Author: bugman
Date: Wed Jan 28 12:29:05 2015
New Revision: 27338
URL: http://svn.gna.org/viewcvs/relax?rev=27338&view=rev
Log:
Large simplification of the atomic coordinate assembly code in the internal
structural object.
This is in the lib.structure.internal.coordinates.assemble_coord_array()
function. The logic of the
function has recently changed due to the introduction of the pairwise sequence
alignments. This
caused a lot of code to now be redundant, and also incorrect in certain cases.
This simplification
fixes the problem caught by the Structure.test_align_molecules2 system test.
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=27338&r1=27337&r2=27338&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Wed Jan 28 12:29:05 2015
@@ -65,7 +65,6 @@
# Assemble the atomic coordinates of all structures.
print("Assembling all atomic coordinates:")
ids = []
- atom_ids = []
atom_pos = []
mol_names = []
res_names = []
@@ -95,28 +94,6 @@
# Printout.
print(" Model: %s" % model.num)
- # Create a new structure ID for all the molecules of this model
(if the molecules argument is not supplied).
- if molecules == None:
- if len(object_names) > 1 and num_models > 1:
- ids.append('%s, model %i' % (object_names[struct_index],
model.num))
- elif len(object_names) > 1:
- ids.append('%s' % (object_names[struct_index]))
- elif num_models > 1:
- ids.append('model %i' % (model.num))
- else:
- ids.append(None)
-
- # Extend the lists.
- if molecules == None:
- atom_names.append([])
- atom_ids.append([])
- atom_pos.append([])
- if seq_info_flag:
- mol_names.append([])
- res_names.append([])
- res_nums.append([])
- elements.append([])
-
# Add all coordinates and elements.
current_mol = ''
current_res = None
@@ -138,26 +115,23 @@
one_letter_codes.append(objects[struct_index].one_letter_codes(mol_name=mol_name))
# Extend the lists.
- if molecules != None:
- atom_names.append([])
- atom_ids.append([])
- atom_pos.append([])
- if seq_info_flag:
- mol_names.append([])
- res_names.append([])
- res_nums.append([])
- elements.append([])
+ atom_names.append([])
+ atom_pos.append([])
+ if seq_info_flag:
+ mol_names.append([])
+ res_names.append([])
+ res_nums.append([])
+ elements.append([])
# Create a new structure ID.
- if molecules != None:
- if len(object_names) > 1 and num_models > 1:
- ids.append('%s, model %i, %s' %
(object_names[struct_index], model.num, mol_name))
- elif len(object_names) > 1:
- ids.append('%s, %s' % (object_names[struct_index],
mol_name))
- elif num_models > 1:
- ids.append('model %i, %s' % (model.num, mol_name))
- else:
- ids.append('%s' % mol_name)
+ if len(object_names) > 1 and num_models > 1:
+ ids.append('%s, model %i, %s' %
(object_names[struct_index], model.num, mol_name))
+ elif len(object_names) > 1:
+ ids.append('%s, %s' % (object_names[struct_index],
mol_name))
+ elif num_models > 1:
+ ids.append('model %i, %s' % (model.num, mol_name))
+ else:
+ ids.append('%s' % mol_name)
# A new residue.
if res_num != current_res:
@@ -166,7 +140,6 @@
# Extend the lists.
atom_names[-1].append([])
- atom_ids[-1].append({})
atom_pos[-1].append({})
if seq_info_flag:
mol_names[-1].append({})
@@ -174,15 +147,8 @@
res_nums[-1].append({})
elements[-1].append({})
- # A unique identifier.
- if molecules != None:
- id = ":%s&%s@%s" % (res_num, res_name, atom_name)
- else:
- id = "#%s:%s&%s@%s" % (mol_name, res_num, res_name,
atom_name)
-
# Store the per-structure ID and coordinate.
atom_names[-1][-1].append(atom_name)
- atom_ids[-1][-1][atom_name] = id
atom_pos[-1][-1][atom_name] = pos[0]
# Store the per-structure sequence information.
@@ -193,7 +159,7 @@
elements[-1][-1][atom_name] = elem
# The total number of molecules.
- num_mols = len(atom_ids)
+ num_mols = len(atom_names)
# Sequence alignment.
if algorithm == 'NW70':
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