bio_tools 0.1.3

Install, run, and inspect computational biology and chemistry tools, e.g. AlphaFold, Boltz, RFdiffusion3, and ProteinMPNN
Documentation 
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use crate::{
    LaunchType, License, LicenseCategory, ProcessExpense, SpecData, ToolCategory,
    tool_definitions::{
        Tool,
        catalog::{CatalogEntry, DataType, Identity, PrimaryInput},
    },
};

/// Property prediction first: it scores mutations rather than producing
/// sequences, and is used to triage a design campaign's output rather than
/// to generate it.
pub const ENTRY: CatalogEntry = CatalogEntry {
    identity: Identity::Installed(Tool::ThermoMpnn),
    categories: &[
        ToolCategory::PropertyPrediction,
        ToolCategory::ProteinDesign,
    ],
    launch_type: LaunchType::PythonBasedApp,
    license_type: LicenseCategory::Permissive,
    expense: ProcessExpense::Moderate,
    primary_output: Some(DataType::Csv),
    primary_inputs: &[PrimaryInput::new("pdb", &[DataType::Pdb])],
    top_choice: true,
    spec: SpecData {
        summary: "A graph neural network (GNN) trained using transfer learning to predict changes in stability for protein point mutants",
        description: "A deep learning–based method for predicting thermostability changes quickly and accurately given \
        only an initial protein structure.",
        availability: "Installed by setup_system.sh into its own uv environment; weights ship with the checkout",
        license_details: "MIT (Kuhlman Lab), weights included, over MIT-licensed ProteinMPNN. Commercial use is unrestricted.",
        repo_url: Some("https://github.com/Kuhlman-Lab/ThermoMPNN"),
        home_url: None,
        docs_url: Some("https://github.com/Kuhlman-Lab/ThermoMPNN#readme"),
        input_params_url: Some(
            "https://github.com/Kuhlman-Lab/ThermoMPNN/blob/main/analysis/custom_inference.py",
        ),
        examples_url: Some("https://github.com/Kuhlman-Lab/ThermoMPNN/tree/main/examples"),
        paper_url: Some("https://www.pnas.org/doi/10.1073/pnas.2314853121"),
        license: License::Mit,
        license_url: None,
        tested: true,
    },
};