Author: bugman
Date: Fri Nov 21 19:51:14 2014
New Revision: 26698
URL: http://svn.gna.org/viewcvs/relax?rev=26698&view=rev
Log:
Modified the Frame_order.test_pdb_model_iso_cone_z_axis system test to have a
cone angle.
The cone opening half-angle was previously 0.0. The test now checks the
geometric object in the PDB
file for a cone opening half-angle of 2.0.
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=26698&r1=26697&r2=26698&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 Fri Nov
21 19:51:14 2014
@@ -1810,6 +1810,9 @@
axis_phi = 0.0
print("Rotor axis: %s" % create_rotor_axis_spherical(axis_theta,
axis_phi))
+ # Cone parameters.
+ theta = 2.0
+
# Set the average domain position translation parameters.
self.interpreter.value.set(param='ave_pos_x', val=0.0)
self.interpreter.value.set(param='ave_pos_y', val=0.0)
@@ -1819,17 +1822,28 @@
self.interpreter.value.set(param='ave_pos_gamma', val=0.0)
self.interpreter.value.set(param='axis_theta', val=axis_theta)
self.interpreter.value.set(param='axis_phi', val=axis_phi)
- self.interpreter.value.set(param='cone_theta', val=0.0)
+ self.interpreter.value.set(param='cone_theta', val=theta)
self.interpreter.value.set(param='cone_sigma_max', val=0.0)
# Set the pivot.
self.interpreter.frame_order.pivot(pivot=pivot, fix=True)
# Create the PDB.
- self.interpreter.frame_order.pdb_model(dir=ds.tmpdir, inc=1, size=l)
+ self.interpreter.frame_order.pdb_model(dir=ds.tmpdir, inc=10, size=l)
# The files.
files = ['frame_order_A.pdb', 'frame_order_B.pdb']
+
+ # The xy-plane vectors.
+ inc = 2.0 * pi / 10.0
+ vectors = zeros((10, 3), float64)
+ for i in range(10):
+ # The angle phi.
+ phi = inc * i
+
+ # The xy-plane, starting along the x-axis.
+ vectors[i, 0] = cos(phi)
+ vectors[i, 1] = sin(phi)
# The data, as it should be with everything along the z-axis, shifted
from the origin to the pivot.
neg = [False, True]
@@ -1837,7 +1851,10 @@
data = []
for i in range(2):
data.append([
+ # The pivot.
[ 1, 'PIV', 1, 'Piv', pivot],
+
+ # The rotor.
[ 1, 'RTX', 2, 'CTR', pivot],
[ 2, 'RTX', 3, 'PRP', self.rotate_from_Z(origin=pivot,
length=l_rotor, angle=axis_theta, neg=neg[i])],
[ 3, 'RTB', 4, 'BLO', self.rotate_from_Z(origin=pivot,
length=l_rotor, angle=axis_theta, neg=neg[i])],
@@ -1845,10 +1862,22 @@
[ 5, 'RTB', 368, 'BLO', self.rotate_from_Z(origin=pivot,
length=l_rotor, angle=axis_theta, neg=neg[i])],
[ 6, 'RTB', 550, 'BLO', self.rotate_from_Z(origin=pivot,
length=l_rotor-2.0, angle=axis_theta, neg=neg[i])],
[ 7, 'RTL', 732, 'z-ax', self.rotate_from_Z(origin=pivot,
length=l_rotor+2.0, angle=axis_theta, neg=neg[i])],
+
+ # The cone edge.
[ 3, 'CNE', 733, 'APX', pivot],
- [ 3, 'CNE', 734, 'H2', self.rotate_from_Z(origin=pivot,
length=l, angle=axis_theta, neg=neg[i])],
- [ 4, 'CON', 735, 'H3', self.rotate_from_Z(origin=pivot,
length=l, angle=axis_theta, neg=neg[i])],
- [ 1, 'TLE', 736, tle[i], self.rotate_from_Z(origin=pivot,
length=l+10, angle=axis_theta, neg=neg[i])]
+ [ 3, 'CNE', 734, 'H2', self.rotate_from_Z(origin=pivot,
length=l, angle=theta, axis=vectors[0], neg=neg[i])],
+ [ 3, 'CNE', 735, 'H3', self.rotate_from_Z(origin=pivot,
length=l, angle=theta, axis=vectors[1], neg=neg[i])],
+ [ 3, 'CNE', 736, 'H4', self.rotate_from_Z(origin=pivot,
length=l, angle=theta, axis=vectors[2], neg=neg[i])],
+ [ 3, 'CNE', 737, 'H5', self.rotate_from_Z(origin=pivot,
length=l, angle=theta, axis=vectors[3], neg=neg[i])],
+ [ 3, 'CNE', 738, 'H6', self.rotate_from_Z(origin=pivot,
length=l, angle=theta, axis=vectors[4], neg=neg[i])],
+ [ 3, 'CNE', 739, 'H7', self.rotate_from_Z(origin=pivot,
length=l, angle=theta, axis=vectors[5], neg=neg[i])],
+ [ 3, 'CNE', 740, 'H8', self.rotate_from_Z(origin=pivot,
length=l, angle=theta, axis=vectors[6], neg=neg[i])],
+ [ 3, 'CNE', 741, 'H9', self.rotate_from_Z(origin=pivot,
length=l, angle=theta, axis=vectors[7], neg=neg[i])],
+ [ 3, 'CNE', 742, 'H10', self.rotate_from_Z(origin=pivot,
length=l, angle=theta, axis=vectors[8], neg=neg[i])],
+ [ 3, 'CNE', 743, 'H11', self.rotate_from_Z(origin=pivot,
length=l, angle=theta, axis=vectors[9], neg=neg[i])],
+
+ # Titles.
+ [ 1, 'TLE', 804, tle[i], self.rotate_from_Z(origin=pivot,
length=l+10, angle=axis_theta, neg=neg[i])]
])
# Loop over the representations.
@@ -1867,8 +1896,13 @@
if atom_name == 'BLD':
continue
+ # Skip the cone interior (checking the edge will be
sufficient).
+ if res_name == 'CON':
+ continue
+
# Checks.
print("Checking residue %s %s, atom %s %s, at position %s." %
(data[i][index][0], data[i][index][1], data[i][index][2], data[i][index][3],
data[i][index][4]))
+ print(" to residue %s %s, atom %s %s, at position %s." %
(res_num, res_name, atom_num, atom_name, pos[0]))
self.assertEqual(data[i][index][0], res_num)
self.assertEqual(data[i][index][1], res_name)
self.assertEqual(data[i][index][2], atom_num)
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