Author: bugman
Date: Fri Mar 22 17:35:56 2013
New Revision: 19003
URL: http://svn.gna.org/viewcvs/relax?rev=19003&view=rev
Log:
Next block of the manual merger of the frame_order_testing branch.
The commands used were:
svn merge -r18892:18893
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18916:18917
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18917:18918
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18920:18921
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18921:18922
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18933:18934
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18934:18935
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18935:18936
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
The console messages were:
[edau@localhost relax-trunk]$ svn merge -r18892:18893
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18893 into '.':
U specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18916:18917
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
[edau@localhost relax-trunk]$ svn merge -r18917:18918
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18918 into '.':
G specific_fns/frame_order.py
U auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18920:18921
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18921 into '.':
G specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18921:18922
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18922 into '.':
G auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18933:18934
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18934 into '.':
G specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18934:18935
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18935 into '.':
U test_suite/system_tests/scripts/frame_order/rigid_test.py
[edau@localhost relax-trunk]$ svn merge -r18935:18936
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18936 into '.':
G specific_fns/frame_order.py
[edau@localhost relax-trunk]$
Modified:
trunk/auto_analyses/frame_order.py
trunk/specific_fns/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/rigid_test.py
Modified: trunk/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=19003&r1=19002&r2=19003&view=diff
==============================================================================
--- trunk/auto_analyses/frame_order.py (original)
+++ trunk/auto_analyses/frame_order.py Fri Mar 22 17:35:56 2013
@@ -35,6 +35,7 @@
from data import Relax_data_store; ds = Relax_data_store()
from generic_fns.angles import wrap_angles
from generic_fns.pipes import cdp_name, get_pipe
+from lib.text.sectioning import section, subsection, title
from maths_fns.coord_transform import spherical_to_cartesian
from prompt.interpreter import Interpreter
from relax_errors import RelaxError
@@ -86,10 +87,7 @@
status.exec_lock.acquire(pipe_bundle, mode='auto-analysis')
# Initial printout.
- text = "# Frame order auto-analysis #"
- print("\n\n\n\n\n\n\n" + "#"*len(text))
- print("%s" % text)
- print("#"*len(text))
+ title(file=sys.stdout, text="Frame order auto-analysis", prespace=7)
# Store the args.
self.data_pipe_full = data_pipe_full
@@ -331,8 +329,8 @@
# The model title.
title = model[0].upper() + model[1:]
- # Print out.
- self.print_title(title)
+ # Printout.
+ section(file=sys.stdout, text="%s frame order model"%title,
prespace=5)
# The data pipe name.
self.pipe_name_dict[model] = '%s - %s' % (title,
self.pipe_bundle)
@@ -404,7 +402,7 @@
title = model[0].upper() + model[1:]
# Print out.
- self.print_title(title)
+ section(file=sys.stdout, text="%s frame order model"%title,
prespace=5)
# The data pipe name.
self.pipe_name_dict[model] = '%s - %s' % (title, self.pipe_bundle)
@@ -526,19 +524,6 @@
sys.stdout.write("\n")
- def print_title(self, name):
- """Title printout for each frame order model.
-
- @param name: The frame order model name.
- @type name: str
- """
-
- text = "# %s frame order model #" % name
- print("\n\n\n\n\n" + "#"*len(text))
- print("%s" % text)
- print("#"*len(text) + "\n")
-
-
def read_results(self, model=None, pipe_name=None):
"""Attempt to read old results files.
@@ -587,6 +572,7 @@
self.interpreter.frame_order.pdb_model(dir=self.results_dir+model,
force=True)
# Create the visualisation script.
+ subsection(file=sys.stdout, text="Creating a PyMOL visualisation
script.")
script = open_write_file(file_name='pymol_display.py',
dir=self.results_dir+model, force=True)
# Add a comment for the user.
Modified: trunk/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/frame_order.py?rev=19003&r1=19002&r2=19003&view=diff
==============================================================================
--- trunk/specific_fns/frame_order.py (original)
+++ trunk/specific_fns/frame_order.py Fri Mar 22 17:35:56 2013
@@ -44,6 +44,8 @@
from generic_fns.structure.cones import Iso_cone, Pseudo_elliptic
from generic_fns.structure.mass import centre_of_mass
from generic_fns.structure.internal import Internal
+from lib.structure.rotor import rotor_pdb
+from lib.text.sectioning import subsection
from maths_fns import frame_order, order_parameters
from maths_fns.coord_transform import spherical_to_cartesian
from maths_fns.rotation_matrix import euler_to_R_zyz, two_vect_to_R
@@ -957,6 +959,9 @@
@type force: bool
"""
+ # Printout.
+ subsection(file=sys.stdout, text="Creating a PDB file with the
moving domains shifted to the average position.")
+
# Make a copy of the structural object (so as to preserve the
original structure).
structure = deepcopy(cdp.structure)
@@ -966,7 +971,11 @@
euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma, R)
else:
euler_to_R_zyz(0.0, cdp.ave_pos_beta, cdp.ave_pos_gamma, R)
- structure.rotate(R=R, origin=cdp.pivot,
atom_id=self._domain_moving())
+ if cdp.ave_pos_pivot == 'com':
+ origin = centre_of_mass(atom_id=self._domain_moving(),
verbosity=0)
+ else:
+ origin = cdp.pivot
+ structure.rotate(R=R, origin=origin, atom_id=self._domain_moving())
# Then translate the moving domain.
if not self._translation_fixed():
@@ -988,6 +997,10 @@
@keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
@type force: bool
"""
+
+ # Printout.
+ subsection(file=sys.stdout, text="Creating a PDB file of a
distribution of positions coving the full dynamics of the moving domain.")
+
def _pdb_geometric_rep(self, file=None, dir=None, size=30.0, inc=36,
force=False, neg_cone=True):
@@ -1007,6 +1020,9 @@
@type neg_cone: bool
"""
+ # Printout.
+ subsection(file=sys.stdout, text="Creating a PDB file containing a
geometric object representing the frame order dynamics.")
+
# Monte Carlo simulation flag.
sim = False
num_sim = 0
@@ -1025,8 +1041,38 @@
if neg_cone:
model_neg = structure.add_model(model=2)
+ # The rotor object.
+ if cdp.model in ['rotor', 'free rotor', 'iso cone', 'iso cone, free
rotor', 'pseudo-ellipse']:
+ # The rotor angle.
+ if cdp.model in ['free rotor', 'iso cone, free rotor']:
+ rotor_angle = pi
+ else:
+ rotor_angle = cdp.cone_sigma_max
+
+ # Generate the rotor axis.
+ if cdp.model in ['rotor', 'free rotor', 'iso cone', 'iso cone,
free rotor']:
+ axis = zeros(3, float64)
+ spherical_to_cartesian([1.0, cdp.axis_theta, cdp.axis_phi],
axis)
+ else:
+ axes = zeros((3, 3), float64)
+ euler_to_R_zyz(cdp.eigen_alpha, cdp.eigen_beta,
cdp.eigen_gamma, axes)
+ axis = axes[:,2]
+
+ # Get the CoM of the entire molecule to use as the centre of the
rotor.
+ com = centre_of_mass(verbosity=0)
+
+ # 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)
+
+ # 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
+
# Create the molecule.
- structure.add_molecule(name=cdp.model)
+ structure.add_molecule(name='rest')
# Alias the molecules.
mol = model.mol[0]
Modified: trunk/test_suite/system_tests/scripts/frame_order/rigid_test.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/rigid_test.py?rev=19003&r1=19002&r2=19003&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/frame_order/rigid_test.py (original)
+++ trunk/test_suite/system_tests/scripts/frame_order/rigid_test.py Fri Mar
22 17:35:56 2013
@@ -121,9 +121,6 @@
# Set the reference domain.
self._execute_uf(uf_name='frame_order.ref_domain', ref='fixed')
-# Link the domains to the PDB files.
-self._execute_uf(uf_name='frame_order.domain_to_pdb', domain='fixed',
pdb='displaced.pdb')
-
# Set up the mechanics of the displacement to the average domain position.
self._execute_uf(uf_name='frame_order.average_position', pivot='com',
translation=True)
r19003 - in /trunk: auto_analyses/ specific_fns/ test_suite/system_tests/scripts/frame_order/