Module simulation
source code
Module for simulating the frame order motions.
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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
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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
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__package__ = 'lib.frame_order' |
Imports:
cos,
pi,
sin,
sqrt,
dot,
eye,
float64,
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
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
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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.
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uniform_distribution(file=None,
model=None,
structure=None,
parameters={},
eigenframe=None,
pivot=None,
atom_id=None,
total=1000,
max_rotations=100000)
| source code
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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.
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