Example #1
0
def lmod(root, amber_prmtop, messages):
    """ Prepares a prmtop file for use with lmod """
    response = askyesno('lmod', 'Do you want to adjust LJ A-coefficients for '
                                'use with lmod?')
    if response:
        action = actions.lmod(amber_prmtop, ArgumentList(''))
        action.execute()
        messages.write('%s\n' % action)
Example #2
0
def deletepdb(root, amber_prmtop, messages):
    """ Asks the user if they want to delete the sections added by addPDB """
    response = askyesno('deletePDB',
                        'Do you want to delete the addPDB flags from %s?' %
                        amber_prmtop.parm)
    if response:
        action = actions.deletePDB(amber_prmtop, ArgumentList(''))
        action.execute()
        messages.write('%s\n' % action)
Example #3
0
def addatomicnumber(root, amber_prmtop, messages):
    """ Asks the user if they want to add ATOMIC_NUMBER to the prmtop """
    response = askyesno('addAtomicNumber',
                        'Do you want to add the ATOMIC_NUMBER section to %s?' % 
                        amber_prmtop.parm)
    if response:
        action = actions.addAtomicNumber(amber_prmtop, ArgumentList(''))
        action.execute()
        messages.write('%s\n' % action)