Package lib :: Package frame_order :: Module simulation
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Module simulation

source code

Module for simulating the frame order motions.

Functions [hide private]
 
brownian(file=None, model=None, structure=None, parameters={}, eigenframe=None, pivot=None, atom_id=None, step_size=2.0, snapshot=10, total=1000)
Pseudo-Brownian dynamics simulation of the frame order motions.
source code
 
mode_distribution(file=None, structure=None, axis=None, angle=None, pivot=None, atom_id=None, angle_inc=0.0174532925199, total=None, reverse=False, mirror=False)
Linear distribution of a single component of the frame order motions.
source code
 
uniform_distribution(file=None, model=None, structure=None, parameters={}, eigenframe=None, pivot=None, atom_id=None, total=1000, max_rotations=100000)
Uniform distribution of the frame order motions.
source code
Variables [hide private]
  __package__ = 'lib.frame_order'

Imports: cos, modf, pi, sin, sqrt, arange, array, concatenate, dot, eye, float64, linspace, transpose, zeros, sys, warn, RelaxError, RelaxWarning, MODEL_DOUBLE_ROTOR, wrap_angles, axis_angle_to_R, R_random_hypersphere, R_to_tilt_torsion, tilt_torsion_to_R, random_unit_vector


Function Details [hide private]

brownian(file=None, model=None, structure=None, parameters={}, eigenframe=None, pivot=None, atom_id=None, step_size=2.0, snapshot=10, total=1000)

source code 

Pseudo-Brownian dynamics simulation of the frame order motions.

Parameters:
  • file (str) - The opened and writable file object to place the snapshots into.
  • structure (lib.structure.internal.object.Internal instance) - The internal structural object containing the domain to simulate as a single model.
  • model (str) - The frame order model to simulate.
  • parameters (dict of float) - The dictionary of model parameter values. The key is the parameter name and the value is the value.
  • eigenframe (numpy rank-2, 3D float64 array) - The full 3D eigenframe of the frame order motions.
  • pivot (numpy rank-2 (N, 3) float64 array) - The list of pivot points of the frame order motions.
  • atom_id (None or str) - The atom ID string for the atoms in the structure to rotate - i.e. the moving domain.
  • step_size (float) - The rotation will be of a random direction but with this fixed angle. The value is in degrees.
  • snapshot (int) - The number of steps in the simulation when snapshots will be taken.
  • total (int) - The total number of snapshots to take before stopping the simulation.

mode_distribution(file=None, structure=None, axis=None, angle=None, pivot=None, atom_id=None, angle_inc=0.0174532925199, total=None, reverse=False, mirror=False)

source code 

Linear distribution of a single component of the frame order motions.

Parameters:
  • file (str) - The opened and wrlib/frame_order/simulation.pyitable file object to place the PDB models of the representation into.
  • structure (lib.structure.internal.object.Internal instance) - The internal structural object to convert into an ensemble along the mode of motion.
  • axis (numpy 3D float64 array) - The rotation axis.
  • angle (float) - The rotation angle in radian (structures will be rotated +/- this angle).
  • pivot (numpy 3D float64 array) - The pivot point for the given motional mode.
  • atom_id (None or str) - The atom ID string for the atoms in the structure to rotate - i.e. the moving domain.
  • angle_inc (float) - The angle between rotated representations. The default is 1 degree.
  • total (int) - The total number of structures to distribute along the motional modes. This overrides angle_inc.
  • reverse (bool or list of bool) - Set this to reverse the ordering of the models distributed along the motional mode. Use a list of Booleans to selectively reverse each motional mode.
  • mirror (bool) - Set this to have the models distributed along the motional mode shift from the negative angle to positive angle, and then return to the negative angle.

uniform_distribution(file=None, model=None, structure=None, parameters={}, eigenframe=None, pivot=None, atom_id=None, total=1000, max_rotations=100000)

source code 

Uniform distribution of the frame order motions.

Parameters:
  • file (str) - The opened and writable file object to place the PDB models of the distribution into.
  • structure (lib.structure.internal.object.Internal instance) - The internal structural object containing the domain to distribute as a single model.
  • model (str) - The frame order model to distribute.
  • parameters (dict of float) - The dictionary of model parameter values. The key is the parameter name and the value is the value.
  • eigenframe (numpy rank-2, 3D float64 array) - The full 3D eigenframe of the frame order motions.
  • pivot (numpy rank-2 (N, 3) float64 array) - The list of pivot points of the frame order motions.
  • atom_id (None or str) - The atom ID string for the atoms in the structure to rotate - i.e. the moving domain.
  • total (int) - The total number of states in the distribution.
  • max_rotations (int) - The maximum number of rotations to generate the distribution from. This prevents an execution for an infinite amount of time when a frame order amplitude parameter is close to zero so that the subset of all rotations within the distribution is close to zero.