Use absolute paths for input PDB and output prefix in native RFDiffusion

runs

Author: lyskov

src/app/rfdiffusion.rs

@@ -22,25 +22,34 @@ pub fn native_spec(mut app_args: Vec<String>, working_dir: &Path) -> NativeRunSp
     const INPUT_PDB_PREFIX: &str = "inference.input_pdb=";
     const OUTPUT_PREFIX: &str = "inference.output_prefix=";
 
+    let mut output_prefix_present = false;
     for arg in &mut app_args {
         if arg.starts_with(INPUT_PDB_PREFIX) {
             let input_pdb = arg.split_at(INPUT_PDB_PREFIX.len()).1;
 
             let input_pdb_path = PathBuf::from(input_pdb);
             if !input_pdb_path.is_absolute() {
                 let abs_input_pdb = working_dir.join(input_pdb_path);
-                arg.replace_range(
-                    ..,
-                    &format!("inference.input_pdb={}", abs_input_pdb.to_str().unwrap()),
+                *arg = format!("inference.input_pdb={}", abs_input_pdb.to_str().unwrap());
+            }
+        } else if arg.starts_with(OUTPUT_PREFIX) {
+            let output_prefix = arg.split_at(OUTPUT_PREFIX.len()).1;
+
+            let output_prefix_path = PathBuf::from(output_prefix);
+            if !output_prefix_path.is_absolute() {
+                let abs_output_prefix = working_dir.join(output_prefix_path);
+                *arg = format!(
+                    "inference.output_prefix={}",
+                    abs_output_prefix.to_str().unwrap()
                 );
             }
-
-            // let input_pdb = arg.split_once('=').unwrap().1;
-            // arg.replace_range(.., format!("inference.input_pdb={input_pdb}"));
+            output_prefix_present = true;
         }
     }
 
-    app_args.extend_from_slice(&[format!("{OUTPUT_PREFIX}{}", working_dir.to_str().unwrap())]);
+    if !output_prefix_present {
+        app_args.extend_from_slice(&[format!("{OUTPUT_PREFIX}{}/", working_dir.to_str().unwrap())]);
+    }
 
     NativeRunSpec::new(include_asset!("pixi/rfdiffusion.toml"), app_args)
 }