Issues

• Bug: Adding feature_transforms with the 'transform' value non None causes ASCII errors during training

  bug
  DeepRank/deeprank2#653 · Filter by author Norgent opened on Oct 17, 2025
  5

• No preclustering logic when loading pre-trained model for inference

  stale
  DeepRank/deeprank2#652 · Filter by author Norgent opened on Oct 1, 2025
  1

• Improvements to PyPi listing/pyproject.toml

  docsstale
  DeepRank/deeprank2#648 · Filter by author DaniBodor opened on Jan 14, 2025
  1

• re-order add_feature arguments

  covariatesdiscstale
  DeepRank/deeprank2#633 · Filter by author DaniBodor opened on Jul 22, 2024
  3

• Add single proteins/molecules class

  stale
  DeepRank/deeprank2#605 · Filter by author gcroci2 opened on May 21, 2024

• Provide the trained models for various scenarios.

  featurestale
  DeepRank/deeprank2#602 · Filter by author amjjbonvin opened on Mar 22, 2024
  5

• Create a tutorial for the antibody-antigen docking models use case

  blocked
  DeepRank/deeprank2#556 · Filter by author gcroci2 opened on Jan 15, 2024 · M1.4: Tutorials&Datasets

• Create a tutorial for the protein-ligand complexes use case

  blocked
  DeepRank/deeprank2#555 · Filter by author gcroci2 opened on Jan 15, 2024 · M1.4: Tutorials&Datasets

• Add example data for antibody-antigen docking models use case

  discneeds infostale
  DeepRank/deeprank2#553 · Filter by author gcroci2 opened on Jan 15, 2024 · M1.4: Tutorials&Datasets
  1

• Add example data for protein-ligand complexes use case

  discneeds infostale
  DeepRank/deeprank2#552 · Filter by author gcroci2 opened on Jan 15, 2024 · M1.4: Tutorials&Datasets
  1

• Create tests and docs for multiple-chain graphs

  blocked
  DeepRank/deeprank2#551 · Filter by author gcroci2 opened on Jan 15, 2024 · M1.3: Multiple-chains

• Create tests and docs for protein-ligand graphs

  blocked
  DeepRank/deeprank2#550 · Filter by author gcroci2 opened on Jan 15, 2024 · M1.2: Protein-ligands

• Deal with residue features in protein-ligand graphs

  blocked
  DeepRank/deeprank2#548 · Filter by author DaniBodor opened on Jan 15, 2024 · M1.2: Protein-ligands

• Allow for multiple-chain graphs

  blockingdiscstale
  DeepRank/deeprank2#547 · Filter by author gcroci2 opened on Jan 15, 2024 · M1.3: Multiple-chains
  6

• Consider allowing mixed resolution graphs for protein-ligand graphs

  blockeddisc
  DeepRank/deeprank2#546 · Filter by author gcroci2 opened on Jan 15, 2024 · M1.2: Protein-ligands

• Create tests and docs for protein-nucleic acid graphs

  blocked
  DeepRank/deeprank2#545 · Filter by author DaniBodor opened on Jan 15, 2024 · M1.1: Protein-nucleic acids

• Allow for none-residue atom entries for protein-ligand graphs

  blockingstale
  DeepRank/deeprank2#544 · Filter by author gcroci2 opened on Jan 15, 2024 · M1.2: Protein-ligands
  1

• Add nucleotides to aminoacidlist for protein-nucleic acid graphs

  blockingstale
  DeepRank/deeprank2#543 · Filter by author DaniBodor opened on Jan 15, 2024 · M1.1: Protein-nucleic acids
  4

• Fix build for Python 3.11

  blockedbugCI
  DeepRank/deeprank2#540 · Filter by author gcroci2 opened on Jan 3, 2024
  3

  

• Make MapMethod an attribute of GridSettings in deeprank2.grid module

  nice to havestale
  DeepRank/deeprank2#516 · Filter by author DaniBodor opened on Nov 1, 2023
  1

• make _set_feature_modules to return ModuleType objects

  nice to havestale
  DeepRank/deeprank2#512 · Filter by author DaniBodor opened on Oct 9, 2023
  1

• variant residue is only added to atomic graphs, but not residue graphs

  bugneeds infostale
  DeepRank/deeprank2#511 · Filter by author DaniBodor opened on Oct 9, 2023
  1

• Integrate PDBprep

  featurestaletools
  DeepRank/deeprank2#509 · Filter by author DaniBodor opened on Oct 4, 2023
  2

  

• Refactor deeprank2.tools.target.add_targets function

  nice to havestale
  DeepRank/deeprank2#499 · Filter by author gcroci2 opened on Sep 20, 2023
  1

• Create feature classes

  nice to havestale
  DeepRank/deeprank2#486 · Filter by author DaniBodor opened on Sep 5, 2023
  2