Author: bugman
Date: Sat Jan 31 15:17:09 2015
New Revision: 27429
URL: http://svn.gna.org/viewcvs/relax?rev=27429&view=rev
Log:
Created the Structure.test_sequence_alignment_residue_number system test.
This will be used to test the structure.sequence_alignment user function
together with the 'residue
number' MSA algorithm. This is simply a copy of the
Structure.test_sequence_alignment_central_star_nw70_blosum62 system test with a
few small changes.
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=27429&r1=27428&r2=27429&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Sat Jan 31 15:17:09 2015
@@ -4719,6 +4719,82 @@
self.assertEqual(ds.sequence_alignments[0].end_gap_extend_penalty,
end_gap_extend_penalty)
+ def test_sequence_alignment_residue_number(self):
+ """Test of the structure.sequence_alignment user function using the
'residue number' MSA algorithm."""
+
+ # 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')
+
+ # Delete some residues.
+ self.interpreter.structure.delete("#CaM B:82")
+ self.interpreter.structure.delete("#CaM A:100-120")
+
+ # Perform the alignment.
+ self.interpreter.structure.sequence_alignment(pipes=['mf'],
models=[[1, 1]], molecules=[['CaM A', 'CaM B']], msa_algorithm='residue number')
+
+ # 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.
+ pipes = ['mf', 'mf']
+ models = [1, 1]
+ molecules = ['CaM A', 'CaM B']
+ ids = ["Object 'mf'; Model 1; Molecule 'CaM A'", "Object 'mf'; Model
1; Molecule 'CaM B'"]
+ sequences = [
+ 'EEEIREAFRVFDKDGNGYVDEMIREADIDGDGQVNYEEFVQMMTAK**',
+
'EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
+ ]
+ strings = [
+
'EEEIREAFRVFDKDGNGY---------------------VDEMIREADIDGDGQVNYEEFVQMMTAK**',
+
'-EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
+ ]
+ gaps = []
+ for i in range(len(strings)):
+ gaps.append([])
+ for j in range(len(strings[0])):
+ gaps[i].append(0)
+ for i in range(18, 39):
+ gaps[0][i] = 1
+ gaps[1][0] = 1
+ 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], pipes[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])
+ for j in range(len(strings[0])):
+ self.assertEqual(ds.sequence_alignments[0].gaps[i, j],
gaps[i][j])
+ 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."""
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