Add ProteinMPNN support and tests

Author: lyskov

src/executor.rs

@@ -128,14 +128,27 @@ pub fn run(
             Image("rosettacommons/rfdiffusion".into()),
             {
                 //app_args.insert(0, "inference.output_prefix=/w".into()); // /motifscaffolding
-                app_args.extend([
-                    "inference.output_prefix=/w/".into(),
-                    "inference.model_directory_path=/app/RFdiffusion/models".into(),
-                ]);
+                app_args.splice(
+                    0..0,
+                    [
+                        "inference.output_prefix=/w/".into(),
+                        "inference.model_directory_path=/app/RFdiffusion/models".into(),
+                    ],
+                );
                 app_args
             },
             Some("/app/RFdiffusion/schedules".into()),
         ),
+
+        App::Proteinmpnn => (
+            Image("rosettacommons/proteinmpnn".into()),
+            {
+                //app_args.extend(["--out_folder=/w/".into()]);
+                app_args.splice(0..0, ["--out_folder=/w/".into()]);
+                app_args
+            },
+            None,
+        ),
         //_ => todo!(),
     };
 

src/main.rs

@@ -85,6 +85,10 @@ enum App {
     /// Run the RFdiffusion command https://github.com/RosettaCommons/RFdiffusion
     #[value(aliases = ["Rfdiffusion"])]
     Rfdiffusion,
+
+    /// Run the RFdiffusion command https://github.com/RosettaCommons/RFdiffusion
+    #[value(aliases = ["ProteinMPNN"])]
+    Proteinmpnn,
 }
 
 fn main() -> Result<()> {

tests/proteinmpnn.rs

@@ -0,0 +1,54 @@
+use assert_cmd::{assert::OutputAssertExt, cargo::cargo_bin_cmd};
+use assert_fs::TempDir;
+
+mod common;
+
+common::engine_tests!(proteinmpnn);
+
+fn proteinmpnn(engine: &str) {
+    use assert_fs::assert::PathAssert;
+
+    let root = std::path::PathBuf::from("target/proteinmpnn").join(engine);
+    std::fs::create_dir_all(&root).expect("create engine testing dir");
+    let work_dir = TempDir::new_in(root).expect("create temp dir");
+
+    let pdb_id = "3htn";
+    let pdb_file = pdb_id.to_string() + ".pdb";
+
+    let pdb_path = work_dir.path().join(&pdb_file);
+    std::fs::write(
+        pdb_path,
+        reqwest::blocking::get(format!("https://files.rcsb.org/download/{pdb_file}"))
+            .unwrap()
+            .bytes()
+            .unwrap(),
+    )
+    .unwrap();
+
+    let cmd = cargo_bin_cmd!()
+        .args([
+            "run",
+            "--container-engine",
+            engine,
+            "-w",
+            work_dir.path().to_str().unwrap(),
+            "proteinmpnn",
+            "--pdb_path",
+            &pdb_file,
+            "--pdb_path_chains",
+            "A B",
+        ])
+        .unwrap();
+    cmd.assert().success();
+
+    use assert_fs::prelude::PathChild;
+
+    work_dir
+        .child(".0000.rc.log")
+        .assert(predicates::path::exists());
+
+    let o_pdb = work_dir.child("seqs/3htn.fa");
+    o_pdb.assert(predicates::path::exists());
+
+    // std::thread::sleep(std::time::Duration::from_secs(60));
+}