Author: bugman
Date: Sat Feb 14 11:22:17 2015
New Revision: 27644
URL: http://svn.gna.org/viewcvs/relax?rev=27644&view=rev
Log:
Added the frame_order.distribute user function to the auto-analysis results
output.
This will allow both the pseudo-Brownian simulation and uniform distribution
PDB files to be
available to the user in all results directories (excluding the intermediate
results for speed).
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=27644&r1=27643&r2=27644&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/frame_order.py (original)
+++ branches/frame_order_cleanup/auto_analyses/frame_order.py Sat Feb 14
11:22:17 2015
@@ -385,7 +385,7 @@
# Debugging and test suite variables.
_final_state = True
- def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, pre_run_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, results_compress_type=0, rigid_grid_split=False,
store_intermediate=True, nested_params_ave_dom_pos=True):
+ def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, pre_run_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, distribution_total=1000, results_compress_type=0,
rigid_grid_split=False, store_intermediate=True,
nested_params_ave_dom_pos=True):
"""Perform the full frame order analysis.
@param data_pipe_full: The name of the data pipe
containing all of the RDC and PCS data.
@@ -416,6 +416,8 @@
@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
+ @keyword distribution_total: The total argument for the uniform
distribution frame_order.distribute user function.
+ @type distribution_total: int
@keyword results_compress_type: The type of compression to use
when creating the results files. See the results.write user function for
details.
@type results_compress_type: int
@keyword rigid_grid_split: A flag which if True will cause
the grid search for the rigid model to be split so that the rotation is
optimised first followed by the translation. When combined with grid zooming,
this can save optimisation time. However it may result in the global minimum
being missed.
@@ -446,6 +448,7 @@
self.brownian_step_size = brownian_step_size
self.brownian_snapshot = brownian_snapshot
self.brownian_total = brownian_total
+ self.distribution_total = distribution_total
self.results_compress_type = results_compress_type
self.rigid_grid_split = rigid_grid_split
self.store_intermediate = store_intermediate
@@ -1415,6 +1418,10 @@
script.write("pymol.frame_order()\n")
script.close()
+ # The uniform distribution of structures.
+ if simulation:
+ self.interpreter.frame_order.distribute(dir=dir,
total=self.distribution_total, force=True)
+
# The pseudo-Brownian dynamics simulation.
if simulation:
self.interpreter.frame_order.simulate(dir=dir,
step_size=self.brownian_step_size, snapshot=self.brownian_snapshot,
total=self.brownian_total, force=True)
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