Author: bugman
Date: Mon Jan 26 19:11:26 2015
New Revision: 27317
URL: http://svn.gna.org/viewcvs/relax?rev=27317&view=rev
Log:
Bug fixes for the new lib.structure.internal.coordinates.common_residues()
function.
This function for determining the common residues between multiple sets of
pairwise alignments was
failing in quite a number of cases. The logic has been updated to handle these.
Modified:
trunk/lib/structure/internal/coordinates.py
Modified: trunk/lib/structure/internal/coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/coordinates.py?rev=27317&r1=27316&r2=27317&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Mon Jan 26 19:11:26 2015
@@ -339,6 +339,11 @@
if skip[0][j]:
sys.stdout.write("-")
+ # A gap, so skip the residue.
+ elif gap_matrices[0][0, j]:
+ sys.stdout.write("-")
+ sys.stdout.write(one_letter_codes[0][j])
+
# Keep the residue.
else:
sys.stdout.write(one_letter_codes[0][j])
@@ -355,12 +360,7 @@
# Loop over the residues of alignment mol_index.
seq1_index = -1
seq2_index = -1
- for j in range(max(res_counts)):
- # No more residues.
- if j >= len(gap_matrices[mol_index-1][1]):
- sys.stdout.write("-")
- continue
-
+ for j in range(len(gap_matrices[mol_index-1][0])):
# Increment the sequence indices.
if not gap_matrices[mol_index-1][0, j]:
seq1_index += 1
@@ -386,7 +386,7 @@
# Already skipped in the first molecule.
elif skip[0][seq1_index] and not gap_matrices[mol_index-1][1, j]:
- skip[mol_index][seq2_index] = 1
+ skip[mol_index][seq1_index] = 1
skip_counts[mol_index] += 1
sys.stdout.write("-")
_______________________________________________
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
