Module geometric

Module for handling the geometric representation of the frame order motions.

Functions

add_axes(structure=None, representation=None, size=None, sims=False)
Add the axis system for the current frame order model to the structural object.

add_cones(structure=None, representation=None, size=None, inc=None, sims=False)
Add the cone geometric object for the current frame order model to the structural object.

add_pivots(structure=None, sims=False)
Add the pivots for the current frame order model to the structural object.

add_titles(structure=None, representation=None, displacement=40.0, sims=False)
Add atoms to be used for the titles for the frame order geometric objects.

add_rotors(structure=None, representation=None, size=None, sims=False)
Add all rotor objects for the current frame order model to the structural object.

average_position(structure=None, models=None, sim=None)
Shift the given structural object to the average position.

create_ave_pos(format='PDB', file=None, dir=None, compress_type=0, model=1, force=False)
Create a PDB file of the molecule with the moving domains shifted to the average position.

create_geometric_rep(format='PDB', file=None, dir=None, compress_type=0, size=30.0, inc=36, force=False)
Create a PDB file containing a geometric object representing the frame order dynamics.

frame_from_axis(axis, frame)
Build a full 3D frame from the single axis.

numpy rank-2, 3D float64 array generate_axis_system(sim_index=None)
Generate and return the full 3D axis system for the current frame order model.

Variables

__package__ = 'specific_analyses.frame_order'

Imports: deepcopy, pi, cross, dot, eye, float64, zeros, norm, sys, warn, RelaxFault, create_rotor_axis_alpha, create_rotor_axis_spherical, MODEL_DOUBLE_ROTOR, MODEL_FREE_ROTOR, MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR, MODEL_ISO_CONE_TORSIONLESS, MODEL_LIST_DOUBLE, MODEL_LIST_FREE_ROTORS, MODEL_LIST_ISO_CONE, MODEL_LIST_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE_FREE_ROTOR, MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_ROTOR, euler_to_R_zyz, open_write_file, Iso_cone, Pseudo_elliptic, generate_vector_residues, Internal, cone, rotor, subsection, subsubsection, RelaxWarning, pipe_centre_of_mass, check_parameters, domain_moving, generate_pivot

Function Details

add_axes(structure=None, representation=None, size=None, sims=False)

Add the axis system for the current frame order model to the structural object.

Parameters:

• structure (lib.structure.internal.object.Internal instance) - The internal structural object to add the rotor objects to.
• representation (None or str) - The representation to create. If this is set to None or 'A', the standard representation will be created. If set to 'B', the axis system will be inverted.
• size (float) - The size of the geometric object in Angstroms.
• sims (bool) - A flag which if True will add the Monte Carlo simulation rotors to the structural object. There must be one model for each Monte Carlo simulation already present in the structural object.

add_cones(structure=None, representation=None, size=None, inc=None, sims=False)

Add the cone geometric object for the current frame order model to the structural object.

Parameters:

• structure (lib.structure.internal.object.Internal instance) - The internal structural object to add the rotor objects to.
• representation (str) - The representation to create. If this is set to None or 'A', the standard representation will be created. If set to 'B', the axis system will be inverted.
• size (float) - The size of the geometric object in Angstroms.
• inc (int) - The number of increments for the filling of the cone objects.
• sims (bool) - A flag which if True will add the Monte Carlo simulation pivots to the structural object. There must be one model for each Monte Carlo simulation already present in the structural object.

add_pivots(structure=None, sims=False)

Add the pivots for the current frame order model to the structural object.

Parameters:

• structure (lib.structure.internal.object.Internal instance) - The internal structural object to add the rotor objects to.
• sims (bool) - A flag which if True will add the Monte Carlo simulation pivots to the structural object. There must be one model for each Monte Carlo simulation already present in the structural object.

add_titles(structure=None, representation=None, displacement=40.0, sims=False)

Add atoms to be used for the titles for the frame order geometric objects.

Parameters:

• structure (lib.structure.internal.object.Internal instance) - The internal structural object to add the rotor objects to.
• representation (None or str) - The representation to title.
• displacement (float) - The distance away from the pivot point, in Angstrom, to place the title. The simulation title will be shifted by a few extra Angstrom to avoid clashes.
• sims (bool) - A flag which if True will add the Monte Carlo simulation pivots to the structural object. There must be one model for each Monte Carlo simulation already present in the structural object.

add_rotors(structure=None, representation=None, size=None, sims=False)

Add all rotor objects for the current frame order model to the structural object.

Parameters:

• structure (lib.structure.internal.object.Internal instance) - The internal structural object to add the rotor objects to.
• representation (None or str) - The representation to create. If this is set to None, the rotor will be dumbbell shaped with propellers at both ends. If set to 'A' or 'B', only half of the rotor will be shown.
• size (float) - The size of the geometric object in Angstroms.
• sims (bool) - A flag which if True will add the Monte Carlo simulation rotors to the structural object. There must be one model for each Monte Carlo simulation already present in the structural object.

average_position(structure=None, models=None, sim=None)

Shift the given structural object to the average position.

Parameters:

• structure (lib.structure.internal.object.Internal instance) - The structural object to operate on.
• models (list of int) - The list of models to shift.
• sim (bool) - A flag which if True will use the Monte Carlo simulation results. In this case, the model list should be set to the simulation indices plus 1 and the structural object should have one model per simulation already set up.

create_ave_pos(format='PDB', file=None, dir=None, compress_type=0, model=1, force=False)

Create a PDB file of the molecule with the moving domains shifted to the average position.

Parameters:

• format (str) - The format for outputting the geometric representation. Currently only the 'PDB' format is supported.
• file (str) - The name of the file for the average molecule structure.
• dir (str) - The name of the directory to place the PDB file into.
• compress_type (int) - The compression type. The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression.
• model (int) - Only one model from an analysed ensemble can be used for the PDB representation of the Monte Carlo simulations, as these consists of one model per simulation.
• force (bool) - Flag which if set to True will cause any pre-existing file to be overwritten.

create_geometric_rep(format='PDB', file=None, dir=None, compress_type=0, size=30.0, inc=36, force=False)

Create a PDB file containing a geometric object representing the frame order dynamics.

Parameters:

• format (str) - The format for outputting the geometric representation. Currently only the 'PDB' format is supported.
• file (str) - The name of the file of the PDB representation of the frame order dynamics to create.
• dir (str) - The name of the directory to place the PDB file into.
• compress_type (int) - The compression type. The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression.
• size (float) - The size of the geometric object in Angstroms.
• inc (int) - The number of increments for the filling of the cone objects.
• force (bool) - Flag which if set to True will cause any pre-existing file to be overwritten.

frame_from_axis(axis, frame)

Build a full 3D frame from the single axis.

Parameters:

• axis (numpy rank-1, 3D array) - The Z-axis of the system.
• frame (numpy rank-2, 3D array) - The empty frame to populate.

generate_axis_system(sim_index=None)

Generate and return the full 3D axis system for the current frame order model.

Parameters:

• sim_index (None or int) - The optional MC simulation index to obtain the frame for a given simulation.

Returns: numpy rank-2, 3D float64 array

The full 3D axis system for the model.