8. Generation an Ensemble of Structure Instance

class EnsembleGeneration.EnsembleGeneration

A class to create ensemble of structure instance

anglar_sweep(struct, axis, translation_vector, no_of_structs, loc_rotation_angle, output_template, atom_com_ind=False, write=False)

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:

struct

Input Structure Instance

axis

3-ple, 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)

output_template

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.

circular_sweep_with_fixed_spin(struct, axis, point, ang_range, no_of_structs, output_template, loc_axis=False, loc_ang_range=False, atom_com_ind=False, write=False)

Generate an ensemble of Structure Instance

Arguments:

struct

Input Structure Instance

axis

3-ple, axis around which the large scale rotation will be done

point

3-ple, point around which large scale rotation will be done

ang_range

tuple, rotation range (degrees)

no_of_structs

int, number of structures to output

output_template

string, prefix name for outputted pdb files

loc_axis

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

loc_ang_range

tuple, rotation range for local rotation (degrees)

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.

circular_sweep_with_tangential_spin(struct, axis, point, ang_range, no_of_structs, output_template, loc_ang_range=False, atom_com_ind=False, write=False)

Generate an ensemble of Structure Instance

Arguments:

struct

Input Structure Instance

axis

3-ple, axis around which the large scale rotation will be done

point

3-ple, point around which large scale rotation will be done

ang_range

tuple, rotation range (degrees)

no_of_structs

int, number of structures to output

output_template

string, prefix name for outputted pdb files

loc_ang_range

tuple, rotation range for local rotation (degrees)

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.

randomise_structs(struct, no_of_structs, max_trans, max_rot, v_grain=30, rad=False)

Generate an ensemble of Structure Instance.

Arguments:

struct

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 vetors (default=30)

spiral_sweep(struct, axis, dist, no_of_structs, loc_ang_range, loc_axis, output_template, atom_com_ind=False, write=False)

Generate an ensemble of Structure Instance

Arguments:

struct

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)

output_template

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.