Collection of Utility Tools

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

from chemsh import *
tools.takeSnapshots(fragObj[, dcd='_namd.dcd', xst='_namd.xst', pbc_wrap='non-solvent', nsnapshots=20, ff='charmm'])

Parameters:

  • fragObj: A Fragment instance (object), typically created from a PSF or PDB file for biomolecular dynamics simulations

  • dcd: DCD filename

  • 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