Author: bugman
Date: Fri Nov 21 19:19:53 2014
New Revision: 26696
URL: http://svn.gna.org/viewcvs/relax?rev=26696&view=rev
Log:
Created the Frame_order.test_pdb_model_pseudo_ellipse_xz_plane_tilt system
test.
This checks the PDB file created by the frame_order.pdb_model user function
for the pseudo-ellipse
model with a xz-plane tilt. To properly construct the coordinates, the
rotate_from_Z() method was
modified to accept a rotation matrix argument to allow the geometric shape to
be rotated.
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=26696&r1=26695&r2=26696&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 19:19:53 2014
@@ -23,7 +23,7 @@
from math import cos, pi, sin, sqrt
import platform
import numpy
-from numpy import array, float64, transpose, zeros
+from numpy import array, dot, float64, transpose, zeros
from os import sep
from tempfile import mkdtemp
@@ -237,7 +237,7 @@
return string
- def rotate_from_Z(self, origin=origin, length=0.0, angle=0.0,
axis=x_axis, neg=False):
+ def rotate_from_Z(self, origin=origin, length=0.0, angle=0.0,
axis=x_axis, R=None, neg=False):
"""Rotate a vector along Z-axis around the origin.
@keyword origin: The origin of the final vector.
@@ -248,6 +248,8 @@
@type angle: float
@keyword axis: The direction in the xy-plane to rotate the
vector along.
@type axis: numpy 3D, rank-1 array
+ @keyword R: A rotation matrix to be used before adding the
origin.
+ @type R: numpy 3D, rank-2 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.
@@ -268,6 +270,10 @@
if neg:
for i in range(3):
point[i] = -point[i]
+
+ # Rotation.
+ if R != None:
+ point = dot(R, point)
# Extend the length and add the origin.
for i in range(3):
@@ -1836,6 +1842,149 @@
index += 1
+ def test_pdb_model_pseudo_ellipse_xz_plane_tilt(self):
+ """Check the frame_order.pdb_model user function PDB file for the
pseudo-ellipse model with a xz-plane tilt."""
+
+ # Init.
+ pivot = array([1, -2, 1.1], float64)
+ l = 50.0
+ l_rotor = l + 5.0
+
+ # Create a data pipe.
+ self.interpreter.pipe.create(pipe_name='PDB model', pipe_type='frame
order')
+
+ # Select the model.
+ self.interpreter.frame_order.select_model('pseudo-ellipse')
+
+ # The axis parameters, and printout.
+ eigen_alpha = 0.0
+ eigen_beta = -pi/2.0
+ eigen_gamma = 0.0
+ R = zeros((3, 3), float64)
+ euler_to_R_zyz(eigen_alpha, eigen_beta, eigen_gamma, R)
+ print("Motional eigenframe:\n%s" % R)
+
+ # Cone parameters.
+ theta_x = 2.0
+ theta_y = 0.1
+
+ # 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)
+ self.interpreter.value.set(param='ave_pos_z', val=0.0)
+ self.interpreter.value.set(param='ave_pos_alpha', val=0.0)
+ self.interpreter.value.set(param='ave_pos_beta', val=0.0)
+ self.interpreter.value.set(param='ave_pos_gamma', val=0.0)
+ self.interpreter.value.set(param='eigen_alpha', val=eigen_alpha)
+ self.interpreter.value.set(param='eigen_beta', val=eigen_beta)
+ self.interpreter.value.set(param='eigen_gamma', val=eigen_gamma)
+ self.interpreter.value.set(param='cone_theta_x', val=theta_x)
+ self.interpreter.value.set(param='cone_theta_y', val=theta_y)
+ 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=10, size=l)
+
+ # The files.
+ files = ['frame_order_A.pdb', 'frame_order_B.pdb']
+
+ # The xy-plane vectors and angles.
+ inc = 2.0 * pi / 10.0
+ vectors = zeros((10, 3), float64)
+ theta_max = zeros(10, 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 cone opening angle.
+ theta_max[i] = theta_x * theta_y / sqrt((cos(phi)*theta_y)**2 +
(sin(phi)*theta_x)**2)
+
+ # The data, as it should be with everything along the z-axis,
shifted from the origin to the pivot.
+ neg = [False, True]
+ tle = ['a', 'b']
+ 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=eigen_beta, neg=neg[i])],
+ [ 3, 'RTB', 4, 'BLO', self.rotate_from_Z(origin=pivot,
length=l_rotor, angle=eigen_beta, neg=neg[i])],
+ [ 4, 'RTB', 186, 'BLO', self.rotate_from_Z(origin=pivot,
length=l_rotor-2.0, angle=eigen_beta, neg=neg[i])],
+ [ 5, 'RTB', 368, 'BLO', self.rotate_from_Z(origin=pivot,
length=l_rotor, angle=eigen_beta, neg=neg[i])],
+ [ 6, 'RTB', 550, 'BLO', self.rotate_from_Z(origin=pivot,
length=l_rotor-2.0, angle=eigen_beta, neg=neg[i])],
+ [ 7, 'RTL', 732, 'z-ax', self.rotate_from_Z(origin=pivot,
length=l_rotor+2.0, angle=eigen_beta, neg=neg[i])],
+
+ # The axis system.
+ [ 1, 'AXE', 733, 'R', pivot],
+ [ 2, 'AXE', 734, 'R', pivot],
+ [ 2, 'AXE', 735, 'x-ax', self.rotate_from_Z(origin=pivot,
length=l, angle=pi/2.0+eigen_beta, neg=neg[i])],
+ [ 2, 'AXE', 736, 'x-ax', self.rotate_from_Z(origin=pivot,
length=l*1.1, angle=pi/2.0+eigen_beta, neg=neg[i])],
+ [ 2, 'AXE', 737, 'R', pivot],
+ [ 2, 'AXE', 738, 'y-ax', self.rotate_from_Z(origin=pivot,
length=l, angle=pi/2.0, axis=y_axis, neg=neg[i])],
+ [ 2, 'AXE', 739, 'y-ax', self.rotate_from_Z(origin=pivot,
length=l*1.1, angle=pi/2.0, axis=y_axis, neg=neg[i])],
+
+ # The cone edge.
+ [ 3, 'CNE', 740, 'APX', pivot],
+ [ 3, 'CNE', 741, 'H2', self.rotate_from_Z(origin=pivot,
length=l, angle=theta_max[0], axis=vectors[0], R=R, neg=neg[i])],
+ [ 3, 'CNE', 742, 'H3', self.rotate_from_Z(origin=pivot,
length=l, angle=theta_max[1], axis=vectors[1], R=R, neg=neg[i])],
+ [ 3, 'CNE', 743, 'H4', self.rotate_from_Z(origin=pivot,
length=l, angle=theta_max[2], axis=vectors[2], R=R, neg=neg[i])],
+ [ 3, 'CNE', 744, 'H5', self.rotate_from_Z(origin=pivot,
length=l, angle=theta_max[3], axis=vectors[3], R=R, neg=neg[i])],
+ [ 3, 'CNE', 745, 'H6', self.rotate_from_Z(origin=pivot,
length=l, angle=theta_max[4], axis=vectors[4], R=R, neg=neg[i])],
+ [ 3, 'CNE', 746, 'H7', self.rotate_from_Z(origin=pivot,
length=l, angle=theta_max[5], axis=vectors[5], R=R, neg=neg[i])],
+ [ 3, 'CNE', 747, 'H8', self.rotate_from_Z(origin=pivot,
length=l, angle=theta_max[6], axis=vectors[6], R=R, neg=neg[i])],
+ [ 3, 'CNE', 748, 'H9', self.rotate_from_Z(origin=pivot,
length=l, angle=theta_max[7], axis=vectors[7], R=R, neg=neg[i])],
+ [ 3, 'CNE', 749, 'H10', self.rotate_from_Z(origin=pivot,
length=l, angle=theta_max[8], axis=vectors[8], R=R, neg=neg[i])],
+ [ 3, 'CNE', 750, 'H11', self.rotate_from_Z(origin=pivot,
length=l, angle=theta_max[9], axis=vectors[9], R=R, neg=neg[i])],
+
+ # Titles.
+ [ 1, 'TLE', 811, tle[i], self.rotate_from_Z(origin=pivot,
length=l+10, angle=eigen_beta, neg=neg[i])]
+ ])
+
+ # Loop over the representations.
+ for i in range(2):
+ # Delete all structural data.
+ self.interpreter.structure.delete()
+
+ # Read the contents of the file.
+ self.interpreter.structure.read_pdb(file=files[i], dir=ds.tmpdir)
+
+ # Check the atomic coordinates.
+ selection = cdp.structure.selection()
+ index = 0
+ for res_num, res_name, atom_num, atom_name, pos in
cdp.structure.atom_loop(selection=selection, res_num_flag=True,
res_name_flag=True, atom_num_flag=True, atom_name_flag=True, pos_flag=True):
+ # Skip the propeller blades.
+ 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)
+ self.assertEqual(data[i][index][3], atom_name)
+ self.assertAlmostEqual(data[i][index][4][0], pos[0][0], 3)
+ self.assertAlmostEqual(data[i][index][4][1], pos[0][1], 3)
+ self.assertAlmostEqual(data[i][index][4][2], pos[0][2], 3)
+
+ # Increment the index.
+ index += 1
+
+
def test_pdb_model_pseudo_ellipse_z_axis(self):
"""Check the frame_order.pdb_model user function PDB file for the
pseudo-ellipse model along the z-axis."""
r26696 - /branches/frame_order_cleanup/test_suite/system_tests/frame_order.py