r27426 - in /trunk: lib/sequence_alignment/msa.py pipe_control/structure/main.py -- January 31, 2015 - 13:13

Author: bugman
Date: Sat Jan 31 13:13:38 2015
New Revision: 27426

URL: http://svn.gna.org/viewcvs/relax?rev=27426&view=rev
Log:
Shifted the residue skipping data structure construction into the relax 
library.

The code was originally in 
pipe_control.structure.main.assemble_structural_coordinates() but has
been shifted into the new lib.sequence_alignment.msa.msa_residue_skipping() 
function.  This will
also for greater code reuse.  The lib.sequence_alignment.msa module is also a 
better location for
such functionality.


Modified:
    trunk/lib/sequence_alignment/msa.py
    trunk/pipe_control/structure/main.py

Modified: trunk/lib/sequence_alignment/msa.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence_alignment/msa.py?rev=27426&r1=27425&r2=27426&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/msa.py (original)
+++ trunk/lib/sequence_alignment/msa.py Sat Jan 31 13:13:38 2015
@@ -228,3 +228,50 @@
 
     # Return the results.
     return strings, gaps
+
+
+def msa_residue_skipping(sequences=None, strings=None, gaps=None):
+    """Create the residue skipping data structure. 
+
+    @keyword sequences: The list of residue sequences as one letter codes.
+    @type sequences:    list of str
+    @keyword strings:   The list of alignment strings.
+    @type strings:      list of str
+    @keyword gaps:      The gap matrix.
+    @type gaps:         numpy rank-2 int array
+    @return:            The residue skipping data structure.  The first 
dimension is the molecule and the second is the residue.  As opposed to zero, 
a value of one means the residue should skipped.
+    @rtype:             list of lists of int
+    # 
+    """
+
+    # initialise.
+    skip = []
+    num_mols = len(sequences)
+
+    # Loop over each molecule.
+    for mol_index in range(num_mols):
+        skip.append([])
+        for i in range(len(sequences[0])):
+            # Create the empty residue skipping data structure.
+            if strings == None:
+                skip[mol_index].append(0)
+                continue
+
+            # No residue in the current sequence.
+            if gaps[mol_index][i]:
+                continue
+
+            # A gap in one of the other sequences.
+            gap = False
+            for mol_index2 in range(num_mols):
+                if gaps[mol_index2][i]:
+                    gap = True
+
+            # Skip the residue.
+            if gap:
+                skip[mol_index].append(1)
+            else:
+                skip[mol_index].append(0)
+
+    # Return the data structure.
+    return skip

Modified: trunk/pipe_control/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27426&r1=27425&r2=27426&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py        (original)
+++ trunk/pipe_control/structure/main.py        Sat Jan 31 13:13:38 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, msa_residue_numbers
+from lib.sequence_alignment.msa import central_star, msa_residue_numbers, 
msa_residue_skipping
 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
@@ -178,30 +178,7 @@
         strings, gaps = msa_residue_numbers(one_letter_codes, 
residue_numbers=res_num_list)
 
     # Create the residue skipping data structure. 
-    skip = []
-    for mol_index in range(num_mols):
-        skip.append([])
-        for i in range(len(one_letter_codes[0])):
-            # Create the empty residue skipping data structure.
-            if strings == None:
-                skip[mol_index].append(0)
-                continue
-
-            # No residue in the current sequence.
-            if gaps[mol_index][i]:
-                continue
-
-            # A gap in one of the other sequences.
-            gap = False
-            for mol_index2 in range(num_mols):
-                if gaps[mol_index2][i]:
-                    gap = True
-
-            # Skip the residue.
-            if gap:
-                skip[mol_index].append(1)
-            else:
-                skip[mol_index].append(0)
+    skip = msa_residue_skipping(sequences=one_letter_codes, strings=strings, 
gaps=gaps)
 
     # Assemble and return the atomic coordinates and common atom information.
     coord, mol_name_common, res_name_common, res_num_common, 
atom_name_common, element_common = assemble_coord_array(atom_pos=atom_pos, 
mol_names=mol_names, res_names=res_names, res_nums=res_nums, 
atom_names=atom_names, elements=elements, sequences=one_letter_codes, 
skip=skip)