Author: bugman
Date: Sat Jan 31 12:41:37 2015
New Revision: 27422
URL: http://svn.gna.org/viewcvs/relax?rev=27422&view=rev
Log:
Modified the internal structural object one_letter_codes() method.
This now validates the models to make sure all models match, and the method
requires the selection
object so that residue subsets can be handled.
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=27422&r1=27421&r2=27422&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Sat Jan 31 12:41:37 2015
@@ -2295,11 +2295,13 @@
return len(self.structural_data[0].mol)
- def one_letter_codes(self, mol_name=None):
+ def one_letter_codes(self, mol_name=None, selection=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
+ @keyword selection: The internal structural selection object. This is
obtained by calling the selection() method with the atom ID string.
+ @type selection: lib.structure.internal.Internal_selection instance
@return: The one letter code sequence for the given
molecule.
@rtype: str
"""
@@ -2307,11 +2309,17 @@
# Initialise.
codes = ''
+ # Validate the models.
+ self.validate_models(verbosity=0)
+
# Use the first model.
model = self.structural_data[0]
+ # Residue numbers.
+ res_nums = []
+
# Loop over the molecules.
- for mol_index in range(len(model.mol)):
+ for mol_index, i in selection.loop():
# Alias.
mol = model.mol[mol_index]
@@ -2319,9 +2327,13 @@
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)
+ # Not a new residue.
+ if mol.res_num[i] in res_nums:
+ continue
+
+ # Convert to the one letter code and store the residue number.
+ codes += aa_codes_three_to_one(mol.res_name[i])
+ res_nums.append(mol.res_num[i])
# Return the codes.
return codes
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