Author: bugman
Date: Thu Dec 18 09:11:29 2014
New Revision: 27119
URL: http://svn.gna.org/viewcvs/relax?rev=27119&view=rev
Log:
Created the Structure.test_atomic_fluctuations system test.
This will be used to implement the idea of the structure.atomic_fluctuations
user function.
Modified:
trunk/test_suite/system_tests/structure.py
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27119&r1=27118&r2=27119&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Thu Dec 18 09:11:29 2014
@@ -21,7 +21,8 @@
# Python module imports.
from math import sqrt
-from numpy import array, float64, zeros
+from numpy import array, float64, std, zeros
+from numpy.linalg import norm
from os import sep
from re import search
import sys
@@ -307,6 +308,33 @@
# Load the file, load the spins, and attach the protons.
self.assertRaises(RelaxError, self.interpreter.structure.read_pdb,
'1OGT_trunc.pdb', dir=path)
+
+
+ def test_atomic_fluctuations(self):
+ """Check the operation of the U{structure.rmsd user
function<http://www.nmr-relax.com/manual/structure_rmsd.html>}."""
+
+ # Load the file.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+ self.interpreter.structure.read_pdb('web_of_motion.pdb', dir=path)
+
+ # Run the structure.atomic_fluctuations user function and collect the
results in a dummy file object.
+ file = DummyFileObject()
+ self.interpreter.structure.atomic_fluctuations(atom_id='@N,CA',
file=file, format='text')
+
+ # The fluctuations.
+ n = array([[ 9.464, -9.232, 27.573], [ 9.211, -9.425, 26.970], [
7.761, -6.392, 27.161]], float64)
+ ca = array([[10.302, -8.195, 26.930], [10.077, -8.221, 26.720], [
9.256, -6.332, 27.183]], float64)
+ sd = std(array([norm(n[0] - ca[0]), norm(n[1] - ca[1]), norm(n[2] -
ca[2])], float64), ddof=1)
+ expected = []
+ expected.append("# %18s %20s\n" % (":4@N", ":4@CA"))
+ expected.append("%20.15f %20.15f\n" % (sd, 0.0))
+ expected.append("%20.15f %20.15f\n" % (0.0, sd))
+
+ # Check the file.
+ lines = file.readlines()
+ self.assertEqual(len(expected), len(lines))
+ for i in range(len(lines)):
+ self.assertEqual(expected[i]+'\n', lines[i])
def test_bug_sr_2998_broken_conect_records(self):
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