fix: allow direct scheme with XTC; add CSS alias to single_bead.yaml

assets/single_bead.yaml

@@ -824,6 +824,7 @@ HLYS: { ff: !Alias LYS }
 HTYR: { ff: !Alias TYR }
 HCYS: { ff: !Alias CYS }
 CYX: { ff: !Alias CYS }
+CSS: { radius: 3.6, formfactor: !Alias CYS }
 
 # PDB atom name aliases — map multi-character PDB names to their
 # element form factors so atomic-resolution structures work with

src/cli.rs

@@ -47,8 +47,8 @@ pub enum Commands {
         #[clap(short = 'p', long, default_value = "6")]
         pmax: usize,
         /// Cubic box side length (Å)
-        #[clap(short = 'b', long = "box", default_value = "200.0")]
-        side_length: f64,
+        #[clap(short = 'b', long = "box")]
+        side_length: Option<f64>,
         #[clap(flatten)]
         solvent: SolventArgs,
     },
@@ -291,7 +291,7 @@ fn command_to_scheme(
             solvent,
         } => (
             IntensityScheme::Direct { pmax },
-            Some([side_length; 3]),
+            side_length.map(|s| [s; 3]),
             solvent.to_config(),
         ),
         Commands::Multipole {

src/lib.rs

@@ -212,6 +212,8 @@ impl Pripps {
                 ));
             }
             structure.box_sides = Some(Vector3::from(box_sides));
+        } else if xtcfile.is_none() {
+            structure.box_sides = Some(Vector3::from([200.0; 3]));
         }
 
         let active_solvent = solvent.filter(|cfg| cfg.is_active());