Author: bugman
Date: Fri Dec 19 11:01:02 2014
New Revision: 27143
URL: http://svn.gna.org/viewcvs/relax?rev=27143&view=rev
Log:
Created the Structure.test_atomic_fluctuations_angle system test.
This will be used to implement the mapping of inter-atomic vector angular
fluctuations between
structures via a new 'measure' keyword argument for 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=27143&r1=27142&r2=27143&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Fri Dec 19 11:01:02 2014
@@ -21,7 +21,7 @@
# Python module imports.
from math import sqrt
-from numpy import array, float64, std, zeros
+from numpy import array, average, float64, std, zeros
from numpy.linalg import norm
from os import sep
from re import search
@@ -31,8 +31,9 @@
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from pipe_control.mol_res_spin import count_spins, return_spin, spin_loop
+from lib.errors import RelaxError, RelaxNoPdbError
from lib.geometry.rotations import axis_angle_to_R, euler_to_R_zyz
-from lib.errors import RelaxError, RelaxNoPdbError
+from lib.geometry.vectors import vector_angle_acos
from lib.io import DummyFileObject
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
@@ -328,6 +329,49 @@
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" % (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_atomic_fluctuations_angle(self):
+ """Check the angular fluctuations calculated by the
structure.atomic_fluctuations user function.
+
+ This checks the text file (with the format argument set to text) of
interatomic angle 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='angles',
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 angles to the average.
+ vect_ave = average(vectors, axis=0)
+ angles = [
+ vector_angle_acos(vect_ave, vectors[0]),
+ vector_angle_acos(vect_ave, vectors[1]),
+ vector_angle_acos(vect_ave, vectors[2])
+ ]
+
+ # The fluctuations.
+ sd = std(array(angles, float64), ddof=1)
expected = []
expected.append("# %18s %20s\n" % (":4@N", ":4@CA"))
expected.append("%20.15f %20.15f\n" % (0.0, sd))
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