Author: bugman
Date: Wed Oct 1 19:44:08 2014
New Revision: 26104
URL: http://svn.gna.org/viewcvs/relax?rev=26104&view=rev
Log:
Created the Structure.test_align system test.
This will be used to test the yet to be implemented structure.align user
function. This user
function will be similar to the structure.superimpose user function but will be
designed so that
structures with different primary and atomic sequences can be superimposed.
Modified:
trunk/test_suite/system_tests/structure.py
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=26104&r1=26103&r2=26104&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Wed Oct 1 19:44:08 2014
@@ -21,14 +21,14 @@
# Python module imports.
from math import sqrt
-from numpy import float64, zeros
+from numpy import array, float64, zeros
from os import sep
from tempfile import mkdtemp, mktemp
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from pipe_control.mol_res_spin import count_spins, return_spin, spin_loop
-from lib.geometry.rotations import euler_to_R_zyz
+from lib.geometry.rotations import axis_angle_to_R, euler_to_R_zyz
from lib.errors import RelaxError
from lib.io import DummyFileObject
from status import Status; status = Status()
@@ -57,6 +57,47 @@
# Rebuild the list.
lines[:] = [x for x in lines if x[:6] != 'REMARK']
+
+
+ def test_align(self):
+ """Test the U{structure.align user
function<http://www.nmr-relax.com/manual/structure_align.html>}."""
+
+ # Reset relax.
+ self.interpreter.reset()
+
+ # Path of the PDB file.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'diffusion_tensor'+sep+'spheroid'
+
+ # Create a data pipe for the reference structure, then load it.
+ self.interpreter.pipe.create('ref', 'N-state')
+ self.interpreter.structure.read_pdb('uniform.pdb', dir=path)
+
+ # Delete a residue and atom.
+ self.interpreter.structure.delete(":8")
+ self.interpreter.structure.delete(":2@N")
+
+ # Create a second data pipe for the structures to align and
superimpose.
+ self.interpreter.pipe.create('align', 'N-state')
+
+ # Load the PDB twice as different models.
+ self.interpreter.structure.read_pdb('uniform.pdb', dir=path,
set_model_num=1)
+ self.interpreter.structure.read_pdb('uniform.pdb', dir=path,
set_model_num=2)
+
+ # Delete a residue and atom.
+ self.interpreter.structure.delete(":12")
+ self.interpreter.structure.delete(":20@H")
+
+ # Translate and rotate the models.
+ R = zeros((3, 3), float64)
+ self.interpreter.structure.translate(T=[1., 1., 1.], model=1)
+ self.interpreter.structure.translate(T=[0., 0., 1.], model=2)
+ axis_angle_to_R(array([1, 0, 0], float64), 1.0, R)
+ self.interpreter.structure.rotate(R=R, model=1)
+ axis_angle_to_R(array([0, 0, 1], float64), 2.0, R)
+ self.interpreter.structure.rotate(R=R, model=2)
+
+ # The alignment.
+ self.interpreter.structure.align(pipes=['ref', 'align'], method='fit
to mean', atom_id='@N,H')
def test_alt_loc_missing(self):
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