Author: bugman
Date: Thu Apr 10 12:19:32 2014
New Revision: 22672
URL: http://svn.gna.org/viewcvs/relax?rev=22672&view=rev
Log:
The frame order pivot points are now stored differently in the current data
pipe.
Instead of being stored as a list or array of numbers in cdp.pivot, the point
is now stored as
cdp.pivot_x, cdp.pivot_y and cdp.pivot_z. The second pivot cdp.pivot2 is now
stored as
cdp.pivot_x_2, cdp.pivot_y_2 and cdp.pivot_z_2.
This is to simplify the automated handling of optimisation parameters.
Rather than having to
convert the pivot_x, pivot_y, and pivot_z parameters to and from a list, the
same mechanisms can now
be used for all of the optimised frame order parameters. This will be used
to hugely simplify many
of the functions in the specific_analyses.frame_order.parameters module and
eliminate a large source
of bugs.
Modified:
trunk/specific_analyses/frame_order/api.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/specific_analyses/frame_order/parameters.py
trunk/specific_analyses/frame_order/uf.py
trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
Modified: trunk/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/api.py?rev=22672&r1=22671&r2=22672&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/api.py (original)
+++ trunk/specific_analyses/frame_order/api.py Thu Apr 10 12:19:32 2014
@@ -409,14 +409,14 @@
# The pivot point.
if cdp.params[i] == 'pivot_x':
- lower = cdp.pivot[0] - 10.0
- upper = cdp.pivot[0] + 10.0
+ lower = cdp.pivot_x - 10.0
+ upper = cdp.pivot_x + 10.0
elif cdp.params[i] == 'pivot_y':
- lower = cdp.pivot[1] - 10.0
- upper = cdp.pivot[1] + 10.0
+ lower = cdp.pivot_y - 10.0
+ upper = cdp.pivot_y + 10.0
elif cdp.params[i] == 'pivot_z':
- lower = cdp.pivot[2] - 10.0
- upper = cdp.pivot[2] + 10.0
+ lower = cdp.pivot_z - 10.0
+ upper = cdp.pivot_z + 10.0
# Average domain position translation (in a +/- 5 Angstrom box).
if cdp.params[i] in ['ave_pos_x', 'ave_pos_y', 'ave_pos_z']:
@@ -493,13 +493,8 @@
for j in range(n):
# Fixed parameter.
if grid[j] == None:
- # Get the current parameter value (pivot, assuming the
pivot point is always at the start of the parameter array).
- if cdp.params[j] in ['pivot_x', 'pivot_y', 'pivot_z']:
- pts[i, j] = cdp.pivot[j] / scaling_matrix[j, j]
-
- # Get the current parameter value (normal parameter).
- else:
- pts[i, j] = getattr(cdp, cdp.params[j]) /
scaling_matrix[j, j]
+ # Get the current parameter value.
+ pts[i, j] = getattr(cdp, cdp.params[j]) /
scaling_matrix[j, j]
# Add the point coordinate.
else:
Modified: trunk/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/optimisation.py?rev=22672&r1=22671&r2=22672&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/optimisation.py (original)
+++ trunk/specific_analyses/frame_order/optimisation.py Thu Apr 10 12:19:32
2014
@@ -667,13 +667,13 @@
# The fixed pivot point.
pivot = None
- if hasattr(cdp, 'pivot'):
- pivot = cdp.pivot
+ if hasattr(cdp, 'pivot_x'):
+ pivot = array([cdp.pivot_x, cdp.pivot_y, cdp.pivot_z])
# The second pivot.
pivot2 = None
- if hasattr(cdp, 'pivot2'):
- pivot2 = cdp.pivot2
+ if hasattr(cdp, 'pivot_x_2'):
+ pivot2 = array([cdp.pivot_x_2, cdp.pivot_y_2, cdp.pivot_z_2])
# Pivot optimisation.
pivot_opt = True
@@ -764,7 +764,9 @@
# Pivot point.
if not pivot_fixed():
# Store the pivot.
- cdp.pivot = param_vector[:3]
+ cdp.pivot_x = param_vector[0]
+ cdp.pivot_y = param_vector[1]
+ cdp.pivot_z = param_vector[2]
# Then remove it from the params.
param_vector = param_vector[3:]
Modified: trunk/specific_analyses/frame_order/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/parameters.py?rev=22672&r1=22671&r2=22672&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/parameters.py (original)
+++ trunk/specific_analyses/frame_order/parameters.py Thu Apr 10 12:19:32
2014
@@ -59,8 +59,9 @@
# Pivot point.
if not pivot_fixed():
- for i in range(3):
- param_vect.append(cdp.pivot[i])
+ param_vect.append(cdp.pivot_x)
+ param_vect.append(cdp.pivot_y)
+ param_vect.append(cdp.pivot_z)
# Normal values.
if sim_index == None:
Modified: trunk/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/uf.py?rev=22672&r1=22671&r2=22672&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/uf.py (original)
+++ trunk/specific_analyses/frame_order/uf.py Thu Apr 10 12:19:32 2014
@@ -107,7 +107,7 @@
if cdp.ave_pos_pivot == 'com':
origin = pipe_centre_of_mass(atom_id=domain_moving(), verbosity=0)
else:
- origin = cdp.pivot
+ origin = array([cdp.pivot_x, cdp.pivot_y, cdp.pivot_z])
structure.rotate(R=R, origin=origin, atom_id=domain_moving())
# Then translate the moving domain.
@@ -173,6 +173,9 @@
if neg_cone:
model_neg = structure.add_model(model=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']:
# The rotor angle.
@@ -186,14 +189,14 @@
# Generate the rotor axis.
if cdp.model in ['rotor']:
- axis = create_rotor_axis_alpha(alpha=cdp.axis_alpha,
pivot=cdp.pivot, point=com)
+ axis = create_rotor_axis_alpha(alpha=cdp.axis_alpha,
pivot=pivot, point=com)
elif cdp.model in ['free rotor', '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)
# Add the rotor object to the structure as a new molecule.
- rotor_pdb(structure=structure, rotor_angle=rotor_angle, axis=axis,
axis_pt=cdp.pivot, centre=com, span=2e-9, blade_length=5e-10, staggered=False)
+ rotor_pdb(structure=structure, rotor_angle=rotor_angle, axis=axis,
axis_pt=pivot, centre=com, span=2e-9, blade_length=5e-10, staggered=False)
# FIXME: Temporary write out and exit.
print("\nGenerating the PDB file.")
@@ -215,7 +218,7 @@
##################
# Add the pivot point.
- 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')
+ structure.add_atom(mol_name=cdp.model, pdb_record='HETATM', atom_num=1,
atom_name='R', res_name='PIV', res_num=1, pos=pivot, element='C')
# The axes.
@@ -251,11 +254,11 @@
# Generate the axis vectors.
print("\nGenerating the axis vectors.")
- res_num = geometric.generate_vector_residues(mol=mol,
vector=axis_pos, atom_name='z-ax', res_name_vect='AXE',
sim_vectors=axis_sim_pos, res_num=2, origin=cdp.pivot, scale=size)
+ res_num = geometric.generate_vector_residues(mol=mol,
vector=axis_pos, atom_name='z-ax', res_name_vect='AXE',
sim_vectors=axis_sim_pos, res_num=2, origin=pivot, scale=size)
# The negative.
if neg_cone:
- res_num = geometric.generate_vector_residues(mol=mol_neg,
vector=axis_neg, atom_name='z-ax', res_name_vect='AXE',
sim_vectors=axis_sim_neg, res_num=2, origin=cdp.pivot, scale=size)
+ res_num = geometric.generate_vector_residues(mol=mol_neg,
vector=axis_neg, atom_name='z-ax', res_name_vect='AXE',
sim_vectors=axis_sim_neg, res_num=2, origin=pivot, scale=size)
# The full axis system.
else:
@@ -300,9 +303,9 @@
axis_sim_neg = axes_sim_neg[:,:, j]
# The vectors.
- res_num = geometric.generate_vector_residues(mol=mol,
vector=axes_pos[:, j], atom_name='%s-ax'%label[j], res_name_vect='AXE',
sim_vectors=axis_sim_pos, res_num=2, origin=cdp.pivot, scale=size)
+ res_num = geometric.generate_vector_residues(mol=mol,
vector=axes_pos[:, j], atom_name='%s-ax'%label[j], res_name_vect='AXE',
sim_vectors=axis_sim_pos, res_num=2, origin=pivot, scale=size)
if neg_cone:
- res_num = geometric.generate_vector_residues(mol=mol_neg,
vector=axes_neg[:, j], atom_name='%s-ax'%label[j], res_name_vect='AXE',
sim_vectors=axis_sim_neg, res_num=2, origin=cdp.pivot, scale=size)
+ res_num = geometric.generate_vector_residues(mol=mol_neg,
vector=axes_neg[:, j], atom_name='%s-ax'%label[j], res_name_vect='AXE',
sim_vectors=axis_sim_neg, res_num=2, origin=pivot, scale=size)
# The cone object.
@@ -337,11 +340,11 @@
cone = Iso_cone(cone_theta)
# Create the positive and negative cones.
- geometric.create_cone_pdb(mol=mol, cone=cone,
start_res=mol.res_num[-1]+1, apex=cdp.pivot, R=R_pos, inc=inc,
distribution='regular', axis_flag=False)
+ geometric.create_cone_pdb(mol=mol, cone=cone,
start_res=mol.res_num[-1]+1, apex=pivot, R=R_pos, inc=inc,
distribution='regular', axis_flag=False)
# The negative.
if neg_cone:
- geometric.create_cone_pdb(mol=mol_neg, cone=cone,
start_res=mol_neg.res_num[-1]+1, apex=cdp.pivot, R=R_neg, inc=inc,
distribution='regular', axis_flag=False)
+ geometric.create_cone_pdb(mol=mol_neg, cone=cone,
start_res=mol_neg.res_num[-1]+1, apex=pivot, R=R_neg, inc=inc,
distribution='regular', axis_flag=False)
# Create the PDB file.
@@ -421,15 +424,21 @@
# Check the pivot validity.
is_float_array(pivot, name='pivot point', size=3)
- # Store the pivot point. and fixed flag.
+ # Store the pivot point and fixed flag.
if order == 1:
- cdp.pivot = pivot
+ cdp.pivot_x = pivot[0]
+ cdp.pivot_y = pivot[1]
+ cdp.pivot_z = pivot[2]
else:
- # The variable name.
- name = 'pivot%i' % order
-
- # Store the variable.
- setattr(cdp, name, pivot)
+ # The variable names.
+ name_x = 'pivot_x_%i' % order
+ name_y = 'pivot_y_%i' % order
+ name_z = 'pivot_z_%i' % order
+
+ # Store the variables.
+ setattr(cdp, name_x, pivot[0])
+ setattr(cdp, name_y, pivot[1])
+ setattr(cdp, name_z, pivot[2])
def quad_int(flag=False):
Modified: trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=22672&r1=22671&r2=22672&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
(original)
+++ trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
Thu Apr 10 12:19:32 2014
@@ -351,7 +351,7 @@
print("Rotation matrix:\n%s\n" % R)
R = transpose(R)
print("Inverted rotation:\n%s\n" % R)
- pivot = cdp.pivot
+ pivot = array([cdp.pivot_x, cdp.pivot_y, cdp.pivot_z])
# Delete the data pipe (if a loaded state has been used).
if self.LOAD_STATE:
r22672 - in /trunk: specific_analyses/frame_order/ test_suite/system_tests/scripts/frame_order/cam/