Package pipe_control :: Package structure :: Module geometric
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Module geometric

source code

Functions [hide private]
 
create_rotor_pdb(file=None, dir=None, rotor_angle=None, axis=None, axis_pt=True, centre=None, span=2e-09, blade_length=5e-10, force=False, staggered=False)
Create a PDB representation of a rotor motional model.
source code
 
create_vector_dist(length=None, symmetry=True, file=None, dir=None, force=False)
Create a PDB representation of the vector distribution.
source code
Variables [hide private]
  status = Status()
  __package__ = 'pipe_control.structure'

Imports: pi, getcwd, RelaxNoPdbError, RelaxNoSequenceError, RelaxNoVectorsError, get_file_path, open_write_file, Internal, rotor, interatomic_loop, exists_mol_res_spin_data, return_spin, check_pipe, pipe_centre_of_mass, Status


Function Details [hide private]

create_rotor_pdb(file=None, dir=None, rotor_angle=None, axis=None, axis_pt=True, centre=None, span=2e-09, blade_length=5e-10, force=False, staggered=False)

source code 

Create a PDB representation of a rotor motional model.

Parameters:
  • file (str) - The name of the PDB file to create.
  • dir (str) - The name of the directory to place the PDB file into.
  • rotor_angle (float) - The angle of the rotor motion in degrees.
  • axis (numpy rank-1, 3D array) - The vector defining the rotor axis.
  • axis_pt (numpy rank-1, 3D array) - A point lying anywhere on the rotor axis. This is used to define the position of the axis in 3D space.
  • centre (numpy rank-1, 3D array) - The central point of the representation. If this point is not on the rotor axis, then the closest point on the axis will be used for the centre.
  • span (float) - The distance from the central point to the rotor blades (meters).
  • blade_length (float) - The length of the representative rotor blades.
  • force (bool) - A flag which if set will overwrite any pre-existing file.
  • staggered (bool) - A flag which if True will cause the rotor blades to be staggered. This is used to avoid blade overlap.

create_vector_dist(length=None, symmetry=True, file=None, dir=None, force=False)

source code 

Create a PDB representation of the vector distribution.

Parameters:
  • length (float) - The length to set the vectors to in the PDB file.
  • symmetry (bool) - The symmetry flag which if set will create a second PDB chain 'B' which is the same as chain 'A' but with the vectors reversed.
  • file (str) - The name of the PDB file to create.
  • dir (str) - The name of the directory to place the PDB file into.
  • force (bool) - Flag which if set will overwrite any pre-existing file.