From e0b0ecd1c3e72fb25a86fc332a8091f12efc335b Mon Sep 17 00:00:00 2001
From: Sebastian Pineda <sebastian@dell7050>
Date: Mon, 4 May 2026 14:08:18 +0200
Subject: [PATCH] fix: allow direct scheme with XTC by making box length
 optional; add CSS alias
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- `--box` for `direct` is now optional (no default_value in clap); when
  omitted without an XTC the 200 Å fallback is applied in lib.rs, preserving
  existing single-frame behaviour
- Removes the hard error that fired even when -b was not supplied, allowing
  trajectory-averaged SAXS via `direct` without specifying a box
- Add CSS (disulfide-bonded cysteine) as an alias for CYS in single_bead.yaml

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 assets/single_bead.yaml | 1 +
 src/cli.rs              | 6 +++---
 src/lib.rs              | 2 ++
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/assets/single_bead.yaml b/assets/single_bead.yaml
index d417599..1ae15b3 100644
--- a/assets/single_bead.yaml
+++ b/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
diff --git a/src/cli.rs b/src/cli.rs
index e577088..56b4f47 100644
--- a/src/cli.rs
+++ b/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 {
diff --git a/src/lib.rs b/src/lib.rs
index 01b2aad..806c0bc 100644
--- a/src/lib.rs
+++ b/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());