Author: bugman
Date: Thu Feb 18 17:30:01 2010
New Revision: 10747
URL: http://svn.gna.org/viewcvs/relax?rev=10747&view=rev
Log:
Added a system test script for testing the relative stereochemistry analysis.
Added:
1.3/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
Added:
1.3/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py?rev=10747&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
(added)
+++ 1.3/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
Thu Feb 18 17:30:01 2010
@@ -1,0 +1,160 @@
+###############################################################################
+#
#
+# Copyright (C) 2010 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+"""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.
+
+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.
+"""
+
+# Python module imports.
+from os import rename, sep
+from tempfile import mkdtemp
+
+# relax module imports.
+from auto_analyses.stereochem_analysis import Stereochem_analysis
+
+
+# Path of the data files.
+path = sys.path[-1] + sep + 'test_suite' + sep + 'shared_data'
+path_str = path + sep + 'structures' + sep + 'phthalic_acid' + sep +
'snapshots' + sep
+path_noe = path + sep + 'noe_restraints' + sep
+path_rdc = path + sep + 'rdc_data' + sep
+
+# Number of ensembles.
+NUM_ENS = 3
+
+# Ensemble size.
+NUM_MODELS = 2
+
+# Configurations.
+CONFIGS = ["R", "S"]
+
+# Snapshot directories (corresponding to CONFIGS).
+SNAPSHOT_DIR = [path_str + "snapshots", path_str + "snapshots"]
+
+# Min and max number of the snapshots (corresponding to CONFIGS).
+SNAPSHOT_MIN = [0, 0]
+SNAPSHOT_MAX = [5, 5]
+
+# Pseudo-atoms.
+PSEUDO = [
+["Q7", ["@H16", "@H17", "@H18"]],
+["Q9", ["@H20", "@H21", "@H22"]],
+["Q10", ["@H23", "@H24", "@H25"]]
+]
+
+# NOE file.
+NOE_FILE = path_noe + "phthalic_acid"
+
+# RDC file info.
+RDC_NAME = "PAN"
+RDC_FILE = path_rdc + "PAN_phthalic_acid"
+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
+
+# Results directory.
+RESULTS_DIR = mkdtemp()
+
+# Set up and code execution.
+analysis = Stereochem_analysis(
+ stage=1,
+ results_dir=RESULTS_DIR,
+ num_ens=NUM_ENS,
+ num_models=NUM_MODELS,
+ configs=CONFIGS,
+ snapshot_dir=SNAPSHOT_DIR,
+ snapshot_min=SNAPSHOT_MIN,
+ snapshot_max=SNAPSHOT_MAX,
+ pseudo=PSEUDO,
+ noe_file=NOE_FILE,
+ rdc_name=RDC_NAME,
+ rdc_file=RDC_FILE,
+ rdc_spin_id_col=RDC_SPIN_ID_COL,
+ rdc_mol_name_col=RDC_MOL_NAME_COL,
+ rdc_res_num_col=RDC_RES_NUM_COL,
+ rdc_res_name_col=RDC_RES_NAME_COL,
+ rdc_spin_num_col=RDC_SPIN_NUM_COL,
+ rdc_spin_name_col=RDC_SPIN_NAME_COL,
+ rdc_data_col=RDC_DATA_COL,
+ rdc_error_col=RDC_ERROR_COL,
+ bond_length=BOND_LENGTH,
+ log=LOG,
+ bucket_num=BUCKET_NUM,
+ lower_lim_noe=LOWER_LIM_NOE,
+ upper_lim_noe=UPPER_LIM_NOE,
+ lower_lim_rdc=LOWER_LIM_RDC,
+ upper_lim_rdc=UPPER_LIM_RDC
+)
+
+# Execute all stages.
+try:
+ for i in range(1, 6):
+ # Set the stage.
+ print "\n\n\nStage %i\n\n" % i
+ analysis.stage = i
+
+ # Execute the stage.
+ if i != 3:
+ analysis.run()
+ else:
+ print("Renaming '%s' to '%s'." % (RESULTS_DIR+sep+'ensembles',
RESULTS_DIR+sep+'ensembles_superimposed'))
+ rename(RESULTS_DIR+sep+'ensembles',
RESULTS_DIR+sep+'ensembles_superimposed')
r10747 - /1.3/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py