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)