Scripts.DatabankLib.form_factor module

Module form_factor serves for bilayer form factor calculations.

class Scripts.DatabankLib.form_factor.NumpyArrayEncoder(*args, **kwargs)

Bases: CompactJSONEncoder

encode(o)

Encode JSON object o with respect to single line lists.

class Scripts.DatabankLib.form_factor.FormFactor(conf, traj, nbin, output, system: System, density_type='electron')

Bases: object

Calculates form factors from density profiles.

Further development will include thickness of the membrane from the intersection of lipid density and water density. Already enables to calculate electrom/mass/number densities

Density could be calculated only from the final form factor profile - testing is needed to see stability for rare species.

Examination of FF error spikes is needed!

static get_electrons(mapping_name)

residue_electrons_all(molecule)

Return list of electrons

assign_electrons()

calculate_weight()

Creates an array of weights for all atoms in the simulation.

For electron densities:

• creates dictonary of atom types and number of electrons loaded form an external file –> in the future it backmaps

  the atom names to mapping files and automaticaly assigns # of electrons

Number densities:

• all weights are 1

Mass densities:

• reads masses from u.atoms.masses

calculate_density()

fourier(ff_density, box_z, ff_range, d_ff)

Calculates fourier transform of ff_density in the FF_range. It calculates a “height” of a bin for FF puroposes; in this case the number of bins is constant and the bin width changes.

Parameters:

• ff_density (_type_) – TODO: fill

• box_z (_type_) – TODO: fill

• ff_range (_type_) – TODO: fill

• d_ff (_type_) – TODO: fill

Returns:

TODO: fill

Return type:

_type_