Class NDX

source code

     object --+        
              |        
           dict --+    
                  |    
        odict.odict --+
                      |
         object --+   |
                  |   |
utilities.FileUtils --+
                      |
                     NDX

Known Subclasses:

• uniqueNDX

Gromacs index file.

Represented as a ordered dict where the keys are index group names and
values are numpy arrays of atom numbers.

Use the :meth:`NDX.read` and :meth:`NDX.write` methods for
I/O. Access groups by name via the :meth:`NDX.get` and
:meth:`NDX.set` methods.

Alternatively, simply treat the :class:`NDX` instance as a
dictionary. Setting a key automatically transforms the new value
into a integer 1D numpy array (*not* a set, as would be the
:program:`make_ndx` behaviour).

.. Note:: The index entries themselves are ordered and can contain 
          duplicates so that output from NDX can be easily used for 
          :program:`g_dih` and friends. If you need set-like behaviour
          you will have do use :class:`gromacs.formats.uniqueNDX` or
          :class:`gromacs.cbook.IndexBuilder` (which uses
          :program:`make_ndx` throughout).

**Example**

  Read index file, make new group and write to disk::

    ndx = NDX()
    ndx.read('system.ndx')
    print ndx['Protein']       
    ndx['my_group'] = [2, 4, 1, 5]   # add new group
    ndx.write('new.ndx')

  Or quicker (replacing the input file ``system.ndx``)::

    ndx = NDX('system')          # suffix .ndx is automatically added
    ndx['chi1'] = [2, 7, 8, 10]
    ndx.write()

new empty dictionary

Return a list of groups in the same format as  :func:`gromacs.cbook.get_ndx_groups`.

Format:
   [ {'name': group_name, 'natoms': number_atoms, 'nr':  # group_number}, ....]