r10719 - /1.3/sample_scripts/stereochem_analysis_config.py -- February 18, 2010 - 13:53

Author: bugman
Date: Thu Feb 18 13:53:39 2010
New Revision: 10719

URL: http://svn.gna.org/viewcvs/relax?rev=10719&view=rev
Log:
Added the relative stereochemistry analysis configuration file.

This will be converted into a relax script.


Added:
    1.3/sample_scripts/stereochem_analysis_config.py

Added: 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 (added)
+++ 1.3/sample_scripts/stereochem_analysis_config.py Thu Feb 18 13:53:39 2010
@@ -1,0 +1,77 @@
+"""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