Author: bugman
Date: Tue May 27 17:17:56 2014
New Revision: 23476
URL: http://svn.gna.org/viewcvs/relax?rev=23476&view=rev
Log:
Completed the frame_order.pdb_model user function backend for the frame order
PDB representation.
Most of this backend, including the axes and cone representations, had been
broken for quite a while
and were being skipped with an early return statement. This has now been
made functional and a few
fixes have been made.
For the 'rotor' and 'free rotor' model, the neg_cone argument is now ignored
so that only one model
is produced in the final frame order PDB representation file. For all other
models, the rotor
representation is no longer centred to the point on axis closest to the
centre of mass, as the pivot
is unambiguously defined. The rotor representation has also been made larger
in these models so
that it is outside of the cone, and the propeller blades are now staggered.
Modified:
trunk/specific_analyses/frame_order/uf.py
Modified: trunk/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/uf.py?rev=23476&r1=23475&r2=23476&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/uf.py (original)
+++ trunk/specific_analyses/frame_order/uf.py Tue May 27 17:17:56 2014
@@ -36,11 +36,12 @@
from lib.io import open_write_file
from lib.order import order_parameters
from lib.structure.cones import Iso_cone, Pseudo_elliptic
+from lib.structure.geometric import generate_vector_residues
from lib.structure.internal.object import Internal
+from lib.structure.represent.cone import cone
from lib.structure.represent.rotor import rotor_pdb
from lib.text.sectioning import subsection
from pipe_control import pipes
-from pipe_control.structure import geometric
from pipe_control.structure.mass import pipe_centre_of_mass
from specific_analyses.frame_order.data import domain_moving,
translation_fixed
from specific_analyses.frame_order.parameters import update_model
@@ -148,7 +149,7 @@
@type inc: int
@keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
@type force: bool
- @keyword neg_cone: A flag which if True will cause the negative
cone to be added to the representation.
+ @keyword neg_cone: A flag which if True will cause the negative
cone to be added to the representation. This is ignored for the rotor models.
@type neg_cone: bool
"""
@@ -169,9 +170,13 @@
structure = Internal()
# Create model for the positive and negative images.
+ if cdp.model in ['rotor', 'free rotor']:
+ neg_cone = False
model = structure.add_model(model=1)
+ model_num = 1
if neg_cone:
model_neg = structure.add_model(model=2)
+ model_num = 2
# The pivot point.
pivot = array([cdp.pivot_x, cdp.pivot_y, cdp.pivot_z])
@@ -185,7 +190,9 @@
rotor_angle = cdp.cone_sigma_max
# Get the CoM of the entire molecule to use as the centre of the
rotor.
- com = pipe_centre_of_mass(verbosity=0)
+ 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']:
@@ -195,15 +202,14 @@
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
+
# 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=2e-9, blade_length=5e-10, staggered=False)
-
- # FIXME: Temporary write out and exit.
- print("\nGenerating the PDB file.")
- pdb_file = open_write_file(file, dir, force=force)
- structure.write_pdb(pdb_file)
- pdb_file.close()
- return
+ rotor_pdb(structure=structure, rotor_angle=rotor_angle, axis=axis,
axis_pt=pivot, centre=com, span=span, blade_length=5e-10, staggered=True)
# Create the molecule.
structure.add_molecule(name='rest')
@@ -254,11 +260,11 @@
# 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=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=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=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=pivot, scale=size)
# The full axis system.
else:
@@ -303,9 +309,9 @@
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=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=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=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=pivot, scale=size)
# The cone object.
@@ -326,7 +332,7 @@
# The pseudo-ellipse cone object.
if cdp.model in ['pseudo-ellipse', 'pseudo-ellipse, torsionless',
'pseudo-ellipse, free rotor']:
- cone = Pseudo_elliptic(cdp.cone_theta_x, cdp.cone_theta_y)
+ cone_obj = Pseudo_elliptic(cdp.cone_theta_x, cdp.cone_theta_y)
# The isotropic cone object.
else:
@@ -337,14 +343,14 @@
cone_theta =
order_parameters.iso_cone_S_to_theta(cdp.cone_s1)
# The object.
- cone = Iso_cone(cone_theta)
+ cone_obj = 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=pivot, R=R_pos, inc=inc,
distribution='regular', axis_flag=False)
+ cone(mol=mol, cone_obj=cone_obj, 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=pivot, R=R_neg, inc=inc,
distribution='regular', axis_flag=False)
+ cone(mol=mol_neg, cone_obj=cone_obj,
start_res=mol_neg.res_num[-1]+1, apex=pivot, R=R_neg, inc=inc,
distribution='regular', axis_flag=False)
# Create the PDB file.
r23476 - /trunk/specific_analyses/frame_order/uf.py