Author: bugman
Date: Sat Jan 31 12:24:09 2015
New Revision: 27421
URL: http://svn.gna.org/viewcvs/relax?rev=27421&view=rev
Log:
The residue number based sequence alignment is now executed when assembling
atomic coordinates.
This is in the assemble_structural_coordinates() function of the
pipe_control.structure.main module.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27421&r1=27420&r2=27421&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Sat Jan 31 12:24:09 2015
@@ -38,7 +38,7 @@
from lib.plotting.api import correlation_matrix
from lib.selection import tokenise
from lib.sequence import write_spin_data
-from lib.sequence_alignment.msa import central_star
+from lib.sequence_alignment.msa import central_star, msa_residue_numbers
from lib.structure.internal.coordinates import assemble_atomic_coordinates,
assemble_coord_array, loop_coord_structures
from lib.structure.internal.displacements import Displacements
from lib.structure.internal.object import Internal
@@ -152,6 +152,10 @@
for i in range(len(align.object_ids)):
print(align.strings[i])
+ # Alias the required data structures.
+ strings = align.strings
+ gaps = align.gaps
+
# Handle sequence alignments - no alignment required.
elif len(objects) == 1 and same_mol:
# Printout.
@@ -184,13 +188,13 @@
continue
# No residue in the current sequence.
- if align.gaps[mol_index][i]:
+ if gaps[mol_index][i]:
continue
# A gap in one of the other sequences.
gap = False
for mol_index2 in range(num_mols):
- if align.gaps[mol_index2][i]:
+ if gaps[mol_index2][i]:
gap = True
# Skip the residue.
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