r23161 - /trunk/sample_scripts/n_state_model/stereochem_analysis.py -- May 13, 2014 - 23:19

Author: bugman
Date: Tue May 13 23:19:44 2014
New Revision: 23161

URL: http://svn.gna.org/viewcvs/relax?rev=23161&view=rev
Log:
Docstring improvements for the stereochem_analysis.py N-state model sample 
script.

The paragraphs are now all on one line and 'Q-factor' has been changed to 'Q 
factor'.


Modified:
    trunk/sample_scripts/n_state_model/stereochem_analysis.py

Modified: trunk/sample_scripts/n_state_model/stereochem_analysis.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/sample_scripts/n_state_model/stereochem_analysis.py?rev=23161&r1=23160&r2=23161&view=diff
==============================================================================
--- trunk/sample_scripts/n_state_model/stereochem_analysis.py   (original)
+++ trunk/sample_scripts/n_state_model/stereochem_analysis.py   Tue May 13 
23:19:44 2014
@@ -21,35 +21,25 @@
 
 """Script for the determination of relative stereochemistry.
 
-The analysis is preformed by using multiple ensembles of structures, 
randomly sampled from a given
-set of structures.  The discrimination is performed by comparing the sets of 
ensembles using NOE
-violations and RDC Q-factors.
+The analysis is preformed by using multiple ensembles of structures, 
randomly sampled from a given set of structures.  The discrimination is 
performed by comparing the sets of ensembles using NOE violations and RDC Q 
factors.
 
 This script is split into multiple stages:
 
-    1.  The random sampling of the snapshots to generate the N ensembles 
(NUM_ENS, usually 10,000 to
-    100,000) of M members (NUM_MODELS, usually ~10).  The original snapshot 
files are expected to be
-    named the SNAPSHOT_DIR + CONFIG + a number from SNAPSHOT_MIN to 
SNAPSHOT_MAX + ".pdb", e.g.
-    "snapshots/R647.pdb".  The ensembles will be placed into the "ensembles" 
directory.
+    1.  The random sampling of the snapshots to generate the N ensembles 
(NUM_ENS, usually 10,000 to 100,000) of M members (NUM_MODELS, usually ~10).  
The original snapshot files are expected to be named the SNAPSHOT_DIR + 
CONFIG + a number from SNAPSHOT_MIN to SNAPSHOT_MAX + ".pdb", e.g. 
"snapshots/R647.pdb".  The ensembles will be placed into the "ensembles" 
directory.
 
     2.  The NOE violation analysis.
 
-    3.  The superimposition of ensembles.  For each ensemble, Molmol is used 
for superimposition
-    using the fit to first algorithm.  The superimposed ensembles will be 
placed into the
-    "ensembles_superimposed" directory.  This stage is not necessary for the 
NOE analysis.
+    3.  The superimposition of ensembles.  For each ensemble, Molmol is used 
for superimposition using the fit to first algorithm.  The superimposed 
ensembles will be placed into the "ensembles_superimposed" directory.  This 
stage is not necessary for the NOE analysis.
 
-    4.  The RDC Q-factor analysis.
+    4.  The RDC Q factor analysis.
 
     5.  Generation of Grace graphs.
 
-    6.  Final ordering of ensembles using the combined RDC and NOE 
Q-factors, whereby the NOE
-    Q-factor is defined as::
+    6.  Final ordering of ensembles using the combined RDC and NOE Q 
factors, whereby the NOE Q factor is defined as::
 
         Q^2 = U / sum(NOE_i^2),
 
-    where U is the quadratic flat bottom well potential - the NOE violation 
in Angstrom^2. The
-    denominator is the sum of all squared NOEs - this must be given as the 
value of NOE_NORM.  The
-    combined Q is given by::
+    where U is the quadratic flat bottom well potential - the NOE violation 
in Angstrom^2. The denominator is the sum of all squared NOEs - this must be 
given as the value of NOE_NORM.  The combined Q is given by::
 
         Q_total^2 = Q_NOE^2 + Q_RDC^2.
 """