Author: bugman
Date: Fri Jan 23 11:09:41 2015
New Revision: 27290
URL: http://svn.gna.org/viewcvs/relax?rev=27290&view=rev
Log:
Sequence alignment is now performed in
lib.structure.internal.coordinates.assemble_coord_array().
This is a pairwise alignment to the first molecule of the list. The alignments
are not yet used for
anything. The assemble_coord_array() function is used by the structure.align
user function, as well
as a few other structure user functions.
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=27290&r1=27289&r2=27290&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Fri Jan 23 11:09:41 2015
@@ -1,6 +1,6 @@
###############################################################################
# #
-# Copyright (C) 2014 Edward d'Auvergne #
+# Copyright (C) 2014-2015 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -24,6 +24,9 @@
# Python module imports.
from numpy import array, float64
+
+# relax module imports.
+from lib.sequence_alignment.align_protein import align_pairwise
def assemble_coord_array(objects=None, object_names=None, molecules=None,
models=None, atom_id=None, algorithm='NW70', matrix='BLOSUM62',
gap_open_penalty=1.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0,
end_gap_extend_penalty=0.0, seq_info_flag=False):
@@ -67,6 +70,7 @@
res_nums = []
atom_names = []
elements = []
+ one_letter_codes = []
for struct_index in range(len(objects)):
# Printout.
print(" Data pipe: %s" % object_names[struct_index])
@@ -126,6 +130,9 @@
# Change the current molecule name.
current_mol = mol_name
+ # Store the one letter codes for sequence alignment.
+
one_letter_codes.append(objects[struct_index].one_letter_codes(mol_name=mol_name))
+
# Extend the lists.
if molecules != None:
atom_ids.append([])
@@ -165,6 +172,14 @@
res_nums[-1][id] = res_num
atom_names[-1][id] = atom_name
elements[-1][id] = elem
+
+ # Sequence alignment.
+ print("\nPairwise sequence alignment to the first molecule:\n")
+ gap_matrices = []
+ for i in range(1, len(one_letter_codes)):
+ print("Molecules 1-%i" % (i+1))
+ align1, align2, gaps = align_pairwise(one_letter_codes[0],
one_letter_codes[i], matrix='BLOSUM62', gap_open_penalty=5.0,
gap_extend_penalty=1.0)
+ gap_matrices.append(gaps)
# Set up the structures for the superimposition algorithm.
num = len(atom_ids)
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