def view_trajectory(self):
"""
Output the trajectory as a DCD file and views it in VMD
"""
if self.args['grid_LJr'].endswith('.nc') and (not os.path.isfile(self.args['grid_LJr'][:-2]+'dx')):
import AlGDock.IO
IO_Grid = AlGDock.IO.Grid()
IO_Grid.read(self.args['grid_LJr'])
IO_Grid.write(self.args['grid_LJr'][:-2]+'dx')
scriptFN = 'script.vmd'
script = ''
script += 'set ligand [mol new '+self.args['ligand_prmtop']+']\n'
script += 'mol addfile '+self.args['output_dcd']+' type dcd waitfor all\n'
script += 'mol new {%s} type {dx} first 0 last -1 step 1 waitfor 1\n'%(self.args['grid_LJr'][:-2]+'dx')
script += 'mol modstyle 0 1 Isosurface 10.000000 0 2 0 1 1\n'
scriptF = open(scriptFN,'w')
scriptF.write(script)
scriptF.close()
import AlGDock
vmdFN = AlGDock.findPaths(['vmd'])['vmd']
vmd_args = [vmdFN] + ['-e', scriptFN]
import subprocess
p = subprocess.call(vmd_args)
