Author: bugman
Date: Wed Dec 3 11:09:52 2014
New Revision: 26913
URL: http://svn.gna.org/viewcvs/relax?rev=26913&view=rev
Log:
Expanded all of the Frame_order.test_simulate_* system tests.
Two atoms have been added to the origin [0, 0, 0], one in the moving domain,
the other in the
reference non-moving domain. The positions of these atoms are checked to
make sure that the domain
systems are correctly handled.
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=26913&r1=26912&r2=26913&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 Wed
Dec 3 11:09:52 2014
@@ -389,7 +389,7 @@
# Create a data pipe.
self.interpreter.pipe.create(pipe_name='PDB model', pipe_type='frame
order')
- # Create a 6 atom structure with the CoM at [0, 0, 0].
+ # Create a 8 atom structure with the CoM at [0, 0, 0].
atom_pos = 100.0 * eye(3)
self.interpreter.structure.add_atom(mol_name='axes', atom_name='N',
res_name='X', res_num=1, pos=atom_pos[0], element='N')
self.interpreter.structure.add_atom(mol_name='axes', atom_name='N',
res_name='Y', res_num=2, pos=atom_pos[1], element='N')
@@ -397,6 +397,8 @@
self.interpreter.structure.add_atom(mol_name='axes', atom_name='N',
res_name='nX', res_num=4, pos=-atom_pos[0], element='N')
self.interpreter.structure.add_atom(mol_name='axes', atom_name='N',
res_name='nY', res_num=5, pos=-atom_pos[1], element='N')
self.interpreter.structure.add_atom(mol_name='axes', atom_name='N',
res_name='nZ', res_num=6, pos=-atom_pos[2], element='N')
+ self.interpreter.structure.add_atom(mol_name='axes', atom_name='N',
res_name='C', res_num=7, pos=[0.0, 0.0, 0.0], element='N')
+ self.interpreter.structure.add_atom(mol_name='axes', atom_name='Ti',
res_name='O', res_num=8, pos=[0.0, 0.0, 0.0], element='Ti')
# Set up the domains.
self.interpreter.domain(id='moving', spin_id=':1-7')
@@ -3214,8 +3216,11 @@
# 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, 1.0, 4)
+ # The vector lengths.
+ if res_name in ['X', 'Y', 'Z', 'Xn', 'Yn', 'Zn']:
+ self.assertAlmostEqual(r/100.0, 1.0, 4)
+ elif res_name == 'C':
+ self.assertAlmostEqual(r, 0.0, 4)
# Check the X vector.
if res_name == 'X':
@@ -3232,6 +3237,18 @@
self.assertAlmostEqual(new_pos[0], 0.0, 3)
self.assertAlmostEqual(new_pos[1], 0.0, 3)
self.assertAlmostEqual(new_pos[2], 100.0, 3)
+
+ # Check the centre.
+ elif res_name == 'C':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == 'C':
+ self.assertAlmostEqual(pos[0], 0.0, 3)
+ self.assertAlmostEqual(pos[1], 0.0, 3)
+ self.assertAlmostEqual(pos[2], 0.0, 3)
def test_simulate_iso_cone_z_axis(self):
@@ -3275,8 +3292,11 @@
# 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, 1.0, 4)
+ # The vector lengths.
+ if res_name in ['X', 'Y', 'Z', 'Xn', 'Yn', 'Zn']:
+ self.assertAlmostEqual(r/100.0, 1.0, 4)
+ elif res_name == 'C':
+ self.assertAlmostEqual(r, 0.0, 4)
# Check the X vector.
if res_name == 'X':
@@ -3297,6 +3317,18 @@
# Check the Z vector (should be in the cone defined by
theta).
elif res_name == 'Z':
self.assert_(theta <= cone_theta + epsilon)
+
+ # Check the centre.
+ elif res_name == 'C':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == 'C':
+ self.assertAlmostEqual(pos[0], 0.0, 3)
+ self.assertAlmostEqual(pos[1], 0.0, 3)
+ self.assertAlmostEqual(pos[2], 0.0, 3)
# Print out the maximum phi value.
print("Maximum phi for X and Y: %s" % max_phi)
@@ -3346,8 +3378,11 @@
# 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, 1.0, 4)
+ # The vector lengths.
+ if res_name in ['X', 'Y', 'Z', 'Xn', 'Yn', 'Zn']:
+ self.assertAlmostEqual(r/100.0, 1.0, 4)
+ elif res_name == 'C':
+ self.assertAlmostEqual(r, 0.0, 4)
# Check the X vector.
if res_name == 'X':
@@ -3370,6 +3405,18 @@
elif res_name == 'Z':
self.assert_(theta <= cone_theta + epsilon)
+ # Check the centre.
+ elif res_name == 'C':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == 'C':
+ self.assertAlmostEqual(pos[0], 0.0, 3)
+ self.assertAlmostEqual(pos[1], 0.0, 3)
+ self.assertAlmostEqual(pos[2], 0.0, 3)
+
# Print out the maximum phi value.
print("Maximum phi for X and Y: %s" % max_phi)
@@ -3412,8 +3459,11 @@
# 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, 1.0, 4)
+ # The vector lengths.
+ if res_name in ['X', 'Y', 'Z', 'Xn', 'Yn', 'Zn']:
+ self.assertAlmostEqual(r/100.0, 1.0, 4)
+ elif res_name == 'C':
+ self.assertAlmostEqual(r, 0.0, 4)
# Check the X vector.
if res_name == 'X':
@@ -3428,6 +3478,18 @@
# Check the Z vector (should be in the cone defined by
theta).
elif res_name == 'Z':
self.assert_(theta <= cone_theta + epsilon)
+
+ # Check the centre.
+ elif res_name == 'C':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == 'C':
+ self.assertAlmostEqual(pos[0], 0.0, 3)
+ self.assertAlmostEqual(pos[1], 0.0, 3)
+ self.assertAlmostEqual(pos[2], 0.0, 3)
def test_simulate_iso_cone_torsionless_z_axis(self):
@@ -3470,8 +3532,11 @@
# 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, 1.0, 4)
+ # The vector lengths.
+ if res_name in ['X', 'Y', 'Z', 'Xn', 'Yn', 'Zn']:
+ self.assertAlmostEqual(r/100.0, 1.0, 4)
+ elif res_name == 'C':
+ self.assertAlmostEqual(r, 0.0, 4)
# Check the X vector.
if res_name == 'X':
@@ -3492,6 +3557,18 @@
# Check the Z vector (should be in the cone defined by
theta).
elif res_name == 'Z':
self.assert_(theta <= cone_theta + epsilon)
+
+ # Check the centre.
+ elif res_name == 'C':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == 'C':
+ self.assertAlmostEqual(pos[0], 0.0, 3)
+ self.assertAlmostEqual(pos[1], 0.0, 3)
+ self.assertAlmostEqual(pos[2], 0.0, 3)
# Print out the maximum phi value.
print("Maximum phi for X and Y: %s" % max_phi)
@@ -3542,8 +3619,11 @@
# Printout.
print("Checking residue %s %s, atom %s %s, at shifted
position [%8.3f, %8.3f, %8.3f], with spherical coordinates [%8.3f, %8.3f,
%8.3f]." % (res_num, res_name, atom_num, atom_name, new_pos[0], new_pos[1],
new_pos[2], r, theta, phi))
- # The vector length.
- self.assertAlmostEqual(r/100.0, 1.0, 4)
+ # The vector lengths.
+ if res_name in ['X', 'Y', 'Z', 'Xn', 'Yn', 'Zn']:
+ self.assertAlmostEqual(r/100.0, 1.0, 4)
+ elif res_name == 'C':
+ self.assertAlmostEqual(r, 0.0, 4)
# Check the X vector.
if res_name == 'X':
@@ -3563,6 +3643,18 @@
elif res_name == 'Z':
theta_max = cone_theta_x * cone_theta_y /
sqrt((cos(phi)*cone_theta_y)**2 + (sin(phi)*cone_theta_x)**2)
self.assert_(theta <= theta_max + epsilon)
+
+ # Check the centre.
+ elif res_name == 'C':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == 'C':
+ self.assertAlmostEqual(pos[0], 0.0, 3)
+ self.assertAlmostEqual(pos[1], 0.0, 3)
+ self.assertAlmostEqual(pos[2], 0.0, 3)
# Print out the maximum phi value.
print("Maximum phi-pi/2.0 for Y: %s" % max_phi)
@@ -3610,8 +3702,11 @@
# Printout.
print("Checking residue %s %s, atom %s %s, at shifted
position [%8.3f, %8.3f, %8.3f], with spherical coordinates [%8.3f, %8.3f,
%8.3f]." % (res_num, res_name, atom_num, atom_name, new_pos[0], new_pos[1],
new_pos[2], r, theta, phi))
- # The vector length.
- self.assertAlmostEqual(r/100.0, 1.0, 4)
+ # The vector lengths.
+ if res_name in ['X', 'Y', 'Z', 'Xn', 'Yn', 'Zn']:
+ self.assertAlmostEqual(r/100.0, 1.0, 4)
+ elif res_name == 'C':
+ self.assertAlmostEqual(r, 0.0, 4)
# Check the X vector.
if res_name == 'X':
@@ -3631,6 +3726,18 @@
elif res_name == 'Z':
theta_max = cone_theta_x * cone_theta_y /
sqrt((cos(phi)*cone_theta_y)**2 + (sin(phi)*cone_theta_x)**2)
self.assert_(theta <= theta_max + epsilon)
+
+ # Check the centre.
+ elif res_name == 'C':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == 'C':
+ self.assertAlmostEqual(pos[0], 0.0, 3)
+ self.assertAlmostEqual(pos[1], 0.0, 3)
+ self.assertAlmostEqual(pos[2], 0.0, 3)
# Print out the maximum phi value.
print("Maximum phi-pi/2.0 for Y: %s" % max_phi)
@@ -3675,8 +3782,11 @@
# Printout.
print("Checking residue %s %s, atom %s %s, at shifted
position [%8.3f, %8.3f, %8.3f], with spherical coordinates [%8.3f, %8.3f,
%8.3f]." % (res_num, res_name, atom_num, atom_name, new_pos[0], new_pos[1],
new_pos[2], r, theta, phi))
- # The vector length.
- self.assertAlmostEqual(r/100.0, 1.0, 4)
+ # The vector lengths.
+ if res_name in ['X', 'Y', 'Z', 'Xn', 'Yn', 'Zn']:
+ self.assertAlmostEqual(r/100.0, 1.0, 4)
+ elif res_name == 'C':
+ self.assertAlmostEqual(r, 0.0, 4)
# Check the X and Y vectors.
if res_name in ['X', 'Y']:
@@ -3687,6 +3797,18 @@
elif res_name == 'Z':
theta_max = cone_theta_x * cone_theta_y /
sqrt((cos(phi)*cone_theta_y)**2 + (sin(phi)*cone_theta_x)**2)
self.assert_(theta <= theta_max + epsilon)
+
+ # Check the centre.
+ elif res_name == 'C':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == 'C':
+ self.assertAlmostEqual(pos[0], 0.0, 3)
+ self.assertAlmostEqual(pos[1], 0.0, 3)
+ self.assertAlmostEqual(pos[2], 0.0, 3)
# Print out the maximum phi value.
print("Maximum phi-pi/2.0 for Y: %s" % max_phi)
@@ -3733,8 +3855,11 @@
# Printout.
print("Checking residue %s %s, atom %s %s, at shifted
position [%8.3f, %8.3f, %8.3f], with spherical coordinates [%8.3f, %8.3f,
%8.3f]." % (res_num, res_name, atom_num, atom_name, new_pos[0], new_pos[1],
new_pos[2], r, theta, phi))
- # The vector length.
- self.assertAlmostEqual(r/100.0, 1.0, 4)
+ # The vector lengths.
+ if res_name in ['X', 'Y', 'Z', 'Xn', 'Yn', 'Zn']:
+ self.assertAlmostEqual(r/100.0, 1.0, 4)
+ elif res_name == 'C':
+ self.assertAlmostEqual(r, 0.0, 4)
# Check the X vector.
if res_name == 'X':
@@ -3755,6 +3880,18 @@
theta_max = cone_theta_x * cone_theta_y /
sqrt((cos(phi)*cone_theta_y)**2 + (sin(phi)*cone_theta_x)**2)
self.assert_(theta <= theta_max + epsilon)
+ # Check the centre.
+ elif res_name == 'C':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == 'C':
+ self.assertAlmostEqual(pos[0], 0.0, 3)
+ self.assertAlmostEqual(pos[1], 0.0, 3)
+ self.assertAlmostEqual(pos[2], 0.0, 3)
+
# Print out the maximum phi value.
print("Maximum phi-pi/2.0 for Y: %s" % max_phi)
@@ -3798,8 +3935,11 @@
# 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, 1.0, 4)
+ # The vector lengths.
+ if res_name in ['X', 'Y', 'Z', 'Xn', 'Yn', 'Zn']:
+ self.assertAlmostEqual(r/100.0, 1.0, 4)
+ elif res_name == 'C':
+ self.assertAlmostEqual(r, 0.0, 4)
# Check the X vector.
if res_name == 'X':
@@ -3820,6 +3960,18 @@
self.assertAlmostEqual(new_pos[0], 0.0, 3)
self.assertAlmostEqual(new_pos[1], 0.0, 3)
self.assertAlmostEqual(new_pos[2], 100.0, 3)
+
+ # Check the centre.
+ elif res_name == 'C':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == 'C':
+ self.assertAlmostEqual(pos[0], 0.0, 3)
+ self.assertAlmostEqual(pos[1], 0.0, 3)
+ self.assertAlmostEqual(pos[2], 0.0, 3)
def test_sobol_setup(self):
r26913 - /branches/frame_order_cleanup/test_suite/system_tests/frame_order.py