• Fix HPC completed percentage by @rvhonorato in #193
• Sort tasks while initializing libparallel by @rvhonorato in #197
• Small tweaks to the benchmark scripts by @rvhonorato in #195
• Fix sorting of paralel jobs by @rvhonorato in #202
• Updates clarifies install instructions by @joaomcteixeira in #203
• Refactor code to allow for scoring by @rvhonorato in #199
• Use MODDIR instead of MODRUN rigidbody.cns by @amjjbonvin in #207
• Do not delete the run dir. by @joaomcteixeira ...

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

Alpha 1

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