Generation an Ensemble of Structure Instance

class EnsembleGeneration.EnsembleGeneration[source]

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)[source]

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)[source]

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)[source]

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)[source]

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]