Module uf
source code
Module for all of the frame order specific user functions.
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decompose(root=' decomposed ' ,
dir=None,
atom_id=None,
model=1,
total=100,
reverse=False,
mirror=False,
force=True)
Structural representation of the individual frame order motional
components. |
source code
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distribute(file=' distribution.pdb.bz2 ' ,
dir=None,
atom_id=None,
total=1000,
max_rotations=100000,
model=1,
force=True)
Create a uniform distribution of structures for the frame order
motions. |
source code
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pdb_model(ave_pos=' ave_pos ' ,
rep=' frame_order ' ,
dir=None,
compress_type=0,
size=30.0,
inc=36,
model=1,
force=False)
Create 3 different PDB files for representing the frame order
dynamics of the system. |
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permute_axes(permutation=' A ' )
Permute the axes of the motional eigenframe to switch between local
minima. |
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pivot(pivot=None,
order=1,
fix=False)
Set the pivot point for the 2 body motion. |
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quad_int(flag=False)
Turn the high precision Scipy quadratic numerical integration on or
off. |
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simulate(file=' simulation.pdb.bz2 ' ,
dir=None,
step_size=2.0,
snapshot=10,
total=1000,
model=1,
force=True)
Pseudo-Brownian dynamics simulation of the frame order motions. |
source code
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sobol_setup(max_num=200,
oversample=100)
Oversampling setup for the quasi-random Sobol' sequence used for
numerical PCS integration. |
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__package__ = ' specific_analyses.frame_order '
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Imports:
deepcopy,
pi,
argsort,
array,
float64,
ones,
transpose,
zeros,
warn,
is_float_array,
is_float,
RelaxError,
RelaxFault,
brownian,
mode_distribution,
uniform_distribution,
MODEL_DOUBLE_ROTOR,
MODEL_ISO_CONE,
MODEL_LIST,
MODEL_LIST_FREE_ROTORS,
MODEL_LIST_ISO_CONE,
MODEL_LIST_PSEUDO_ELLIPSE,
MODEL_LIST_RESTRICTED_TORSION,
MODEL_PSEUDO_ELLIPSE,
MODEL_RIGID,
cartesian_to_spherical,
R_to_euler_zyz,
open_write_file,
RelaxWarning,
check_pipe,
check_domain,
check_model,
check_parameters,
check_pivot,
domain_moving,
generate_pivot,
average_position,
create_ave_pos,
create_geometric_rep,
generate_axis_system,
count_sobol_points,
assemble_param_vector,
update_model
decompose(root=' decomposed ' ,
dir=None,
atom_id=None,
model=1,
total=100,
reverse=False,
mirror=False,
force=True)
| source code
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Structural representation of the individual frame order motional
components.
- Parameters:
root (str) - The file root for the PDB files created. Each motional component
will be represented by a different PDB file appended with
'_mode1.pdb', '_mode2.pdb', '_mode3.pdb', etc.
dir (str or None) - The directory name to place the file into.
atom_id (None or str) - The atom identification string to allow the decomposition to be
applied to subset of all atoms.
model (int) - Only one model from an analysed ensemble of structures can be
used for the decomposition, as the corresponding PDB file
consists of one model per state.
total (int) - The total number of structures to distribute along the motional
modes. This overrides a default fixed angle incrementation.
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.
force (bool) - A flag which, if set to True, will overwrite the any pre-existing
file.
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distribute(file=' distribution.pdb.bz2 ' ,
dir=None,
atom_id=None,
total=1000,
max_rotations=100000,
model=1,
force=True)
| source code
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Create a uniform distribution of structures for the frame order
motions.
- Parameters:
file (str) - The PDB file for storing the frame order motional distribution.
The compression is determined automatically by the file
extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
dir (str or None) - The directory name to place the file into.
atom_id (None or str) - The atom identification string to allow the distribution to be a
subset of all atoms.
total (int) - The total number of states/model/structures 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.
model (int) - Only one model from an analysed ensemble of structures can be
used for the distribution, as the corresponding PDB file consists
of one model per state.
force (bool) - A flag which, if set to True, will overwrite the any pre-existing
file.
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pdb_model(ave_pos=' ave_pos ' ,
rep=' frame_order ' ,
dir=None,
compress_type=0,
size=30.0,
inc=36,
model=1,
force=False)
| source code
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Create 3 different PDB files for representing the frame order dynamics
of the system.
- Parameters:
ave_pos (str or None) - The file root for the average molecule structure.
rep (str or None) - The file root of the PDB representation of the frame order
dynamics to create.
dist (str or None) - The file root which will contain multiple models spanning the
full dynamics distribution of the frame order model.
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.
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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Permute the axes of the motional eigenframe to switch between local
minima.
- Parameters:
permutation (str) - The permutation to use. This can be either 'A' or 'B' to select
between the 3 permutations, excluding the current combination.
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Set the pivot point for the 2 body motion.
- Parameters:
pivot (list of num) - The pivot point of the two bodies (domains, etc.) in the
structural coordinate system.
order (int) - The ordinal number of the pivot point. The value of 1 is for the
first pivot point, the value of 2 for the second pivot point, and
so on.
fix (bool) - A flag specifying if the pivot point should be fixed during
optimisation.
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Turn the high precision Scipy quadratic numerical integration on or
off.
- Parameters:
flag (bool) - The flag which if True will perform high precision numerical
integration via the scipy.integrate quad(), dblquad() and
tplquad() integration methods rather than the rough quasi-random
numerical integration.
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Set the reference domain for the frame order, multi-domain models.
- Parameters:
ref (str) - The reference domain.
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Select the Frame Order model.
- Parameters:
model (str) - The Frame Order model. This can be one of 'pseudo-ellipse',
'pseudo-ellipse, torsionless', 'pseudo-ellipse, free rotor', 'iso
cone', 'iso cone, torsionless', 'iso cone, free rotor', 'rotor',
'rigid', 'free rotor', 'double rotor'.
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simulate(file=' simulation.pdb.bz2 ' ,
dir=None,
step_size=2.0,
snapshot=10,
total=1000,
model=1,
force=True)
| source code
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Pseudo-Brownian dynamics simulation of the frame order motions.
- Parameters:
file (str) - The PDB file for storing the frame order pseudo-Brownian dynamics
simulation. The compression is determined automatically by the
file extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
dir (str or None) - The directory name to place the file into.
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.
model (int) - Only one model from an analysed ensemble of structures can be
used for the pseudo-Brownian simulation, as the simulation and
corresponding PDB file consists of one model per simulation.
force (bool) - A flag which, if set to True, will overwrite the any pre-existing
file.
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Oversampling setup for the quasi-random Sobol' sequence used for
numerical PCS integration.
- Parameters:
max_num (int) - The maximum number of integration points N.
oversample (int) - The oversampling factor Ov used for the N * Ov * 10**M, where M
is the number of dimensions or torsion-tilt angles for the
system.
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