Update imports in examples.

examples/amber/simulate_amber_gb.py

@@ -8,13 +8,12 @@ import simtk.openmm as mm
 import simtk.openmm.app as app
 
 # ParmEd Imports
-from chemistry.amber import AmberParm
-from chemistry.openmm.reporters import StateDataReporter, NetCDFReporter
-from chemistry import unit as u
+from parmed import load_file, unit as u
+from parmed.openmm import StateDataReporter, NetCDFReporter
 
 # Load the Amber files
 print('Loading AMBER files...')
-ala5_gas = AmberParm('ala5_gas.parm7', 'ala5_gas.rst7')
+ala5_gas = load_file('ala5_gas.parm7', 'ala5_gas.rst7')
 
 # Create the OpenMM system
 print('Creating OpenMM System')

examples/amber/simulate_amber_pme.py

@@ -8,13 +8,12 @@ import simtk.openmm as mm
 import simtk.openmm.app as app
 
 # ParmEd Imports
-from chemistry.amber import AmberParm
-from chemistry.openmm.reporters import StateDataReporter, NetCDFReporter
-from chemistry import unit as u
+from parmed import load_file, unit as u
+from parmed.openmm import StateDataReporter, NetCDFReporter
 
 # Load the Amber files
 print('Loading AMBER files...')
-ala2_solv = AmberParm('ala2_solv.parm7', 'ala2_solv.rst7')
+ala2_solv = load_file('ala2_solv.parm7', 'ala2_solv.rst7')
 
 # Create the OpenMM system
 print('Creating OpenMM System')

examples/charmm/simulate_charmm_gb.py

@@ -8,15 +8,15 @@ import simtk.openmm as mm
 import simtk.openmm.app as app
 
 # ParmEd Imports
-from chemistry.charmm import CharmmPsfFile, CharmmCrdFile, CharmmParameterSet
-from chemistry.openmm import StateDataReporter
-from chemistry import unit as u
+from parmed import load_file, unit as u
+from parmed.charmm import CharmmParameterSet
+from parmed.openmm import StateDataReporter
 
 # Load the CHARMM files
 print('Loading CHARMM files...')
 params = CharmmParameterSet('toppar/par_all36_prot.prm')
-ala5_gas = CharmmPsfFile('ala5_autopsf.psf')
-ala5_crds = app.PDBFile('ala5_autopsf.pdb')
+ala5_gas = load_file('ala5_autopsf.psf')
+ala5_crds = load_file('ala5_autopsf.pdb')
 
 # NOTE NOTE
 # The parameter set we used here is the CHARMM 36 force field, but this is

examples/charmm/simulate_charmm_gui.py

@@ -8,16 +8,16 @@ import simtk.openmm as mm
 import simtk.openmm.app as app
 
 # ParmEd Imports
-from chemistry.charmm import CharmmPsfFile, CharmmCrdFile, CharmmParameterSet
-from chemistry.openmm.reporters import StateDataReporter
-from chemistry import unit as u
+from parmed import load_file, unit as u
+from parmed.charmm import CharmmParameterSet
+from parmed.openmm import StateDataReporter
 
 # Load the CHARMM files
 print('Loading CHARMM files...')
 params = CharmmParameterSet('toppar/par_all36_prot.prm',
                             'toppar/toppar_water_ions.str')
-ala2_solv = CharmmPsfFile('ala2_charmmgui.psf')
-ala2_crds = CharmmCrdFile('ala2_charmmgui.crd')
+ala2_solv = load_file('ala2_charmmgui.psf')
+ala2_crds = load_file('ala2_charmmgui.crd')
 
 # NOTE NOTE
 # The parameter set we used here is the CHARMM 36 force field, but this is

examples/gromacs/simulate_gromacs_gb.py

@@ -8,14 +8,13 @@ import simtk.openmm as mm
 import simtk.openmm.app as app
 
 # ParmEd Imports
-from chemistry import load_file
-from chemistry.openmm.reporters import NetCDFReporter
-from chemistry import unit as u
+from parmed import load_file
+from parmed.openmm.reporters import NetCDFReporter
+from parmed import unit as u
 
 # Load the Gromacs files
 print('Loading Gromacs files...')
-top = load_file('dhfr_gas.top')
-gro = load_file('dhfr_gas.gro')
+top = load_file('dhfr_gas.top', xyz='dhfr_gas.gro')
 
 # Create the OpenMM system
 print('Creating OpenMM System')
@@ -40,7 +39,7 @@ prop = dict(CudaPrecision='mixed') # Use mixed single/double precision
 sim = app.Simulation(top.topology, system, integrator, platform, prop)
 
 # Set the particle positions
-sim.context.setPositions(gro.positions)
+sim.context.setPositions(top.positions)
 
 # Minimize the energy
 print('Minimizing energy')

examples/gromacs/simulate_gromacs_pme.py

@@ -8,17 +8,13 @@ import simtk.openmm as mm
 import simtk.openmm.app as app
 
 # ParmEd Imports
-from chemistry import load_file
-from chemistry.openmm.reporters import NetCDFReporter
-from chemistry import unit as u
+from parmed import load_file
+from parmed.openmm.reporters import NetCDFReporter
+from parmed import unit as u
 
 # Load the Gromacs files
 print('Loading Gromacs files...')
-top = load_file('dhfr_pme.top')
-gro = load_file('dhfr_pme.gro')
-
-# Transfer the unit cell information from the GRO file to the top object
-top.box = gro.box[:]
+top = load_file('dhfr_pme.top', xyz='dhfr_pme.gro')
 
 # Create the OpenMM system
 print('Creating OpenMM System')
@@ -43,7 +39,7 @@ prop = dict(CudaPrecision='mixed') # Use mixed single/double precision
 sim = app.Simulation(top.topology, system, integrator, platform, prop)
 
 # Set the particle positions
-sim.context.setPositions(gro.positions)
+sim.context.setPositions(top.positions)
 
 # Minimize the energy
 print('Minimizing energy')

examples/rosetta/simulate_ala12_mutant.py

@@ -8,7 +8,7 @@ from simtk.openmm.app import *
 from simtk.unit import *
 
 # ParmEd imports
-from chemistry import load_rosetta
+from parmed import load_rosetta
 
 # PyRosetta imports
 from toolbox import mutate_residue