Module simulation
source code
Module for simulating the frame order motions.
|
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
|
|
|
__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
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.
|