Disctransformation.transform package

Submodules

Disctransformation.transform.DTransform module

Disctransformation.transform.DTransform.DTransform(mdl)

Takes a model object and performs Linear transformation suitable for Disctransformation

Parameters:

mdl (pdbclass) – Model object to the file for Disctransform

Returns:

mdl – Modified model object after Disctransform

Return type:

pdbclass

Disctransformation.transform.DTransform.GetDiscRepresentation(mdl)

Takes a model object and adds a pseudoatom for every CA atom. This atom will be CA atom with Residue DTA. This can be used for the visualization in pdb format

Parameters:

mdl (pdbclass) – Model object of the file to add pseudoatom

Returns:

mdl – Modified model object after pseudoatom addition

Return type:

pdbclass

Disctransformation.transform.DTransform.GetDiscRepresentation_nthCA(mdl, nthCA=4)

Takes a model object and adds a pseudoatom for every nth CA atom. This atom will be CA atom with Residue DTA. This can be used for the visualization in pdb format

Parameters:

  • mdl (pdbclass) – Model object of the file to add pseudoatom

  • nthCA (int, optional) – Description

Returns:

mdl – Modified model object after pseudoatom addition

Return type:

pdbclass

Disctransformation.transform.DTransform.sqrdistance(a1, a2)

Summary

Parameters:

  • a1 (TYPE) – Description

  • a2 (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.transform.pdbclass module

class Disctransformation.transform.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

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.transform.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

Module contents