Package specific_analyses :: Package n_state_model :: Module uf
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Module uf

source code

The N-state model or structural ensemble analysis user functions.

Functions [hide private]
 
CoM(pivot_point=None, centre=None)
Centre of mass analysis.
source code
 
cone_pdb(cone_type=None, scale=1.0, file=None, dir=None, force=False)
Create a PDB file containing a geometric object representing the various cone models.
source code
Variables [hide private]
  __package__ = 'specific_analyses.n_state_model'

Imports: acos, cos, pi, array, dot, float64, zeros, norm, RelaxError, euler_to_R_zyz, two_vect_to_R, open_write_file, Iso_cone, Internal, generate_vector_dist, generate_vector_residues, cone_edge, check_pipe, centre_of_mass


Function Details [hide private]

CoM(pivot_point=None, centre=None)

source code 

Centre of mass analysis.

This function does an analysis of the centre of mass (CoM) of the N states. This includes calculating the order parameter associated with the pivot-CoM vector, and the associated cone of motions. The pivot_point argument must be supplied. If centre is None, then the CoM will be calculated from the selected parts of the loaded structure. Otherwise it will be set to the centre arg.

Parameters:
  • pivot_point (list of float of length 3) - The pivot point in the structural file(s).
  • centre (list of float of length 3) - The optional centre of mass vector.

cone_pdb(cone_type=None, scale=1.0, file=None, dir=None, force=False)

source code 

Create a PDB file containing a geometric object representing the various cone models.

Currently the only cone types supported are 'diff in cone' and 'diff on cone'.

Parameters:
  • cone_type (str) - The type of cone model to represent.
  • scale (float) - The size of the geometric object is eqaul to the average pivot-CoM vector length multiplied by this scaling factor.
  • file (str) - The name of the PDB file to create.
  • dir (str) - The name of the directory to place the PDB file into.
  • force (int) - Flag which if set to True will cause any pre-existing file to be overwritten.