Merge multiple --atomfile files; split gaussian_atoms.yaml by mlund · Pull Request #14 · mlund/pripps

mlund · 2026-06-18T16:21:58Z

Form-factor definitions composed from several YAML files: repeat --atomfile (or pass a list to the Python Pripps constructor). Files merge in order; last file wins on duplicate species (logged). Merging happens before symbolic resolution, so an !Alias/!United/!Linear in one file can reference a species from another.

Also splits gaussian_atoms.yaml into an atomic/UA-only table — drops the 20 CG residue beads (duplicates of poly_amino_acid.yaml) and 8 unused residue aliases. CG consumers load poly_amino_acid.yaml (or merge it in).

Resolves the mixed-representation file from #7; supersedes #11.

Verified: cargo fmt/clippy clean, 103 Rust tests pass, maturin develop + 10 pytest pass.

Closes #7

Form-factor definitions can now be composed from several YAML files. Repeat --atomfile (or pass several paths), or give the Python Pripps constructor a list. Files are merged in order; on a duplicate species the last file wins and a warning is logged. Merging happens before symbolic resolution, so an !Alias/!United/!Linear in one file may reference a species defined in another. - formfactor.rs: split read_formfactors into parse_specs + finalize_specs; add read_formfactors_merged. - lib.rs: add Pripps::from_yaml_files; from_yaml delegates via from_formfactors. - cli.rs: --atomfile becomes Vec<PathBuf> (repeatable, order-preserving). - pripps-py: Pripps(...) accepts a str or list[str]. Split gaussian_atoms.yaml into an atomic/united-atom-only table: drop the 20 coarse-grained residue beads (byte-identical duplicates of poly_amino_acid.yaml) and 8 unused residue-level aliases, and rewrite the header. Residue-bead consumers load poly_amino_acid.yaml (or merge it with the atomic file). This resolves the mixed-representation file and supersedes the rename-only approach in #11. Closes #7

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A newly added test writes to fixed filenames in the global temp directory, which can cause flaky failures under parallel test execution.

Pull request overview

Adds support for composing form-factor definitions from multiple YAML files (merged in order with “last file wins” on duplicate species), updates the CLI and Python bindings to accept multiple inputs, and cleans up shipped assets by splitting coarse-grained residue beads out of assets/gaussian_atoms.yaml into the dedicated residue table.

Changes:

Implement pre-resolution merging of multiple YAML form-factor spec files (read_formfactors_merged) and expose it via Pripps::from_yaml_files.
Update CLI (--atomfile/-a) and Python constructor to accept one or more form-factor files.
Split assets/gaussian_atoms.yaml to be atomic/UA-only and update docs/tests to use the residue table where appropriate.

File summaries

File	Description
`src/lib.rs`	Adds `from_yaml_files` constructor and updates a test to use the CG residue form-factor table.
`src/formfactor.rs`	Refactors YAML loading into parse/finalize stages and adds merged multi-file loader + test.
`src/cli.rs`	Changes `--atomfile/-a` to accept multiple paths and wires it to `from_yaml_files`.
`README.md`	Documents multi-file merging behavior and updates the shipped form-factor table descriptions/examples.
`pripps-py/src/lib.rs`	Allows Python `Pripps(...)` to accept either a single path or a list of paths.
`assets/gaussian_atoms.yaml`	Removes CG residue beads/aliases so the file is atomic/united-atom only, with updated header guidance.

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Comments generated: 1

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mlund · 2026-06-18T16:25:44Z

+given — repeat `--atomfile` (or pass several paths) on the CLI, or pass a
+list to the Python constructor:
+
+```bash


No need to give examples, just keep this brief

mlund · 2026-06-18T16:26:50Z

 | 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 |


Perhaps a better name is pepsi_atoms.yaml? It would be more useful to end user. But is it true?

mlund · 2026-06-18T16:28:24Z

@@ -1,364 +1,8 @@
-# Amino acid single bead approximation for atomistic scattering


Mention origin of these values? pepsi?

- Rename gaussian_atoms.yaml -> pepsi_atoms.yaml and document provenance: atomic five-Gaussians are Waasmaier & Kirfel (1995); united-atom groups and K=4π solvent convention are PepsiSAXS (Grudinin et al. 2017). Update all references (tests, script, README) and link DOIs inline. - Trim the README "Merging multiple files" section per review. - Use tempfile::tempdir() in the merge test to avoid fixed temp-file names colliding under parallel test runs.

mlund · 2026-06-19T07:44:44Z

Addressed in 21580ec:

Renamed gaussian_atoms.yaml → pepsi_atoms.yaml and documented provenance. Confirmed the atomic five-Gaussians are the Waasmaier & Kirfel (1995) parametrization (valid sinθ/λ ∈ [0,6] Å⁻¹, matching the qrange), used with PepsiSAXS united-atom groups and the K=4π convention. Header + README updated, DOIs linked inline; all references updated.
README merging section trimmed to be brief (dropped the examples).
Merge test now uses tempfile::tempdir() instead of fixed temp filenames, so it won't collide under parallel runs.

cargo fmt/clippy clean, 103 Rust tests + 10 pytest pass.

Copilot AI review requested due to automatic review settings June 18, 2026 16:21

Copilot started reviewing on behalf of mlund June 18, 2026 16:22 View session

mlund mentioned this pull request Jun 18, 2026

renamed gaussian_atoms.yaml #11

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Copilot AI reviewed Jun 18, 2026

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Comment thread src/formfactor.rs Outdated

mlund commented Jun 18, 2026

View reviewed changes

Clarify gaussian ff in readme

851ad9b

mlund merged commit 4b6a1a7 into master Jun 19, 2026
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mlund deleted the split-atomfiles-merge branch June 19, 2026 08:02

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Merge multiple --atomfile files; split gaussian_atoms.yaml#14

Merge multiple --atomfile files; split gaussian_atoms.yaml#14
mlund merged 3 commits into
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		@@ -1,364 +1,8 @@
		# Amino acid single bead approximation for atomistic scattering

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