Author: bugman
Date: Tue Jul 1 16:17:10 2014
New Revision: 24377
URL: http://svn.gna.org/viewcvs/relax?rev=24377&view=rev
Log:
Redesign of the axis geometric representation for the frame order motions.
This is now much more model dependent to avoid clashes with the rotor objects
and other
representations:
- For the torsionless isotropic cone, a single z-axis is created.
- For the double rotor, a single z-axis is produced connecting the two
pivots, from pivot2 to pivot1.
- For the pseudo-ellipse and free rotor pseudo-ellipse, the x and y-axes are
created.
- For the torsionless pseudo-ellipse, all three x, y and z-axes are created.
- For all other models, no axis system is produced as this has been made
redundant by the rotor
objects.
Modified:
branches/frame_order_cleanup/lib/structure/internal/object.py
branches/frame_order_cleanup/pipe_control/pymol_control.py
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Modified: branches/frame_order_cleanup/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/object.py?rev=24377&r1=24376&r2=24377&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/internal/object.py
(original)
+++ branches/frame_order_cleanup/lib/structure/internal/object.py Tue
Jul 1 16:17:10 2014
@@ -207,6 +207,7 @@
| CNC | Apex or centre of the cone geometric object |
| CNX | Axis of the cone geometric object |
| CNE | Edge of the cone geometric object |
+ | AXE | The axis geometric object |
|________|________________________________________________|
For any other residues, no description is returned.
@@ -232,6 +233,7 @@
"CNC": "Apex or centre of the cone geometric object",
"CNX": "Axis of the cone geometric object",
"CNE": "Edge of the cone geometric object",
+ "AXE": "The axis geometric object",
}
# Return the description, if one exists.
Modified: branches/frame_order_cleanup/pipe_control/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pymol_control.py?rev=24377&r1=24376&r2=24377&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pymol_control.py (original)
+++ branches/frame_order_cleanup/pipe_control/pymol_control.py Tue Jul 1
16:17:10 2014
@@ -566,8 +566,8 @@
if id == None:
raise RelaxError("The PyMOL object ID must be supplied.")
- # Select the AVE, CNX, and SIM residues.
- pymol_obj.exec_cmd("select (%s & resn AVE,CNX,SIM)" % id)
+ # Select the AXE residues.
+ pymol_obj.exec_cmd("select (%s & resn AXE)" % id)
# Show the vector as a stick.
pymol_obj.exec_cmd("show stick, 'sele'")
@@ -576,7 +576,7 @@
pymol_obj.exec_cmd("color cyan, 'sele'")
# Select the atom used for labelling.
- pymol_obj.exec_cmd("select (%s & resn AVE,CNX,SIM and symbol N)" % id)
+ pymol_obj.exec_cmd("select (%s & resn AXE and symbol N)" % id)
# Hide the atom.
pymol_obj.exec_cmd("hide ('sele')")
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=24377&r1=24376&r2=24377&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Tue Jul 1 16:17:10 2014
@@ -52,34 +52,30 @@
@type size: float
"""
- # The pivot point.
- pivot = generate_pivot(order=1)
-
# Create the molecule.
- structure.add_molecule(name='axes')
+ mol_name = 'axes'
+ structure.add_molecule(name=mol_name)
+
+ # The pivot points.
+ pivot1 = generate_pivot(order=1)
+ pivot2 = generate_pivot(order=2)
# Alias the molecules.
- mol = structure.get_molecule('axes', model=1)
+ mol = structure.get_molecule(mol_name, model=1)
mol_neg = None
if structure.num_models() == 2:
- mol_neg = structure.get_molecule('axes', model=2)
+ mol_neg = structure.get_molecule(mol_name, model=2)
# The inversion matrix.
inv_mat = -eye(3)
- # 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=pivot, element='C')
-
- # The spherical angles.
- if cdp.model in ['iso cone', 'free rotor', 'iso cone, torsionless', 'iso
cone, free rotor', 'rotor']:
+ # A single z-axis, when no rotor object is present.
+ if cdp.model in ['iso cone, torsionless']:
# Print out.
print("\nGenerating the z-axis system.")
# The axis.
- if cdp.model in ['rotor', 'free rotor']:
- axis = create_rotor_axis_alpha(alpha=cdp.axis_alpha,
pivot=pivot, point=com)
- else:
- axis = create_rotor_axis_spherical(theta=cdp.axis_theta,
phi=cdp.axis_phi)
+ axis = create_rotor_axis_spherical(theta=cdp.axis_theta,
phi=cdp.axis_phi)
print(("Central axis: %s." % axis))
# Rotations and inversions.
@@ -96,7 +92,7 @@
# Fill the structure.
for i in range(cdp.sim_number):
if cdp.model in ['rotor', 'free rotor']:
- axis_sim[i] =
create_rotor_axis_alpha(alpha=cdp.axis_alpha_sim[i], pivot=pivot, point=com)
+ axis_sim[i] =
create_rotor_axis_alpha(alpha=cdp.axis_alpha_sim[i], pivot=pivot1, point=com)
else:
axis_sim[i] =
create_rotor_axis_spherical(theta=cdp.axis_theta_sim[i],
phi=cdp.axis_phi_sim[i])
@@ -106,16 +102,32 @@
# 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='AXE', sim_vectors=axis_sim_pos, res_num=2,
origin=pivot, scale=size)
+ res_num = 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=pivot1, scale=size)
# The negative.
if mol_neg != None:
- res_num = 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)
+ res_num = 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=pivot1, scale=size)
+
+ # The z-axis connecting two motional modes.
+ elif cdp.model in ['double rotor']:
+ # Printout.
+ print("\nGenerating the z-axis linking the two pivot points.")
+
+ # The axis.
+ axis = pivot1 - pivot2
+ print(("Interconnecting axis: %s." % axis))
+
+ # Generate the axis vectors.
+ print("\nGenerating the axis vectors.")
+ res_num = generate_vector_residues(mol=mol, vector=axis,
atom_name='z-ax', res_name_vect='AXE', res_num=1, origin=pivot2)
# The full axis system.
- else:
+ elif cdp.model in ['pseudo-ellipse', 'pseudo-ellipse, torsionless',
'pseudo-ellipse, free rotor']:
# Print out.
print("\nGenerating the full axis system.")
+
+ # Add the pivot point.
+ structure.add_atom(mol_name=mol_name, pdb_record='HETATM',
atom_num=1, atom_name='R', res_name='AXE', res_num=1, pos=pivot1, element='C')
# The axis system.
axes = zeros((3, 3), float64)
@@ -143,9 +155,13 @@
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])
+ # The axes to create.
+ label = ['x', 'y']
+ if cdp.model in ['pseudo-ellipse, torsionless']:
+ label = ['x', 'y', 'z']
+
# Generate the axis vectors.
print("\nGenerating the axis vectors.")
- label = ['x', 'y', 'z']
for j in range(len(label)):
# The simulation data.
axis_sim_pos = None
@@ -155,9 +171,9 @@
axis_sim_neg = axes_sim_neg[:,:, j]
# The vectors.
- res_num = 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)
+ res_num = 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=pivot1, scale=size)
if mol_neg != None:
- res_num = 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)
+ res_num = 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=pivot1, scale=size)
def add_cones(structure=None, size=None, inc=None):
r24377 - in /branches/frame_order_cleanup: lib/structure/internal/ pipe_control/ specific_analyses/frame_order/