use crate::{
LaunchType, License, LicenseCategory, ProcessExpense, SpecData, ToolCategory,
tool_definitions::{
Tool,
catalog::{CatalogEntry, DataType, Identity, PrimaryInput},
},
};
pub const ENTRY: CatalogEntry = CatalogEntry {
identity: Identity::Installed(Tool::Placer),
categories: &[
ToolCategory::ProteinDesign,
ToolCategory::StructurePrediction,
],
launch_type: LaunchType::PythonBasedApp,
license_type: LicenseCategory::Permissive,
expense: ProcessExpense::Moderate,
primary_output: None,
primary_inputs: &[PrimaryInput::new(
"structure_file",
&[DataType::Pdb, DataType::MmCif],
)],
top_choice: false,
spec: SpecData {
summary: "Generate an ensemble of protein-ligand poses and side-chain conformations. Given a \
protein pocket and ligand, estimates how the ligand and sidechains will arrange themselves.",
description: "Runs PLACER (Protein-Ligand Atomistic Conformational Ensemble Resolver), a graph network that denoises corrupted atomic coordinates back to plausible ones. Given a structure and approximate knowledge of the binding site, it samples an ensemble of ligand poses and side-chain conformations rather than a single answer, with a predicted uncertainty (prmsd) per sample.",
availability: "Installed by setup_system.sh into its own uv environment; needs Linux, an NVIDIA GPU, and the checkout (weights are included in it)",
license_details: "BSD 3-Clause (University of Washington, Institute for Protein Design), which the licence explicitly extends to the bundled model weights. Commercial use is unrestricted.",
repo_url: Some("https://github.com/baker-laboratory/PLACER"),
home_url: None,
docs_url: Some("https://www.biorxiv.org/content/10.1101/2024.09.25.614868"),
input_params_url: None,
examples_url: None,
paper_url: Some("https://www.biorxiv.org/content/10.1101/2024.09.25.614868"),
license: License::Bsd3Clause,
license_url: None,
tested: false,
},
};