Author: bugman
Date: Thu Nov 27 16:27:21 2014
New Revision: 26784
URL: http://svn.gna.org/viewcvs/relax?rev=26784&view=rev
Log:
Created an initial version of the Frame_order.test_simulate_rotor_z_axis
system test.
This is to check the frame_order.simulate user function rotor model along the
z-axis. It currently
fails due to a bug in the user function.
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=26784&r1=26783&r2=26784&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 Thu
Nov 27 16:27:21 2014
@@ -23,7 +23,7 @@
from math import cos, pi, sin, sqrt
import platform
import numpy
-from numpy import array, dot, float64, transpose, zeros
+from numpy import array, dot, eye, float64, transpose, zeros
from os import sep
from tempfile import mkdtemp
@@ -32,6 +32,7 @@
import dep_check
from lib.frame_order.conversions import create_rotor_axis_alpha,
create_rotor_axis_spherical
from lib.frame_order.variables import MODEL_DOUBLE_ROTOR, MODEL_FREE_ROTOR,
MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR, MODEL_ISO_CONE_TORSIONLESS,
MODEL_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_RIGID,
MODEL_ROTOR
+from lib.geometry.coord_transform import cartesian_to_spherical
from lib.geometry.rotations import axis_angle_to_R, euler_to_R_zyz,
R_to_euler_zyz
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
@@ -388,6 +389,20 @@
# Create a data pipe.
self.interpreter.pipe.create(pipe_name='PDB model', pipe_type='frame
order')
+ # Convert the pivot to a numpy array.
+ pivot = array(pivot)
+
+ # The 3 atomic positions.
+ atom_pos = 100.0 * eye(3)
+
+ # Create a single atom structure.
+ self.interpreter.structure.add_atom(mol_name='axes', atom_name='N',
res_name='X', res_num=1, pos=atom_pos[0]+pivot, element='N')
+ self.interpreter.structure.add_atom(mol_name='axes', atom_name='N',
res_name='Y', res_num=2, pos=atom_pos[1]+pivot, element='N')
+ self.interpreter.structure.add_atom(mol_name='axes', atom_name='N',
res_name='Z', res_num=3, pos=atom_pos[2]+pivot, element='N')
+
+ # Set up the moving domain.
+ self.interpreter.domain(id='X', spin_id=':1')
+
# Select the model.
self.interpreter.frame_order.select_model(model)
@@ -3159,6 +3174,69 @@
self.assertAlmostEqual(cdp.chi2, 0.011377487066752203, 5)
+ def test_simulate_rotor_z_axis(self):
+ """Check the frame_order.simulate user function PDB file for the
rotor model along the z-axis."""
+
+ # Init.
+ cone_sigma_max = 0.3
+ pivot = array([1, 0, 0], float64)
+ l = 30.0
+ sim_num = 500
+
+ # The axis alpha parameter, and printout.
+ axis_alpha = pi / 2.0
+ axis = create_rotor_axis_alpha(pi/2, pivot, array([0, 0, 0],
float64))
+ print("\nRotor axis: %s" % axis)
+ print("Rotor apex (100*axis + [1, 0, 0]):\n %s" % (l*axis +
pivot))
+
+ # Set up.
+ self.setup_model(pipe_name='PDB model', model='rotor', pivot=pivot,
ave_pos_x=0.0, ave_pos_y=0.0, ave_pos_z=0.0, ave_pos_alpha=0.0,
ave_pos_beta=0.0, ave_pos_gamma=0.0, axis_alpha=axis_alpha,
cone_sigma_max=cone_sigma_max)
+
+ # Create the PDB.
+ self.interpreter.frame_order.simulate(file='simulation.pdb',
dir=ds.tmpdir, step_size=10.0, snapshot=10, total=sim_num)
+
+ # Delete all structural data.
+ self.interpreter.structure.delete()
+
+ # Read the contents of the file.
+ self.interpreter.structure.read_pdb(file='simulation.pdb',
dir=ds.tmpdir)
+
+ # Check the atomic coordinates.
+ selection = cdp.structure.selection()
+ 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):
+ # Loop over all positions.
+ for i in range(sim_num):
+ # Shift the position back to the origin, and decompose into
spherical coordinates.
+ new_pos = pos[i] - pivot
+ r, theta, phi = cartesian_to_spherical(new_pos)
+
+ # Printout.
+ print("Checking residue %s %s, atom %s %s, at shifted
position %s, with spherical coordinates %s." % (res_num, res_name, atom_num,
atom_name, new_pos, [r, theta, phi]))
+
+ # The vector length.
+ self.assertAlmostEqual(r, 100.0, 3)
+
+ # Check the X vector.
+ if res_name == 'X':
+ self.assertAlmostEqual(theta, pi/2.0, 3)
+ self.assert_(phi >= -cone_sigma_max)
+ self.assert_(phi <= cone_sigma_max)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the Y vector.
+ elif res_name == 'Y':
+ self.assertAlmostEqual(theta, pi/2.0, 3)
+ self.assert_(phi-pi/2.0 >= -cone_sigma_max)
+ self.assert_(phi-pi/2.0 <= cone_sigma_max)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the Z vector (should not move).
+ elif res_name == 'Z':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 100.0, 3)
+
+
def test_sobol_setup(self):
"""Check the basic operation of the frame_order.sobol_setup user
function."""
r26784 - /branches/frame_order_cleanup/test_suite/system_tests/frame_order.py