Author: bugman
Date: Thu Jan 29 19:19:00 2015
New Revision: 27372
URL: http://svn.gna.org/viewcvs/relax?rev=27372&view=rev
Log:
Merged revisions 27370-27371 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27370 | bugman | 2015-01-29 18:30:04 +0100 (Thu, 29 Jan 2015) | 6 lines
Corrections for the Structure.test_align_CaM_BLOSUM62 system test.
The CaM N and C domains can not be aligned together in a global MSA as they
would align very well to
themselves, causing the atomic coordinate assembly function to fail.
........
r27371 | bugman | 2015-01-29 19:18:23 +0100 (Thu, 29 Jan 2015) | 6 lines
Improvement for the lib.sequence_alignment.msa.central_star() function.
The strings and gap matrix returned by the function have been reordered to
match the input
sequences.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/sequence_alignment/msa.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/structure_align.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Jan 29 19:19:00 2015
@@ -1 +1 @@
-/trunk:1-27368
+/trunk:1-27371
Modified: branches/frame_order_cleanup/lib/sequence_alignment/msa.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/sequence_alignment/msa.py?rev=27372&r1=27371&r2=27372&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/sequence_alignment/msa.py (original)
+++ branches/frame_order_cleanup/lib/sequence_alignment/msa.py Thu Jan 29
19:19:00 2015
@@ -141,12 +141,19 @@
# Rebuild the alignment lists and create a gap matrix.
strings = []
M = len(Sc_prime)
- gaps = zeros((N, M), int16)
strings.append(Sc_prime)
for i in range(N-1):
strings.append(''.join(string_lists[i]))
for i in range(N):
strings[i] = strings[i].replace('X', '-')
+
+ # Restore the original sequence ordering.
+ string = strings.pop(0)
+ strings.insert(Sc_index, string)
+
+ # Create the gap matrix.
+ gaps = zeros((N, M), int16)
+ for i in range(N):
for j in range(M):
if strings[i][j] == '-':
gaps[i, j] = 1
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/structure_align.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/structure_align.py?rev=27372&r1=27371&r2=27372&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/structure_align.py
(original)
+++
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/structure_align.py
Thu Jan 29 19:19:00 2015
@@ -16,8 +16,11 @@
# Load the structure.
structure.read_pdb('%s.pdb' % code, dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures')
-# Backbone heavy atom align all structures.
-structure.align(pipes=codes, atom_id='@N,C,CA,O', method='fit to first',
matrix='BLOSUM62', gap_open_penalty=10.0, gap_extend_penalty=1.0,
end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
+# First align the N-domains - aligning 1OSA onto 1J70 to act as a scaffold.
+structure.align(pipes=['1J7O', '1OSA'], atom_id='@N,C,CA,O', method='fit to
first', matrix='BLOSUM62', gap_open_penalty=10.0, gap_extend_penalty=1.0,
end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
+
+# Then align the C-domains - aligning 1J7P onto the 1OSA scaffold.
+structure.align(pipes=['1OSA', '1J7P'], atom_id='@N,C,CA,O', method='fit to
first', matrix='BLOSUM62', gap_open_penalty=10.0, gap_extend_penalty=1.0,
end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
# Write out the result.
structure.write_pdb('devnull', force=True)
r27372 - in /branches/frame_order_cleanup: ./ lib/sequence_alignment/ test_suite/system_tests/scripts/n_state_model/