Author: bugman
Date: Fri Jan 30 12:46:23 2015
New Revision: 27390
URL: http://svn.gna.org/viewcvs/relax?rev=27390&view=rev
Log:
Renamed the Sequence.test_align_molecules system test to
Structure.test_sequence_alignment_molecules.
As the sequence alignment is dependent on the structural data in the relax
data store, the user
function for sequence alignment would be better named as
structure.sequence_alignment. The
sequence.align user function is not appropriate as all other sequence user
functions relate to the
molecule, residue, and spin data structure of each data pipe rather than to
the structural data.
Modified:
trunk/test_suite/system_tests/sequence.py
trunk/test_suite/system_tests/structure.py
Modified: trunk/test_suite/system_tests/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/sequence.py?rev=27390&r1=27389&r2=27390&view=diff
==============================================================================
--- trunk/test_suite/system_tests/sequence.py (original)
+++ trunk/test_suite/system_tests/sequence.py Fri Jan 30 12:46:23 2015
@@ -37,73 +37,6 @@
# Create the data pipe.
self.interpreter.pipe.create('mf', 'mf')
-
-
- def test_align_molecules(self):
- """Test of the sequence.align user function."""
-
- # Path of the structure file.
- path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'
-
- # Load the two rotated structures.
- self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path,
set_model_num=1, set_mol_name='CaM A')
- self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=path,
set_model_num=1, set_mol_name='CaM B')
-
- # Perform the alignment.
- self.interpreter.sequence.align(msa_algorithm='Central Star',
algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=10.0,
gap_extend_penalty=1.0, end_gap_open_penalty=0.5, end_gap_extend_penalty=0.1)
-
- # Save the relax state.
- self.tmpfile = mktemp()
- self.interpreter.state.save(self.tmpfile, dir=None, force=True)
-
- # Reset relax.
- self.interpreter.reset()
-
- # Load the results.
- self.interpreter.state.load(self.tmpfile)
-
- # The real data.
- object_ids = ['mf', 'mf']
- models = [1, 1]
- molecules = ['CaM A', 'CaM B']
- sequences = [
-
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK***',
-
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK***'
- ]
- strings = [
-
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK***',
-
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK***'
- ]
- gaps = []
- for i in range(len(strings)):
- gaps.append([])
- for j in range(len(strings[0])):
- gaps[i].append(0)
- msa_algorithm = 'Central Star'
- pairwise_algorithm = 'NW70'
- matrix = 'BLOSUM62'
- gap_open_penalty = 10.0
- gap_extend_penalty = 1.0
- end_gap_open_penalty = 0.5
- end_gap_extend_penalty = 0.1
-
- # Check the data.
- for i in range(2):
- print("Checking \"%s\"" % molecules[i])
- self.assertEqual(ds.sequence_alignments[0].ids[i], ids[i])
- self.assertEqual(ds.sequence_alignments[0].object_ids[i],
object_ids[i])
- self.assertEqual(ds.sequence_alignments[0].models[i], models[i])
- self.assertEqual(ds.sequence_alignments[0].molecules[i],
molecules[i])
- self.assertEqual(ds.sequence_alignments[0].sequences[i],
sequences[i])
- self.assertEqual(ds.sequence_alignments[0].strings[i],
strings[i])
- self.assertEqual(ds.sequence_alignments[0].gaps[i], gaps[i])
- self.assertEqual(ds.sequence_alignments[0].msa_algorithm,
msa_algorithm)
- self.assertEqual(ds.sequence_alignments[0].pairwise_algorithm,
pairwise_algorithm)
- self.assertEqual(ds.sequence_alignments[0].matrix, matrix)
- self.assertEqual(ds.sequence_alignments[0].gap_open_penalty,
gap_open_penalty)
- self.assertEqual(ds.sequence_alignments[0].gap_extend_penalty,
gap_extend_penalty)
- self.assertEqual(ds.sequence_alignments[0].end_gap_open_penalty,
end_gap_open_penalty)
-
self.assertEqual(ds.sequence_alignments[0].end_gap_extend_penalty,
end_gap_extend_penalty)
def test_load_protein_asp_atoms_from_pdb(self):
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27390&r1=27389&r2=27390&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Fri Jan 30 12:46:23 2015
@@ -4643,6 +4643,73 @@
self.assertAlmostEqual(cdp.structure.rmsd, 0.77282758781333061)
+ def test_sequence_alignment_molecules(self):
+ """Test of the structure.sequence_alignment user function."""
+
+ # Path of the structure file.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'
+
+ # Load the two rotated structures.
+ self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir=path,
set_model_num=1, set_mol_name='CaM A')
+ self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=path,
set_model_num=1, set_mol_name='CaM B')
+
+ # Perform the alignment.
+ self.interpreter.structure.sequence_alignment(msa_algorithm='Central
Star', algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=10.0,
gap_extend_penalty=1.0, end_gap_open_penalty=0.5, end_gap_extend_penalty=0.1)
+
+ # Save the relax state.
+ self.tmpfile = mktemp()
+ self.interpreter.state.save(self.tmpfile, dir=None, force=True)
+
+ # Reset relax.
+ self.interpreter.reset()
+
+ # Load the results.
+ self.interpreter.state.load(self.tmpfile)
+
+ # The real data.
+ object_ids = ['mf', 'mf']
+ models = [1, 1]
+ molecules = ['CaM A', 'CaM B']
+ sequences = [
+
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK***',
+
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK***'
+ ]
+ strings = [
+
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK***',
+
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK***'
+ ]
+ gaps = []
+ for i in range(len(strings)):
+ gaps.append([])
+ for j in range(len(strings[0])):
+ gaps[i].append(0)
+ msa_algorithm = 'Central Star'
+ pairwise_algorithm = 'NW70'
+ matrix = 'BLOSUM62'
+ gap_open_penalty = 10.0
+ gap_extend_penalty = 1.0
+ end_gap_open_penalty = 0.5
+ end_gap_extend_penalty = 0.1
+
+ # Check the data.
+ for i in range(2):
+ print("Checking \"%s\"" % molecules[i])
+ self.assertEqual(ds.sequence_alignments[0].ids[i], ids[i])
+ self.assertEqual(ds.sequence_alignments[0].object_ids[i],
object_ids[i])
+ self.assertEqual(ds.sequence_alignments[0].models[i], models[i])
+ self.assertEqual(ds.sequence_alignments[0].molecules[i],
molecules[i])
+ self.assertEqual(ds.sequence_alignments[0].sequences[i],
sequences[i])
+ self.assertEqual(ds.sequence_alignments[0].strings[i],
strings[i])
+ self.assertEqual(ds.sequence_alignments[0].gaps[i], gaps[i])
+ self.assertEqual(ds.sequence_alignments[0].msa_algorithm,
msa_algorithm)
+ self.assertEqual(ds.sequence_alignments[0].pairwise_algorithm,
pairwise_algorithm)
+ self.assertEqual(ds.sequence_alignments[0].matrix, matrix)
+ self.assertEqual(ds.sequence_alignments[0].gap_open_penalty,
gap_open_penalty)
+ self.assertEqual(ds.sequence_alignments[0].gap_extend_penalty,
gap_extend_penalty)
+ self.assertEqual(ds.sequence_alignments[0].end_gap_open_penalty,
end_gap_open_penalty)
+
self.assertEqual(ds.sequence_alignments[0].end_gap_extend_penalty,
end_gap_extend_penalty)
+
+
def test_superimpose_fit_to_first(self):
"""Test of the structure.superimpose user function, fitting to the
first structure."""
r27390 - in /trunk/test_suite/system_tests: sequence.py structure.py