Author: bugman
Date: Thu Sep 25 10:20:42 2014
New Revision: 26026
URL: http://svn.gna.org/viewcvs/relax?rev=26026&view=rev
Log:
Improved logic in the auto_analyses.frame_order.summarise() function.
The model names, directories and titles are now being auto-generated from the
full list of frame
order models in lib.frame_order.variables.MODEL_LIST.
To create a common mechanism for determining the model directory name, the
Frame_order_analysis.model_directory() method has been converted into a module
function.
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=26026&r1=26025&r2=26026&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/frame_order.py (original)
+++ branches/frame_order_cleanup/auto_analyses/frame_order.py Thu Sep 25
10:20:42 2014
@@ -53,7 +53,7 @@
from lib.arg_check import is_bool, is_float, is_int, is_str
from lib.errors import RelaxError
from lib.frame_order.conversions import convert_axis_alpha_to_spherical
-from lib.frame_order.variables import MODEL_DOUBLE_ROTOR, MODEL_FREE_ROTOR,
MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR, MODEL_ISO_CONE_TORSIONLESS,
MODEL_LIST_FREE_ROTORS, MODEL_LIST_ISO_CONE, MODEL_LIST_NONREDUNDANT,
MODEL_LIST_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE_FREE_ROTOR, MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_RIGID,
MODEL_ROTOR
+from lib.frame_order.variables import MODEL_DOUBLE_ROTOR, MODEL_FREE_ROTOR,
MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR, MODEL_ISO_CONE_TORSIONLESS,
MODEL_LIST, MODEL_LIST_FREE_ROTORS, MODEL_LIST_ISO_CONE,
MODEL_LIST_NONREDUNDANT, MODEL_LIST_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE,
MODEL_PSEUDO_ELLIPSE_FREE_ROTOR, MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_RIGID,
MODEL_ROTOR
from lib.geometry.coord_transform import spherical_to_cartesian
from lib.io import open_write_file
from lib.order.order_parameters import iso_cone_theta_to_S
@@ -68,6 +68,29 @@
+def model_directory(model, base_dir=None):
+ """Return the directory to be used for the model.
+
+ @param model: The frame order model name.
+ @type model: str
+ @keyword base_dir: The optional base directory to prepend to the file
name.
+ @type base_dir: None or str
+ """
+
+ # Convert the model name.
+ dir = model.replace(' ', '_')
+ dir = dir.replace(',', '')
+
+ # Process the base directory.
+ if base_dir == None:
+ base_dir = ''
+ elif base_dir[-1] != sep:
+ base_dir += sep
+
+ # Return the full path.
+ return base_dir + dir
+
+
def summarise(file_name='summary', dir=None, force=True):
"""Summarise the frame order auto-analysis results.
@@ -76,48 +99,36 @@
@keyword file_name: The file to save the table into.
@type file_name: str
- @keyword dir: The optional directory to place the file into.
+ @keyword dir: The optional directory to place the file into. If
specified, the results files will also be searched for in this directory.
@type dir: None or str
@keyword force: A flag which if True will cause any preexisting
file to be overwritten.
@type force: bool
"""
- # The model names and directories.
- model_names = [
- 'Rigid',
- 'Free rotor',
- 'Rotor',
- 'Iso cone, free rotor',
- 'Iso cone, torsionless',
- 'Iso cone, torsionless (perm A)',
- 'Iso cone',
- 'Iso cone (perm A)',
- 'Pseudo ellipse, torsionless',
- 'Pseudo ellipse, torsionless (perm A)',
- 'Pseudo ellipse, torsionless (perm B)',
- 'Pseudo ellipse',
- 'Pseudo ellipse (perm A)',
- 'Pseudo ellipse (perm B)',
- 'Double rotor'
- ]
- model_dirs = {
- 'Rigid': 'rigid',
- 'Free rotor': 'free_rotor',
- 'Rotor': 'rotor',
- 'Iso cone, free rotor': 'iso_cone, free_rotor',
- 'Iso cone, torsionless': 'iso_cone_torsionless',
- 'Iso cone, torsionless (perm A)': 'iso_cone_torsionless_permutation_A',
- 'Iso cone': 'iso_cone',
- 'Iso cone (perm A)': 'iso_cone_permutation_A',
- 'Pseudo ellipse, torsionless': 'pseudo-ellipse_torsionless',
- 'Pseudo ellipse, torsionless (perm A)':
'pseudo-ellipse_torsionless_permutation_A',
- 'Pseudo ellipse, torsionless (perm B)':
'pseudo-ellipse_torsionless_permutation_B',
- 'Pseudo ellipse': 'pseudo-ellipse',
- 'Pseudo ellipse (perm A)': 'pseudo-ellipse_permutation_A',
- 'Pseudo ellipse (perm B)': 'pseudo-ellipse_permutation_B',
- 'Double rotor': 'double_rotor'
- }
-
+ # The model names, titles and directories, including axis permutations.
+ models = []
+ model_titles = []
+ dirs = []
+ for model in MODEL_LIST:
+ # Add the base model.
+ models.append(model)
+ title = model[0].upper() + model[1:]
+ model_titles.append(title)
+ dirs.append(model_directory(model, base_dir=dir))
+
+ # Axis permutations.
+ if model in MODEL_LIST_ISO_CONE + MODEL_LIST_PSEUDO_ELLIPSE:
+ # The A permutation.
+ models.append("%s permutation A" % model)
+ model_titles.append(title + ' (perm A)')
+ dirs.append(model_directory(models[-1], base_dir=dir))
+
+ # The B permutation.
+ if model in MODEL_LIST_PSEUDO_ELLIPSE:
+ models.append("%s permutation B" % model)
+ model_titles.append(title + ' (perm B)')
+ dirs.append(model_directory(models[-1], base_dir=dir))
+
# The analysis directory and structures.
contents = []
contents.append(["Analysis directory", getcwd()])
@@ -136,23 +147,23 @@
# Loop over the models.
contents1 = []
contents2 = []
- for i in range(len(model_names)):
+ for i in range(len(models)):
# No file.
- if not access(model_dirs[model_names[i]]+'/results.bz2', F_OK):
+ if not access(dirs[i]+sep+'results.bz2', F_OK):
continue
# Create a data pipe.
- pipes.create(model_names[i], 'frame order')
+ pipes.create(models[i], 'frame order')
# Load the data.
- results.read(file='results', dir=model_dirs[model_names[i]])
+ results.read(file='results', dir=dirs[i])
# Number of params.
k = len(cdp.params)
# Format the model information.
- contents1.append([model_names[i], k, cdp.chi2, cdp.chi2 + 2*k, None,
None, None, None, None, None, None])
- contents2.append([model_names[i], 0.0, 0.0, 0.0, None, None, None,
None, None, None])
+ contents1.append([model_titles[i], k, cdp.chi2, cdp.chi2 + 2*k, None,
None, None, None, None, None, None])
+ contents2.append([model_titles[i], 0.0, 0.0, 0.0, None, None, None,
None, None, None])
# Eigen alpha.
if hasattr(cdp, 'eigen_alpha') and cdp.eigen_alpha != None:
@@ -211,9 +222,11 @@
string += format_table(headings=headings1, contents=contents1,
custom_format=[None, None, "%.2f", "%.2f", "%.3f", "%.3f", "%.3f", "%.2f",
"%.2f", "%.2f", "%.2f"])
string += format_table(headings=headings2, contents=contents2,
custom_format=[None, "%.3f", "%.3f", "%.3f", "%.3f", "%.3f", "%.3f", "%.3f",
"%.3f", "%.3f"])
- # Write out.
+ # Stdout output.
sys.stdout.write("\n\n\n")
sys.stdout.write(string)
+
+ # Save to file.
file = open_write_file(file_name=file_name, dir=dir, force=force)
file.write(string)
file.close()
@@ -422,7 +435,7 @@
self.interpreter.eliminate()
# Save the results.
-
self.interpreter.results.write(dir=self.model_directory(perm_model), force=True)
+ 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)
@@ -514,26 +527,6 @@
# Return the increment list.
return incs
-
-
- def model_directory(self, model, pre_run=False):
- """Return the directory to be used for the model.
-
- @param model: The frame order model.
- @type model: str
- @keyword pre_run: A flag which if True will prepend the pre-run
results directory instead of the current results directory.
- @type pre_run: bool
- """
-
- # Convert the model name.
- dir = model.replace(' ', '_')
- dir = dir.replace(',', '')
-
- # Return the full path.
- if pre_run:
- return self.pre_run_dir + dir
- else:
- return self.results_dir + dir
def nested_params_ave_dom_pos(self, model):
@@ -844,7 +837,7 @@
self.interpreter.eliminate()
# Save the results.
- self.interpreter.results.write(dir=self.model_directory(model),
force=True)
+ 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)
@@ -876,8 +869,8 @@
# 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=self.model_directory(model),
force=True)
-
self.interpreter.frame_order.simulate(dir=self.model_directory(model),
step_size=self.brownian_step_size, snapshot=self.brownian_snapshot,
total=self.brownian_total, force=True)
+ 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)
# Nothing more to do.
return
@@ -935,11 +928,11 @@
self.print_results()
# Save the results.
- self.interpreter.results.write(dir=self.model_directory(model),
force=True)
+ 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=self.model_directory(model),
force=True)
- self.interpreter.frame_order.simulate(dir=self.model_directory(model),
step_size=self.brownian_step_size, snapshot=self.brownian_snapshot,
total=self.brownian_total, force=True)
+ 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)
def print_results(self):
@@ -1036,7 +1029,10 @@
"""
# The file name.
- path = self.model_directory(model, pre_run=pre_run) + sep +
'results.bz2'
+ base_dir = self.results_dir
+ if pre_run:
+ base_dir = self.pre_run_dir
+ path = model_directory(model, base_dir=base_dir) + sep + 'results.bz2'
# The file does not exist.
if not access(path, F_OK):
@@ -1130,12 +1126,12 @@
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=self.model_directory(model),
force=True)
- self.interpreter.frame_order.simulate(dir=self.model_directory(model),
step_size=self.brownian_step_size, snapshot=self.brownian_snapshot,
total=self.brownian_total, force=True)
+ 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=self.model_directory(model), force=True)
+ 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)
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