Releases: haddocking/haddock3
Releases · haddocking/haddock3
2024.10.0b6
What's Changed
- Openmm by @VGPReys in #654
- Interactive rescoring reviewed by @VGPReys in #778
- added chain ID by @mgiulini in #793
- Interactive rescoring and reclustering by @mgiulini in #769
- Zip structures by @mgiulini in #794
- Create action.yml by @amjjbonvin in #797
- Adding mirror pushing to the Castiel EuroHPC GitLab repo by @amjjbonvin in #798
- Add conditional execution for integration job by @rvhonorato in #801
- changed capri columns by @mgiulini in #805
- Side by side2 by @sverhoeven in #799
- Round other cluster + dont add score which was not there before by @sverhoeven in #810
- update codehub sync by @rvhonorato in #812
- Show top 10 ranked clusters + Other cluster by @sverhoeven in #813
- Improve docs by @mgiulini in #803
- Validate example workflows by @mgiulini in #816
- Low level docs by @mgiulini in #815
- Fine tuning Contact map module by @VGPReys in #749
- Mapping TIMEOUT output to failure in libhpc by @VGPReys in #727
- corrected parameter handling for cli-score by @mgiulini in #807
- Calc accessibility by @mgiulini in #820
- Work arround chain matching in IL-RMSDMatrix by @VGPReys in #828
- ordered traceback by @mgiulini in #831
- Fast rmsd by @mgiulini in #809
- Resolves issue #845 - adding missing parameters by @amjjbonvin in #847
- Interactivity fixes by @mgiulini in #823
- Graphical representation of clusters by @VGPReys in #772
- added traceback plot and sum of ranks file by @mgiulini in #850
- Offline mode by @VGPReys in #825
- Fix offlinemode by @VGPReys in #854
- Upgrade contact heatmap by @VGPReys in #855
- changing header info in contact map tsv files by @VGPReys in #856
- Fixing error in caprieval using shapes by @VGPReys in #851
- Fix auto analysis by @mgiulini in #853
- Improved seletopclusts by @VGPReys in #819
- Chain match coords load issue by @VGPReys in #864
- added groups data by @VGPReys in #872
- create new CNSScoringModule class by @VGPReys in #870
- Fair by @VGPReys in #868
- Added alascan modules to tests execution and comparison by @amjjbonvin in #876
- Add prefix to model names from input ensemble by @VGPReys in #878
- Save outputs in case of faulty tolerance by @VGPReys in #880
- Heavy atoms RMSD calculation in caprieval by @VGPReys in #837
- Add
codacy/codacy-coverage-reporter-action
action totests.yml
by @rvhonorato in #875 - Remove faulty outputs before saving io.json by @VGPReys in #883
- Define contact distance cutoff parameter in ilrmsdmatrix by @VGPReys in #881
- corrected absolute path in seletopclusts by @mgiulini in #888
- Improve alascan output by @mgiulini in #889
- Reclusts matrixplot by @VGPReys in #859
- check that file exists before renaming by @VGPReys in #893
- Update CONTRIBUTING.md by @AnnaKravchenko in #890
- Per interface scoring by @amjjbonvin in #896
- updating to latest main version by @amjjbonvin in #899
- Add option to keep the existing b-factor in the input PDB by @amjjbonvin in #898
- Updated CNS installation instructions by @amjjbonvin in #895
- Merge of main branch into the score branch by @amjjbonvin in #902
- Adds the HADDOCK score to the PDB headers - issue #901 by @amjjbonvin in #903
- only run codacy-coverage-reporter-action for same repo by @rvhonorato in #904
- Inverted chains by @mgiulini in #905
- added code of conduct by @mgiulini in #910
- improved postprocessing scaling by @mgiulini in #874
- remove deprecation warnings by @mgiulini in #907
- Reduce number of files in
mode = "local"
by @rvhonorato in #918 - add more good byes by @rvhonorato in #929
- Avoid generating
.seed
files by @rvhonorato in #924 - Makes haddock3 restraints subcommands available as web service by @sverhoeven in #841
- Refactor
rigidbody
module to allow the preparation ofcns_input
to be done in parallel by @rvhonorato in #933 - Use
less_io
parameter incaprieval
by @rvhonorato in #928 - increased max sampling_factor by @mgiulini in #939
- removed duplicated w_air parameter by @amjjbonvin in #946
- Add MPI execution tests by @rvhonorato in #942
- Update repository templates by @rvhonorato in #951
- lazy load MPI module and COMM variable by @rvhonorato in #953
- Refactor
capri.extract_data_from_capri_class
to propagate the model's energy terms by @rvhonorato in #950 - changed min and max clust_cutoff by @mgiulini in #954
- Use
prepare_cns_input_sequential
whenmode
is not local by @rvhonorato in #943 - better description for some modules by @VGPReys in #947
- added ilrmsd to capri clt by @mgiulini in #957
- update
caprieval
integration tests by @rvhonorato in #958 - Handle exceptions in
Worker.run
by @rvhonorato in #962 - Clean intermediate files in batch mode by @VGPReys in #937
- change log level of exceptions in the Worker's run method by @rvhonorato in #966
- Update
caprieval
integration tests with new score values by @rvhonorato in #964 - Fix rescore by @mgiulini in #972
- Add logic to check for incompatible parameters by @rvhonorato in #935
- Propagate cluster related properties in
caprieval
by @rvhonorato in #978 - Ilrmsd onechain clarified by @mgiulini in #922
- Update
README.md
by @rvhonorato in #976 - Change the naming of the phoshpate oxygens to OP1/OP2 by @amjjbonvin in #985
- links to feedbacks by @VGPReys in #997
- Single chain caprieval by @VGPReys in #994
- remove dead code related to DNA in
cm_restraints.cns
by @amjjbonvin in #1001 - modifying amb_scale and unamb_scale parameter names by @VGPReys in #983
- avoid
fileexist
on empty strings by @amjjbonvin in #995 - Fileexist issue update by @amjjbonvin in #1010
- Set tolerance to 5 for non-topoaa modules by @sverhoeven in #1004
- ordering by size in clustrmsd by @mgiulini in #974
- added integration tests for scoring modules by @mgiulini in #968
*...
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 intopoaa
by @joaomcteixeira in #499 - Correct function selection in
topoaa
whenorder=0
andlimit
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
inisort
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 bysortkey
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 thepages.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
fortoml
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 forlocal
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
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 tolibontology
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
fromREMARK
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 updatesCNS_EXE
path tobin/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
tomdref
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
inlightdock.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
andflexref
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 intopoaa/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 ofMODRUN
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)