em_map_utils.structure_size_and_shape

structure_size_and_shape.py

Author:

Ardan Patwardhan

Affiliation:

EMBL-EBI, Wellcome Genome Campus, CB10 1SD, UK

Date:

07/08/2025

Description:

Threshold and align map with a box by determining the principal axes of the structure and then aligning the principal axes to the box. Estimate the size of the molecule using the lengths of the 3 orthogonal line projections. Estimate the asphericity of the structure as a shape measure.

Attributes

logger

map_name_pattern

Functions

read_map_list_from(list_file[, list_dir, file_dir])

max_eccentricity(widths)

Calculate the maximum eccentricity from the longest and smallest

asphericity_coefficient(a, b, c)

Calculate the asphericity coefficient using three orthogonal width

structure_size_and_shape(entry_file[, aligned_file, ...])

Determine the size and shape of a structure.

main()

Module Contents

em_map_utils.structure_size_and_shape.logger
em_map_utils.structure_size_and_shape.map_name_pattern
em_map_utils.structure_size_and_shape.read_map_list_from(list_file, list_dir=None, file_dir=None)
em_map_utils.structure_size_and_shape.max_eccentricity(widths)
Calculate the maximum eccentricity from the longest and smallest

principal axes.

Parameters:

widths – 3 widths along the principal axes.

Returns:

Max eccentricity calculated from the longest and shortest axes.

em_map_utils.structure_size_and_shape.asphericity_coefficient(a, b, c)

Calculate the asphericity coefficient using three orthogonal width measures for a structure. Tha asphericity coefficient is defined as: 1 - [ (V/S) / (V0/S0) ] where: S0 and V0 are the surface area and volume of a sphere with the cube root diameter = (abc)^(1/3), V is the volume of an ellipsoid with the axes a,b,c, S is the surface area of the ellipsoid with axes a,b,c calculated using the Carlson symmetric elliptical integral. What this formula is based on is that the surface area to volume ratio is at a minimum for a sphere compared to any ellipsoid with an equivalent volume and the comparison between the ratios increases the more the ellipsoid deviated from a sphere.

Parameters:

  • a – Width along first axis.

  • b – Width along second axis.

  • c – Width along third axis.

Returns:

Asphericity coefficient.

em_map_utils.structure_size_and_shape.structure_size_and_shape(entry_file, aligned_file=None, plot_profile=True, csv_file=None, csv_mode='a', max_map_size=600)

Determine the size and shape of a structure.

Parameters:

  • entry_file – Name of input MRC file.

  • aligned_file – Optional name of aligned output MRC file.

  • plot_profile – Boolean for plotting line projections.

  • csv_file – Optional name of CSV file to output results to.

  • csv_mode – Whether to (a)ppend or (w) to CSV file.

  • max_map_size – If any dimension of the map is larger than max_map_size, the map is rescaled to make it fit. This option is mainly to reduce the time for processing large maps.

Returns:

Tuple with physical widths of structure along the principal axes, the cube root of these widths (which represents a sphere equivalent average), and the asphericity.

em_map_utils.structure_size_and_shape.main()