Sba formfactors by IVinterbladh · Pull Request #5 · mlund/pripps

IVinterbladh · 2026-05-29T12:02:16Z

Removed incorrect Amino acid form factors from Single_beads.yaml
Added yaml-files for the polynomial form factor for the amino acid and matrini3 beads. Both with and without excluded solvent in addition to pure excluded solvent models.
Added a new excluded solvent method where a polynomial form factor from the yaml-file is used.
Updated python notebook for plotting results.

… such that pripps can read martini structures and the martini form factors. Added a new excluded solvent option 'polynomial', where a yaml file with the polynomial coefficients are given.

Copilot

Pull request overview

This PR adds support for polynomial form-factor tables (including a new “polynomial” excluded-volume model) and updates the structure atom-kind resolution to support residue-scoped coarse-grained names, alongside new/updated test datasets and form-factor assets.

Changes:

Added a new excluded-volume model (ExcludedVolume::Polynomial) that reads per-kind excluded-volume form factors from a dedicated YAML table.
Updated structure atom-kind lookup to prefer residue-scoped keys (RES_ATOM) before falling back to united-atom and atom-name-only lookup (with unit tests).
Added/updated polynomial form-factor YAML/CSV assets and supplemental test/example inputs (lysozyme XYZ, batch fitting script, README updates).

Reviewed changes

Copilot reviewed 22 out of 25 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
tests/lysozyme/lyzexp.dat	Adjusts lysozyme experimental data header/comment line.
tests/lysozyme/6lyz.xyz	Adds an XYZ structure file for lysozyme test/example usage.
src/structure.rs	Adds residue-scoped atom-kind resolution with tests.
src/solvent/polynomial_excluded.rs	Implements polynomial excluded-volume dummy generation from a separate YAML table (+ tests).
src/solvent/mod.rs	Wires the new `ExcludedVolume::Polynomial` variant into solvent dummy generation and scaling.
src/cli.rs	Adds CLI support for `--excluded polynomial` and an optional `--excluded-atomfile` path.
README.md	Documents the new excluded-volume option and `excluded_atomfile` parameter in Python examples/tables.
pripps-py/src/lib.rs	Exposes `excluded_atomfile` and the `polynomial` excluded model in the Python bindings.
pripps-py/examples/batch_sba_sasbdb.py	Adds a batch-fitting helper script for SASBDB cache entries using the polynomial excluded-volume model.
assets/single_bead.yaml	Updates/removes incorrect single-bead form factors and reorganizes amino-acid bead definitions.
assets/poly_martini_excl.yaml	Adds Martini polynomial excluded-volume form-factor table (YAML).
assets/poly_martini_excl.csv	Adds Martini polynomial excluded-volume coefficients source (CSV).
assets/poly_martini_atomic.yaml	Adds Martini polynomial atomic form-factor table (YAML).
assets/poly_martini_atomic.csv	Adds Martini polynomial atomic coefficients source (CSV).
assets/poly_martini_atev.yaml	Adds Martini polynomial ATEV form-factor table (YAML).
assets/poly_martini_atev.csv	Adds Martini polynomial ATEV coefficients source (CSV).
assets/poly_excl.yaml	Adds amino-acid polynomial excluded-volume form-factor table (YAML).
assets/poly_excl.csv	Adds amino-acid polynomial excluded-volume coefficients source (CSV).
assets/poly_atomic.yaml	Adds amino-acid polynomial atomic form-factor table (YAML).
assets/poly_atev.yaml	Adds amino-acid polynomial ATEV form-factor table (YAML).
assets/poly_atev.csv	Adds amino-acid polynomial ATEV coefficients source (CSV).

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…d the pdf files of lysozyme

…rmfactors

…f the same file as the atomistic form factors and not a separate file. Code changed accordingly such that the excluded solvent form factors will be called from the same file as the others.

…ady had it)and added such that all three have the same scaling to experimental data

… hydration shell points from grid method

…nts from the model when using the grid version

…rmfactors

…work

Polynomial excluded volume reads `excluded_solvent` from the per-bead entries in the main atom file, so the separate `excluded_atomfile` / `--excluded-atomfile` parameter is dead surface area. Remove it from the CLI args and from all three pyo3 model constructors plus the `solvent_from_kwargs` helper. Drop the now-orphaned `log` dependency in pripps-py (its only direct use was the deprecation warning). Also: - polynomial_excluded: defer the `kind_name` lookup into the error path - structure: collapse nested `if let` into a let-chain (clippy)

…ders The "polynomial" excluded-volume model named an incidental form-factor representation rather than its mechanism: it reads an explicit per-kind `excluded_solvent` form factor from the table (which need not be a polynomial), unlike the geometry-derived Fraser/FoXS/Grid/Voronoi variants. Rename the model to `PerKind` across the enum, CLI (`--excluded per-kind`), Python bindings (`excluded="per-kind"`), the module file (`per_kind_excluded.rs`), and README. The per-kind `excluded_solvent` field name is unchanged. Also clarify the poly_ asset header comments: the plain files keep the excluded solvent as a separate, fittable `excluded_solvent` term (`--excluded per-kind`), while the `_combined` files fold it into a single form factor (`--excluded disabled`). Fix stale CSV provenance lines to reference the current file names.

The PerKind rename of the excluded-volume model broke the example references to the old `excluded="polynomial"` string. Update the batch script and the notebook source cell to `excluded="per-kind"`. Also rename the cryptic batch_sba_sasbdb.py to batch_single_bead_fit_sasbdb.py (matching the notebook's spelled-out "single-bead") and expand SBA/SASBDB in its docstring.

mlund · 2026-06-16T17:34:14Z

@IVinterbladh assets/gaussian_atoms.yaml (renamed from single_bead.yaml) actually holds two different representations in one file:

20 coarse-grained residue beads (ALA…VAL) as !Polynomial form factors over qrange: [0.0, 0.75] — i.e. single-bead-approximation entries.
the full atomic / united-atom set (N, C, O, H, CH, CH₂, CH₃, …) as !Gaussian / !Alias / !United over qrange: [0.0, 6.0].

So both the filename gaussian_atoms and the header comment # Amino acid single bead approximation for atomistic scattering are a bit misleading — the file is neither purely Gaussian atoms nor purely single-bead.

Could you either split it into separate atomistic and CG-bead files, or at least pick a name that covers both and rewrite the header comment to describe the two parts? Just flagging so the asset names stay self-explanatory.

The `excluded_solvent` form-factor field was shown in the YAML example and the model/shipped-files tables but never explained: add a property- table row and a paragraph describing that it is a second form factor for the displaced bulk solvent, read only by the `per-kind` excluded-volume model. Also add a `!Linear` example to the YAML snippet so every model in the supported-models table is illustrated.

List all seven shipped YAML assets (was three): add stovgaard2010, poly_martini, and both `_combined` variants, pair each `per-kind` file with its `combined` counterpart, and correct the gaussian_atoms entry to note it is a mixed residue-polynomial + atomic-Gaussian table.

These two classes arrived from master (PR #5) after the original docstring commit, so they lacked the class-level `__doc__` that Pripps and MultipoleModel already carry. Mirror the same description.

IVinterbladh added 5 commits April 23, 2026 09:43

Added the Sba form factors for amino acid and martini3 beads. Changed…

876df59

… such that pripps can read martini structures and the martini form factors. Added a new excluded solvent option 'polynomial', where a yaml file with the polynomial coefficients are given.

Updated python notebook for plotting results

446002c

removed the incorrect form factors from the single_bead.yaml

0ee45fd

updated the default excluded_atomfile to the correct file

3252edb

Added the sba amino acid form factors to singel_bead.yaml

b4dbb76

IVinterbladh requested a review from Copilot May 29, 2026 12:22

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IVinterbladh and others added 3 commits May 29, 2026 14:30

Potential fix for pull request finding

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Potential fix for pull request finding

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mlund reviewed Jun 12, 2026

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Comment thread assets/poly_atev.csv Outdated

mlund reviewed Jun 12, 2026

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Comment thread pripps-py/examples/testing_single-bead_approximation.ipynb

mlund reviewed Jun 12, 2026

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Comment thread assets/poly_excl.csv Outdated

mlund reviewed Jun 12, 2026

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Comment thread tests/lysozyme/sba_fit.pdf Outdated

IVinterbladh and others added 15 commits June 12, 2026 14:48

Changed names and structure of csv files with coefficients and remove…

920ace1

…d the pdf files of lysozyme

Merge branch 'sba_formfactors' of github.com:mlund/pripps into sba_fo…

9eed3a3

…rmfactors

changed the structure of the polynomail excluded solvent to be part o…

103824f

…f the same file as the atomistic form factors and not a separate file. Code changed accordingly such that the excluded solvent form factors will be called from the same file as the others.

added the solvation option to debye and direct models (multipole alre…

c6371ca

…ady had it)and added such that all three have the same scaling to experimental data

added some tests and removed unused lyzosyme test files

0b76be9

updated example python notebooks added possibility to print number of…

69a0d3d

… hydration shell points from grid method

Merge branch 'master' into sba_formfactors

7b0dd98

removed the python API of getting number of hydration shell grid poi…

0d59ab6

…nts from the model when using the grid version

Merge branch 'sba_formfactors' of github.com:mlund/pripps into sba_fo…

22b3521

…rmfactors

fixed open parentheses in cli.rs

65458c0

fixed error and added log to Cargo.toml so the python extension will …

416329b

…work

changed name of atomic+excluded to combined for the form factor files

8ef9165

mlund added the enhancement New feature or request label Jun 16, 2026

mlund reviewed Jun 16, 2026

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Comment thread assets/gaussian_atoms.yaml

mlund added 2 commits June 16, 2026 20:28

mlund merged commit f9fae8f into master Jun 16, 2026
1 check passed

mlund deleted the sba_formfactors branch June 16, 2026 18:33

mlund mentioned this pull request Jun 16, 2026

@IVinterbladh assets/gaussian_atoms.yaml (renamed from single_bead.yaml) actually holds two different representations in one file: #7

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Sba formfactors#5

Sba formfactors#5
mlund merged 25 commits into
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mlund commented Jun 16, 2026

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