gromacs.tools.GromacsCommandMultiIndex

Class GromacsCommandMultiIndex

object --+ | core.Command --+ | core.GromacsCommand --+ | GromacsCommandMultiIndex

Instance Methods

[hide private]

__init__(self, **kwargs)
Initialize instance.

source code

run(self, *args, **kwargs)
Run the command; make a combined multi-index file if necessary.

source code

_fake_multi_ndx(self, **kwargs)
Combine multiple index file into a single one and return appropriate kwargs.

source code

__del__(self)
Clean up temporary multi-index files if they were used.

source code

Inherited from core.GromacsCommand: check_failure, transform_args

Inherited from core.GromacsCommand (private): _build_arg_list, _combine_arglist, _combineargs, _get_gmx_docs, _run_command

Inherited from core.Command: Popen, __call__, commandline, help

Inherited from core.Command (private): _commandline

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties

[hide private]

Inherited from core.GromacsCommand: gmxdoc

Inherited from object: __class__

init(self, **kwargs)
(Constructor)

source code

Initialize instance.

1) Sets up the combined index file.
2) Inititialize :class:`~gromacs.core.GromacsCommand` with the 
   new index file.

See the documentation for :class:`gromacs.core.GromacsCommand` for details.

Overrides: object.__init__

run(self, *args, **kwargs)

source code

Run the command; make a combined multi-index file if necessary.

Overrides: core.Command.run

_fake_multi_ndx(self, **kwargs)

source code

Combine multiple index file into a single one and return appropriate kwargs.

Calling the method combines multiple index files into a a single
temporary one so that Gromacs tools that do not (yet) support multi
file input for index files can be used transparently as if they did.

If a temporary index file is required then it is deleted once the
object is destroyed.

:Returns:
  The method returns the input keyword arguments with the necessary
  changes to use the temporary index files.

:Keywords: 
   Only the listed keywords have meaning for the method:

   *n* : filename or list of filenames
      possibly multiple index files; *n* is replaced by the name of 
      the temporary index file.
   *s* : filename
      structure file (tpr, pdb, ...) or ``None``; if a structure file is 
      supplied then the Gromacs default index groups are automatically added
      to the temporary indexs file.

:Example: 
   Used in derived classes that replace the standard
   :meth:`run` (or :meth:`__init__`) methods with something like::

      def run(self,*args,**kwargs):
          kwargs = self._fake_multi_ndx(**kwargs)            
          return super(G_mindist, self).run(*args, **kwargs)

Class GromacsCommandMultiIndex

__init__(self, **kwargs) (Constructor)

run(self, *args, **kwargs)

_fake_multi_ndx(self, **kwargs)

init(self, **kwargs)
(Constructor)