Author: bugman
Date: Tue Feb 10 13:22:15 2015
New Revision: 27619
URL: http://svn.gna.org/viewcvs/relax?rev=27619&view=rev
Log:
Merged revisions 27616-27618 via svnmerge from
svn+ssh://[email protected]/svn/relax/trunk
........
r27616 | bugman | 2015-02-10 13:08:00 +0100 (Tue, 10 Feb 2015) | 6 lines
Created the Structure.test_atomic_fluctuations_no_match system test.
This demonstrates a failure in the operation of the
structure.atomic_fluctuations user function when
the supplied atom ID matches no atoms.
........
r27617 | bugman | 2015-02-10 13:15:55 +0100 (Tue, 10 Feb 2015) | 6 lines
Fixes for the lib.structure.internal.coordinates.assemble_coord_array()
function.
The problem was uncovered by the Structure.test_atomic_fluctuations_no_match
system test. The
function can now handle no data being passed in.
........
r27618 | bugman | 2015-02-10 13:19:26 +0100 (Tue, 10 Feb 2015) | 8 lines
Fixes for the pipe_control.structure.main.assemble_structural_coordinates()
function.
The function will now raise a RelaxError if no structural data matching the
atom ID can be found.
The problem was uncovered by the Structure.test_atomic_fluctuations_no_match
system test. The fix
affects the structure.atomic_fluctuations, structure.displacement,
structure.find_pivot,
structure.rmsd, structure.superimpose, and structure.web_of_motion user
functions.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/structure/internal/coordinates.py
branches/frame_order_cleanup/pipe_control/structure/main.py
branches/frame_order_cleanup/test_suite/system_tests/structure.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Feb 10 13:22:15 2015
@@ -1 +1 @@
-/trunk:1-27614
+/trunk:1-27618
Modified: branches/frame_order_cleanup/lib/structure/internal/coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/coordinates.py?rev=27619&r1=27618&r2=27619&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/internal/coordinates.py
(original)
+++ branches/frame_order_cleanup/lib/structure/internal/coordinates.py Tue Feb
10 13:22:15 2015
@@ -161,6 +161,10 @@
@return: The array of atomic coordinates (first dimension is
the model and/or molecule, the second are the atoms, and the third are the
coordinates); the common list of molecule names; the common list of residue
names; the common list of residue numbers; the common list of atom names; the
common list of element names.
@rtype: numpy rank-3 float64 array, list of str, list of str,
list of int, list of str, list of str
"""
+
+ # No data to assemble.
+ if mol_names == []:
+ return [], [], [], [], [], []
# Set up the structures for common coordinates.
num_mols = len(skip)
Modified: branches/frame_order_cleanup/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/structure/main.py?rev=27619&r1=27618&r2=27619&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/structure/main.py (original)
+++ branches/frame_order_cleanup/pipe_control/structure/main.py Tue Feb 10
13:22:15 2015
@@ -131,6 +131,10 @@
# Assemble the atomic coordinates of all molecules.
ids, object_id_list, model_list, molecule_list, atom_pos, mol_names,
res_names, res_nums, atom_names, elements, one_letter_codes, num_mols =
assemble_atomic_coordinates(objects=objects, object_names=object_names,
molecules=molecules, models=models, atom_id=atom_id)
+
+ # No data.
+ if mol_names == []:
+ raise RelaxError("No structural data matching the atom ID string '%s'
can be found." % atom_id)
# Are all molecules the same?
same_mol = True
Modified: branches/frame_order_cleanup/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/structure.py?rev=27619&r1=27618&r2=27619&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/structure.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/structure.py Tue Feb
10 13:22:15 2015
@@ -559,6 +559,25 @@
self.assertEqual(len(script), len(lines))
for i in range(len(lines)):
self.assertEqual(script[i], lines[i])
+
+
+ def test_atomic_fluctuations_no_match(self):
+ """Check the operation of the structure.atomic_fluctuations user
function when no data matches the atom ID.
+
+ This checks the interatomic distance fluctuations calculated by the
U{structure.atomic_fluctuations user
function<http://www.nmr-relax.com/manual/structure_atomic_fluctuations.html>}.
+ """
+
+ # Load the file.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+ self.interpreter.structure.read_pdb('web_of_motion.pdb', dir=path)
+
+ # Run the structure.atomic_fluctuations user function and collect the
results in a dummy file object.
+ file = DummyFileObject()
+ self.interpreter.structure.atomic_fluctuations(atom_id='@X',
file=file, format='text')
+
+ # Check the file.
+ lines = file.readlines()
+ self.assertEqual(len(lines), 0)
def test_atomic_fluctuations_parallax(self):
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