Disctransformation.align_axis package

Submodules

Disctransformation.align_axis.align module

Disctransformation.align_axis.align.create_orientation_matrix(N)

Summary

Parameters:

N (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.align.get_arbitrary_perpendicular_vector(Ng, P)

Summary

Parameters:

  • Ng (TYPE) – Description

  • P (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.align.main()

Summary

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.fourier_transform module

Disctransformation.align_axis.fourier_transform.avg_zstep_distance(CoordsZ)

Summary

Parameters:

CoordsZ (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.fourier_transform.fourier_transform(mdl, coord_A_iter)

Summary

Parameters:

  • mdl (TYPE) – Description

  • coord_A_iter (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.fourier_transform2D module

Disctransformation.align_axis.fourier_transform2D.avg_zstep_distance(CoordsZ)

Summary

Parameters:

CoordsZ (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.fourier_transform2D.fourier_transform(mdl, coord_A_iter)

Summary

Parameters:

  • mdl (TYPE) – Description

  • coord_A_iter (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.getorientation module

Disctransformation.align_axis.getorientation.getorientation(coord_X)

Summary

Parameters:

coord_X (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.main module

Disctransformation.align_axis.main.align(inputfile, outputfile, alignaxis, chain, align_flag=True)

Summary

Parameters:

  • inputfile (TYPE) – Description

  • outputfile (TYPE) – Description

  • alignaxis (TYPE) – Description

  • chain (TYPE) – Description

  • align_flag (bool, optional) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.main.alignx(N, T, B)

Summary

Parameters:

  • N (TYPE) – Description

  • T (TYPE) – Description

  • B (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.main.aligny(N, T, B)

Summary

Parameters:

  • N (TYPE) – Description

  • T (TYPE) – Description

  • B (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.main.alignz(N, T, B)

Summary

Parameters:

  • N (TYPE) – Description

  • T (TYPE) – Description

  • B (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.main.get_arbitrary_perpendicular_vector(Ng, P)

Summary

Parameters:

  • Ng (TYPE) – Description

  • P (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.makemove module

Disctransformation.align_axis.makemove.move(mdl, OM)

Summary

Parameters:

  • mdl (TYPE) – Description

  • OM (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.parsepdb module

Disctransformation.align_axis.parsepdb.parsepdb(fname, chains)

Summary

Parameters:

  • fname (TYPE) – Description

  • chains (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.pdbclass module

class Disctransformation.align_axis.pdbclass.PDB(filename)

Bases: object

Summary

T()

Summary

Returns:

Description

Return type:

TYPE

aa_length()

Summary

Returns:

Description

Return type:

TYPE

add_atom_in_model(serial, name, resName, chainID, resSeq, x, y, z, T)

Summary

Parameters:

  • serial (TYPE) – Description

  • name (TYPE) – Description

  • resName (TYPE) – Description

  • chainID (TYPE) – Description

  • resSeq (TYPE) – Description

  • x (TYPE) – Description

  • y (TYPE) – Description

  • z (TYPE) – Description

  • T (TYPE) – Description

Returns:

Description

Return type:

TYPE

altLoc()

Summary

Returns:

Description

Return type:

TYPE

chainID()

Summary

Returns:

Description

Return type:

TYPE

iter_length()

Summary

Returns:

Description

Return type:

TYPE

name()

Summary

Returns:

Description

Return type:

TYPE

resName()

Summary

Returns:

Description

Return type:

TYPE

resSeq()

Summary

Returns:

Description

Return type:

TYPE

sequence()

Summary

Returns:

Description

Return type:

TYPE

sequence_map()

Summary

Returns:

Description

Return type:

TYPE

serial()

Summary

Returns:

Description

Return type:

TYPE

set_T(i, value)

Summary

Parameters:

  • i (TYPE) – Description

  • value (TYPE) – Description

set_iter_length(value)

Summary

Parameters:

value (TYPE) – Description

set_x(i, value)

Summary

Parameters:

  • i (TYPE) – Description

  • value (TYPE) – Description

set_y(i, value)

Summary

Parameters:

  • i (TYPE) – Description

  • value (TYPE) – Description

set_z(i, value)

Summary

Parameters:

  • i (TYPE) – Description

  • value (TYPE) – Description

write(outfilename)

Summary

Parameters:

outfilename (TYPE) – Description

Returns:

Description

Return type:

TYPE

writeCA(outfilename, skip_res='DTA')

Summary

Parameters:

  • outfilename (TYPE) – Description

  • skip_res (str, optional) – Description

Returns:

Description

Return type:

TYPE

write_all_chains(outfilename)

Summary

Parameters:

outfilename (TYPE) – Description

Returns:

Description

Return type:

TYPE

write_selection(outfilename, selection)

Summary

Parameters:

  • outfilename (TYPE) – Description

  • selection (TYPE) – Description

Returns:

Description

Return type:

TYPE

write_selection_multimdl(outfilename, selection, modelid)

Summary

Parameters:

  • outfilename (TYPE) – Description

  • selection (TYPE) – Description

  • modelid (TYPE) – Description

Returns:

Description

Return type:

TYPE

x()

Summary

Returns:

Description

Return type:

TYPE

y()

Summary

Returns:

Description

Return type:

TYPE

z()

Summary

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.pdbclass.pdb_line(serial='', name='', resName='', chainID='', resSeq='', x='', y='', z='', occupancy='', T='', element='', charge='', altLoc='', iCode='')

serial, name, resName, resSeq , x, y, z, occupancy, T, element, charge, altLoc, chainID, iCode

Parameters:

  • serial (str, optional) – Description

  • name (str, optional) – Description

  • resName (str, optional) – Description

  • chainID (str, optional) – Description

  • resSeq (str, optional) – Description

  • x (str, optional) – Description

  • y (str, optional) – Description

  • z (str, optional) – Description

  • occupancy (str, optional) – Description

  • T (str, optional) – Description

  • element (str, optional) – Description

  • charge (str, optional) – Description

  • altLoc (str, optional) – Description

  • iCode (str, optional) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.align_axis.rewritepdb2 module

Disctransformation.align_axis.roration_matrix2 module

Disctransformation.align_axis.roration_matrix2.rotation_matrix(axis, theta)

Summary

Parameters:

  • axis (TYPE) – Description

  • theta (TYPE) – Description

Returns:

Description

Return type:

TYPE

Module contents