Author: bugman
Date: Fri Jan 23 11:06:53 2015
New Revision: 27289
URL: http://svn.gna.org/viewcvs/relax?rev=27289&view=rev
Log:
Implemented the internal structural object one_letter_codes() method.
This will create a string of one letter residue codes for the given molecule.
Only proteins are
currently supported. This method uses the new
lib.sequence.aa_codes_three_to_one() relax library
function.
Modified:
trunk/lib/structure/internal/object.py
Modified: trunk/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=27289&r1=27288&r2=27289&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Fri Jan 23 11:06:53 2015
@@ -1,6 +1,6 @@
###############################################################################
# #
-# Copyright (C) 2003-2014 Edward d'Auvergne #
+# Copyright (C) 2003-2015 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -39,6 +39,7 @@
from lib.errors import RelaxError, RelaxNoneIntError, RelaxNoPdbError
from lib.io import file_root, open_read_file
from lib.selection import Selection
+from lib.sequence import aa_codes_three_to_one
from lib.structure import pdb_read, pdb_write
from lib.structure.internal.displacements import Displacements
from lib.structure.internal.models import ModelList
@@ -2266,6 +2267,38 @@
return len(self.structural_data[0].mol)
+ def one_letter_codes(self, mol_name=None):
+ """Generate and return the one letter code sequence for the given
molecule.
+
+ @keyword mol_name: The name of the molecule to return the one letter
codes for.
+ @type mol_name: str
+ @return: The one letter code sequence for the given
molecule.
+ @rtype: str
+ """
+
+ # Initialise.
+ codes = ''
+
+ # Use the first model.
+ model = self.structural_data[0]
+
+ # Loop over the molecules.
+ for mol_index in range(len(model.mol)):
+ # Alias.
+ mol = model.mol[mol_index]
+
+ # Skip non-matching molecules.
+ if mol_name and mol_name != mol.mol_name:
+ continue
+
+ # Loop over the residues.
+ for res_name, res_num in mol.loop_residues():
+ codes += aa_codes_three_to_one(res_name)
+
+ # Return the codes.
+ return codes
+
+
def pack_structs(self, data_matrix, orig_model_num=None,
set_model_num=None, orig_mol_num=None, set_mol_name=None, file_name=None,
file_path=None, file_path_abs=None, verbosity=1, merge=False):
"""From the given structural data, expand the structural data data
structure.
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