Author: bugman
Date: Tue Jul 29 13:58:14 2014
New Revision: 24802
URL: http://svn.gna.org/viewcvs/relax?rev=24802&view=rev
Log:
Created the Frame_order.test_auto_analysis system test.
This will be an extremely quick run through of the frame order auto-analysis
as this is not
currently tested. 1 Sobol' quasi-random integration point will be used for
all models for speed.
The system test uses the rigid CaM test data to perform a full analysis.
Added:
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py
- copied, changed from r24801,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/full_analysis.py
Modified:
branches/frame_order_cleanup/test_suite/system_tests/frame_order.py
Modified: branches/frame_order_cleanup/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/frame_order.py?rev=24802&r1=24801&r2=24802&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/frame_order.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/frame_order.py Tue
Jul 29 13:58:14 2014
@@ -238,6 +238,13 @@
setattr(cdp, param, curr)
+ def test_auto_analysis(self):
+ """Test the frame order auto-analysis using the rigid CaM test
data."""
+
+ # Execute the script.
+
self.interpreter.run(script_file=self.cam_path+'auto_analysis_to_rigid.py')
+
+
def test_cam_double_rotor(self):
"""Test the double rotor frame order model of CaM."""
Copied:
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py
(from r24801,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/full_analysis.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py?p2=branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py&p1=branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/full_analysis.py&r1=24801&r2=24802&rev=24802&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/full_analysis.py
(original)
+++
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py
Tue Jul 29 13:58:14 2014
@@ -19,14 +19,8 @@
#
#
###############################################################################
-"""Script for black-box Frame Order analysis.
-
-This script should be run from the directory where it is found with the
commands:
-
-$ ../../../../../relax full_analysis.py
-
-The free rotor pseudo-elliptic cone model is not used in this script as the
cone X and Y opening angles cannot be differentiated with simply RDC and PCS
data, hence this model is perfectly approximated by the free rotor isotropic
cone.
-"""
+"""Script for black-box Frame Order analysis."""
+
# Python module imports.
from numpy import array
@@ -34,40 +28,41 @@
# relax module imports.
from auto_analyses.frame_order import Frame_order_analysis
+from status import Status; status = Status()
# Analysis variables.
#####################
# The grid search size (the number of increments per dimension).
-GRID_INC = 11
+GRID_INC = 2
# The more precise grid search size for the initial rigid model (the number
of increments per dimension).
-GRID_INC_RIGID = 31
+GRID_INC_RIGID = 2
# The number of Sobol' points for the PCS numerical integration in the grid
searches.
-NUM_INT_PTS_GRID = 50
+NUM_INT_PTS_GRID = 1
# The list of the number of Sobol' points for the PCS numerical integration
to use iteratively in the optimisations after the grid search (for the PCS
data subset).
-NUM_INT_PTS_SUBSET = [100]
+NUM_INT_PTS_SUBSET = [1]
# The minimisation function tolerance cutoff to terminate optimisation (for
the PCS data subset, see the minimise user function).
FUNC_TOL_SUBSET = [1e-2]
# The list of the number of Sobol' points for the PCS numerical integration
to use iteratively in the optimisations after the grid search (for all PCS
and RDC data).
-NUM_INT_PTS_FULL = [100, 1000, 10000]
+NUM_INT_PTS_FULL = [1]
# The minimisation function tolerance cutoff to terminate optimisation (for
all PCS and RDC data, see the minimise user function).
-FUNC_TOL_FULL = [1e-2, 1e-3, 1e-4]
+FUNC_TOL_FULL = [1e-2]
# The optimisation technique.
MIN_ALGOR = 'simplex'
# The number of Monte Carlo simulations to be used for error analysis at the
end of the protocol.
-MC_NUM = 100
+MC_NUM = 3
# The number of Sobol' points for the PCS numerical integration during Monte
Carlo simulations.
-MC_INT_PTS = 100
+MC_INT_PTS = 1
# The minimisation function tolerance cutoff to terminate optimisation
during Monte Carlo simulations.
MC_FUNC_TOL = 1e-2
@@ -81,11 +76,16 @@
'iso cone, free rotor',
'iso cone',
'pseudo-ellipse, torsionless',
- 'pseudo-ellipse'
+ 'pseudo-ellipse',
+ 'double rotor'
]
# Set up the base data pipes.
#############################
+
+# The data paths.
+BASE_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'+sep
+DATA_PATH = BASE_PATH + sep+'rigid'
# The data pipe bundle to group all data pipes.
PIPE_BUNDLE = "Frame Order (%s)" % asctime(localtime())
@@ -95,8 +95,8 @@
pipe.create(pipe_name=SUBSET, pipe_type='frame order', bundle=PIPE_BUNDLE)
# Read the structures.
-structure.read_pdb('1J7O_1st_NH.pdb', dir='..', set_mol_name='N-dom')
-structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..', set_mol_name='C-dom')
+structure.read_pdb('1J7O_1st_NH.pdb', dir=BASE_PATH, set_mol_name='N-dom')
+structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=BASE_PATH,
set_mol_name='C-dom')
# Set up the 15N and 1H spins.
structure.load_spins(spin_id='@N', ave_pos=False)
@@ -147,17 +147,17 @@
# Loop over the alignments.
for i in range(len(ln)):
# Load the RDCs.
- rdc.read(align_id=ln[i], file=rdc_files[i], dir='.', spin_id1_col=1,
spin_id2_col=2, data_col=3, error_col=4)
+ rdc.read(align_id=ln[i], file=rdc_files[i], dir=DATA_PATH,
spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4)
# The PCS (only a subset of ~5 spins for fast initial optimisations).
- pcs.read(align_id=ln[i], file=pcs_files_subset[i], dir='.',
mol_name_col=1, res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+ pcs.read(align_id=ln[i], file=pcs_files_subset[i], dir=DATA_PATH,
mol_name_col=1, res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
# The temperature and field strength.
spectrometer.temperature(id=ln[i], temp=303.0)
spectrometer.frequency(id=ln[i], frq=rdc_frq[i], units="MHz")
# Load the N-domain tensors (the full tensors).
-script('../tensors.py')
+script(BASE_PATH + 'tensors.py')
# Define the domains.
domain(id='N', spin_id="#N-dom")
@@ -199,7 +199,7 @@
# Load the complete PCS data into the already filled data pipe.
for i in range(len(ln)):
- pcs.read(align_id=ln[i], file=pcs_files[i], mol_name_col=1,
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+ pcs.read(align_id=ln[i], file=pcs_files[i], dir=DATA_PATH,
mol_name_col=1, res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
r24802 - in /branches/frame_order_cleanup/test_suite/system_tests: ./ scripts/frame_order/cam/