hikari.dataframes.res

Attributes

res_instructions

Classes

ResInstructionType	Generic enumeration.
ResFrame	This class stores and manipulates basic information present

Module Contents

hikari.dataframes.res.res_instructions

class hikari.dataframes.res.ResInstructionType

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

UNIQUE_INT = 1

UNIQUE_LIST = 2

UNIQUE_MULTILINE = 3

REPEATING_SINGLET = -1

class hikari.dataframes.res.ResFrame

Bases: hikari.dataframes.BaseFrame

This class stores and manipulates basic information present in majority of crystallographic information files such as unit cell parameters stored in scalars and vectors.

BaseFrame utilises the following notation for stored attributes:

• The name begins from a unit cell property we are interested in:

• “a”, “b”, “c” describe unit cell lengths/vectors a, b, c,

• “al”, “be”, “ga” describe unit cell angles alpha, beta, gamma,

• “v” describes unit cell volume,

• “x”, “y”, “z” describe directions - normalised unit cell vectors.

• “A”, “G” describe stacked vector and metric matrix, respectively.

• The unit cell parameter symbol is then followed by an underscore “_”.

• The name ends with a single letter denoting type of space and variable:

• “d” (from Direct) denotes direct space scalars/matrices,

• “r” (from Reciprocal) denotes reciprocal space scalars/matrices,

• “v” (from Vector) denotes direct space vectors,

• ‘w” (similar to “v”) denotes reciprocal space vectors.

The values can be accessed by referencing a given attribute in the object, for example BaseFrame. a_d stores information about the lattice constant a in direct space as a floating point, but BaseFrame. a_v is a direct space vector. Available attributes have been once again presented in a table below:

	Available constants	in direct space	in reciprocal space	Unit (^-1 in reciprocal)
Scalars	a, b, c	a_d, b_d, c_d	a_r, b_r, c_r	Angstrom
	al, be, ga	al_d, be_d, ga_d	al_r, be_r, ga_r	Radian
	v	v_d	v_r	Angstrom^3
Vectors	a, b, c	a_v, b_v, c_v	a_w, b_w, c_w	Angstrom
	x, y, z	x_v, y_v, z_v	x_w, y_w, z_w	Angstrom
Matrices	A	A_d	A_r	Angstrom^2
	G	G_d	G_r	Angstrom^2

data

atomic_form_factor(atom, hkl)

Calculate X-ray atomic form factors for a single atom and a hkl array

Parameters:

• atom (str) – Atom/ion name/identifier interpreted by form factor table

• hkl (np.array) – A 2D array listing all hkls to consider

Returns:

A 1D array listing atomic form factors for desired hkls

Return type:

np.array

temperature_factor(hkl, u)

Calculate temperature factor for single u matrix and a hkl array

Parameters:

• hkl (np.array) – A 2D array listing all hkls to consider

• u (np.array) – A classical anisotropic displacement parameters matrix

Returns:

A 1D array listing temperature factors for desired hkls

Return type:

np.array

form_factor(hkl, space_group)

Calculate form factors based on current structure, hkls, and space group

Parameters:

• hkl (np.array) – A 2D array listing all hkls to consider

• space_group (hikari.symmetry.Group) – Space group describing the internal crystal symmetry

Returns:

A 1D array listing total form factors for desired hkls

Return type:

np.array

read(path)

Read data from specified ins/res file and return an dict

Parameters:

path (str) – Relative or absolute path to the res file to be read

Returns:

None

Return type:

None