Represent multi-subunit component and its density map

class Assembly.Assembly(structList)[source]

A class to represent multi-subunit component and its corresponding density map.

build_maps(resolution, template_map, sig_coeff=0.356)[source]

Build list of maps corresponding to the protein components in the structList.

Arguments:

resolution
Desired resolution of the density map in Angstrom units.
template_map
A map object that will be uesd as the template to build maps of for the individual maps. Usually the input map used for the assembly fitting.
sigma_coeff
the sigma value (multiplied by the resolution) that controls the width of the Gaussian. Default values is 0.356.
combine_maps()[source]

Used to combine the list of map objects into a single map object

combine_structs()[source]

Used to combine the list of structure objects into a single structure object

make_VQ_points(threshold, noOfPoints, lap_fil, epochs=300)[source]

Cluster the density maps in the assembly object into n points using vector quantisation algorithm.

Arguments:

emmap
Map (to be clustered) instance.
threshold
voxels with density above this value are used in the VQ run.
noOfPoints
Number of Vector quantisation points to output.
lap_fil
True if you want to Laplacian filter the map first, False otherwise. Note that filtering the map change the density values of the map, which is relevant for the threshold parameter.
epochs
Number of iterations to run the Vector quantisation algorithm. Default is set to 300
Return:
A list of vector objects containing the vector quatisation points
move_map_and_prot_by_aa(index, rx, ry, rz, ra, tx, ty, tz)[source]

Translate and rotate the structure and map objects in the assembly around its centre given an axis and angle.

Arguments:

index
Index of the structure and map list.
rx,ry,rz
Axis to rotate about, ie. rx,ry,rz = 0,0,1 rotates the structure and map round the xy-plane.
ra
Angle (in degrees) to rotate map.
tx,ty,tz
Distance in Angstroms to move structure and map in respective x, y, and z directions.
move_map_and_prot_by_euler(index, rx, ry, rz, tx, ty, tz)[source]

Translate and rotate the structure and map objects in the assembly around its centre using Euler angles.

Arguments:

index
Index of the structure and map list.
rx,ry,rz
Axis to rotate about, ie. rx,ry,rz = 0,0,1 rotates the structure and map round the xy-plane.
ra
Angle (in degrees) to rotate map.
tx,ty,tz
Distance in Angstroms to move structure and map in respective x, y, and z directions.
move_map_and_prot_by_mat(index, mat, tx, ty, tz)[source]

Translate and rotate the structure and map objects around pivot given by CoM using a translation vector and a rotation matrix respectively.

Arguments:
mat
3x3 matrix used to rotate structure and map objects.
tx,ty,tz
Distance in Angstroms to move structure and map in respective x, y, and z directions.
move_map_and_prot_by_quat(index, tx, ty, tz, q_param, mat)[source]

Translate the structure objects using a translation vector and rotate it using a quaternion object Translate and rotate the map objects around pivot given by CoM using a translation vector and a rotation matrix respectively.

Arguments:
index
Index of the structure and map list.
tx,ty,tz
Distance in Angstroms to move structure and map in respective x, y, and z directions.
q_param
Is a list of type [w, x, y, z] which represents a quaternion vector used for rotation
mat
3x3 matrix used to rotate structure and map objects.
randomise_structs(max_trans, max_rot, v_grain=30, rad=False)[source]

Randomise the position and orientation of the protein components in the structList.

Arguments:

max_trans
Maximum translation permitted
max_rot
Maximum rotation permitted (in degree if rad=False)
v_grain
Graning Level for the generation of random vetors (default=30)
randomise_structs_and_maps(max_trans, max_rot, v_grain=30, rad=False)[source]

Randomise the position and orientation of the protein components and its corresponding map objects.

Arguments:

max_trans
Maximum translation permitted
max_rot
Maximum rotation permitted (in degree if rad=False)
v_grain
Graning Level for the generation of random vetors (default=30)
reset_all()[source]

Reset the map and structure objects to is initial state.

reset_maps()[source]

Undo all the transformations applied to the list of map objects and restore it to its original state.

reset_structs()[source]

Translate the list of structure objects back into initial position.

write_all_to_files(templateName)[source]

Write the all the strucrure and map objects separately to a pdb and mrc formatted file respectively.

Arguments:

templateName
A string representing the prefix of the file name