Author: bugman
Date: Fri Jan 17 11:51:16 2014
New Revision: 22024
URL: http://svn.gna.org/viewcvs/relax?rev=22024&view=rev
Log:
Created the Frame_order.test_generate_rotor2_distribution system test.
This is to test the Frame Order distribution generating base script, used for
creating the synthetic
Frame Order test data, and to demonstrate a failure in handling
back-calculated RDC data.
To implement this, the test_suite/shared_data/frame_order/cam/ path has been
converted into a Python
package (with the addition of the __init__.py files). The base data
generation script
test_suite/shared_data/frame_order/cam/generate_base.py has also been
modified to use the absolute
path for the data files and its run() method now accepts the save_path
argument to allow the files
to be saved into a temporary directory.
Added:
trunk/test_suite/shared_data/frame_order/__init__.py
- copied, changed from r22019, trunk/test_suite/shared_data/__init__.py
trunk/test_suite/shared_data/frame_order/cam/__init__.py
- copied, changed from r22019, trunk/test_suite/shared_data/__init__.py
trunk/test_suite/system_tests/scripts/frame_order/cam/generate_rotor2_distribution.py
- copied, changed from r22019,
trunk/test_suite/shared_data/frame_order/cam/rotor2/generate_distribution.py
Modified:
trunk/test_suite/shared_data/__init__.py
trunk/test_suite/shared_data/frame_order/cam/generate_base.py
trunk/test_suite/system_tests/frame_order.py
Modified: trunk/test_suite/shared_data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/__init__.py?rev=22024&r1=22023&r2=22024&view=diff
==============================================================================
--- trunk/test_suite/shared_data/__init__.py (original)
+++ trunk/test_suite/shared_data/__init__.py Fri Jan 17 11:51:16 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006-2010 Edward d'Auvergne
#
+# Copyright (C) 2006-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -23,4 +23,6 @@
"""The relax test-suite shared data."""
-__all__ = []
+__all__ = [
+ 'frame_order'
+]
Copied: trunk/test_suite/shared_data/frame_order/__init__.py (from r22019,
trunk/test_suite/shared_data/__init__.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/__init__.py?p2=trunk/test_suite/shared_data/frame_order/__init__.py&p1=trunk/test_suite/shared_data/__init__.py&r1=22019&r2=22024&rev=22024&view=diff
==============================================================================
--- trunk/test_suite/shared_data/__init__.py (original)
+++ trunk/test_suite/shared_data/frame_order/__init__.py Fri Jan 17 11:51:16
2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006-2010 Edward d'Auvergne
#
+# Copyright (C) 2006-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -20,7 +20,9 @@
###############################################################################
# Package docstring.
-"""The relax test-suite shared data."""
+"""The relax test-suite shared data for the Frame Order theories."""
-__all__ = []
+__all__ = [
+ 'cam'
+]
Copied: trunk/test_suite/shared_data/frame_order/cam/__init__.py (from
r22019, trunk/test_suite/shared_data/__init__.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/__init__.py?p2=trunk/test_suite/shared_data/frame_order/cam/__init__.py&p1=trunk/test_suite/shared_data/__init__.py&r1=22019&r2=22024&rev=22024&view=diff
==============================================================================
--- trunk/test_suite/shared_data/__init__.py (original)
+++ trunk/test_suite/shared_data/frame_order/cam/__init__.py Fri Jan 17
11:51:16 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006-2010 Edward d'Auvergne
#
+# Copyright (C) 2006-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -20,7 +20,9 @@
###############################################################################
# Package docstring.
-"""The relax test-suite shared data."""
+"""The relax test-suite shared data for the CaM data for the Frame Order
theories."""
-__all__ = []
+__all__ = [
+ 'generate_base'
+]
Modified: trunk/test_suite/shared_data/frame_order/cam/generate_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/generate_base.py?rev=22024&r1=22023&r2=22024&view=diff
==============================================================================
--- trunk/test_suite/shared_data/frame_order/cam/generate_base.py (original)
+++ trunk/test_suite/shared_data/frame_order/cam/generate_base.py Fri Jan 17
11:51:16 2014
@@ -26,18 +26,20 @@
from math import pi
from numpy import array, cross, dot, float16, float64, transpose, zeros
from numpy.linalg import norm
+from os import getcwd, sep
import sys
# relax module imports.
+from lib.frame_order.format import print_frame_order_2nd_degree
+from lib.geometry.coord_transform import cartesian_to_spherical
+from lib.geometry.rotations import axis_angle_to_R, R_to_euler_zyz
+from lib.io import open_write_file
+from lib.linear_algebra.kronecker_product import kron_prod
from pipe_control.angles import wrap_angles
-from lib.frame_order.format import print_frame_order_2nd_degree
+from pipe_control.interatomic import interatomic_loop
from pipe_control.mol_res_spin import spin_loop
-from pipe_control.interatomic import interatomic_loop
-from lib.geometry.coord_transform import cartesian_to_spherical
-from lib.linear_algebra.kronecker_product import kron_prod
-from lib.geometry.rotations import axis_angle_to_R, R_to_euler_zyz
from prompt.interpreter import Interpreter
-from lib.io import open_write_file
+from status import Status; status = Status()
class Main:
@@ -45,8 +47,18 @@
pivot = array([ 37.254, 0.5, 16.7465])
com = array([ 26.83678091, -12.37906417, 28.34154128])
- def run(self):
- """Generate the distribution and alignment data."""
+ def run(self, save_path=None):
+ """Generate the distribution and alignment data.
+
+ @keyword save_path: The path to place the files into. If set to
None, then the current path will be used.
+ @type save_path: None or str
+ """
+
+ # The paths to the files.
+ self.path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'+sep
+ self.save_path = save_path
+ if self.save_path == None:
+ self.save_path = getcwd()
# Load the interpreter.
self.interpreter = Interpreter(show_script=False, quit=False,
raise_relax_error=True)
@@ -72,7 +84,7 @@
"""Calculate the RDCs and PCSs expected for the structural
distribution."""
# Load the tensors.
- self.interpreter.script('../tensors.py')
+ self.interpreter.script(self.path+'tensors.py')
# Set up the model.
self.interpreter.n_state_model.select_model(model='fixed')
@@ -108,8 +120,8 @@
spin.pcs_err[tag] = 0.1
# Write the data.
- self.interpreter.rdc.write(align_id=tag,
file='rdc_%s.txt'%tensors[i], bc=True, force=True)
- self.interpreter.pcs.write(align_id=tag,
file='pcs_%s.txt'%tensors[i], bc=True, force=True)
+ self.interpreter.rdc.write(align_id=tag,
file='rdc_%s.txt'%tensors[i], dir=self.save_path, bc=True, force=True)
+ self.interpreter.pcs.write(align_id=tag,
file='pcs_%s.txt'%tensors[i], dir=self.save_path, bc=True, force=True)
# Store the state.
self.interpreter.state.save('back_calc', force=True)
@@ -138,7 +150,7 @@
self.interpreter.pipe.create('distribution', 'N-state')
# Load the original PDB.
- self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir='..',
set_mol_name='C-dom')
+ self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb',
dir=self.path, set_mol_name='C-dom')
# Set up the 15N and 1H spins.
self.interpreter.structure.load_spins(spin_id='@N', ave_pos=False)
@@ -159,7 +171,7 @@
self.daeg = zeros((9, 9), float64)
# Open the output files.
- rot_file = open_write_file('rotations', compress_type=1, force=True)
+ rot_file = open_write_file('rotations', dir=self.save_path,
compress_type=1, force=True)
# Printout.
sys.stdout.write("\n\nRotating %s states:\n\n" % self.N)
@@ -196,7 +208,7 @@
self.daeg = self.daeg / self.N
# Write out the frame order matrix.
- file = open('frame_order_matrix', 'w')
+ file = open(self.save_path+sep+'frame_order_matrix', 'w')
print_frame_order_2nd_degree(self.daeg, file=file)
@@ -204,7 +216,7 @@
"""Print out of the full system."""
# Open the file.
- file = open('axis_system', 'w')
+ file = open(self.save_path+sep+'axis_system', 'w')
# Header.
file.write("\n")
@@ -274,7 +286,7 @@
self.interpreter.structure.connect_atom(index1=0, index2=3)
# Write out the PDB.
- self.interpreter.structure.write_pdb('axis.pdb', compress_type=0,
force=True)
+ self.interpreter.structure.write_pdb('axis.pdb', dir=self.save_path,
compress_type=0, force=True)
def axes_to_pdb_main_axis(self):
@@ -294,7 +306,7 @@
self.interpreter.structure.connect_atom(index1=0, index2=1)
# Write out the PDB.
- self.interpreter.structure.write_pdb('axis.pdb', compress_type=0,
force=True)
+ self.interpreter.structure.write_pdb('axis.pdb', dir=self.save_path,
compress_type=0, force=True)
def build_axes_alt(self):
Modified: trunk/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/frame_order.py?rev=22024&r1=22023&r2=22024&view=diff
==============================================================================
--- trunk/test_suite/system_tests/frame_order.py (original)
+++ trunk/test_suite/system_tests/frame_order.py Fri Jan 17 11:51:16 2014
@@ -24,6 +24,7 @@
import platform
import numpy
from os import sep
+from tempfile import mkdtemp
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
@@ -113,6 +114,9 @@
# The path to the CaM scripts.
self.cam_path = status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep
+ # Create a temporary directory for dumping files.
+ ds.tmpdir = mkdtemp()
+
def tearDown(self):
"""Clean up after the tests."""
@@ -632,6 +636,13 @@
self.flags(pcs=False)
self.interpreter.run(script_file=self.cam_path+'rotor2.py')
self.check_chi2(0.080669539157379247)
+
+
+ def test_generate_rotor2_distribution(self):
+ """Generate the rotor2 distribution of CaM."""
+
+ # Execute the script.
+
self.interpreter.run(script_file=self.cam_path+'generate_rotor2_distribution.py')
def fixme_test_model_free_rotor(self):
Copied:
trunk/test_suite/system_tests/scripts/frame_order/cam/generate_rotor2_distribution.py
(from r22019,
trunk/test_suite/shared_data/frame_order/cam/rotor2/generate_distribution.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/generate_rotor2_distribution.py?p2=trunk/test_suite/system_tests/scripts/frame_order/cam/generate_rotor2_distribution.py&p1=trunk/test_suite/shared_data/frame_order/cam/rotor2/generate_distribution.py&r1=22019&r2=22024&rev=22024&view=diff
==============================================================================
---
trunk/test_suite/shared_data/frame_order/cam/rotor2/generate_distribution.py
(original)
+++
trunk/test_suite/system_tests/scripts/frame_order/cam/generate_rotor2_distribution.py
Fri Jan 17 11:51:16 2014
@@ -8,17 +8,18 @@
from math import pi
# relax module imports.
+from data_store import Relax_data_store; ds = Relax_data_store()
from lib.geometry.rotations import axis_angle_to_R
# Base module import.
-from generate_base import Main
+from test_suite.shared_data.frame_order.cam.generate_base import Main
class Generate(Main):
# The number of structures.
- ANGLE = 60
- INC = ANGLE / 1000000.0
- N = int(ANGLE / INC) + 1
+ TILT_ANGLE = 60
+ N = 10
+ INC = TILT_ANGLE / float(N - 1)
def __init__(self):
"""Model specific setup."""
@@ -40,4 +41,4 @@
# Execute the code.
generate = Generate()
-generate.run()
+generate.run(save_path=ds.tmpdir)
r22024 - in /trunk/test_suite: shared_data/ shared_data/frame_order/ shared_data/frame_order/cam/ system_tests/ system_tests...