Author: bugman
Date: Thu Nov 20 18:41:46 2014
New Revision: 26671
URL: http://svn.gna.org/viewcvs/relax?rev=26671&view=rev
Log:
Completed the Frame_order.test_pdb_model_rotor system test.
This now sets the rotor axis to the z-axis (with a printout to be sure), sets
the torsion angle to
zero for simplicity, creates a new data pipe and loads the PDB representation
file, then checks all
of the key atom coordinates.
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=26671&r1=26670&r2=26671&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 20 18:41:46 2014
@@ -30,6 +30,7 @@
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
import dep_check
+from lib.frame_order.conversions import create_rotor_axis_alpha
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.rotations import R_to_euler_zyz
from status import Status; status = Status()
@@ -1618,6 +1619,10 @@
# Select the model.
self.interpreter.frame_order.select_model('rotor')
+ # 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)))
+
# 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)
@@ -1625,21 +1630,60 @@
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='axis_theta', val=0.5)
- self.interpreter.value.set(param='axis_phi', val=0.1)
- self.interpreter.value.set(param='cone_theta', val=0.1)
- self.interpreter.value.set(param='cone_sigma_max', val=0.1)
+ self.interpreter.value.set(param='axis_alpha', val=axis_alpha)
+ 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)
# Create the PDB.
- self.interpreter.frame_order.pdb_model(dir=ds.tmpdir)
+ self.interpreter.frame_order.pdb_model(dir=ds.tmpdir, inc=1)
+
+ # Create a data pipe for the new structure.
+ self.interpreter.pipe.create(pipe_name='PDB check', pipe_type='frame
order')
+ self.interpreter.pipe.display()
# Read the contents of the file.
- file = open(ds.tmpfile)
- lines = file.readlines()
- file.close()
+ 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.
+ 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, -30.0]],
+ [ 3, 'RTX', 4, 'PRP', [1.0, 0.0, 30.0]],
+ [ 4, 'RTB', 5, 'BLO', [1.0, 0.0, -30.0]],
+ [ 5, 'RTB', 187, 'BLO', [1.0, 0.0, -28.0]],
+ [ 6, 'RTB', 369, 'BLO', [1.0, 0.0, -30.0]],
+ [ 7, 'RTB', 551, 'BLO', [1.0, 0.0, -28.0]],
+ [ 8, 'RTB', 733, 'BLO', [1.0, 0.0, 30.0]],
+ [ 9, 'RTB', 915, 'BLO', [1.0, 0.0, 28.0]],
+ [10, 'RTB', 1097, 'BLO', [1.0, 0.0, 30.0]],
+ [11, 'RTB', 1279, 'BLO', [1.0, 0.0, 28.0]],
+ [12, 'RTL', 1461, 'z-ax', [1.0, 0.0, -32.0]],
+ [12, 'RTL', 1462, 'z-ax', [1.0, 0.0, 32.0]]
+ ]
+
+ # 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
+
+ # Checks.
+ print("Checking residue %s %s, atom %s %s, at position %s." %
(data[index][0], data[index][1], data[index][2], data[index][3],
data[index][4]))
+ self.assertEqual(data[index][0], res_num)
+ self.assertEqual(data[index][1], res_name)
+ self.assertEqual(data[index][2], atom_num)
+ self.assertEqual(data[index][3], atom_name)
+ self.assertEqual(data[index][4][0], pos[0][0])
+ self.assertEqual(data[index][4][1], pos[0][1])
+ self.assertEqual(data[index][4][2], pos[0][2])
+
+ # Increment the index.
+ index += 1
def test_pseudo_ellipse_zero_cone_angle(self):
r26671 - /branches/frame_order_cleanup/test_suite/system_tests/frame_order.py