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]
 
average_position(pivot='com', translation=True)
Set up the mechanics of the average domain position.
source code
 
num_int_pts(num=200000)
Set the number of integration points to use in the quasi-random Sobol' sequence.
source code
 
pdb_ave_pos(file=None, dir=None, force=False)
Create a PDB file of the molecule with the moving domains shifted to the average position.
source code
 
pdb_distribution(file=None, dir=None, force=False)
Create a PDB file of a distribution of positions coving the full dynamics of the moving domain.
source code
 
pdb_geometric_rep(file=None, dir=None, size=30.0, inc=36, force=False, neg_cone=True)
Create a PDB file containing a geometric object representing the frame order dynamics.
source code
 
pdb_model(ave_pos_file='ave_pos.pdb', rep_file='frame_order.pdb', dist_file='domain_distribution.pdb', dir=None, size=30.0, inc=36, force=False, neg_cone=True)
Create 3 different PDB files for representing the frame order dynamics of the system.
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.
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select_model(model=None)
Select the Frame Order model.
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Variables [hide private]
  __package__ = 'specific_analyses.frame_order'

Imports: deepcopy, pi, array, dot, eye, float64, transpose, zeros, sys, is_float_array, RelaxError, create_rotor_axis_alpha, create_rotor_axis_euler, create_rotor_axis_spherical, euler_to_R_zyz, two_vect_to_R, open_write_file, order_parameters, Iso_cone, Pseudo_elliptic, generate_vector_residues, Internal, cone, rotor_pdb, subsection, pipes, pipe_centre_of_mass, domain_moving, translation_fixed, update_model


Function Details [hide private]

average_position(pivot='com', translation=True)

source code 

Set up the mechanics of the average domain position.

Parameters:
  • pivot (str) - What to use as the motional pivot. This can be 'com' for the centre of mass of the moving domain, or 'motional' to link the pivot of the motion to the rotation of the average domain position.
  • translation (bool) - If True, translation to the average domain position will be allowed. If False, then translation will not occur.

num_int_pts(num=200000)

source code 

Set the number of integration points to use in the quasi-random Sobol' sequence.

Parameters:
  • num (int) - The number of integration points.

pdb_ave_pos(file=None, dir=None, force=False)

source code 

Create a PDB file of the molecule with the moving domains shifted to the average position.

Parameters:
  • file (str) - The name of the file for the average molecule structure.
  • dir (str) - The name of the directory to place the PDB file into.
  • force (bool) - Flag which if set to True will cause any pre-existing file to be overwritten.

pdb_distribution(file=None, dir=None, force=False)

source code 

Create a PDB file of a distribution of positions coving the full dynamics of the moving domain.

Parameters:
  • file (str) - The name of the file 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.
  • force (bool) - Flag which if set to True will cause any pre-existing file to be overwritten.

pdb_geometric_rep(file=None, dir=None, size=30.0, inc=36, force=False, neg_cone=True)

source code 

Create a PDB file containing a geometric object representing the frame order dynamics.

Parameters:
  • file (str) - The name of the file of the PDB representation of the frame order dynamics to create.
  • dir (str) - The name of the directory to place the PDB file into.
  • size (float) - The size of the geometric object in Angstroms.
  • inc (int) - The number of increments for the filling of the cone objects.
  • force (bool) - Flag which if set to True will cause any pre-existing file to be overwritten.
  • neg_cone (bool) - A flag which if True will cause the negative cone to be added to the representation. This is ignored for the rotor models.

pdb_model(ave_pos_file='ave_pos.pdb', rep_file='frame_order.pdb', dist_file='domain_distribution.pdb', dir=None, size=30.0, inc=36, force=False, neg_cone=True)

source code 

Create 3 different PDB files for representing the frame order dynamics of the system.

Parameters:
  • ave_pos_file (str or None) - The name of the file for the average molecule structure.
  • rep_file (str or None) - The name of the file of the PDB representation of the frame order dynamics to create.
  • dist_file (str or None) - The name of the file 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.
  • size (float) - The size of the geometric object in Angstroms.
  • inc (int) - The number of increments for the filling of the cone objects.
  • force (bool) - Flag which if set to True will cause any pre-existing file to be overwritten.
  • neg_cone (bool) - A flag which if True will cause the negative cone to be added to the representation.

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)

source code 

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

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

select_model(model=None)

source code 

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', 'line', 'line, torsionless', 'line, free rotor', 'rotor', 'rigid', 'free rotor', 'double rotor'.