Class IndexBuilder

Build a index group from the selection arguments.

If selections and a structure file are supplied then the individual
selections are constructed with separate calls to
:func:`gromacs.make_ndx`. Use :meth:`IndexBuilder.combine` to combine
them into a joint selection.

:Arguments:

   struct : filename
      Structure file (tpr, pdb, ...)

   selections : list
      The list must contain strings or tuples, which must be be one of
      the following constructs:

         "<1-letter aa code><resid>[:<atom name]"

             Selects the CA of the residue or the specified atom
             name.

             example: ``"S312:OA"`` or ``"A22"`` (equivalent to ``"A22:CA"``)
         
         ("<1-letter aa code><resid>", "<1-letter aa code><resid>, ["<atom name>"])

            Selects a *range* of residues. If only two residue
            identifiers are provided then all atoms are
            selected. With an optional third atom identifier,
            only this atom anme is selected for each residue
            in the range. [EXPERIMENTAL]

         "@<make_ndx selection>"

             The ``@`` letter introduces a verbatim ``make_ndx``
             command. It will apply the given selection without any
             further processing or checks.

             example: ``"@a 6234 - 6238"`` or ``'@"SOL"'`` (note the quoting)
             or ``"@r SER & r 312 & t OA"``.

   names : list
      Strings to name the selections; if not supplied or if individuals
      are ``None`` then a default name is created.

   offset : int, dict
      This number is added to the resids in the first selection scheme; this
      allows names to be the same as in a crystal structure. If offset is a 
      dict then it is used to directly look up the resids.

   ndx : filename or list of filenames
      Optional input index file(s).

   out_ndx : filename
      Output index file.
      

Overrides: object.__init__

Combine individual groups into a single one and write output.

:Keywords:         
   name_all : string
      Name of the combined group, ``None`` generates a name.  [``None``]
   out_ndx : filename
      Name of the output file that will contain the individual groups
      and the combined group. If ``None`` then default from the class
      constructor is used. [``None``]
   operation : character
      Logical operation that is used to generate the combined group from
      the individual groups: "|" (OR) or "&" (AND) ["|"]
   defaultgroups : bool
      ``True``: append everything to the default groups produced by 
      :program:`make_ndx` (or rather, the groups provided in the ndx file on
      initialization --- if this was ``None`` then these are truly default groups);
      ``False``: only use the generated groups

:Returns:
   ``(combinedgroup_name, output_ndx)``, a tuple showing the
   actual group name and the name of the file; useful when all names are autogenerated.

.. Warning:: The order of the atom numbers in the combined group is
             *not* guaranteed to be the same as the selections on input because
             ``make_ndx`` sorts them ascending. Thus you should be careful when
             using these index files for calculations of angles and dihedrals.
             Use :class:`gromacs.formats.NDX` in these cases.

Concatenate input index files.

Generate a new index file that contains the default Gromacs index groups (if a structure file was defined) and all index groups from the input index files.

Parameters:

• out_ndx (filename) - Name of the output index file; if None then use the default provided to the constructore. [None].

RESIDUE

Value:

re.compile(r'(?x)(?P<aa>([ACDEFGHIKLMNPQRSTVWY])|(\S\S\S))(?P<resid>\d +)(:(?P<atom>\w+))?')

offset

*offset* as a number is added to the resids in the first selection
scheme; this
allows names to be the same as in a crystal structure. If *offset* is a
dict then it is used to directly look up the resids. Use :meth:`gmx_resid`
to transform a crystal resid to a gromacs resid.

The attribute may be changed directly after init.

names

Get Method:

unreachable.names(self) - Names of all generated index groups.