Issues

• Update haddock3 version in notebooks before October release

  notebooks
  haddocking/haddock3#1702 · Filter by author VGPReys opened on Sep 30, 2026
  1

• The matrix size check in the contactmap module might overestimate the required memory

  enhancementm|contactmap
  haddocking/haddock3#1699 · Filter by author amjjbonvin opened on Sep 23, 2026
  

• Implement validation of workflows against the general default.yaml

  enhancementworkflow
  Feature

  haddocking/haddock3#1693 · Filter by author amjjbonvin opened on Sep 17, 2026

• ncores = -1 gives error

  bug
  haddocking/haddock3#1691 · Filter by author sverhoeven opened on Sep 16, 2026
  3

• We want caching!

  enhancementplanned-long-term
  haddocking/haddock3#1689 · Filter by author AnnaEngel98 opened on Sep 3, 2026
  

• Add protein-RNA example to haddock3/examples

  examplesplanned-long-term
  haddocking/haddock3#1683 · Filter by author AnnaKravchenko opened on Sep 1, 2026
  

• Hardcoded md timestep - is it intenional?

  m|mdrefm|mdscoringquestionStale
  haddocking/haddock3#1680 · Filter by author AnnaKravchenko opened on Sep 1, 2026
  1

• Restrict libparallel scheduler exception handling to expected task failures

  bug
  haddocking/haddock3#1673 · Filter by author sjdv1982 opened on Aug 28, 2026

• update deeprank module to use upstream v2.0.0

  enhancementm|deeprankplanned-long-term
  haddocking/haddock3#1671 · Filter by author rvhonorato opened on Aug 21, 2026

• ssdihed restrains a larger ange region than intended

  bugdocumentationm|cgtoaam|emrefm|flexrefm|mdrefm|mdscoring
  haddocking/haddock3#1668 · Filter by author AnnaKravchenko opened on Aug 18, 2026
  1

  

• Add automated detection of CG base-pairs to dna-restraints.cns

  enhancementm|cgtoaam|emrefm|flexrefm|mdrefm|mdscoring
  haddocking/haddock3#1659 · Filter by author amjjbonvin opened on Aug 7, 2026
  1

  

• CAPRI eval uses different atom sets for DNA in AA and CG mode

  bugm|caprieval
  haddocking/haddock3#1658 · Filter by author amjjbonvin opened on Aug 7, 2026

• Undeterministic behaviour of the martinize function in topocg

  bugm|topocg
  haddocking/haddock3#1657 · Filter by author amjjbonvin opened on Aug 7, 2026
  

• refactor modularity-breaking implementations

  planned-long-termrefactoring
  haddocking/haddock3#1530 · Filter by author rvhonorato opened on Apr 21, 2026
  2

• Add caching to store RMSD values

  featureplanned-long-term
  haddocking/haddock3#1528 · Filter by author rvhonorato opened on Apr 21, 2026
  5

• Allow handling of molecules with more than 99999 atoms

  enhancementm|topoaaplanned-long-term
  haddocking/haddock3#1506 · Filter by author amjjbonvin opened on Apr 9, 2026
  7

  

• Enable docking of membrane proteins embedded into a bilayer

  featureplanned-long-term
  haddocking/haddock3#1486 · Filter by author amjjbonvin opened on Mar 4, 2026
  2

  

• Add support for custom alignment file in [caprieval]

  featurem|caprievalplanned-long-term
  haddocking/haddock3#1410 · Filter by author AnnaKravchenko opened on Oct 3, 2025
  3

  

• Add an option to restrain non-canonical NA pairs

  CNScommunityenhancementm|emrefm|flexrefm|mdrefplanned-long-term
  Feature

  haddocking/haddock3#1397 · Filter by author AnnaKravchenko opened on Sep 19, 2025
  3

• Refactor align_full in libnotebooks

  enhancementplanned-long-term
  haddocking/haddock3#1375 · Filter by author AnnaKravchenko opened on Sep 4, 2025
  1

• Refinement workflow output contains cns error file, but workflow is not affected

  bugm|emrefm|flexrefm|mdref
  haddocking/haddock3#1349 · Filter by author AnnaKravchenko opened on Aug 13, 2025
  3

• Analsysis module describing interactions

  enhancementfeatureplanned-long-term
  haddocking/haddock3#1336 · Filter by author VGPReys opened on Jul 29, 2025
  7

  

• Add modules that could add/delete molecules within a workflow

  featureplanned-long-termworkflow
  haddocking/haddock3#992 · Filter by author amjjbonvin opened on Sep 2, 2024
  6

  

• haddock3 workflow without starting with topoaa

  executionplanned-long-term
  haddocking/haddock3#932 · Filter by author VGPReys opened on Jul 10, 2024
  3

  

• Add a saxsscore module.

  featurem|saxsscoreplanned-long-term
  haddocking/haddock3#433 · Filter by author rvhonorato opened on May 16, 2022
  9