renamed gaussian_atoms.yaml

README.md

@@ -239,7 +239,7 @@ must define it when `--excluded per-kind` is selected.
 | File | Description | Best for |
 |------|-------------|----------|
 | `assets/foxs_formfactors.yaml` | Cromer-Mann (Int. Tables Vol. C) atomic form factors, FoXS-compatible volumes and SASA radii | Atomic PDBs with `--excluded foxs` |
-| `assets/gaussian_atoms.yaml` | Mixed table: residue single-bead polynomials plus atomic/united-atom Gaussians (CH/CH₂/NH/…) | Atomic PDBs with PepsiSAXS-style solvent models |
+| `assets/poly_aas+gaussian_atoms.yaml` | Mixed table: residue single-bead polynomials plus atomic/united-atom Gaussians (CH/CH₂/NH/…) | Atomic PDBs with PepsiSAXS-style solvent models |
 | `assets/stovgaard2010.yaml` | Per-residue form-factor centroids (one-body model, q ∈ [0, 0.75] Å⁻¹) from Stovgaard et al. 2010, <https://doi.org/10.1186/1471-2105-11-429> | Residue / Cα single-bead models |
 | `assets/poly_amino_acid.yaml` | Amino-acid bead polynomials with a separate `excluded_solvent` polynomial per bead | Cα / single-bead with `--excluded per-kind` |
 | `assets/poly_amino_acid_combined.yaml` | Amino-acid bead polynomials with the excluded solvent already folded into the form factor | Cα / single-bead with `--excluded disabled` |
@@ -254,7 +254,7 @@ their respective tools.
 **Don't mix files with non-matching `--excluded` flags.** Each
 YAML + excluded-volume convention is a self-consistent bundle:
 `foxs_formfactors.yaml` was calibrated jointly with FoXS's
-`K = 16π` Gaussian, while `gaussian_atoms.yaml` was calibrated with
+`K = 16π` Gaussian, while `poly_aas+gaussian_atoms.yaml` was calibrated with
 PepsiSAXS's `K = 4π`. Swapping the denominator gives atomic and
 excluded contributions that were never fit together and yields
 subtly biased intensities.

pripps-py/tests/test_smoke.py

@@ -132,7 +132,7 @@ class TestPepsiFit(unittest.TestCase):
     def setUpClass(cls):
         cls.exp = load_lyzexp()
         q_max = float(cls.exp[-1, 0])
-        pr = pripps.Pripps("../assets/gaussian_atoms.yaml")
+        pr = pripps.Pripps("../assets/poly_aas+gaussian_atoms.yaml")
         cls.model = pr.multipole_model(
             "../tests/lysozyme/4lzt.pdb",
             qmin=0.0,

scripts/sasbdb_bench.py

@@ -62,7 +62,7 @@
 BENCH = REPO / "sasbdb_bench"
 CACHE = BENCH / "cache"
 FF_YAML_DEFAULT = REPO / "assets" / "foxs_formfactors.yaml"
-# Override via --atomfile if you want gaussian_atoms.yaml for the
+# Override via --atomfile if you want poly_aas+gaussian_atoms.yaml for the
 # PepsiSAXS-style K=4π convention.
 
 SASBDB_API = "https://www.sasbdb.org/rest-api/entry/summary/{}/"

src/lib.rs

@@ -775,7 +775,8 @@ mod tests {
         // produce a physically reasonable profile. Not as good as
         // the FoXS pipeline (different coefficients, different
         // denominator) but the shape should be plausible.
-        let pripps = Pripps::from_yaml(std::path::Path::new("assets/gaussian_atoms.yaml")).unwrap();
+        let pripps =
+            Pripps::from_yaml(std::path::Path::new("assets/poly_aas+gaussian_atoms.yaml")).unwrap();
         let pdb = std::path::PathBuf::from("tests/lysozyme/4lzt.pdb");
         let solvent = SolventConfig {
             excluded: ExcludedVolume::Fraser { volume_scale: 1.0 },
@@ -848,7 +849,7 @@ mod tests {
     ///    rescales it back to a full average (not frame 0 × 1/N_frames).
     #[test]
     fn trajectory_stride_and_weights() {
-        let pripps = Pripps::from_yaml(Path::new("assets/gaussian_atoms.yaml")).unwrap();
+        let pripps = Pripps::from_yaml(Path::new("assets/poly_amino_acid.yaml")).unwrap();
         let template = std::path::PathBuf::from("tests/lysozyme/4lzt.xyz");
         let xtc = std::env::temp_dir().join("pripps_stride_test.xtc");
         write_two_frame_xtc(&xtc);