kira-protein-longevity-analysis

Rust CLI tool for physics-informed protein robustness and fragility analysis under environmental conditions (pH, oxidative stress, temperature).

Installation

Install from crates.io (Rust 1.91+ / Windows / Linux / MacOS):

cargo install kira-protein-longevity-analysis

Or

Build from source (Rust 1.91+):

cargo build --release

Usage

kira-protein-longevity-analysis analyze --input <file_or_dir> --ph 5.8 --ros high --temp-c 39

Options:

• --input <file_or_dir>: structure file or directory of .cif/.mmcif/.pdb
• --fasta <file>: optional FASTA (currently unused)
• --ph <float>: environment pH (default 7.4)
• --ros <low|normal|high>: oxidative stress level (default normal)
• --temp-c <float>: temperature in C (default 37.0)
• --threads <usize>: worker threads (default: num_cpus)
• --backend <scalar|simd>: SIMD backend selection
• --format <json|tsv>: output format (default json)
• --out <file>: output file (stdout if omitted)
• --short: reduce output payload
• --verbose: per-stage timing info

Notes

• Heuristic scoring only (no MD or Rosetta).
• Deterministic output for the same inputs.

Sample output (for hen egg-white lysozyme)

.\target\release\kira-protein-longevity-analysis.exe  analyze --input 1LYZ.cif --ph 4.5 --ros normal --temp-c 37 --short
{
  "schema_version": 1,
  "tool": "kira-protein-longevity-analysis",
  "env": {
    "ph": 4.5,
    "ros": "Normal",
    "temp_c": 37.0
  },
  "results": [
    {
      "protein_id": "1LYZ",
      "length": 129,
      "chains": 1,
      "robustness": {
        "score": 0.8534382,
        "delta_vs_neutral": -0.069004476,
        "verdict": "ACCEPT"
      },
      "reasons": [
        {
          "tag": "packing:low_core_packing",
          "value": 0.3029582,
          "details": {
            "contribution": 0.0757395476102829
          }
        },
        {
          "tag": "ph:risk_combined",
          "value": 0.2760181,
          "details": {
            "contribution": 0.06900452822446823,
            "electrostatic_risk": 0.1336318999528885,
            "salt_bridge_loss_fraction": 0.2760181128978729
          }
        },
        {
          "tag": "temp:sensitivity",
          "value": 0.018177493,
          "details": {
            "contribution": 0.0018177492311224341
          }
        },
        {
          "tag": "ph:salt_bridge_loss",
          "value": 0.2760181,
          "details": {
            "lost": 122,
            "total": 442
          }
        },
        {
          "tag": "ros:oxidation_exposed",
          "value": 0.0,
          "details": {
            "contribution": 0.0
          }
        },
        {
          "tag": "strain:high_turn_strain",
          "value": 0.0,
          "details": {
            "contribution": 0.0
          }
        },
        {
          "tag": "surface:exposed_hydrophobic_load",
          "value": 0.0,
          "details": {
            "contribution": 0.0
          }
        }
      ],
      "hotspots_topk": [
        {
          "chain": "A",
          "res_idx": 129,
          "aa": "L",
          "fragility": 0.2744191,
          "flags": [
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 128,
          "aa": "R",
          "fragility": 0.25469586,
          "flags": [
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 21,
          "aa": "R",
          "fragility": 0.23720291,
          "flags": [
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 114,
          "aa": "R",
          "fragility": 0.22168806,
          "flags": [
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 5,
          "aa": "R",
          "fragility": 0.19572324,
          "flags": [
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 45,
          "aa": "R",
          "fragility": 0.19572324,
          "flags": [
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 20,
          "aa": "Y",
          "fragility": 0.18489888,
          "flags": [
            "oxidation_prone",
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 127,
          "aa": "C",
          "fragility": 0.18489888,
          "flags": [
            "oxidation_prone",
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 6,
          "aa": "C",
          "fragility": 0.17529854,
          "flags": [
            "oxidation_prone",
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 13,
          "aa": "K",
          "fragility": 0.16678384,
          "flags": [
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 116,
          "aa": "K",
          "fragility": 0.16678384,
          "flags": [
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 33,
          "aa": "K",
          "fragility": 0.15923193,
          "flags": [
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 115,
          "aa": "C",
          "fragility": 0.15923193,
          "flags": [
            "oxidation_prone",
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 68,
          "aa": "R",
          "fragility": 0.15469585,
          "flags": []
        },
        {
          "chain": "A",
          "res_idx": 18,
          "aa": "D",
          "fragility": 0.15253401,
          "flags": [
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 52,
          "aa": "D",
          "fragility": 0.15253401,
          "flags": [
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 30,
          "aa": "C",
          "fragility": 0.14659348,
          "flags": [
            "oxidation_prone",
            "salt_bridge_loss"
          ]
        },
        {
          "chain": "A",
          "res_idx": 22,
          "aa": "G",
          "fragility": 0.13720292,
          "flags": []
        },
        {
          "chain": "A",
          "res_idx": 48,
          "aa": "D",
          "fragility": 0.13720292,
          "flags": []
        },
        {
          "chain": "A",
          "res_idx": 118,
          "aa": "T",
          "fragility": 0.13720292,
          "flags": []
        }
      ]
    }
  ]
}

Test data provenance

This directory contains protein structure files (pdb & cif) obtained from the Protein Data Bank (PDB, https://www.rcsb.org).

PDB data are in the public domain (CC0 1.0). Original authors retain attribution for experimental determination.

These files are included solely for testing and benchmarking purposes.

License

MIT