Author: bugman
Date: Sat Jan 31 15:15:17 2015
New Revision: 27428
URL: http://svn.gna.org/viewcvs/relax?rev=27428&view=rev
Log:
Modified the Structure.test_sequence_alignment_central_star_nw70_blosum62
system test.
Some residues are now deleted so that the sequences are not identical.
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=27428&r1=27427&r2=27428&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Sat Jan 31 15:15:17 2015
@@ -4644,7 +4644,7 @@
def test_sequence_alignment_central_star_nw70_blosum62(self):
- """Test of the structure.sequence_alignment user function."""
+ """Test of the structure.sequence_alignment user function using the
'Central Star', 'NW70', and 'BLOSUM62' options."""
# Path of the structure file.
path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'
@@ -4652,6 +4652,10 @@
# 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='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)
@@ -4672,18 +4676,21 @@
molecules = ['CaM A', 'CaM B']
ids = ["Object 'mf'; Model 1; Molecule 'CaM A'", "Object 'mf'; Model
1; Molecule 'CaM B'"]
sequences = [
-
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**',
-
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
+ 'EEEIREAFRVFDKDGNGYVDEMIREADIDGDGQVNYEEFVQMMTAK**',
+
'EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
]
strings = [
-
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**',
-
'EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
+
'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'
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
[email protected]
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits
