Coming from coords2sans¶

sinccity takes over coords2sans's features; its names and units differ in places.

coords2sans	sinccity
`Structure.read(path, residues, masses, elements)`	`sinccity.load(path, residues=, masses=, elements=)` or `gsc.load_structure(...)`
`Structure(resids, resnames, names, positions, elements)`	`Structure.from_atoms(xyz, symbols, resids=, resnames=, names=)`
`structure.positions`, `structure.elements` (editable)	`structure.xyz`, `structure.symbols`; `structure.with_symbols(new)`
`structure.sld(deuterated=[...])`	`structure.deuterated([...]).sld`, or `set_params(deuterated=[...])`
`SansCalculator(solvent_sld=6.36e-6)`	`set_params(sld_solvent=6.36)`, in 10⁻⁶ Å⁻²
`q_min`, `q_max`, `q_points`, `q_log`	`set_q_grid(qmin, qmax, npoints, spacing='log' or 'linear')`; the default grid is SasView's, 3e-4 to 0.3 Å⁻¹ in 30 points
`polydispersity`, `size_points`, `SIZE_RANGE`	`size_pd`, `size_pd_n`, `size_pd_nsigma`
`average_amplitude=True`	`kernel='average'`
`BIN_WIDTH` (0.01 Å)	`histogram_bin`, by default at most 0.01 Å and smaller at high q or with a size spread
`calculate(structure, label)` → `Curve`	`set_structure(structure)`, then `calculate(label=)` → `ScatteringProfile`
`Curve.save`, `Curve.plot(ax)`	`profile.save_csv(path)` (the same two columns); `ax.plot(profile.q, profile.intensity)` or `profile.plot()` (plotly)
`SansTask`	`get_settings()` plus a series, run by `from_settings(settings).calculate_series(series)`

Two rules differ on purpose. PDB files without an element column use SasView's name rule (CA is carbon), and in .gro files a two-letter element name counts only in a one-atom residue (so CA in a protein is carbon). \(V_\mathrm{norm}\) is the volume of the atoms that scatter, which equals coords2sans's volume of all atoms unless an atom matches the solvent.