Module uf
source code
The N-state model or structural ensemble analysis user functions.
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CoM(pivot_point=None,
centre=None)
Centre of mass analysis. |
source code
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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
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__package__ = ' specific_analyses.n_state_model '
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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,
stitch_cone_to_edge,
pipes,
centre_of_mass
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.
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cone_pdb(cone_type=None,
scale=1.0,
file=None,
dir=None,
force=False)
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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.
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