Author: bugman
Date: Fri Nov 21 15:00:10 2014
New Revision: 26690
URL: http://svn.gna.org/viewcvs/relax?rev=26690&view=rev
Log:
Improvements for all of the Frame_order.test_pdb_model_* system tests.
The rotate_from_Z() method has been introduced to simplify the determination of
the 3D coordinates
expected for the PDB file. This will allow for more advanced testing of the
PDB for the cone
models.
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=26690&r1=26689&r2=26690&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 15:00:10 2014
@@ -20,10 +20,10 @@
###############################################################################
# Python module imports.
-from math import pi, sqrt
+from math import cos, pi, sin, sqrt
import platform
import numpy
-from numpy import array, float64, transpose
+from numpy import array, float64, transpose, zeros
from os import sep
from tempfile import mkdtemp
@@ -55,6 +55,12 @@
# Set the system to 'Windows' no matter what.
SYSTEM = 'Windows'
+
+# Some vectors.
+x_axis = array([1, 0, 0], float64)
+y_axis = array([0, 1, 0], float64)
+z_axis = array([0, 0, 1], float64)
+origin = array([0, 0, 0], float64)
class Frame_order(SystemTestCase):
@@ -136,6 +142,46 @@
status.skipped_tests.append([methodName, 'Scipy', self._skip_type])
+ def rotate_from_Z(self, origin=origin, length=0.0, angle=0.0, axis=x_axis,
neg=False):
+ """Rotate a vector along Z-axis around the origin.
+
+ @keyword origin: The origin of the final vector.
+ @type origin: numpy 3D, rank-1 array
+ @keyword length: The length of the Z-vector to rotate.
+ @type length: float
+ @keyword angle: The angle in rad to rotate by.
+ @type angle: float
+ @keyword axis: The direction in the xy-plane to rotate the vector
along.
+ @type axis: numpy 3D, rank-1 array
+ @keyword neg: A flag which if True causes the negative Z-axis to
be used.
+ @type neg: bool
+ @return: The final rotated vector shifted by the origin.
+ @rtype: numpy 3D, rank-1 array
+ """
+
+ # The final point.
+ point = zeros(3, float64)
+
+ # Z-axis reduction.
+ point[2] = cos(angle)
+
+ # The X and Y-axis increases.
+ point[0] = axis[0]*sin(angle)
+ point[1] = axis[1]*sin(angle)
+
+ # Inversion.
+ if neg:
+ for i in range(3):
+ point[i] = -point[i]
+
+ # Extend the length and add the origin.
+ for i in range(3):
+ point[i] = point[i]*length + origin[i]
+
+ # Return the point.
+ return point
+
+
def setUp(self):
"""Set up for all the functional tests."""
@@ -1613,12 +1659,10 @@
def test_pdb_model_iso_cone_z_axis(self):
"""Check the frame_order.pdb_model user function PDB file for the
isotropic cone model along the z-axis."""
- # Lengths.
+ # Init.
+ pivot = array([1, 0, -2], float64)
l = 25.0
l_rotor = l + 5.0
- l_in = l_rotor - 2.0
- l_out = l_rotor + 2.0
- label = l + 10.0
# Create a data pipe.
self.interpreter.pipe.create(pipe_name='PDB model', pipe_type='frame
order')
@@ -1644,7 +1688,7 @@
self.interpreter.value.set(param='cone_sigma_max', val=0.0)
# Set the pivot.
- self.interpreter.frame_order.pivot(pivot=[1, 0, 0], fix=True)
+ 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)
@@ -1653,33 +1697,24 @@
files = ['frame_order_A.pdb', 'frame_order_B.pdb']
# The data, as it should be with everything along the z-axis, shifted
from the origin to the pivot.
- data = [[
- [ 1, 'PIV', 1, 'Piv', [1.0, 0.0, 0.0]],
- [ 1, 'RTX', 2, 'CTR', [1.0, 0.0, 0.0]],
- [ 2, 'RTX', 3, 'PRP', [1.0, 0.0, l_rotor]],
- [ 3, 'RTB', 4, 'BLO', [1.0, 0.0, l_rotor]],
- [ 4, 'RTB', 186, 'BLO', [1.0, 0.0, l_in]],
- [ 5, 'RTB', 368, 'BLO', [1.0, 0.0, l_rotor]],
- [ 6, 'RTB', 550, 'BLO', [1.0, 0.0, l_in]],
- [ 7, 'RTL', 732, 'z-ax', [1.0, 0.0, l_out]],
- [ 3, 'CNE', 733, 'APX', [1.0, 0.0, 0.0]],
- [ 3, 'CNE', 734, 'H2', [1.0, 0.0, l]],
- [ 4, 'CON', 735, 'H3', [1.0, 0.0, l]],
- [ 1, 'TLE', 736, 'a', [1.0, 0.0, label]],
- ], [
- [ 1, 'PIV', 1, 'Piv', [1.0, 0.0, 0.0]],
- [ 1, 'RTX', 2, 'CTR', [1.0, 0.0, 0.0]],
- [ 2, 'RTX', 3, 'PRP', [1.0, 0.0, -l_rotor]],
- [ 3, 'RTB', 4, 'BLO', [1.0, 0.0, -l_rotor]],
- [ 4, 'RTB', 186, 'BLO', [1.0, 0.0, -l_in]],
- [ 5, 'RTB', 368, 'BLO', [1.0, 0.0, -l_rotor]],
- [ 6, 'RTB', 550, 'BLO', [1.0, 0.0, -l_in]],
- [ 7, 'RTL', 732, 'z-ax', [1.0, 0.0, -l_out]],
- [ 3, 'CNE', 733, 'APX', [1.0, 0.0, 0.0]],
- [ 3, 'CNE', 734, 'H2', [1.0, 0.0, -l]],
- [ 4, 'CON', 735, 'H3', [1.0, 0.0, -l]],
- [ 1, 'TLE', 736, 'b', [1.0, 0.0, -label]],
- ]]
+ neg = [False, True]
+ tle = ['a', 'b']
+ data = []
+ for i in range(2):
+ data.append([
+ [ 1, 'PIV', 1, 'Piv', pivot],
+ [ 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])],
+ [ 4, 'RTB', 186, 'BLO', self.rotate_from_Z(origin=pivot,
length=l_rotor-2.0, angle=axis_theta, neg=neg[i])],
+ [ 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])],
+ [ 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])]
+ ])
# Loop over the representations.
for i in range(2):
@@ -1714,13 +1749,10 @@
def test_pdb_model_iso_cone_xz_plane_tilt(self):
"""Check the frame_order.pdb_model user function PDB file for the
isotropic cone model with a xz-plane tilt."""
- # Lengths.
+ # Init.
+ pivot = array([1, 1, 1], float64)
l = 45.0
- proj = sqrt(0.5*l**2)
- l_rotor = sqrt(0.5*(l + 5.0)**2)
- l_in = sqrt(0.5*(l + 5.0 - 2.0)**2)
- l_out = sqrt(0.5*(l + 5.0 + 2.0)**2)
- label = sqrt(0.5*(l + 10.0)**2)
+ l_rotor = l + 5.0
# Create a data pipe.
self.interpreter.pipe.create(pipe_name='PDB model', pipe_type='frame
order')
@@ -1746,7 +1778,7 @@
self.interpreter.value.set(param='cone_sigma_max', val=0.0)
# Set the pivot.
- self.interpreter.frame_order.pivot(pivot=[1, 1, 1], fix=True)
+ 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)
@@ -1755,33 +1787,24 @@
files = ['frame_order_A.pdb', 'frame_order_B.pdb']
# The data, as it should be with everything along the z-axis, shifted
from the origin to the pivot.
- data = [[
- [ 1, 'PIV', 1, 'Piv', [ 1.0, 1.0, 1.0]],
- [ 1, 'RTX', 2, 'CTR', [ 1.0, 1.0, 1.0]],
- [ 2, 'RTX', 3, 'PRP', [-l_rotor+1.0, 1.0, l_rotor+1.0]],
- [ 3, 'RTB', 4, 'BLO', [-l_rotor+1.0, 1.0, l_rotor+1.0]],
- [ 4, 'RTB', 186, 'BLO', [-l_in+1.0, 1.0, l_in+1.0]],
- [ 5, 'RTB', 368, 'BLO', [-l_rotor+1.0, 1.0, l_rotor+1.0]],
- [ 6, 'RTB', 550, 'BLO', [-l_in+1.0, 1.0, l_in+1.0]],
- [ 7, 'RTL', 732, 'z-ax', [-l_out+1.0, 1.0, l_out+1.0]],
- [ 3, 'CNE', 733, 'APX', [ 1.0, 1.0, 1.0]],
- [ 3, 'CNE', 734, 'H2', [-proj+1.0, 1.0, proj+1.0]],
- [ 4, 'CON', 735, 'H3', [-proj+1.0, 1.0, proj+1.0]],
- [ 1, 'TLE', 736, 'a', [-label+1.0, 1.0, label+1.0]],
- ], [
- [ 1, 'PIV', 1, 'Piv', [ 1.0, 1.0, 1.0]],
- [ 1, 'RTX', 2, 'CTR', [ 1.0, 1.0, 1.0]],
- [ 2, 'RTX', 3, 'PRP', [ l_rotor+1.0, 1.0, -l_rotor+1.0]],
- [ 3, 'RTB', 4, 'BLO', [ l_rotor+1.0, 1.0, -l_rotor+1.0]],
- [ 4, 'RTB', 186, 'BLO', [ l_in+1.0, 1.0, -l_in+1.0]],
- [ 5, 'RTB', 368, 'BLO', [ l_rotor+1.0, 1.0, -l_rotor+1.0]],
- [ 6, 'RTB', 550, 'BLO', [ l_in+1.0, 1.0, -l_in+1.0]],
- [ 7, 'RTL', 732, 'z-ax', [ l_out+1.0, 1.0, -l_out+1.0]],
- [ 3, 'CNE', 733, 'APX', [ 1.0, 1.0, 1.0]],
- [ 3, 'CNE', 734, 'H2', [ proj+1.0, 1.0, -proj+1.0]],
- [ 4, 'CON', 735, 'H3', [ proj+1.0, 1.0, -proj+1.0]],
- [ 1, 'TLE', 736, 'b', [ label+1.0, 1.0, -label+1.0]],
- ]]
+ neg = [False, True]
+ tle = ['a', 'b']
+ data = []
+ for i in range(2):
+ data.append([
+ [ 1, 'PIV', 1, 'Piv', pivot],
+ [ 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])],
+ [ 4, 'RTB', 186, 'BLO', self.rotate_from_Z(origin=pivot,
length=l_rotor-2.0, angle=axis_theta, neg=neg[i])],
+ [ 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])],
+ [ 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])]
+ ])
# Loop over the representations.
for i in range(2):
@@ -1816,10 +1839,9 @@
def test_pdb_model_rotor_z_axis(self):
"""Check the frame_order.pdb_model user function PDB file for the
rotor model along the z-axis."""
- # Lengths.
+ # Init.
+ pivot = array([1, 0, 0], float64)
l = 30.0
- l2 = l - 2.0
- l3 = l + 2.0
# Create a data pipe.
self.interpreter.pipe.create(pipe_name='PDB model', pipe_type='frame
order')
@@ -1829,7 +1851,8 @@
# The axis alpha parameter, and printout.
axis_alpha = pi / 2.0
- print("Rotor axis: %s" % create_rotor_axis_alpha(pi/2, array([1, 0,
0], float64), array([0, 0, 0], float64)))
+ print("\nRotor axis: %s" % create_rotor_axis_alpha(pi/2, pivot,
array([0, 0, 0], float64)))
+ print("Rotor apex (100*axis + [1, 0, 0]):\n %s" % (100.0*axis +
pivot))
# Set the average domain position translation parameters.
self.interpreter.value.set(param='ave_pos_x', val=0.0)
@@ -1842,7 +1865,7 @@
self.interpreter.value.set(param='cone_sigma_max', val=0.0)
# Set the pivot.
- self.interpreter.frame_order.pivot(pivot=[1, 0, 0], fix=True)
+ 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)
@@ -1856,20 +1879,20 @@
# The data, as it should be with everything along the z-axis, shifted
from the origin to the pivot.
data = [
- [ 1, 'PIV', 1, 'Piv', [1.0, 0.0, 0.0]],
- [ 1, 'RTX', 2, 'CTR', [1.0, 0.0, 0.0]],
- [ 2, 'RTX', 3, 'PRP', [1.0, 0.0, l]],
- [ 3, 'RTX', 4, 'PRP', [1.0, 0.0, -l]],
- [ 4, 'RTB', 5, 'BLO', [1.0, 0.0, l]],
- [ 5, 'RTB', 187, 'BLO', [1.0, 0.0, l2]],
- [ 6, 'RTB', 369, 'BLO', [1.0, 0.0, l]],
- [ 7, 'RTB', 551, 'BLO', [1.0, 0.0, l2]],
- [ 8, 'RTB', 733, 'BLO', [1.0, 0.0, -l]],
- [ 9, 'RTB', 915, 'BLO', [1.0, 0.0, -l2]],
- [10, 'RTB', 1097, 'BLO', [1.0, 0.0, -l]],
- [11, 'RTB', 1279, 'BLO', [1.0, 0.0, -l2]],
- [12, 'RTL', 1461, 'z-ax', [1.0, 0.0, l3]],
- [12, 'RTL', 1462, 'z-ax', [1.0, 0.0, -l3]]
+ [ 1, 'PIV', 1, 'Piv', pivot],
+ [ 1, 'RTX', 2, 'CTR', pivot],
+ [ 2, 'RTX', 3, 'PRP', self.rotate_from_Z(origin=pivot,
length=l, angle=0.0)],
+ [ 3, 'RTX', 4, 'PRP', self.rotate_from_Z(origin=pivot,
length=l, angle=0.0, neg=True)],
+ [ 4, 'RTB', 5, 'BLO', self.rotate_from_Z(origin=pivot,
length=l, angle=0.0)],
+ [ 5, 'RTB', 187, 'BLO', self.rotate_from_Z(origin=pivot,
length=l-2.0, angle=0.0)],
+ [ 6, 'RTB', 369, 'BLO', self.rotate_from_Z(origin=pivot,
length=l, angle=0.0)],
+ [ 7, 'RTB', 551, 'BLO', self.rotate_from_Z(origin=pivot,
length=l-2.0, angle=0.0)],
+ [ 8, 'RTB', 733, 'BLO', self.rotate_from_Z(origin=pivot,
length=l, angle=0.0, neg=True)],
+ [ 9, 'RTB', 915, 'BLO', self.rotate_from_Z(origin=pivot,
length=l-2.0, angle=0.0, neg=True)],
+ [10, 'RTB', 1097, 'BLO', self.rotate_from_Z(origin=pivot,
length=l, angle=0.0, neg=True)],
+ [11, 'RTB', 1279, 'BLO', self.rotate_from_Z(origin=pivot,
length=l-2.0, angle=0.0, neg=True)],
+ [12, 'RTL', 1461, 'z-ax', self.rotate_from_Z(origin=pivot,
length=l+2.0, angle=0.0)],
+ [12, 'RTL', 1462, 'z-ax', self.rotate_from_Z(origin=pivot,
length=l+2.0, angle=0.0, neg=True)]
]
# Check the atomic coordinates.
@@ -1897,6 +1920,10 @@
def test_pdb_model_rotor_xz_plane_tilt(self):
"""Check the frame_order.pdb_model user function PDB file for the
rotor model with a xz-plane tilt."""
+ # Init.
+ pivot = array([1, 0, 1], float64)
+ l = 100.0
+
# Create a data pipe.
self.interpreter.pipe.create(pipe_name='PDB model', pipe_type='frame
order')
@@ -1905,9 +1932,9 @@
# The axis alpha parameter, and printout.
axis_alpha = pi / 2.0
- axis = create_rotor_axis_alpha(pi/2, array([1, 0, 1], float64),
array([0, 0, 0], float64))
+ axis = create_rotor_axis_alpha(pi/2, pivot, array([0, 0, 0], float64))
print("\nRotor axis:\n %s" % axis)
- print("Rotor apex (100*axis + [1, 0, 1]):\n %s" % (100.0*axis +
[1.0, 0.0, 1.0]))
+ print("Rotor apex (100*axis + [1, 0, 1]):\n %s" % (100.0*axis +
pivot))
# Set the average domain position translation parameters.
self.interpreter.value.set(param='ave_pos_x', val=0.0)
@@ -1920,7 +1947,7 @@
self.interpreter.value.set(param='cone_sigma_max', val=0.0)
# Set the pivot.
- self.interpreter.frame_order.pivot(pivot=[1, 0, 1], fix=True)
+ self.interpreter.frame_order.pivot(pivot=pivot, fix=True)
# Create the PDB.
self.interpreter.frame_order.pdb_model(dir=ds.tmpdir, inc=1,
size=100.0)
@@ -1933,25 +1960,21 @@
self.interpreter.structure.read_pdb(file='frame_order.pdb',
dir=ds.tmpdir)
# The data, as it should be with everything along the z-axis, shifted
from the origin to the pivot.
- l = 100.0
- proj = sqrt(0.5*l**2)
- proj2 = sqrt(0.5*(l-2.0)**2)
- proj3 = sqrt(0.5*(l+2.0)**2)
data = [
- [ 1, 'PIV', 1, 'Piv', [ 1.0, 0.0, 1.0]],
- [ 1, 'RTX', 2, 'CTR', [ 1.0, 0.0, 1.0]],
- [ 2, 'RTX', 3, 'PRP', [-proj+1.0, 0.0, proj+1.0]],
- [ 3, 'RTX', 4, 'PRP', [ proj+1.0, 0.0, -proj+1.0]],
- [ 4, 'RTB', 5, 'BLO', [-proj+1.0, 0.0, proj+1.0]],
- [ 5, 'RTB', 187, 'BLO', [-proj2+1.0, 0.0, proj2+1.0]],
- [ 6, 'RTB', 369, 'BLO', [-proj+1.0, 0.0, proj+1.0]],
- [ 7, 'RTB', 551, 'BLO', [-proj2+1.0, 0.0, proj2+1.0]],
- [ 8, 'RTB', 733, 'BLO', [ proj+1.0, 0.0, -proj+1.0]],
- [ 9, 'RTB', 915, 'BLO', [ proj2+1.0, 0.0, -proj2+1.0]],
- [10, 'RTB', 1097, 'BLO', [ proj+1.0, 0.0, -proj+1.0]],
- [11, 'RTB', 1279, 'BLO', [ proj2+1.0, 0.0, -proj2+1.0]],
- [12, 'RTL', 1461, 'z-ax', [-proj3+1.0, 0.0, proj3+1.0]],
- [12, 'RTL', 1462, 'z-ax', [ proj3+1.0, 0.0, -proj3+1.0]]
+ [ 1, 'PIV', 1, 'Piv', pivot],
+ [ 1, 'RTX', 2, 'CTR', pivot],
+ [ 2, 'RTX', 3, 'PRP', self.rotate_from_Z(origin=pivot,
length=l, angle=-pi/4.0)],
+ [ 3, 'RTX', 4, 'PRP', self.rotate_from_Z(origin=pivot,
length=l, angle=-pi/4.0, neg=True)],
+ [ 4, 'RTB', 5, 'BLO', self.rotate_from_Z(origin=pivot,
length=l, angle=-pi/4.0)],
+ [ 5, 'RTB', 187, 'BLO', self.rotate_from_Z(origin=pivot,
length=l-2.0, angle=-pi/4.0)],
+ [ 6, 'RTB', 369, 'BLO', self.rotate_from_Z(origin=pivot,
length=l, angle=-pi/4.0)],
+ [ 7, 'RTB', 551, 'BLO', self.rotate_from_Z(origin=pivot,
length=l-2.0, angle=-pi/4.0)],
+ [ 8, 'RTB', 733, 'BLO', self.rotate_from_Z(origin=pivot,
length=l, angle=-pi/4.0, neg=True)],
+ [ 9, 'RTB', 915, 'BLO', self.rotate_from_Z(origin=pivot,
length=l-2.0, angle=-pi/4.0, neg=True)],
+ [10, 'RTB', 1097, 'BLO', self.rotate_from_Z(origin=pivot,
length=l, angle=-pi/4.0, neg=True)],
+ [11, 'RTB', 1279, 'BLO', self.rotate_from_Z(origin=pivot,
length=l-2.0, angle=-pi/4.0, neg=True)],
+ [12, 'RTL', 1461, 'z-ax', self.rotate_from_Z(origin=pivot,
length=l+2.0, angle=-pi/4.0)],
+ [12, 'RTL', 1462, 'z-ax', self.rotate_from_Z(origin=pivot,
length=l+2.0, angle=-pi/4.0, neg=True)]
]
# Check the atomic coordinates.
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