Author: bugman
Date: Mon Dec 22 09:09:57 2014
New Revision: 27149
URL: http://svn.gna.org/viewcvs/relax?rev=27149&view=rev
Log:
Created the Structure.test_atomic_fluctuations_parallax system test.
This is to demonstrate that the parallax shift fluctuations are not implemented
correctly.
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=27149&r1=27148&r2=27149&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Mon Dec 22 09:09:57 2014
@@ -21,7 +21,7 @@
# Python module imports.
from math import sqrt
-from numpy import array, average, float64, std, zeros
+from numpy import array, average, dot, float64, std, zeros
from numpy.linalg import norm
from os import sep
from re import search
@@ -446,6 +446,54 @@
for i in range(len(lines)):
self.assertEqual(script[i], lines[i])
+
+ def test_atomic_fluctuations_parallax(self):
+ """Check the parallax shift fluctuations calculated by the
structure.atomic_fluctuations user function.
+
+ This checks the text file (with the format argument set to text) of
interatomic parallax shift fluctuations calculated by the
U{structure.atomic_fluctuations user
function<http://www.nmr-relax.com/manual/structure_atomic_fluctuations.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(measure='parallax
shift', atom_id='@N,CA', file=file, format='text')
+
+ # The atom positions.
+ 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)
+
+ # The interatom vectors.
+ vectors = ca - n
+
+ # The inter-vector projections to the average.
+ vect_ave = average(vectors, axis=0)
+ unit = vect_ave / norm(vect_ave)
+ proj = [
+ dot(vectors[0], unit) * unit,
+ dot(vectors[1], unit) * unit,
+ dot(vectors[2], unit) * unit
+ ]
+ shift = [
+ vectors[0] - proj[0],
+ vectors[1] - proj[1],
+ vectors[2] - proj[2]
+ ]
+
+ # The fluctuations.
+ sd = std(array(shift, float64), ddof=1)
+ expected = []
+ expected.append("# %18s %20s\n" % (":4@N", ":4@CA"))
+ expected.append("%20.15f %20.15f\n" % (0.0, sd))
+ expected.append("%20.15f %20.15f\n" % (sd, 0.0))
+
+ # Check the file.
+ lines = file.readlines()
+ self.assertEqual(len(expected), len(lines))
+ for i in range(len(lines)):
+ self.assertEqual(expected[i], lines[i])
def test_bug_sr_2998_broken_conect_records(self):
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