Top level Python module is now "openmm" (#3000)

* Top level Python module is now "openmm"

* Updated module names in examples

* Updated module names in documentation

* Updated module in CI scripts

* Added deprecation warning

wrappers/python/simtk/openmm/app/dcdfile.py → wrappers/python/openmm/app/dcdfile.py

@@ -37,9 +37,9 @@ import os
 import time
 import struct
 import math
-from simtk.unit import picoseconds, nanometers, angstroms, is_quantity, norm
-from simtk.openmm import Vec3
-from simtk.openmm.app.internal.unitcell import computeLengthsAndAngles
+from openmm.unit import picoseconds, nanometers, angstroms, is_quantity, norm
+from openmm import Vec3
+from openmm.app.internal.unitcell import computeLengthsAndAngles
 
 class DCDFile(object):
     """DCDFile provides methods for creating DCD files.

wrappers/python/simtk/openmm/app/dcdreporter.py → wrappers/python/openmm/app/dcdreporter.py

@@ -32,9 +32,9 @@ from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
-import simtk.openmm as mm
-from simtk.openmm.app import DCDFile
-from simtk.unit import nanometer
+import openmm as mm
+from openmm.app import DCDFile
+from openmm.unit import nanometer
 
 class DCDReporter(object):
     """DCDReporter outputs a series of frames from a Simulation to a DCD file.

wrappers/python/simtk/openmm/app/desmonddmsfile.py → wrappers/python/openmm/app/desmonddmsfile.py

@@ -29,17 +29,17 @@ from __future__ import print_function
 import os
 import math
 
-from simtk import openmm as mm
-from simtk.openmm.app import forcefield as ff
-from simtk.openmm.app import Element, Topology, PDBFile
-from simtk.openmm.app.element import hydrogen
-from simtk.unit import (nanometer, angstrom, dalton, radian,
+import openmm as mm
+from openmm.app import forcefield as ff
+from openmm.app import Element, Topology, PDBFile
+from openmm.app.element import hydrogen
+from openmm.unit import (nanometer, angstrom, dalton, radian,
                         kilocalorie_per_mole, kilojoule_per_mole,
                         degree, elementary_charge, femtosecond)
 
-from simtk.openmm.app.amberprmtopfile import HCT
-from simtk.openmm.app.internal.customgbforces import GBSAHCTForce
-import simtk.unit as u
+from openmm.app.amberprmtopfile import HCT
+from openmm.app.internal.customgbforces import GBSAHCTForce
+import openmm.unit as u
 
 
 class DesmondDMSFile(object):

wrappers/python/simtk/openmm/app/element.py → wrappers/python/openmm/app/element.py

@@ -34,7 +34,7 @@ __version__ = "1.0"
 
 import sys
 from collections import OrderedDict
-from simtk.unit import daltons, is_quantity
+from openmm.unit import daltons, is_quantity
 if sys.version_info >= (3, 0):
     import copyreg
 else:
@@ -44,7 +44,7 @@ else:
 class Element(object):
     """An Element represents a chemical element.
 
-    The simtk.openmm.app.element module contains objects for all the standard chemical elements,
+    The openmm.app.element module contains objects for all the standard chemical elements,
     such as element.hydrogen or element.carbon.  You can also call the static method Element.getBySymbol() to
     look up the Element with a particular chemical symbol.
 

wrappers/python/simtk/openmm/app/forcefield.py → wrappers/python/openmm/app/forcefield.py

@@ -41,12 +41,12 @@ import warnings
 from math import sqrt, cos
 from copy import deepcopy
 from collections import defaultdict
-import simtk.openmm as mm
-import simtk.unit as unit
+import openmm as mm
+import openmm.unit as unit
 from . import element as elem
-from simtk.openmm.app import Topology
-from simtk.openmm.app.internal.singleton import Singleton
-from simtk.openmm.app.internal import compiled
+from openmm.app import Topology
+from openmm.app.internal.singleton import Singleton
+from openmm.app.internal import compiled
 
 # Directories from which to load built in force fields.
 
@@ -497,7 +497,7 @@ class ForceField(object):
         ::
            success = generator(forcefield, residue)
 
-        where ``forcefield`` is the calling ``ForceField`` object and ``residue`` is a simtk.openmm.app.topology.Residue object.
+        where ``forcefield`` is the calling ``ForceField`` object and ``residue`` is a openmm.app.topology.Residue object.
 
         ``generator`` must conform to the following API:
 
@@ -506,9 +506,9 @@ class ForceField(object):
 
            Parameters
            ----------
-           forcefield : simtk.openmm.app.ForceField
+           forcefield : openmm.app.ForceField
                The ForceField object to which residue templates and/or parameters are to be added.
-           residue : simtk.openmm.app.Topology.Residue
+           residue : openmm.app.Topology.Residue
                The residue topology for which a template is to be generated.
 
            Returns

wrappers/python/simtk/openmm/app/gromacsgrofile.py → wrappers/python/openmm/app/gromacsgrofile.py

@@ -34,10 +34,10 @@ __version__ = "1.0"
 
 import os
 import sys
-from simtk.openmm import Vec3
-from simtk.openmm.app.internal.unitcell import reducePeriodicBoxVectors
+from openmm import Vec3
+from openmm.app.internal.unitcell import reducePeriodicBoxVectors
 from re import sub, match
-from simtk.unit import nanometers, angstroms, Quantity
+from openmm.unit import nanometers, angstroms, Quantity
 from . import element as elem
 try:
     import numpy

wrappers/python/simtk/openmm/app/gromacstopfile.py → wrappers/python/openmm/app/gromacstopfile.py

@@ -32,13 +32,13 @@ from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
-from simtk.openmm.app import Topology
-from simtk.openmm.app import PDBFile
+from openmm.app import Topology
+from openmm.app import PDBFile
 from . import forcefield as ff
 from . import element as elem
 from . import amberprmtopfile as prmtop
-import simtk.unit as unit
-import simtk.openmm as mm
+import openmm.unit as unit
+import openmm as mm
 import math
 import os
 import re

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py → wrappers/python/openmm/app/internal/amber_file_parser.py

@@ -50,11 +50,11 @@ try:
 except:
     np = None
 
-import simtk.unit as units
-import simtk.openmm
-from simtk.openmm.app import element as elem
-from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
-from simtk.openmm.vec3 import Vec3
+import openmm.unit as units
+import openmm
+from openmm.app import element as elem
+from openmm.app.internal.unitcell import computePeriodicBoxVectors
+from openmm.vec3 import Vec3
 from . import customgbforces as customgb
 
 #=============================================================================================
@@ -659,7 +659,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
 
     # Use pyopenmm implementation of OpenMM by default.
     if mm is None:
-        mm = simtk.openmm
+        mm = openmm
 
     # Create OpenMM System.
     if verbose: print("Creating OpenMM system...")