Author: bugman
Date: Tue Jul 1 11:59:05 2014
New Revision: 24370
URL: http://svn.gna.org/viewcvs/relax?rev=24370&view=rev
Log:
Improvements to the internal structural object _get_chemical_name() method.
This now uses a translation table to convert the hetID or residue name into a
description, for
example as used in the PDB HETNAM records to give a human readable
description of the residue inside
the PDB file itself. The new rotor RTX and RTB residue names have been added
to the table as well.
Modified:
branches/frame_order_cleanup/lib/structure/internal/object.py
Modified: branches/frame_order_cleanup/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/object.py?rev=24370&r1=24369&r2=24370&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/internal/object.py
(original)
+++ branches/frame_order_cleanup/lib/structure/internal/object.py Tue
Jul 1 11:59:05 2014
@@ -189,19 +189,21 @@
"""Return 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 |
- | PIV | Pivot point |
- | CON | Cone object |
- | AVE | Average vector |
- |________|_____________________________________|
+ ___________________________________________________________
+ | | |
+ | hetID | Chemical name |
+ |________|________________________________________________|
+ | | |
+ | TNS | Tensor |
+ | COM | Centre of mass |
+ | AXS | Tensor axes |
+ | SIM | Monte Carlo simulation tensor axes |
+ | PIV | Pivot point |
+ | CON | Cone object |
+ | AVE | Average vector |
+ | RTX | Axis of the rotor geometric object |
+ | RTB | Propeller blades of the rotor geometric object |
+ |________|________________________________________________|
For any other residues, no description is returned.
@@ -211,33 +213,22 @@
@rtype: str or None
"""
- # 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'
+ # Translation table.
+ table = {
+ "TNS": "Tensor",
+ "COM": "Centre of mass",
+ "AXS": "Tensor axes",
+ "SIM": "Monte Carlo simulation tensor axes",
+ "PIV": "Pivot point",
+ "CON": "Cone object",
+ "AVE": "Average vector",
+ "RTX": "Axis of the rotor geometric object",
+ "RTB": "Propeller blades of the rotor geometric object"
+ }
+
+ # Return the description, if one exists.
+ if hetID in table:
+ return table[hetID]
def _parse_models_gaussian(self, file_path, verbosity=1):
r24370 - /branches/frame_order_cleanup/lib/structure/internal/object.py