Author: bugman
Date: Mon Sep 22 12:19:36 2014
New Revision: 25950
URL: http://svn.gna.org/viewcvs/relax?rev=25950&view=rev
Log:
Added new arguments to the frame order auto-analysis for the
frame_order.simulate user function.
These are the brownian_step_size, brownian_snapshot and brownian_total
arguments which are passed
directly into the frame_order.simulate user function. This gives the user
more control, as well as
allowing the test suite to speed up this part of the analysis.
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=25950&r1=25949&r2=25950&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/frame_order.py (original)
+++ branches/frame_order_cleanup/auto_analyses/frame_order.py Mon Sep 22
12:19:36 2014
@@ -56,7 +56,7 @@
class Frame_order_analysis:
"""The frame order auto-analysis protocol."""
- def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, opt_rigid=None, opt_subset=None,
opt_full=None, opt_mc=None, mc_sim_num=500, models=MODEL_LIST_NONREDUNDANT):
+ def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, opt_rigid=None, opt_subset=None,
opt_full=None, opt_mc=None, mc_sim_num=500, models=MODEL_LIST_NONREDUNDANT,
brownian_step_size=2.0, brownian_snapshot=10, brownian_total=1000):
"""Perform the full frame order analysis.
@param data_pipe_full: The name of the data pipe containing
all of the RDC and PCS data.
@@ -79,6 +79,12 @@
@type mc_sim_num: int
@keyword models: The frame order models to use in the
analysis. The 'rigid' model must be included as this is essential for the
analysis.
@type models: list of str
+ @keyword brownian_step_size: The step_size argument for the
pseudo-Brownian dynamics simulation frame_order.simulate user function.
+ @type brownian_step_size: float
+ @keyword brownian_snapshot: The snapshot argument for the
pseudo-Brownian dynamics simulation frame_order.simulate user function.
+ @type brownian_snapshot: int
+ @keyword brownian_total: The total argument for the
pseudo-Brownian dynamics simulation frame_order.simulate user function.
+ @type brownian_total: int
"""
# Execution lock.
@@ -98,6 +104,9 @@
self.opt_full = opt_full
self.opt_mc = opt_mc
self.mc_sim_num = mc_sim_num
+ self.brownian_step_size = brownian_step_size
+ self.brownian_snapshot = brownian_snapshot
+ self.brownian_total = brownian_total
# Re-order the models to enable the parameter nesting protocol.
self.models = self.reorder_models(models)
@@ -673,7 +682,7 @@
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),
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)
# Nothing more to do.
return
@@ -725,7 +734,7 @@
# 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),
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)
def print_results(self):
@@ -915,7 +924,7 @@
# 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),
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)
# Create the visualisation script.
subsection(file=sys.stdout, text="Creating a PyMOL visualisation
script.")
r25950 - /branches/frame_order_cleanup/auto_analyses/frame_order.py