Author: bugman
Date: Fri Jun 27 17:47:15 2014
New Revision: 24352
URL: http://svn.gna.org/viewcvs/relax?rev=24352&view=rev
Log:
Shifted the rotor generation for the frame order geometric representation
into its own function.
This is the specific_analyses.frame_order.geometric.add_rotors() function
which adds the rotors are
new structures to a given internal structural object. The code has been
extended to add support for
the double rotor model.
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=24352&r1=24351&r2=24352&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Fri Jun 27 17:47:15 2014
@@ -45,8 +45,99 @@
from lib.warnings import RelaxWarning
from pipe_control import pipes
from pipe_control.structure.mass import pipe_centre_of_mass
-from specific_analyses.frame_order.data import domain_moving
+from specific_analyses.frame_order.data import domain_moving, generate_pivot
from specific_analyses.frame_order.parameters import update_model
+
+
+def add_rotors(structure=None):
+ """Add all rotor objects for the current frame order model to the
structural object.
+
+ @keyword structure: The internal structural object to add the rotor
objects to.
+ @type structure: lib.structure.internal.object.Internal instance
+ """
+
+ # Initialise the list structures for the rotor data.
+ axis = []
+ span = []
+ staggered = []
+ pivot = []
+ rotor_angle = []
+ com = []
+
+ # The pivot points.
+ pivot1 = generate_pivot(order=1)
+ pivot2 = generate_pivot(order=2)
+
+ # The single rotor models.
+ if cdp.model in ['rotor', 'free rotor', 'iso cone', 'iso cone, free
rotor', 'pseudo-ellipse', 'pseudo-ellipse, free rotor']:
+ # The rotor angle.
+ if cdp.model in ['free rotor', 'iso cone, free rotor',
'pseudo-ellipse, free rotor']:
+ rotor_angle.append(pi)
+ else:
+ rotor_angle.append(cdp.cone_sigma_max)
+
+ # Get the CoM of the entire molecule to use as the centre of the
rotor.
+ if cdp.model in ['rotor', 'free rotor']:
+ com.append(pipe_centre_of_mass(verbosity=0))
+ else:
+ com.append(pivot1)
+
+ # Generate the rotor axis.
+ if cdp.model in ['rotor', 'free rotor']:
+ axis.append(create_rotor_axis_alpha(alpha=cdp.axis_alpha,
pivot=pivot, point=com))
+ elif cdp.model in ['iso cone', 'iso cone, free rotor']:
+ axis.append(create_rotor_axis_spherical(theta=cdp.axis_theta,
phi=cdp.axis_phi))
+ else:
+ axis.append(create_rotor_axis_euler(alpha=cdp.eigen_alpha,
beta=cdp.eigen_beta, gamma=cdp.eigen_gamma))
+
+ # The size of the rotor, taking the 30 Angstrom cone representation
into account.
+ if cdp.model in ['rotor', 'free rotor']:
+ span.append(20e-10)
+ else:
+ span.append(35e-10)
+
+ # Stagger the propeller blades.
+ if cdp.model in ['free rotor', 'iso cone, free rotor',
'pseudo-ellipse, free rotor']:
+ staggered.append(False)
+ else:
+ staggered.append(True)
+
+ # The pivot.
+ pivot.append(pivot1)
+
+ # The double rotor models.
+ elif cdp.model in ['double rotor']:
+ # Add both rotor angles (the 2nd must come first).
+ rotor_angle.append(cdp.cone_sigma_max_2)
+ rotor_angle.append(cdp.cone_sigma_max)
+
+ # Set the com to the pivot points.
+ com.append(pivot2)
+ com.append(pivot1)
+
+ # Generate the eigenframe of the motion.
+ frame = zeros((3, 3), float64)
+ euler_to_R_zyz(cdp.eigen_alpha, cdp.eigen_beta, cdp.eigen_gamma,
frame)
+
+ # Add the x and y axes.
+ axis.append(frame[:,0])
+ axis.append(frame[:,1])
+
+ # The rotor size.
+ span.append(20e-10)
+ span.append(20e-10)
+
+ # Stagger the propeller blades.
+ staggered.append(True)
+ staggered.append(True)
+
+ # The pivot points.
+ pivot.append(pivot2)
+ pivot.append(pivot1)
+
+ # Add each rotor to the structure as a new molecule.
+ for i in range(len(axis)):
+ rotor_pdb(structure=structure, rotor_angle=rotor_angle[i],
axis=axis[i], axis_pt=pivot[i], centre=com[i], span=span[i],
blade_length=5e-10, staggered=staggered[i])
def create_ave_pos(format='PDB', file=None, dir=None, force=False):
@@ -149,42 +240,10 @@
model_num = 2
# The pivot point.
- pivot = array([cdp.pivot_x, cdp.pivot_y, cdp.pivot_z])
-
- # The rotor object.
- if cdp.model in ['rotor', 'free rotor', 'iso cone', 'iso cone, free
rotor', 'pseudo-ellipse', 'pseudo-ellipse, free rotor']:
- # The rotor angle.
- if cdp.model in ['free rotor', 'iso cone, free rotor',
'pseudo-ellipse, free rotor']:
- rotor_angle = pi
- else:
- rotor_angle = cdp.cone_sigma_max
-
- # Get the CoM of the entire molecule to use as the centre of the
rotor.
- com = pivot
- if cdp.model in ['rotor', 'free rotor']:
- com = pipe_centre_of_mass(verbosity=0)
-
- # Generate the rotor axis.
- if cdp.model in ['rotor', 'free rotor']:
- axis = create_rotor_axis_alpha(alpha=cdp.axis_alpha,
pivot=pivot, point=com)
- elif cdp.model in ['iso cone', 'iso cone, free rotor']:
- axis = create_rotor_axis_spherical(theta=cdp.axis_theta,
phi=cdp.axis_phi)
- else:
- axis = create_rotor_axis_euler(alpha=cdp.eigen_alpha,
beta=cdp.eigen_beta, gamma=cdp.eigen_gamma)
-
- # The size of the rotor, taking the 30 Angstrom cone representation
into account.
- if cdp.model in ['rotor', 'free rotor']:
- span = 20e-10
- else:
- span = 35e-10
-
- # Stagger the propeller blades.
- staggered = True
- if cdp.model in ['free rotor', 'iso cone, free rotor',
'pseudo-ellipse, free rotor']:
- staggered = False
-
- # Add the rotor object to the structure as a new molecule.
- rotor_pdb(structure=structure, rotor_angle=rotor_angle, axis=axis,
axis_pt=pivot, centre=com, span=span, blade_length=5e-10, staggered=staggered)
+ pivot = generate_pivot(order=1)
+
+ # Add all rotor objects.
+ add_rotors(structure=structure)
# Create the molecule.
structure.add_molecule(name='rest')
r24352 - /branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py