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)
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