form_factor_table module

Form factors and scattering vs. resolution.

Usage: import form_factor_table (main program performs rudimentary test).

Module author: Michael S. Chapman <chapmanms@missouri.edu>

Module author: Andrew Trzynka <trzynkaa@ohsu.edu>

Authors:

Michael S. Chapman <chapmanms@missouri.edu>

Oregon Health & Science University & University of Missouri

Version:

1, Nov 15, 2025

Changed in version 2/11/10: Started

Changed in version 0.3.7: 11/25/12

Changed in version 0.5.0: 4/30/15 restructured text documentation.

Changed in version 1.0.0: 11/18/20 Python 2.7 –> 3.6

Deprecated since version 1.0.8: 12/18/25 internal XTNT support

class form_factor_table.FormFactorTable(source)

Bases: object

Scattering factors obtained from a resolution-dependent look-up table.

Several tables supported: x-ray, neutron & electron scattering, determined empirically or through quantum calculation by others.

Internal support of TNT form factors has been deprecated, as incompatible with copyleft licensing (perhaps). The XTNT option now prompts the user for a file name.

Loads one of several form factor tables ready to support look-up:

  • “XCCP4” - X-ray scattering factors from the CCP4 distribution.

  • “NCCP4” - Neutron scattering factors from the CCP4 distribution.

  • “ERSRef” - (Few-atom) Electron scattering factors from RSRef EM (unknown attribution).

  • “ELECTRON” - Electron scattering factors, neutral atoms, Int. Tab.

  • “XTNT” - X-ray scattering factors from TNT distribution

    (XTNT prompts for a user-provided file).

Excellent introduction to electron scattering factors in Int. Tables Vol.C sect 4.3.2 (p.262).

Parameters:

source (str) – defines which of the supported tables (above) is used.

class Counter

Bases: dict

Counter for references to each entry in form-factor table.

increment(name)
at_dstar(dstar, atom_type='C', type_num=None, b=0.0)

Form factor at d*.

Parameters:

  • atom_type (str)

  • type_num (int) – number corresponding to atom_type, takes predence over atom_type unless “None”.

  • b (float) – temperature factor (including overall B / envelope function), Å2

Returns:

form factor at d*.

Return type:

float

at_dstar_array = <numpy.vectorize object>
at_dstar_sq(dstar_sq, atom_type='C', type_num=None, b=0.0)

Form factor at d*2.

Parameters:

  • atom_type (str)

  • type_num (int) – number corresponding to atom_type, takes predence over atom_type unless “None”.

  • b (float) – flaot temperature factor (including overall B / envelope function), Å2

Returns:

form factor at d*2.

Return type:

float

at_dstar_sq_array = <numpy.vectorize object>
at_s(s, atom_type='C', type_num=None, b=0.0)

Form factor at S.

Parameters:

  • atom_type (str)

  • type_num (int) – number corresponding to atom_type, takes predence over atom_type unless “None”.

  • b (float) – temperature factor (including overall B / envelope function), Å2

Returns:

form factor at S=sin(θ/λ).

Return type:

float

at_s_array = <numpy.vectorize object>
at_s_sq(s_sq, atom_type='C', type_num=None, b=0.0)

Form factor at S2.

Parameters:

  • atom_type (str)

  • type_num (int) – number corresponding to atom_type, takes predence over atom_type unless “None”.

  • b (float float) – temperature factor (including overall B / envelope function), Å2

Returns:

form factor at S2 = (sin(θ/λ))2

Return type:

float

at_s_sq_array = <numpy.vectorize object>
findtype(atom_type=None, atom_name=None, verbose=True)

Find the formfactor atom type that is the best match.

Parameters:

  • atom_type (str) – from the input coordinates.

  • atom_name (str) – optional IUPAC or other name.

  • verbose (bool) – print warning messages for ambigous names.

Returns:

new type:

  • (silently) atom_type if there is an exact match.

  • (silently) atom_type pseudonym (eg. Ca++ for Ca2+) if exists.

  • (silently) results of prior match of the same atom_type/_name.

  • (w/ warning) 1st non-ambiguous match as the common part of atom_type and atom_name is progressively shortened. (Avoiding accidental matches such as CD (delta) to Cadmium.)

  • (w/ warning) 1st non-ambigous match to a shortened atom_type if there are no characters in common with atom_name.

  • Exception if none found.

Return type:

string

name2type(atom_name='C', shorten=True, verbose=True, exception=True)

Best guess of atom type from atom name.

Parameters:

  • atom_name (str) – IUPAC or other name (or arbitrary string).

  • shorten (bool) – shorten atom_name until a match is found.

  • exception (bool) – throw an exception if no match, else return None.

  • verbose (bool) – print warning messages for ambigous names.

Returns:

atom type or None

Return type:

string

recognized(atom_name='C')

Checks if atom type in the form factor table.

Returns:

found.

Return type:

bool

type_number(atom_type='C', atom_name=None)

Returns the index of the atom type in the form factor table.