Author: bugman
Date: Thu Feb 21 11:23:02 2008
New Revision: 5095
URL: http://svn.gna.org/viewcvs/relax?rev=5095&view=rev
Log:
Renaming of a number of variables for the CoM analysis.
These names are more logical.
Modified:
1.3/specific_fns/n_state_model.py
Modified: 1.3/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=5095&r1=5094&r2=5095&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Thu Feb 21 11:23:02 2008
@@ -140,21 +140,21 @@
# Multiply by the probability.
vectors[c] = vectors[c] * cdp.probs[c]
- # Total weighted vector.
- cdp.red_CoM = sum(vectors)
+ # Average of the unit vectors.
+ cdp.ave_unit_pivot_CoM = sum(vectors)
# The length reduction.
- len_red = norm(cdp.red_CoM)
-
- # The full length rotated CoM vector.
- cdp.rot_CoM = norm(cdp.CoM) * cdp.red_CoM / len_red
+ cdp.ave_pivot_CoM_red = norm(cdp.ave_unit_pivot_CoM)
+
+ # The aveage pivot-CoM vector.
+ cdp.ave_pivot_CoM = norm(cdp.pivot_CoM) * cdp.ave_unit_pivot_CoM /
cdp.ave_pivot_CoM_red
# The cone angle for diffusion on an axially symmetric cone.
- cdp.theta_diff_on_cone = acos(len_red)
+ cdp.theta_diff_on_cone = acos(cdp.ave_pivot_CoM_red)
cdp.S_diff_on_cone = (3.0*cos(cdp.theta_diff_on_cone)**2 - 1.0) / 2.0
# The cone angle and order parameter for diffusion in an axially
symmetric cone.
- cdp.theta_diff_in_cone = acos(2.*len_red - 1.)
+ cdp.theta_diff_in_cone = acos(2.*cdp.ave_pivot_CoM_red - 1.)
cdp.S_diff_in_cone = cos(cdp.theta_diff_in_cone) * (1 +
cos(cdp.theta_diff_in_cone)) / 2.0
# Print out.
@@ -162,9 +162,9 @@
print "%-40s %-20s" % ("Moving domain CoM (prior to rotation):",
`cdp.CoM`)
print "%-40s %-20s" % ("Pivot-CoM vector", `cdp.pivot_CoM`)
print "%-40s %-20s" % ("Pivot-CoM unit vector:", `unit_vect`)
- print "%-40s %-20s" % ("Reduced CoM vector:", `cdp.red_CoM`)
- print "%-40s %-20s" % ("Full length rotated CoM vector:",
`cdp.rot_CoM`)
- print "%-40s %-20s" % ("Length reduction from unity:", `len_red`)
+ print "%-40s %-20s" % ("Average of the unit pivot-CoM vectors:",
`cdp.ave_unit_pivot_CoM`)
+ print "%-40s %-20s" % ("Average of the pivot-CoM vector:",
`cdp.ave_pivot_CoM`)
+ print "%-40s %-20s" % ("Length reduction from unity:",
`cdp.ave_pivot_CoM_red`)
print "%-40s %.5f rad (%.5f deg)" % ("Cone angle (diffusion on a
cone)", cdp.theta_diff_on_cone, cdp.theta_diff_on_cone / (2*pi) *360.)
print "%-40s S_cone = %.5f (S^2 = %.5f)" % ("S_cone (diffusion on a
cone)", cdp.S_diff_on_cone, cdp.S_diff_on_cone**2)
print "%-40s %.5f rad (%.5f deg)" % ("Cone angle (diffusion in a
cone)", cdp.theta_diff_in_cone, cdp.theta_diff_in_cone / (2*pi) *360.)
@@ -216,16 +216,16 @@
# Generate the average pivot-CoM vectors.
sim_vectors = None
- if hasattr(cdp, 'rot_CoM_sim'):
- sim_vectors = cdp.rot_CoM_sim
- res_num =
generic_fns.structure.generate_vector_residues(atomic_data=atomic_data,
vector=cdp.rot_CoM, atom_name='Ave', res_name_vect='AVE',
sim_vectors=sim_vectors, res_num=2, origin=cdp.pivot_point, scale=scale)
+ if hasattr(cdp, 'ave_pivot_CoM_sim'):
+ sim_vectors = cdp.ave_pivot_CoM_sim
+ res_num =
generic_fns.structure.generate_vector_residues(atomic_data=atomic_data,
vector=cdp.ave_pivot_CoM, atom_name='Ave', res_name_vect='AVE',
sim_vectors=sim_vectors, res_num=2, origin=cdp.pivot_point, scale=scale)
# Generate the cone outer edge.
if cone_type == 'diff in cone':
angle = cdp.theta_diff_in_cone
elif cone_type == 'diff on cone':
angle = cdp.theta_diff_on_cone
- generic_fns.structure.cone_edge(atomic_data=atomic_data,
res_num=res_num, apex=cdp.pivot_point, axis=cdp.rot_CoM/norm(cdp.rot_CoM),
angle=angle, length=norm(cdp.pivot_CoM), inc=20)
+ generic_fns.structure.cone_edge(atomic_data=atomic_data,
res_num=res_num, apex=cdp.pivot_point,
axis=cdp.ave_pivot_CoM/norm(cdp.ave_pivot_CoM), angle=angle,
length=norm(cdp.pivot_CoM), inc=20)
# Terminate the chain.
generic_fns.structure.terminate(atomic_data=atomic_data,
res_num=res_num)
r5095 - /1.3/specific_fns/n_state_model.py