Package specific_analyses :: Package frame_order :: Module uf
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Module uf

source code

Module for all of the frame order specific user functions.

Functions [hide private]
 
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
 
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
 
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.
source code
 
permute_axes(permutation='A')
Permute the axes of the motional eigenframe to switch between local minima.
source code
 
pivot(pivot=None, order=1, fix=False)
Set the pivot point for the 2 body motion.
source code
 
quad_int(flag=False)
Turn the high precision Scipy quadratic numerical integration on or off.
source code
 
ref_domain(ref=None)
Set the reference domain for the frame order, multi-domain models.
source code
 
select_model(model=None)
Select the Frame Order model.
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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
 
sobol_setup(max_num=200, oversample=100)
Oversampling setup for the quasi-random Sobol' sequence used for numerical PCS integration.
source code
Variables [hide private]
  __package__ = 'specific_analyses.frame_order'

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


Function Details [hide private]

decompose(root='decomposed', dir=None, atom_id=None, model=1, total=100, reverse=False, mirror=False, force=True)

source code 

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.

distribute(file='distribution.pdb.bz2', dir=None, atom_id=None, total=1000, max_rotations=100000, model=1, force=True)

source code 

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.

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 

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.

permute_axes(permutation='A')

source code 

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.

pivot(pivot=None, order=1, fix=False)

source code 

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.

quad_int(flag=False)

source code 

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.

ref_domain(ref=None)

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Set the reference domain for the frame order, multi-domain models.

Parameters:
  • ref (str) - The reference domain.

select_model(model=None)

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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'.

simulate(file='simulation.pdb.bz2', dir=None, step_size=2.0, snapshot=10, total=1000, model=1, force=True)

source code 

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.

sobol_setup(max_num=200, oversample=100)

source code 

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.