Issues

• Use gemmi instead of PyMOL to generate symmetry mates

  enhancement
  prism-science/WaterFlow#108 · Filter by author vratins opened on Aug 22, 2026

• Formalize constants everywhere

  prism-science/WaterFlow#104 · Filter by author vratins opened on Aug 20, 2026

• Extract the new inference dataset helpers into a common module for datasets.

  enhancement
  prism-science/WaterFlow#103 · Filter by author vratins opened on Aug 20, 2026

• Clean up the pre-processing method in dataset.py

  prism-science/WaterFlow#87 · Filter by author vratins opened on Jul 16, 2026

• Track waters in the dataset that have no EDIA data when the EDIA file exists

  enhancementlow priority
  prism-science/WaterFlow#76 · Filter by author vratins opened on Mar 26, 2026

• Add instructions to generate EDIA data

  buglow priority
  prism-science/WaterFlow#75 · Filter by author vratins opened on Mar 25, 2026

• Dockerfile runtime stage runs as root — output files on host owned by root

  prism-science/WaterFlow#73 · Filter by author coderabbitai opened on Mar 25, 2026

• Dealing with alt-locs and partial occupancy for waters

  enhancement
  prism-science/WaterFlow#71 · Filter by author vratins opened on Mar 25, 2026

• Deciding exact methodology for selecting waters and their positions with crystal contacts.

  enhancement
  prism-science/WaterFlow#68 · Filter by author vratins opened on Mar 24, 2026

• Store the processing metadata when generating cache

  enhancement
  prism-science/WaterFlow#66 · Filter by author vratins opened on Mar 23, 2026

• Cleaning up structure of input files to the pipeline

  enhancement
  prism-science/WaterFlow#65 · Filter by author vratins opened on Mar 20, 2026

• Re-factor code to avoid repeated code

  enhancement
  prism-science/WaterFlow#60 · Filter by author vratins opened on Mar 19, 2026

• Track RBF cutoff/radius in checkpoint args dict

  bug
  prism-science/WaterFlow#59 · Filter by author vratins opened on Mar 19, 2026

• Add correctness tests for Euler/RK4 integration

  enhancement
  prism-science/WaterFlow#58 · Filter by author vratins opened on Mar 19, 2026

• Add tests to increase coverage of gvp_encoder.py and utils.py to > 80%

  enhancement
  prism-science/WaterFlow#56 · Filter by author vratins opened on Mar 18, 2026

• Fix ty github action for unresolved-imports

  bug
  prism-science/WaterFlow#55 · Filter by author vratins opened on Mar 18, 2026

• Set up tests to use GPUs and test forward passes with it

  enhancement
  prism-science/WaterFlow#52 · Filter by author vratins opened on Mar 18, 2026

• Rename CLI flags to be consistent between train.py and inference.py

  documentationenhancement
  prism-science/WaterFlow#50 · Filter by author DorisMai opened on Mar 10, 2026

• Clarify usage of duplicate_single_sample flag

  prism-science/WaterFlow#49 · Filter by author DorisMai opened on Mar 10, 2026

• Accept general pdb/cif file names as input

  enhancement
  prism-science/WaterFlow#48 · Filter by author DorisMai opened on Mar 10, 2026

• Refactor the src directory into submodules

  enhancement
  prism-science/WaterFlow#46 · Filter by author DorisMai opened on Mar 9, 2026

• create cache manager class to handle caching directories, names, paths etc.

  enhancement
  prism-science/WaterFlow#41 · Filter by author vratins opened on Feb 27, 2026

• ESM embeddings should handle/account for alt-locs

  enhancement
  prism-science/WaterFlow#40 · Filter by author vratins opened on Feb 27, 2026
  2

• SLAE should be installable as a site-package

  bug
  prism-science/WaterFlow#34 · Filter by author vratins opened on Feb 26, 2026

• Rename <atom_type>_x to <atom_type>_feat for clarity

  enhancement
  prism-science/WaterFlow#32 · Filter by author vratins opened on Feb 25, 2026