Author: bugman
Date: Sat Jan 31 12:04:18 2015
New Revision: 27419
URL: http://svn.gna.org/viewcvs/relax?rev=27419&view=rev
Log:
Implemented the residue number based alignment in the atomic assembly function.
This is in the new
pipe_control.structure.main.assemble_structural_coordinates() function. The
code
for creating the residue skipping data structure is now shared between the
three sequence alignment
options.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27419&r1=27418&r2=27419&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Sat Jan 31 12:04:18 2015
@@ -32,7 +32,7 @@
from data_store import Relax_data_store; ds = Relax_data_store()
from data_store.seq_align import Sequence_alignments
from lib.check_types import is_float
-from lib.errors import RelaxError, RelaxFileError, RelaxImplementError
+from lib.errors import RelaxError, RelaxFileError
from lib.geometry.vectors import vector_angle_atan2
from lib.io import get_file_path, open_write_file, write_data
from lib.plotting.api import correlation_matrix
@@ -138,6 +138,10 @@
if mol != molecule_list[0]:
same_mol = False
+ # Init.
+ strings = None
+ gaps = None
+
# Handle sequence alignments - retrieve the alignment.
align = None
if hasattr(ds, 'sequence_alignments'):
@@ -148,46 +152,52 @@
for i in range(len(align.object_ids)):
print(align.strings[i])
- # 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])):
- # No residue in the current sequence.
- if align.gaps[mol_index][i]:
- continue
-
- # A gap in one of the other sequences.
- gap = False
- for mol_index2 in range(num_mols):
- if align.gaps[mol_index2][i]:
- gap = True
-
- # Skip the residue.
- if gap:
- skip[mol_index].append(1)
- else:
- skip[mol_index].append(0)
-
# Handle sequence alignments - no alignment required.
elif len(objects) == 1 and same_mol:
# Printout.
print("\nSequence alignment disabled as only models with identical
molecule, residue and atomic sequences are being superimposed.")
- # Create the empty residue skipping data structure.
- skip = []
- for mol_index in range(num_mols):
- skip.append([])
- for i in range(len(one_letter_codes[0])):
- skip[mol_index].append(0)
-
# Handle sequence alignments - fall back alignment based on residue
numbering.
else:
# Printout.
print("\nSequence alignment cannot be found - falling back to a
residue number based alignment.")
- raise RelaxImplementError
-
+ # Convert the residue number data structure.
+ res_num_list = []
+ for mol_index in range(num_mols):
+ res_num_list.append([])
+ for i in range(len(one_letter_codes[0])):
+ key = res_nums[mol_index][i].keys()[0]
+ res_num_list[mol_index].append(res_nums[mol_index][i][key])
+
+ # Sequence alignment.
+ 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 align.gaps[mol_index][i]:
+ continue
+
+ # A gap in one of the other sequences.
+ gap = False
+ for mol_index2 in range(num_mols):
+ if align.gaps[mol_index2][i]:
+ gap = True
+
+ # Skip the residue.
+ if gap:
+ skip[mol_index].append(1)
+ else:
+ skip[mol_index].append(0)
# 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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