SincCity¶

The orientationally averaged I(q) of a real-space structure, by the Debye formula: atoms from a PDB or GROMACS GRO file, pixels from a SasView SLD file, or the cells of a legacy ASCII VTK mesh. It is the nuclear, 1D part of SasView's Generic Scattering Calculator, as a plain Python package for scripts and notebooks. There are no 2D, magnetic or polarisation options.

sinccity is developed alongside IQuana but does not depend on it. The two meet through profile.to_data1d(), which returns a sasdata Data1D that IQuana.set_data (or any other sasdata consumer) accepts.

Installation¶

pip install sinccity                  # numpy and periodictable only
pip install "sinccity[plot,sasdata]"  # plus plotly (plots) and sasdata (Data1D output)

The required dependencies are numpy and periodictable (scattering lengths and densities of atoms). Two extras are optional: plot installs plotly, which plot_points and plot_profile need, and sasdata installs sasdata, which to_data1d needs. Without them those calls raise an ImportError that names the extra.

Quick start¶

from sinccity import GenericScatteringCalculator

gsc = GenericScatteringCalculator()
gsc.load_structure('particle.sld')  # .pdb, .gro, .sld or .vtk
gsc.plot_points()  # SasView's "Draw Points", in 3D
gsc.set_q_grid(3e-4, 0.3, 30)  # optional: SasView's defaults
gsc.set_params(sld_solvent=6.34)  # optional: 10^-6 Å^-2, D2O here
profile = gsc.calculate()
profile.describe()
gsc.plot_profile()  # or gsc.plot_profile(data=some_data1d)
data = profile.to_data1d()  # a sasdata Data1D, ready for a fit

An aggregate from a molecular-dynamics run, in several contrasts:

gsc.load_structure(
    'CTA178-eq5.gro',
    residues=['CTA'],  # the micelle, not its solvent
    masses={'CTA': cta_masses},  # from the topology, in atom order
)
gsc.set_params(scale=0.01, size_pd=0.1)
profiles = gsc.calculate_series([
    {'label': 'h-CTA in D2O', 'params': {'sld_solvent': 6.36}},
    {'label': 'h-CTA in H2O', 'params': {'sld_solvent': -0.56}},
    {'label': 'd-CTA in H2O', 'params': {'sld_solvent': -0.56, 'deuterated': ['CTA']}},
])

Where to go next¶

Structures: the file formats, residue selection, elements and periodic boxes.
Calculation: the formula, units, normalisation, size polydispersity, deuteration and the kernels.
Series and reproducibility: contrast series, settings records and worker processes.
Coming from coords2sans: the names that changed.
API reference: every public class and function.

Licence¶

BSD 3-Clause, like IQuana. The readers follow SasView's (sas.sascalc.calculator.sas_gen, BSD-3-Clause, Copyright (c) 2009-2026, SasView Developers), and the test structures are SasView test data under the same licence.