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)
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)
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)