Author: bugman
Date: Thu Dec 29 16:10:41 2011
New Revision: 15112
URL: http://svn.gna.org/viewcvs/relax?rev=15112&view=rev
Log:
Changed the design of the cone PDB object for the frame order models.
The change affects the models which consist of the full motional eigenframe.
Modified:
branches/frame_order_testing/specific_fns/frame_order.py
Modified: branches/frame_order_testing/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/frame_order.py?rev=15112&r1=15111&r2=15112&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/frame_order.py (original)
+++ branches/frame_order_testing/specific_fns/frame_order.py Thu Dec 29
16:10:41 2011
@@ -305,60 +305,50 @@
structure.add_atom(mol_name=cdp.model, pdb_record='HETATM',
atom_num=1, atom_name='R', res_name='PIV', res_num=1, pos=cdp.pivot,
element='C')
- # The central axis.
- ###################
-
- # Print out.
- print("\nGenerating the central axis.")
+ # The axes.
+ ###########
# The spherical angles.
if cdp.model in ['iso cone', 'free rotor', 'iso cone, torsionless',
'iso cone, free rotor', 'rotor']:
- theta_name = 'axis_theta'
- phi_name = 'axis_phi'
+ # Print out.
+ print("\nGenerating the z-axis system.")
+
+ # The axis.
+ axis = zeros(3, float64)
+ spherical_to_cartesian([1.0, getattr(cdp, 'axis_theta'),
getattr(cdp, 'axis_phi')], axis)
+ print(("Central axis: %s." % axis))
+
+ # Rotations and inversions.
+ axis_pos = axis
+ axis_neg = dot(inv_mat, axis)
+
+ # Simulation central axis.
+ axis_sim_pos = None
+ axis_sim_neg = None
+ if sim:
+ # Init.
+ axis_sim = zeros((cdp.sim_number, 3), float64)
+
+ # Fill the structure.
+ for i in range(cdp.sim_number):
+ spherical_to_cartesian([1.0, getattr(cdp,
'axis_theta_sim')[i], getattr(cdp, 'axis_phi_sim')[i]], axis_sim[i])
+
+ # Inversion.
+ axis_sim_pos = axis_sim
+ axis_sim_neg = transpose(dot(inv_mat,
transpose(axis_sim_pos)))
+
+ # Generate the axis vectors.
+ print("\nGenerating the axis vectors.")
+ res_num = generate_vector_residues(mol=mol, vector=axis_pos,
atom_name='z-ax', res_name_vect='ZAX', sim_vectors=axis_sim_pos, res_num=2,
origin=cdp.pivot, scale=size)
+
+ # The negative.
+ if neg_cone:
+ res_num = generate_vector_residues(mol=mol_neg,
vector=axis_neg, atom_name='z-ax', res_name_vect='ZAX',
sim_vectors=axis_sim_neg, res_num=2, origin=cdp.pivot, scale=size)
+
+ # The full axis system.
else:
- theta_name = 'eigen_beta'
- phi_name = 'eigen_gamma'
-
- # The axis.
- axis = zeros(3, float64)
- spherical_to_cartesian([1.0, getattr(cdp, theta_name), getattr(cdp,
phi_name)], axis)
- print(("Central axis: %s." % axis))
-
- # Rotations and inversions.
- axis_pos = axis
- axis_neg = dot(inv_mat, axis)
-
- # Simulation central axis.
- axis_sim_pos = None
- axis_sim_neg = None
- if sim:
- # Init.
- axis_sim = zeros((cdp.sim_number, 3), float64)
-
- # Fill the structure.
- for i in range(cdp.sim_number):
- spherical_to_cartesian([1.0, getattr(cdp,
theta_name+'_sim')[i], getattr(cdp, phi_name+'_sim')[i]], axis_sim[i])
-
- # Inversion.
- axis_sim_pos = axis_sim
- axis_sim_neg = transpose(dot(inv_mat, transpose(axis_sim_pos)))
-
- # Generate the axis vectors.
- print("\nGenerating the axis vectors.")
- res_num = generate_vector_residues(mol=mol, vector=axis_pos,
atom_name='z-ax', res_name_vect='ZAX', sim_vectors=axis_sim_pos, res_num=2,
origin=cdp.pivot, scale=size)
-
- # The negative.
- if neg_cone:
- res_num = generate_vector_residues(mol=mol_neg, vector=axis_neg,
atom_name='z-ax', res_name_vect='ZAX', sim_vectors=axis_sim_neg, res_num=2,
origin=cdp.pivot, scale=size)
-
-
- # The x and y axes.
- ###################
-
- # Skip models missing the full eigenframe.
- if cdp.model not in ['iso cone', 'free rotor', 'iso cone,
torsionless', 'iso cone, free rotor', 'rotor']:
# Print out.
- print("\nGenerating the x and y axes.")
+ print("\nGenerating the full axis system.")
# The axis system.
axes = zeros((3, 3), float64)
@@ -369,36 +359,45 @@
axes_pos = axes
axes_neg = dot(inv_mat, axes)
- # Simulation central axis.
+ # Simulations
axes_sim_pos = None
axes_sim_neg = None
if sim:
# Init.
- axes_sim_pos = zeros((3, cdp.sim_number, 3), float64)
- axes_sim_neg = zeros((3, cdp.sim_number, 3), float64)
+ axes_sim_pos = zeros((cdp.sim_number, 3, 3), float64)
+ axes_sim_neg = zeros((cdp.sim_number, 3, 3), float64)
# Fill the structure.
for i in range(cdp.sim_number):
# The positive system.
- euler_to_R_zyz(cdp.eigen_alpha_sim[i],
cdp.eigen_beta_sim[i], cdp.eigen_gamma_sim[i], axes_sim_pos[:, i])
+ euler_to_R_zyz(cdp.eigen_alpha_sim[i],
cdp.eigen_beta_sim[i], cdp.eigen_gamma_sim[i], axes_sim_pos[i])
# The negative system.
- euler_to_R_zyz(cdp.eigen_alpha_sim[i],
cdp.eigen_beta_sim[i], cdp.eigen_gamma_sim[i], axes_sim_neg[:, i])
- axes_sim_neg[:, i] = dot(inv_mat, axes_sim_neg[:, i])
+ euler_to_R_zyz(cdp.eigen_alpha_sim[i],
cdp.eigen_beta_sim[i], cdp.eigen_gamma_sim[i], axes_sim_neg[i])
+ axes_sim_neg[i] = dot(inv_mat, axes_sim_neg[i])
# Generate the axis vectors.
print("\nGenerating the axis vectors.")
- label = ['x', 'y']
- for i in range(2):
- # Simulation structures.
- if sim:
- axis_sim_pos = axes_sim_pos[:, i]
- axis_sim_neg = axes_sim_neg[:, i]
-
+ label = ['x', 'y', 'z']
+ for j in range(len(label)):
# The vectors.
- res_num = generate_vector_residues(mol=mol,
vector=axes_pos[:, i], atom_name='%s-ax'%label[i],
res_name_vect='%sAX'%upper(label[i]), sim_vectors=axis_sim_pos,
res_num=res_num+1, origin=cdp.pivot, scale=size)
+ res_num = generate_vector_residues(mol=mol,
vector=axes_pos[:, j], atom_name='%s-ax'%label[j], res_name_vect='AXE',
sim_vectors=None, res_num=2, origin=cdp.pivot, scale=size)
if neg_cone:
- res_num = generate_vector_residues(mol=mol_neg,
vector=axes_neg[:, i], atom_name='%s-ax'%label[i],
res_name_vect='%sAX'%upper(label[i]), sim_vectors=axis_sim_neg,
res_num=res_num, origin=cdp.pivot, scale=size)
+ res_num = generate_vector_residues(mol=mol_neg,
vector=axes_neg[:, j], atom_name='%s-ax'%label[j], res_name_vect='AXE',
sim_vectors=None, res_num=2, origin=cdp.pivot, scale=size)
+
+
+ # Simulation data.
+ if sim:
+ for i in range(cdp.sim_number):
+ label = ['x', 'y', 'z']
+ for j in range(len(label)):
+ axis_sim_pos = axes_sim_pos[i, :, j]
+ axis_sim_neg = axes_sim_neg[i, :, j]
+
+ # The vectors.
+ res_num = generate_vector_residues(mol=mol,
vector=axis_sim_pos, atom_name='%s-ax'%label[j], res_name_vect='SIM',
sim_vectors=None, res_num=3+i, origin=cdp.pivot, scale=size)
+ if neg_cone:
+ res_num = generate_vector_residues(mol=mol_neg,
vector=axis_sim_neg, atom_name='%s-ax'%label[j], res_name_vect='SIM',
sim_vectors=None, res_num=3+i, origin=cdp.pivot, scale=size)
# The cone object.
r15112 - /branches/frame_order_testing/specific_fns/frame_order.py