Author: bugman
Date: Thu Jan 29 13:26:00 2015
New Revision: 27347
URL: http://svn.gna.org/viewcvs/relax?rev=27347&view=rev
Log:
Attempt at fixing the lib.structure.internal.coordinates.common_residues()
function.
This function still does not work correctly.
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=27347&r1=27346&r2=27347&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Thu Jan 29 13:26:00 2015
@@ -23,7 +23,7 @@
"""Module for handling atomic coordinate information."""
# Python module imports.
-from numpy import array, float64
+from numpy import array, float64, int16, zeros
# relax module imports.
from lib.errors import RelaxFault
@@ -271,11 +271,10 @@
# Initialise the residue skipping structures.
skip = []
- skip_counts = []
- res_counts = []
+ skip_counts = zeros(num_mols, int16)
+ res_counts = zeros(num_mols, int16)
for mol_index in range(num_mols):
- res_counts.append(len(one_letter_codes[mol_index]))
- skip_counts.append(0)
+ res_counts[mol_index] = len(one_letter_codes[mol_index])
skip.append([])
for j in range(res_counts[mol_index]):
skip[mol_index].append(0)
@@ -295,23 +294,37 @@
# Initialise the gapped strings data structure for the first molecule.
gapped_strings = ['']
- for j in range(max(res_counts)):
- # No more residues.
- if j >= res_counts[0]:
+ string_length = max(res_counts)
+ offsets = zeros((num_mols-1), int16)
+ prev_offsets = zeros((num_mols-1), int16)
+ for seq_index in range(res_counts[0]):
+ # Increment the offsets indices.
+ for mol_index in range(1, num_mols):
+ while gap_matrices[mol_index-1][0, seq_index+offsets[mol_index-1]]:
+ offsets[mol_index-1] += 1
+
+ # A gap.
+ for i in range(max(offsets - prev_offsets)):
gapped_strings[0] += "-"
- continue
-
- # A skip.
- if skip[0][j]:
+
+ # Missing in one of the other molecule.
+ missing = False
+ for mol_index in range(1, num_mols):
+ if gap_matrices[mol_index-1][1, seq_index+offsets[mol_index-1]]:
+ missing = True
+ if missing:
gapped_strings[0] += "-"
-
- # A gap, so skip the residue.
- elif gap_matrices[0][0, j]:
- gapped_strings[0] += "-" + one_letter_codes[0][j]
# Keep the residue.
else:
- gapped_strings[0] += one_letter_codes[0][j]
+ gapped_strings[0] += one_letter_codes[0][seq_index]
+
+ # Store the old offsets.
+ prev_offsets = offsets * 1
+
+ # Final padding.
+ for j in range(max(res_counts) - res_counts[0] - 1):
+ gapped_strings[0] += "-"
# Update the first molecule skip counts.
skip_counts[0] = sum(skip[0])
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