Author: bugman
Date: Sat Sep 27 17:25:28 2014
New Revision: 26090
URL: http://svn.gna.org/viewcvs/relax?rev=26090&view=rev
Log:
Improvements, fixes, and expansion of the results and data visualisation file
creation.
This is for the frame order auto-analysis. The visualisation() method has
been renamed to
results_output() and its scope expanded. The function previously only called
the
frame_order.pdb_model and frame_order.simulation user functions for creating
PDB representations of
the frame order motions and performing a pseudo-Brownian frame order dynamics
simulate. This has
been extended to also call the results.write user function for outputting
results files and the
rdc.corr_plot and pcs_corr_plot for generating correlation plots of the
measured vs. back-calculated
data.
All parts of the auto-analysis were output files are required now call this
method. This ensures
that all output files are always created, and are placed into the correct
directories.
Modified:
branches/frame_order_cleanup/auto_analyses/frame_order.py
Modified: branches/frame_order_cleanup/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/frame_order.py?rev=26090&r1=26089&r2=26090&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/frame_order.py (original)
+++ branches/frame_order_cleanup/auto_analyses/frame_order.py Sat Sep 27
17:25:28 2014
@@ -458,14 +458,15 @@
self.interpreter.eliminate()
self.interpreter.monte_carlo.error_analysis()
- # Finish.
- self.interpreter.results.write(file='results',
dir=self.results_dir+'final', force=True)
+ # Create the output and visualisation files.
+ self.results_output(model='final',
dir=self.results_dir+'final', results_file=True)
+
+ # Regenerate the output and visualisation files for the final
results.
+ else:
+ self.results_output(model='final',
dir=self.results_dir+'final', results_file=False)
# Output the finishing time.
self.interpreter.time()
-
- # Visualisation of the final results.
- self.visualisation(model='final')
# Save the final program state.
if self._final_state:
@@ -518,13 +519,16 @@
self.pipe_name_dict[perm_model] = '%s permutation %s - %s' %
(title, perm, self.pipe_bundle)
self.pipe_name_list.append(self.pipe_name_dict[perm_model])
+ # The output directory.
+ dir = model_directory(perm_model, base_dir=self.results_dir)
+
# The results file already exists, so read its contents instead.
if self.read_results(model=perm_model,
pipe_name=self.pipe_name_dict[perm_model]):
# Re-perform model elimination just in case.
self.interpreter.eliminate()
- # The PDB representation of the model and visualisation
script (in case this was not completed correctly).
- self.visualisation(model=perm_model)
+ # Recreate the output and visualisation files (in case this
was not completed correctly).
+ self.results_output(model=perm_model, dir=dir,
results_file=False)
# Jump to the next permutation.
continue
@@ -556,11 +560,8 @@
# Model elimination.
self.interpreter.eliminate()
- # Save the results.
- self.interpreter.results.write(dir=model_directory(perm_model,
base_dir=self.results_dir), force=True)
-
- # The PDB representation of the model and visualisation script.
- self.visualisation(model=perm_model)
+ # Create the output and visualisation files.
+ self.results_output(model=perm_model, dir=dir, results_file=True)
def check_vars(self):
@@ -867,13 +868,16 @@
self.pipe_name_dict[model] = '%s - %s' % (title,
self.pipe_bundle)
self.pipe_name_list.append(self.pipe_name_dict[model])
+ # The output directory.
+ dir = model_directory(model, base_dir=self.results_dir)
+
# The results file already exists, so read its contents instead.
if self.read_results(model=model,
pipe_name=self.pipe_name_dict[model]):
# Re-perform model elimination just in case.
self.interpreter.eliminate()
- # The PDB representation of the model and visualisation
script (in case this was not completed correctly).
- self.visualisation(model=model)
+ # Recreate the output files (in case this was not completed
correctly).
+ self.results_output(model=model, dir=dir, results_file=False)
# Perform the axis permutation analysis.
self.axis_permutation_analysis(model=model)
@@ -958,11 +962,8 @@
# Model elimination.
self.interpreter.eliminate()
- # Save the results.
- self.interpreter.results.write(dir=model_directory(model,
base_dir=self.results_dir), force=True)
-
- # The PDB representation of the model and visualisation script.
- self.visualisation(model=model)
+ # Create the output and visualisation files.
+ self.results_output(model=model, dir=dir, results_file=True)
# Perform the axis permutation analysis.
self.axis_permutation_analysis(model=model)
@@ -988,11 +989,13 @@
self.pipe_name_dict[model] = '%s - %s' % (title, self.pipe_bundle)
self.pipe_name_list.append(self.pipe_name_dict[model])
+ # The output directory.
+ dir = model_directory(model, base_dir=self.results_dir)
+
# The results file already exists, so read its contents instead.
if self.read_results(model=model,
pipe_name=self.pipe_name_dict[model]):
- # The PDB representation of the model and the pseudo-Brownian
dynamics simulation (in case this was not completed correctly).
-
self.interpreter.frame_order.pdb_model(dir=model_directory(model,
base_dir=self.results_dir), force=True)
- self.interpreter.frame_order.simulate(dir=model_directory(model,
base_dir=self.results_dir), step_size=self.brownian_step_size,
snapshot=self.brownian_snapshot, total=self.brownian_total, force=True)
+ # Recreate the output and visualisation files (in case this was
not completed correctly).
+ self.results_output(model=model, dir=dir, results_file=False)
# Nothing more to do.
return
@@ -1049,11 +1052,8 @@
# Results printout.
self.print_results()
- # Save the results.
- self.interpreter.results.write(dir=model_directory(model,
base_dir=self.results_dir), force=True)
-
- # The PDB representation of the model and the pseudo-Brownian
dynamics simulation.
- self.interpreter.frame_order.pdb_model(dir=model_directory(model,
base_dir=self.results_dir), force=True)
+ # Create the output and visualisation files.
+ self.results_output(model=model, dir=dir, results_file=True)
def print_results(self):
@@ -1210,6 +1210,58 @@
return new
+ def results_output(self, dir=None, model=None, results_file=True):
+ """Create visual representations of the frame order results for the
given model.
+
+ This will call the following user functions:
+
+ - results.write to output a results file (turned off if the
results_file argument is False).
+ - rdc.corr_plot and pcs.corr_plot to visualise the quality of
the data and fit as 2D Grace correlation plots.
+ - frame_order.pdb_model to generate a PDB representation of the
frame order motions.
+ - frame_order.simulate to perform a pseudo-Brownian frame order
dynamics simulation.
+
+ A relax script called 'pymol_display.py' will be created for easily
visualising the PDB representation from the frame_order.pdb_model user
function.
+
+
+ This includes a PDB representation of the motions (the 'cone.pdb'
file located in each model directory) together with a relax script for
displaying the average domain positions together with the cone/motion
representation in PyMOL (the 'pymol_display.py' file, also created in the
model directory).
+
+ @keyword dir: The output directory.
+ @type dir: str
+ @keyword model: The frame order model. This should match
the model of the current data pipe, unless the special value of 'final' is
used to indicate the visualisation of the final results.
+ @type model: str
+ @keyword results_file: A flag which if True will cause a results
file to be created via the results.write user function.
+ @type results_file: bool
+ """
+
+ # Printout.
+ subsection(file=sys.stdout, text="Generating the results and data
visualisation files")
+
+ # Sanity check.
+ if model != 'final' and model.replace(' permutation A',
'').replace(' permutation B', '') != cdp.model:
+ raise RelaxError("The model '%s' does not match the model '%s'
of the current data pipe." % (model.replace(' permuted', ''), cdp.model))
+
+ # The results file.
+ if results_file:
+ self.interpreter.results.write(dir=dir, force=True)
+
+ # The RDC and PCS correlation plots.
+ self.interpreter.rdc.corr_plot(dir=dir, force=True)
+ self.interpreter.pcs.corr_plot(dir=dir, force=True)
+
+ # The PDB representation of the model.
+ self.interpreter.frame_order.pdb_model(dir=dir, force=True)
+
+ # Create the visualisation script for the PDB representation.
+ script = open_write_file(file_name='pymol_display.py', dir=dir,
force=True)
+ script.write("# relax script for displaying the frame order results
of this '%s' model in PyMOL.\n\n" % model)
+ script.write("# PyMOL visualisation.\n")
+ script.write("pymol.frame_order()\n")
+ script.close()
+
+ # The pseudo-Brownian dynamics simulation.
+ self.interpreter.frame_order.simulate(dir=dir,
step_size=self.brownian_step_size, snapshot=self.brownian_snapshot,
total=self.brownian_total, force=True)
+
+
def sobol_setup(self, info=None):
"""Correctly handle the frame_order.sobol_setup user function.
@@ -1231,38 +1283,6 @@
# Full setup.
else:
self.interpreter.frame_order.sobol_setup(max_num=max_num,
oversample=oversample)
-
-
- def visualisation(self, model=None):
- """Create visual representations of the frame order results for the
given model.
-
- This includes a PDB representation of the motions (the 'cone.pdb'
file located in each model directory) together with a relax script for
displaying the average domain positions together with the cone/motion
representation in PyMOL (the 'pymol_display.py' file, also created in the
model directory).
-
- @keyword model: The frame order model to visualise. This should
match the model of the current data pipe, unless the special value of 'final'
is used to indicate the visualisation of the final results.
- @type model: str
- """
-
- # Sanity check.
- if model != 'final' and model.replace(' permutation A',
'').replace(' permutation B', '') != cdp.model:
- raise RelaxError("The model '%s' does not match the model '%s'
of the current data pipe." % (model.replace(' permuted', ''), cdp.model))
-
- # The PDB representation of the model and the pseudo-Brownian
dynamics simulation.
- self.interpreter.frame_order.pdb_model(dir=model_directory(model,
base_dir=self.results_dir), force=True)
- self.interpreter.frame_order.simulate(dir=model_directory(model,
base_dir=self.results_dir), step_size=self.brownian_step_size,
snapshot=self.brownian_snapshot, total=self.brownian_total, 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=model_directory(model, base_dir=self.results_dir), force=True)
-
- # Add a comment for the user.
- script.write("# relax script for displaying the frame order results
of this '%s' model in PyMOL.\n\n" % model)
-
- # The script contents.
- script.write("# PyMOL visualisation.\n")
- script.write("pymol.frame_order()\n")
-
- # Close the file.
- script.close()
r26090 - /branches/frame_order_cleanup/auto_analyses/frame_order.py