Module uf
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Module for all of the frame order specific user functions.
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num_int_pts(num=200000)
Set the number of integration points to use in the quasi-random
Sobol' sequence. |
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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. |
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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. |
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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. |
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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. |
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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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__package__ = ' specific_analyses.frame_order '
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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
average_position(pivot=' com ' ,
translation=True)
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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.
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Set the number of integration points to use in the quasi-random Sobol'
sequence.
- Parameters:
num (int) - The number of integration points.
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pdb_ave_pos(file=None,
dir=None,
force=False)
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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.
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pdb_distribution(file=None,
dir=None,
force=False)
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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.
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pdb_geometric_rep(file=None,
dir=None,
size=30.0,
inc=36,
force=False,
neg_cone=True)
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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.
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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)
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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.
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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', 'line',
'line, torsionless', 'line, free rotor', 'rotor', 'rigid', 'free
rotor', 'double rotor'.
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