Author: bugman
Date: Fri Dec 12 10:48:40 2014
New Revision: 27103
URL: http://svn.gna.org/viewcvs/relax?rev=27103&view=rev
Log:
Modified the Structure.test_align_molecules system test to catch a bug.
This is the failure of the displace_id argument of the structure.align user
function when the
molecules argument is supplied - all atoms are being displaced instead of a
subset.
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=27103&r1=27102&r2=27103&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Fri Dec 12 10:48:40 2014
@@ -223,8 +223,12 @@
self.interpreter.structure.translate(T=[1., 1., 1.], atom_id='#1')
self.interpreter.structure.translate(T=[0., 0., 1.], atom_id='#2')
+ # Add some atoms that should not be aligned.
+ self.interpreter.structure.add_atom(mol_name='1', atom_name='Ti',
res_name='TST', res_num=1, pos=[1.0, 2.0, 3.0], element='Ti',
pdb_record='HETATM')
+ self.interpreter.structure.add_atom(mol_name='2', atom_name='Ti',
res_name='TST', res_num=1, pos=[1.0, 2.0, 3.0], element='Ti',
pdb_record='HETATM')
+
# The alignment.
- self.interpreter.structure.align(pipes=['ref', 'align'],
molecules=[['ref'], ['1', '2']], method='fit to first', atom_id='@N,H')
+ self.interpreter.structure.align(pipes=['ref', 'align'],
molecules=[['ref'], ['1', '2']], method='fit to first', atom_id='@N,H',
displace_id='@N,H')
# Output PDB to stdout to help in debugging.
self.interpreter.structure.write_pdb(file=sys.stdout)
@@ -270,7 +274,8 @@
["N", "NH", 19, 0.000, 0.000, 0.000],
["H", "NH", 19, 0.273, -0.840, 0.510],
["N", "NH", 20, 0.000, 0.000, 0.000],
- #["H", "NH", 20, 0.000, -0.000, 1.020]
+ #["H", "NH", 20, 0.000, -0.000, 1.020],
+ ["Ti", "TST", 1, 1.000, 2.000, 3.000]
]
# The selection object.
@@ -281,6 +286,7 @@
self.assertEqual(len(data),
len(cdp.structure.structural_data[0].mol[1].atom_name))
current_mol = ''
for mol_name, res_num, res_name, atom_name, pos in
cdp.structure.atom_loop(selection=selection, mol_name_flag=True,
res_num_flag=True, res_name_flag=True, atom_name_flag=True, pos_flag=True):
+ print("Molecule '%s', residue '%s %s', atom '%s', position %s" %
(mol_name, res_num, res_name, atom_name, pos))
if mol_name != current_mol:
current_mol = mol_name
i = 0
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