
***************************
Collection of Utility Tools
***************************


The module `tools` contains a collection of convenience functions and will be
loaded when doing::

   from chemsh import *

.. py:module:: tools

.. py:function:: takeSnapshots(fragObj[, dcd='_namd.dcd', xst='_namd.xst', pbc_wrap='non-solvent', nsnapshots=20, ff='charmm'])

   Parameters:
   
   * fragObj: A :py:class:`Fragment` instance (object), typically created from a PSF or PDB file for biomolecular dynamics simulations
   
   * dcd: :py:attr:`DCD <dcd>` filename
   
   * xst: :py:attr:`XST <xst>` filename
   
   * pbc_wrap: Common names for selecting what to PBC wrap around. Currently supported names include: ``'non-solvent'`` (default, where solvent also includes ions), ``'protein'``, ``'water'``, and ``'ions'``. 
   
   * nsnapshots: Number of snapshots to take

   * ff: Forcefield scheme name
