BagelFitter

BagelFitter Class

class src.BagelFitter.BagelFitter

Bases: object

Fits a torus onto a nuclear membrane by searching for the best parameters.

best_torus

The best-fitting torus found during the fitting process.

Type:

Torus

dmap

Input density map of the nuclear membrane.

Type:

IMP.em.DensityMap

dmap_out

Output density map after fitting.

Type:

IMP.em.DensityMap

dmap_out_binary_flag

Flag indicating if the density map is binary.

Type:

bool

input_map_path

Path to the input density map file.

Type:

str

voxel_size

Size of each voxel in the density map (default is 10).

Type:

int

calculate_dice_coefficient(dmap1: DensityMap, dmap2: DensityMap) → float

Computes the Dice Coefficient (F1 Score) for binary overlap between two density maps.

Parameters:

  • dmap1 (IMP.em.DensityMap) – First density map.

  • dmap2 (IMP.em.DensityMap) – Second density map.

Returns:

Dice Coefficient representing the overlap of the two maps.

Return type:

float

create_blank_density_map(n_voxels: int) → DensityMap

Creates an empty density map centered at (0,0,0).

Parameters:

n_voxels (int) – Number of voxels in each dimension.

Returns:

A blank density map with specified voxel size.

Return type:

IMP.em.DensityMap

fill_binary_density(torus: Torus) → None

Generates a binary density map based on the torus parameters.

Parameters:

torus (Torus) – Torus object used to define the density map.

fill_nonbinary_density(torus: Torus) → None

Generates a non-binary density (extracted from the input map) map based on the torus parameters.

Parameters:

torus (Torus) – Torus object used to define the density map.

fit_binary_torus(tor_R_range: tuple = (670, 680, 10), tor_r_range: tuple = (160, 180, 20), tor_th_range: tuple = (85.0, 95, 10), extension: float = 0.0) → Torus

Fits a binary torus to the density map by searching for optimal parameters.

Parameters:

  • tor_R_range (tuple, optional) – Range of major radius values (start, stop, step).

  • tor_r_range (tuple, optional) – Range of minor radius values (start, stop, step).

  • tor_th_range (tuple, optional) – Range of thickness values (start, stop, step).

  • extension (float, optional) – Additional extension factor (default is 0.0).

Returns:

Best-fitting torus object based on maximum cross-correlation coefficient.

Return type:

Torus

fit_nonbinary_torus(tor_R_range: tuple = (670, 680, 10), tor_r_range: tuple = (160, 180, 20), tor_th_range: tuple = (85.0, 95, 10), extension: float = 0.0) → Torus

Fits a non-binary torus to the density map by searching for optimal parameters.

Parameters:

  • tor_R_range (tuple, optional) – Range of major radius values (start, stop, step).

  • tor_r_range (tuple, optional) – Range of minor radius values (start, stop, step).

  • tor_th_range (tuple, optional) – Range of thickness values (start, stop, step).

  • extension (float, optional) – Additional extension factor (default is 0.0).

Returns:

Best-fitting torus object based on maximum cross-correlation coefficient.

Return type:

Torus

generate_binary_torus(tor_R: float, tor_r: float, tor_th: float, extension: float = 0.0, boundingbox_length: float = 2240, voxel_size: float = 10, outmap_fname: str = 'torus_yeast_fitted.mrc') → Torus

Generates and writes a binary torus density map based on input parameters.

Parameters:

  • tor_R (float) – Major radius of the torus.

  • tor_r (float) – Minor radius of the torus.

  • tor_th (float) – Thickness of the bilipid layer.

  • extension (float, optional) – Additional extension factor (default is 0.0).

  • boundingbox_length (float, optional) – Length of the bounding box for Torus centered at (0,0,0). Default value 2240 Å.

  • voxel_size (float, optional) – Individual voxel size in the output map file. Default value 10 Å.

  • outmap_fname (str, optional) – Output map file name of the torus. Default is “torus_yeast_fitted.mrc” in the current directory.

Returns:

Torus object based on input parameters.

Return type:

Torus

load_exprimental_map(input_map_path: str, voxel_size: int | None = None) → None

Loads an experimental density map for processing.

Parameters:

  • input_map_path (str) – Path to the input density map file.

  • voxel_size (int, optional) – Size of each voxel (default is determined from the map).

plot_voxel_values() → None

Plots the histogram of voxel intensity values in the density map.

score_torus_maps(map1: str, map2: str) → float

Computes the cross-correlation coefficient between two torus maps.

Parameters:

  • map1 (str) – Path to the first torus density map.

  • map2 (str) – Path to the second torus density map.

Returns:

Cross-correlation coefficient indicating similarity between the two maps.

Return type:

float

write_torusmap_to_file(outmap_fname: str) → None

Saves the torus density map to a file.

Parameters:

outmap_fname (str) – Filename to save the torus density map.

Torus Class

Summary

class src.Torus.Torus(R: float, r: float, thickness: float, extension: float = 0.0)

Bases: object

Represents a toroidal shape characterized by its major radius (R), minor radius (r), and thickness.

R

Major radius of the torus.

Type:

float

r

Minor radius of the torus.

Type:

float

thickness

Thickness of the torus.

Type:

float

extension

Optional extension parameter (default is 0.0).

Type:

float

eps

Small constant to avoid division by zero errors.

Type:

float

dmap

Data map for storing computed values (if applicable).

Type:

Any

contains_point(x: float, y: float, z: float) → bool

Determines whether a point (x, y, z) lies within the toroidal volume.

Parameters:

  • x (float) – X-coordinate of the point.

  • y (float) – Y-coordinate of the point.

  • z (float) – Z-coordinate of the point.

Returns:

True if the point is inside the torus, False otherwise.

Return type:

bool

contains_point2(x: float, y: float, z: float) → bool

Alternative method to check if a point (x, y, z) lies within the toroidal volume.

Parameters:

  • x (float) – X-coordinate of the point.

  • y (float) – Y-coordinate of the point.

  • z (float) – Z-coordinate of the point.

Returns:

True if the point is inside the torus, False otherwise.

Return type:

bool

distance(x: float, y: float, z: float, d2_xy: float) → float

Computes the shortest distance from a point (x, y, z) to the torus.

Parameters:

  • x (float) – X-coordinate of the point.

  • y (float) – Y-coordinate of the point.

  • z (float) – Z-coordinate of the point.

  • d2_xy (float) – Squared distance from the torus center in the xy-plane.

Returns:

Shortest distance from the given point to the torus.

Return type:

float