Author: bugman
Date: Mon Apr 7 13:49:36 2008
New Revision: 5346
URL: http://svn.gna.org/viewcvs/relax?rev=5346&view=rev
Log:
Made one of the methods private by renaming to __get_chemical_name().
Modified:
1.3/generic_fns/structure/internal_pdb.py
Modified: 1.3/generic_fns/structure/internal_pdb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal_pdb.py?rev=5346&r1=5345&r2=5346&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal_pdb.py (original)
+++ 1.3/generic_fns/structure/internal_pdb.py Mon Apr 7 13:49:36 2008
@@ -51,6 +51,60 @@
# Identification string.
id = 'internal pdb'
+
+
+ def __get_chemical_name(self, hetID):
+ """Method for returning the chemical name corresponding to the given
residue ID.
+
+ The following names are currently returned:
+ ________________________________________________
+ | | |
+ | hetID | Chemical name |
+ |________|_____________________________________|
+ | | |
+ | TNS | Tensor |
+ | COM | Centre of mass |
+ | AXS | Tensor axes |
+ | SIM | Monte Carlo simulation tensor axes |
+ |________|_____________________________________|
+
+
+ @param res: The residue ID.
+ @type res: str
+ @return: The chemical name.
+ @rtype: str
+ """
+
+ # Tensor.
+ if hetID == 'TNS':
+ return 'Tensor'
+
+ # Centre of mass.
+ if hetID == 'COM':
+ return 'Centre of mass'
+
+ # Tensor axes.
+ if hetID == 'AXS':
+ return 'Tensor axes'
+
+ # Monte Carlo simulation tensor axes.
+ if hetID == 'SIM':
+ return 'Monte Carlo simulation tensor axes'
+
+ # Pivot point.
+ if hetID == 'PIV':
+ return 'Pivot point'
+
+ # Cone object.
+ if hetID == 'CON':
+ return 'Cone'
+
+ # Average vector.
+ if hetID == 'AVE':
+ return 'Average vector'
+
+ # Unknown hetID.
+ raise RelaxError, "The residue ID (hetID) " + `hetID` + " is not
recognised."
def atom_add(self, atom_id=None, record_name='', atom_name='',
res_name='', chain_id='', res_num=None, pos=[None, None, None],
segment_id='', element=''):
@@ -131,60 +185,6 @@
self.structural_data[bonded_id].append(atom_num)
- def get_chemical_name(self, hetID):
- """Method for returning the chemical name corresponding to the given
residue ID.
-
- The following names are currently returned:
- ________________________________________________
- | | |
- | hetID | Chemical name |
- |________|_____________________________________|
- | | |
- | TNS | Tensor |
- | COM | Centre of mass |
- | AXS | Tensor axes |
- | SIM | Monte Carlo simulation tensor axes |
- |________|_____________________________________|
-
-
- @param res: The residue ID.
- @type res: str
- @return: The chemical name.
- @rtype: str
- """
-
- # Tensor.
- if hetID == 'TNS':
- return 'Tensor'
-
- # Centre of mass.
- if hetID == 'COM':
- return 'Centre of mass'
-
- # Tensor axes.
- if hetID == 'AXS':
- return 'Tensor axes'
-
- # Monte Carlo simulation tensor axes.
- if hetID == 'SIM':
- return 'Monte Carlo simulation tensor axes'
-
- # Pivot point.
- if hetID == 'PIV':
- return 'Pivot point'
-
- # Cone object.
- if hetID == 'CON':
- return 'Cone'
-
- # Average vector.
- if hetID == 'AVE':
- return 'Average vector'
-
- # Unknown hetID.
- raise RelaxError, "The residue ID (hetID) " + `hetID` + " is not
recognised."
-
-
def terminate(self, atom_id_ext='', res_num=None):
"""Method for terminating the chain by adding a TER record to the
structral data object.
@@ -301,7 +301,7 @@
residues.append(het[1])
# Get the chemical name.
- chemical_name = get_chemical_name(het[1])
+ chemical_name = self.__get_chemical_name(het[1])
# Write the HETNAM records.
file.write("%-6s %2s %3s %-55s\n" % ('HETNAM', '', het[1],
chemical_name))
r5346 - /1.3/generic_fns/structure/internal_pdb.py