Author: bugman
Date: Mon Sep 22 12:26:32 2014
New Revision: 25952
URL: http://svn.gna.org/viewcvs/relax?rev=25952&view=rev
Log:
Spun out the code for shifting to the average frame order position into a new
function.
The old code of the create_ave_pos() of the
specific_analyses.frame_order.geometric module has been
shifted into the new average_position() function. This will allow the code to
be reused by other
parts of relax to obtain the average frame order structures.
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py?rev=25952&r1=25951&r2=25952&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Mon Sep 22 12:26:32 2014
@@ -544,6 +544,42 @@
rotor(structure=structure, rotor_angle=rotor_angle[i], axis=dot(T,
axis[i]), axis_pt=pivot[i], label=label[i], centre=com[i], span=span[i],
blade_length=5e-10, model_num=models[i], staggered=staggered[i],
half_rotor=half_rotor)
+def average_position(structure=None, models=None, sim=None):
+ """Shift the given structural object to the average position.
+
+ @keyword structure: The structural object to operate on.
+ @type structure: lib.structure.internal.object.Internal instance
+ @keyword models: The list of models to shift.
+ @type models: list of int
+ @keyword sim: A flag which if True will use the Monte Carlo
simulation results. In this case, the model list should be set to the
simulation indices plus 1 and the structural object should have one model per
simulation already set up.
+ @type sim: bool
+ """
+
+ # Loop over each model.
+ for i in range(len(models)):
+ # First rotate the moving domain to the average position.
+ R = zeros((3, 3), float64)
+ if hasattr(cdp, 'ave_pos_alpha'):
+ if sim:
+ euler_to_R_zyz(cdp.ave_pos_alpha_sim[i],
cdp.ave_pos_beta_sim[i], cdp.ave_pos_gamma_sim[i], R)
+ else:
+ euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma, R)
+ else:
+ if sim:
+ euler_to_R_zyz(0.0, cdp.ave_pos_beta_sim[i],
cdp.ave_pos_gamma_sim[i], R)
+ else:
+ euler_to_R_zyz(0.0, cdp.ave_pos_beta, cdp.ave_pos_gamma, R)
+ origin = pipe_centre_of_mass(atom_id=domain_moving(), verbosity=0)
+ structure.rotate(R=R, origin=origin, model=models[i],
atom_id=domain_moving())
+
+ # Then translate the moving domain.
+ if sim:
+ T = [cdp.ave_pos_x_sim[i], cdp.ave_pos_y_sim[i],
cdp.ave_pos_z_sim[i]]
+ else:
+ T = [cdp.ave_pos_x, cdp.ave_pos_y, cdp.ave_pos_z]
+ structure.translate(T=T, model=models[i], atom_id=domain_moving())
+
+
def create_ave_pos(format='PDB', file=None, dir=None, compress_type=0,
model=1, force=False):
"""Create a PDB file of the molecule with the moving domains shifted to
the average position.
@@ -615,29 +651,8 @@
elif models[i][j] != None:
structures[i].add_model(model=models[i][j])
- # Loop over each model.
- for j in range(len(models[i])):
- # First rotate the moving domain to the average position.
- R = zeros((3, 3), float64)
- if hasattr(cdp, 'ave_pos_alpha'):
- if sims[i]:
- euler_to_R_zyz(cdp.ave_pos_alpha_sim[j],
cdp.ave_pos_beta_sim[j], cdp.ave_pos_gamma_sim[j], R)
- else:
- euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma, R)
- else:
- if sims[i]:
- euler_to_R_zyz(0.0, cdp.ave_pos_beta_sim[j],
cdp.ave_pos_gamma_sim[j], R)
- else:
- euler_to_R_zyz(0.0, cdp.ave_pos_beta, cdp.ave_pos_gamma, R)
- origin = pipe_centre_of_mass(atom_id=domain_moving(), verbosity=0)
- structures[i].rotate(R=R, origin=origin, model=models[i][j],
atom_id=domain_moving())
-
- # Then translate the moving domain.
- if sims[i]:
- T = [cdp.ave_pos_x_sim[j], cdp.ave_pos_y_sim[j],
cdp.ave_pos_z_sim[j]]
- else:
- T = [cdp.ave_pos_x, cdp.ave_pos_y, cdp.ave_pos_z]
- structures[i].translate(T=T, model=models[i][j],
atom_id=domain_moving())
+ # Shift to the average position.
+ average_position(structure=structures[i], models=models[i],
sim=sims[i])
# Output to PDB format.
if format == 'PDB':
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