TEMPy.optimisation package

Submodules

TEMPy.optimisation.ensemble_generation module

class EnsembleGeneration

Bases: object

A class to create ensemble of structure instance

anglar_sweep(structure_instance, axis, translation_vector, no_of_structs, loc_rotation_angle, flag='mod', atom_com_ind=False, write=False, filename=None)

Generate an ensemble of Structure Instance

NOTE - Chose the number of structures for the ensemble accordingly with the angular increment step (loc_rotation_angle/no_of_structs) and translational increment step (translation_vector/no_of_structs) required. Default setting is around the center of mass.

Arguments:
structure_instance

Input Structure Instructure_instance

axis

3-tuple, axis for translation

translation_vector

3-ple, vector for translation

no_of_structs

int, number of structures to output

loc_rotation_angle

tuple, rotation angle for local rotation (degrees)

flag

string, prefix name for outputted pdb files

atom_com_ind

int, index of atom to rotate around. If False, rotates around centre of mass

write

True will write out each Structure Instance in the ensemble as single PDB.

Return:

list of Structure Instance in which each item is [structure_instance_name,structure_instance]

loadEnsemble(path_dir, file_name_flag, hetatm=False, water=False, verbose=False, pdb=True)

Load an ensemble of Structure Instance from the directory path_dir. Arguments:

path_dir

directory name

file_name_flag

name or suffix of the files.

randomise_structs(structure_instance, no_of_structs, max_trans, max_rot, v_grain=30, rad=False, flag='mod', write=False)

Generate an ensemble of Structure Instance.

Arguments:
structure_instance

Input Structure Instance

no_of_structs

int, number of structures to output

max_trans

Maximum translation permitted

max_rot

Maximum rotation permitted (in degree if rad=False)

v_grain

Graning Level for the generation of random vectors (default=30)

write

True will write out each structure_instanceure Instance in the ensemble as single PDB.

Return:

list of Structure Instance in which each item is [structure_instance_name,structure_instance]

spiral_sweep(structure_instance, axis, dist, no_of_structs, loc_ang_range, loc_axis, flag, atom_com_ind=False, write=False)

Generate an ensemble of Structure Instance

Arguments:
structure_instance

Input Structure Instance

axis

3-ple, axis for translation

dist

int, translation range (Angstroms)

no_of_structs

int, number of structures to output

loc_axis

3-ple, axis for local rotation around centre of mass

loc_ang_range

tuple, rotation range for local rotation (degrees)

flag

string, prefix name for outputted pdb files

atom_com_ind

int, index of atom to rotate around. If False, rotates around centre of mass.

write

True will write out each Structure Instance in the ensemble as single PDB.

Return:

list of Structure Instance in which each item is [structure_instance_name,structure_instance]

Module contents