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},
    },
};

/// Both: the binders are mini-proteins of 65-120 residues rather than
/// peptides, but PeptideBinderDesign is the registry's general "binder
/// design" category, which is what a campaign against a named target is.
pub const ENTRY: CatalogEntry = CatalogEntry {
    identity: Identity::Installed(Tool::BindCraft),
    categories: &[ToolCategory::PeptideBinderDesign],
    launch_type: LaunchType::CondaBasedApp,
    license_type: LicenseCategory::NonCommercial,
    expense: ProcessExpense::Expensive,
    primary_output: None,
    primary_inputs: &[PrimaryInput::new("target_pdb", &[DataType::Pdb])],
    top_choice: true,
    spec: SpecData {
        summary: "Design de novo protein or peptide binders against a target structure.",
        description: "Builds a BindCraft target/advanced/filter settings trio and runs the official pipeline end to end (hallucination, ProteinMPNN redesign, AlphaFold2 validation, and filtering).",
        availability: "Linux, Conda/Mamba, AlphaFold weights, and a large GPU are required",
        license_details: "BindCraft itself is MIT, but it cannot run without PyRosetta, which is free only for non-commercial and academic use and needs a paid licence from the University of Washington otherwise. The AlphaFold2 weights it uses are CC BY 4.0.",
        repo_url: Some("https://github.com/martinpacesa/BindCraft"),
        home_url: None,
        docs_url: Some("https://github.com/martinpacesa/BindCraft/wiki"),
        input_params_url: None,
        examples_url: None,
        paper_url: Some("https://www.biorxiv.org/content/10.1101/2024.09.30.615802"),
        license: License::Mit,
        license_url: None,
        tested: false,
    },
};