r10720 - in /1.3/sample_scripts: stereochem_analysis.py stereochem_analysis_config.py -- February 18, 2010 - 13:54

Author: bugman
Date: Thu Feb 18 13:54:12 2010
New Revision: 10720

URL: http://svn.gna.org/viewcvs/relax?rev=10720&view=rev
Log:
Renamed the stereochem_analysis_config.py file to the stereochem_analysis.py 
relax script.


Added:
    1.3/sample_scripts/stereochem_analysis.py
      - copied unchanged from r10719, 
1.3/sample_scripts/stereochem_analysis_config.py
Removed:
    1.3/sample_scripts/stereochem_analysis_config.py

Removed: 1.3/sample_scripts/stereochem_analysis_config.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/stereochem_analysis_config.py?rev=10719&view=auto
==============================================================================
--- 1.3/sample_scripts/stereochem_analysis_config.py (original)
+++ 1.3/sample_scripts/stereochem_analysis_config.py (removed)
@@ -1,77 +1,0 @@
-"""Configuration for the stereochem_analysis.py script.
-
-All user settings should be placed here.
-
-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.
-
-    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.
-
-    4.  The RDC Q-factor analysis.
-
-    5.  Generation of Grace graphs.
-"""
-
-# Stage of analysis (see the docstring above for the options).
-STAGE = 5
-
-# Number of ensembles.
-NUM_ENS = 100000
-
-# Ensemble size.
-NUM_MODELS = 10
-
-# Configurations.
-CONFIGS = ["R", "S"]
-
-# Snapshot directories (corresponding to CONFIGS).
-SNAPSHOT_DIR = ["snapshots", "snapshots"]
-
-# Min and max number of the snapshots (corresponding to CONFIGS).
-SNAPSHOT_MIN = [0, 0]
-SNAPSHOT_MAX = [76, 71]
-
-# Pseudo-atoms.
-PSEUDO = [
-["Q7", ["@H16", "@H17", "@H18"]],
-["Q9", ["@H20", "@H21", "@H22"]],
-["Q10", ["@H23", "@H24", "@H25"]]
-]
-
-# NOE file.
-NOE_FILE = "noes"
-
-# RDC file info.
-RDC_NAME = "PAN"
-RDC_FILE = "pan_rdcs"
-RDC_SPIN_ID_COL = 1
-RDC_MOL_NAME_COL = None
-RDC_RES_NUM_COL = None
-RDC_RES_NAME_COL = None
-RDC_SPIN_NUM_COL = None
-RDC_SPIN_NAME_COL = None
-RDC_DATA_COL = 2
-RDC_ERROR_COL = None
-
-# Bond length.
-BOND_LENGTH = 1.117 * 1e-10
-
-# Log file output (only for certain stages).
-LOG = True
-
-# Number of buckets for the distribution plots.
-BUCKET_NUM = 200
-
-# Distribution plot limits.
-LOWER_LIM_NOE = 0.0
-UPPER_LIM_NOE = 600.0
-LOWER_LIM_RDC = 0.0
-UPPER_LIM_RDC = 1.0