{
  "project": "PXDesign-main",
  "layout": {
    "conf": "Configuration files, example inputs, license files, and reproduction notes.",
    "model": "PXDesign source code, bundled Protenix/PXDesignBench source trees, original README, and assets.",
    "scripts": "Installation, dependency, Docker, and download scripts.",
    "weight": "Model checkpoints, CCD cache, AF2/ProteinMPNN external tool weights, and MSA cache."
  },
  "paths": {
    "pxdesign_package": "model/pxdesign",
    "protenix_source": "model/Protenix-pxd",
    "pxdesignbench_source": "model/PXDesignBench",
    "example_yaml": "conf/examples/PDL1_quick_start.yaml",
    "checkpoint_dir": "weight/release_data/checkpoint",
    "ccd_cache_dir": "weight/release_data/ccd_cache",
    "tool_weights_root": "weight/tool_weights",
    "af2_weights": "weight/tool_weights/af2",
    "mpnn_weights": "weight/tool_weights/mpnn",
    "reproduction_notes": "conf/PXDESIGN_REPRODUCTION_NOTES.md",
    "original_readme": "model/README.md"
  },
  "environment": {
    "conda_env_used": "model_bio",
    "tool_weights_root_env": "TOOL_WEIGHTS_ROOT=$PWD/weight/tool_weights",
    "protenix_data_root_env": "PROTENIX_DATA_ROOT_DIR=$PWD/weight/release_data/ccd_cache"
  },
  "validated_tasks": [
    "pxdesign check-input",
    "pxdesign parse-target",
    "pxdesign infer",
    "pxdesign pipeline --preset preview",
    "pxdesign pipeline --preset extended"
  ],
  "hpc_runtime_overrides": {
    "use_fast_ln": false,
    "use_deepspeed_evo_attention": false,
    "reason": "The DTK/HIP environment failed to build fastfold_layer_norm_cuda with CUDA compiler flags."
  }
}