Author: bugman
Date: Sat Jan 31 17:26:57 2015
New Revision: 27430
URL: http://svn.gna.org/viewcvs/relax?rev=27430&view=rev
Log:
Corrections and simplifications for the
Structure.test_sequence_alignment_residue_number system test.
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=27430&r1=27429&r2=27430&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Sat Jan 31 17:26:57 2015
@@ -4732,6 +4732,7 @@
# Delete some residues.
self.interpreter.structure.delete("#CaM B:82")
self.interpreter.structure.delete("#CaM A:100-120")
+ self.interpreter.structure.delete(":CA")
# Perform the alignment.
self.interpreter.structure.sequence_alignment(pipes=['mf'],
models=[[1, 1]], molecules=[['CaM A', 'CaM B']], msa_algorithm='residue number')
@@ -4752,12 +4753,12 @@
molecules = ['CaM A', 'CaM B']
ids = ["Object 'mf'; Model 1; Molecule 'CaM A'", "Object 'mf'; Model
1; Molecule 'CaM B'"]
sequences = [
- 'EEEIREAFRVFDKDGNGYVDEMIREADIDGDGQVNYEEFVQMMTAK**',
-
'EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
+ 'EEEIREAFRVFDKDGNGYVDEMIREADIDGDGQVNYEEFVQMMTAK',
+
'EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK'
]
strings = [
-
'EEEIREAFRVFDKDGNGY---------------------VDEMIREADIDGDGQVNYEEFVQMMTAK**',
-
'-EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK**'
+
'EEEIREAFRVFDKDGNGY---------------------VDEMIREADIDGDGQVNYEEFVQMMTAK',
+
'-EEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK'
]
gaps = []
for i in range(len(strings)):
@@ -4767,13 +4768,13 @@
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
+ msa_algorithm = 'residue number'
+ pairwise_algorithm = None
+ matrix = None
+ gap_open_penalty = None
+ gap_extend_penalty = None
+ end_gap_open_penalty = None
+ end_gap_extend_penalty = None
# Check the data.
for i in range(2):
_______________________________________________
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
