Module geometric
source code
Module for handling the geometric representation of the frame order
motions.
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add_axes(structure=None,
representation=None,
size=None,
sims=False)
Add the axis system for the current frame order model to the
structural object. |
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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. |
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add_pivots(structure=None,
sims=False)
Add the pivots for the current frame order model to the structural
object. |
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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. |
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add_rotors(structure=None,
representation=None,
size=None,
sims=False)
Add all rotor objects for the current frame order model to the
structural object. |
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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. |
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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. |
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numpy rank-2, 3D float64 array
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__package__ = ' specific_analyses.frame_order '
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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
add_axes(structure=None,
representation=None,
size=None,
sims=False)
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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.
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add_cones(structure=None,
representation=None,
size=None,
inc=None,
sims=False)
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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.
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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.
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add_titles(structure=None,
representation=None,
displacement=40.0,
sims=False)
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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.
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add_rotors(structure=None,
representation=None,
size=None,
sims=False)
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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.
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average_position(structure=None,
models=None,
sim=None)
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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.
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create_ave_pos(format=' PDB ' ,
file=None,
dir=None,
compress_type=0,
model=1,
force=False)
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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.
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create_geometric_rep(format=' PDB ' ,
file=None,
dir=None,
compress_type=0,
size=30.0,
inc=36,
force=False)
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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.
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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.
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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.
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