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refactor modularity-breaking implementations

refactoringcode improvements without functionality changescode improvements without functionality changes

Status: Open.

#1530 In haddocking/haddock3;

· rvhonorato opened on Apr 21, 2026

Add caching to store RMSD values

featureAdding something new to the codebaseAdding something new to the codebase

Status: Open.

#1528 In haddocking/haddock3;

· rvhonorato opened on Apr 21, 2026

Filter models based on global RMDS

enhancementImproving something in the codebaseImproving something in the codebase

m|filter

planned-long-termIssues that will be eventually done, used to mark issues as TODO itemsIssues that will be eventually done, used to mark issues as TODO items

yaml default parametersAnything related to the YAML configuration files for default parametersAnything related to the YAML configuration files for default parameters

Status: Open.

Feature

#1525 In haddocking/haddock3;

· AnnaKravchenko opened on Apr 17, 2026

Allow handling of molecules with more than 99999 atoms

enhancementImproving something in the codebaseImproving something in the codebase

m|topoaatopoaa moduletopoaa module

Status: Open.

#1506 In haddocking/haddock3;

· amjjbonvin opened on Apr 9, 2026

Enable docking of membrane proteins embedded into a bilayer

featureAdding something new to the codebaseAdding something new to the codebase

planned-long-termIssues that will be eventually done, used to mark issues as TODO itemsIssues that will be eventually done, used to mark issues as TODO items

Status: Open.

#1486 In haddocking/haddock3;

· amjjbonvin opened on Mar 4, 2026

Add support for custom alignment file in [caprieval]

featureAdding something new to the codebaseAdding something new to the codebase

m|caprievalImprovements in caprieval moduleImprovements in caprieval module

planned-long-termIssues that will be eventually done, used to mark issues as TODO itemsIssues that will be eventually done, used to mark issues as TODO items

Status: Open.

#1410 In haddocking/haddock3;

· AnnaKravchenko opened on Oct 3, 2025

Add an option to restrain non-canonical NA pairs

CNSImprovements in the CNS engineImprovements in the CNS engine

communityFeature requests / contribution / issues from usersFeature requests / contribution / issues from users

enhancementImproving something in the codebaseImproving something in the codebase

m|emrefemref moduleemref module

m|flexrefflexref moduleflexref module

m|mdrefmdref modulemdref module

planned-long-termIssues that will be eventually done, used to mark issues as TODO itemsIssues that will be eventually done, used to mark issues as TODO items

Status: Open.

Feature

#1397 In haddocking/haddock3;

· AnnaKravchenko opened on Sep 19, 2025

Refactor align_full in libnotebooks

enhancementImproving something in the codebaseImproving something in the codebase

planned-long-termIssues that will be eventually done, used to mark issues as TODO itemsIssues that will be eventually done, used to mark issues as TODO items

Status: Open.

#1375 In haddocking/haddock3;

· AnnaKravchenko opened on Sep 4, 2025

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

bugSomething isn't workingSomething isn't working

m|emrefemref moduleemref module

m|flexrefflexref moduleflexref module

m|mdrefmdref modulemdref module

Status: Open.

#1349 In haddocking/haddock3;

· AnnaKravchenko opened on Aug 13, 2025

Analsysis module describing interactions

enhancementImproving something in the codebaseImproving something in the codebase

featureAdding something new to the codebaseAdding something new to the codebase

planned-long-termIssues that will be eventually done, used to mark issues as TODO itemsIssues that will be eventually done, used to mark issues as TODO items

Status: Open.

#1336 In haddocking/haddock3;

· VGPReys opened on Jul 29, 2025

Add modules that could add/delete molecules within a workflow

featureAdding something new to the codebaseAdding something new to the codebase

planned-long-termIssues that will be eventually done, used to mark issues as TODO itemsIssues that will be eventually done, used to mark issues as TODO items

workflowAll the general parts of HADDOCK3 not related to any module in particularAll the general parts of HADDOCK3 not related to any module in particular

Status: Open.

#992 In haddocking/haddock3;

· amjjbonvin opened on Sep 2, 2024

haddock3 workflow without starting with topoaa

executionRelated to execution modes, such as GRID, HPC, local, etc.Related to execution modes, such as GRID, HPC, local, etc.

planned-long-termIssues that will be eventually done, used to mark issues as TODO itemsIssues that will be eventually done, used to mark issues as TODO items

Status: Open.

#932 In haddocking/haddock3;

· VGPReys opened on Jul 10, 2024