Author: bugman
Date: Thu Jan 15 18:42:02 2009
New Revision: 8487
URL: http://svn.gna.org/viewcvs/relax?rev=8487&view=rev
Log:
Shifted __det_pdb_element() to the correct location.
Modified:
branches/multi_structure/generic_fns/structure/internal.py
Modified: branches/multi_structure/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8487&r1=8486&r2=8487&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Thu Jan 15
18:42:02 2009
@@ -1106,6 +1106,43 @@
warn(RelaxWarning("The atom number " + `atom_num` + " from the CONECT
record cannot be found within the ATOM and HETATM records."))
+ def __det_pdb_element(self, atom_name):
+ """Try to determine the element from the PDB atom name.
+
+ @param atom_name: The PDB atom name.
+ @type atom_name: str
+ @return: The element name, or None if unsuccessful.
+ @rtype: str or None
+ """
+
+ # Strip away atom numbering, from the front and end.
+ element = strip(atom_name, digits)
+
+ # Amino acid atom translation table (note, numbers have been stripped
already!).
+ table = {'C': ['CA', 'CB', 'CG', 'CD', 'CE', 'CZ'],
+ 'N': ['NE', 'NH'],
+ 'H': ['HA', 'HB', 'HG', 'HD', 'HE', 'HT'],
+ 'O': ['OG', 'OD', 'OE'],
+ 'S': ['SD']
+ }
+
+ # Translate amino acids.
+ for key in table.keys():
+ if element in table[key]:
+ element = key
+ break
+
+ # Allowed element list.
+ elements = ['H', 'C', 'N', 'O', 'F', 'P', 'S']
+
+ # Return the element, if in the list.
+ if element in elements:
+ return element
+
+ # Else, throw a warning.
+ warn(RelaxWarning("Cannot determine the element associated with atom
'%s'." % atom_name))
+
+
def __parse_pdb_record(self, record):
"""Parse the PDB record string and return an array of the
corresponding atomic information.
@@ -1321,43 +1358,6 @@
self.bonded[index2].append(index1)
- def __det_pdb_element(self, atom_name):
- """Try to determine the element from the PDB atom name.
-
- @param atom_name: The PDB atom name.
- @type atom_name: str
- @return: The element name, or None if unsuccessful.
- @rtype: str or None
- """
-
- # Strip away atom numbering, from the front and end.
- element = strip(atom_name, digits)
-
- # Amino acid atom translation table (note, numbers have been stripped
already!).
- table = {'C': ['CA', 'CB', 'CG', 'CD', 'CE', 'CZ'],
- 'N': ['NE', 'NH'],
- 'H': ['HA', 'HB', 'HG', 'HD', 'HE', 'HT'],
- 'O': ['OG', 'OD', 'OE'],
- 'S': ['SD']
- }
-
- # Translate amino acids.
- for key in table.keys():
- if element in table[key]:
- element = key
- break
-
- # Allowed element list.
- elements = ['H', 'C', 'N', 'O', 'F', 'P', 'S']
-
- # Return the element, if in the list.
- if element in elements:
- return element
-
- # Else, throw a warning.
- warn(RelaxWarning("Cannot determine the element associated with atom
'%s'." % atom_name))
-
-
def fill_object_from_pdb(self, records):
"""Method for generating a complete Structure_container object from
the given PDB records.
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