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

.travis.yml

@@ -212,7 +212,7 @@ script:
       else
           make PythonInstall;
       fi;
-      python -m simtk.testInstallation;
+      python -m openmm.testInstallation;
       (cd python/tests && py.test -v);
     fi
 

devtools/ci/jenkins/install_and_test_cpu.sh

@@ -6,5 +6,5 @@ python devtools/run-ctest.py --job-duration=120 --timeout 300 --in-order -R 'Tes
 
 # Build & test Python
 make PythonInstall
-python -m simtk.testInstallation
+python -m openmm.testInstallation
 cd python/tests && py.test -v

devtools/packaging/install.sh

@@ -54,7 +54,7 @@ then
     echo "Installation is complete.  You should now test your installation to make sure"
     echo "it is working correctly by typing the following command:"
     echo
-    echo "python -m simtk.testInstallation"
+    echo "python -m openmm.testInstallation"
 else
     echo
     echo "INSTALLATION FAILED"

docs-source/api-python/app.rst.jinja2

@@ -20,11 +20,11 @@ Representation and Manipulation
     :toctree: generated/
     :template: class.rst
 
-    ~simtk.openmm.app.topology.Topology
-    ~simtk.openmm.app.topology.Chain
-    ~simtk.openmm.app.topology.Residue
-    ~simtk.openmm.app.topology.Atom
-    ~simtk.openmm.app.modeller.Modeller
+    ~openmm.app.topology.Topology
+    ~openmm.app.topology.Chain
+    ~openmm.app.topology.Residue
+    ~openmm.app.topology.Atom
+    ~openmm.app.modeller.Modeller
 
 Simulation
 ~~~~~~~~~~
@@ -32,8 +32,8 @@ Simulation
     :toctree: generated/
     :template: class.rst
 
-    ~simtk.openmm.app.forcefield.ForceField
-    ~simtk.openmm.app.simulation.Simulation
+    ~openmm.app.forcefield.ForceField
+    ~openmm.app.simulation.Simulation
 
 
 Reporting Output

docs-source/api-python/conf.py

@@ -2,7 +2,7 @@
 
 import sys
 import os
-import simtk.openmm.version
+import openmm.version
 
 extensions = ['sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.autosummary',
               'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'process-docstring',
@@ -18,8 +18,8 @@ master_doc = 'index'
 project = u'OpenMM'
 copyright = u'2015, Stanford University and the Authors'
 
-version = simtk.openmm.version.short_version
-release = simtk.openmm.version.full_version
+version = openmm.version.short_version
+release = openmm.version.full_version
 
 exclude_patterns = ['_build', '_templates']
 html_static_path = ['_static']

docs-source/api-python/index.rst

-.. currentmodule:: simtk.openmm.openmm
+.. currentmodule:: openmm.openmm
 
 OpenMM Python API
 =================

docs-source/api-python/library.rst.jinja2

@@ -11,10 +11,10 @@ Core Objects
     :template: class.rst
     :nosignatures:
 
-    ~simtk.openmm.openmm.System
-    ~simtk.openmm.openmm.Context
-    ~simtk.openmm.openmm.Platform
-    ~simtk.openmm.openmm.State
+    ~openmm.openmm.System
+    ~openmm.openmm.Context
+    ~openmm.openmm.Platform
+    ~openmm.openmm.State
 
 
 Forces

docs-source/api-python/render.py

@@ -8,8 +8,8 @@ from glob import glob
 import inspect
 
 import jinja2
-import simtk.openmm
-import simtk.openmm.app
+import openmm
+import openmm.app
 
 
 
@@ -21,7 +21,7 @@ def library_template_variables():
     """Create the data structure available to the Jinja2 renderer when
     filling in the templates.
 
-    This function extracts all of classes in ``simtk.openmm.openmm`` and returns
+    This function extracts all of classes in ``openmm.openmm`` and returns
     a dictionary with them grouped into three lists, the integrators, the forces,
     and the remainder (library_extras).
 
@@ -35,31 +35,31 @@ def library_template_variables():
         'units': [],
     }
 
-    mm_klasses = inspect.getmembers(simtk.openmm, predicate=inspect.isclass)
+    mm_klasses = inspect.getmembers(openmm, predicate=inspect.isclass)
 
 
     # gather all Force subclasses
     for name, klass in mm_klasses:
-        if issubclass(klass, simtk.openmm.openmm.Force):
+        if issubclass(klass, openmm.openmm.Force):
             data['forces'].append(fullname(klass))
 
     # gather all Integrator subclasses
     for _, klass in mm_klasses:
-        if issubclass(klass, simtk.openmm.openmm.Integrator):
+        if issubclass(klass, openmm.openmm.Integrator):
             data['integrators'].append(fullname(klass))
 
-    # gather all extra subclasses in simtk.openmm.openmm
+    # gather all extra subclasses in openmm.openmm
 
     # core classes that are already included in library.rst.jinja2
-    exclude = ['simtk.openmm.openmm.Platform', 'simtk.openmm.openmm.Context',
-              'simtk.openmm.openmm.System', 'simtk.openmm.openmm.State']
+    exclude = ['openmm.openmm.Platform', 'openmm.openmm.Context',
+              'openmm.openmm.System', 'openmm.openmm.State']
     exclude.extend(data['forces'])
     exclude.extend(data['integrators'])
 
     # these classes are useless and not worth documenting.
     exclude.extend([
-        'simtk.openmm.openmm.SwigPyIterator',
-        'simtk.openmm.openmm.OpenMMException'])
+        'openmm.openmm.SwigPyIterator',
+        'openmm.openmm.OpenMMException'])
 
     for _, klass in mm_klasses:
         full = fullname(klass)
@@ -67,7 +67,7 @@ def library_template_variables():
             data['library_extras'].append(full)
 
     # gather units related classes
-    unit_klasses = inspect.getmembers(simtk.unit, predicate=inspect.isclass)
+    unit_klasses = inspect.getmembers(openmm.unit, predicate=inspect.isclass)
     for name, klass in unit_klasses:
         data['units'].append(fullname(klass))
 
@@ -78,7 +78,7 @@ def app_template_variables():
     """Create the data structure available to the Jinja2 renderer when
     filling in the templates.
 
-    This function extracts all of classes in ``simtk.openmm.app`` and returns
+    This function extracts all of classes in ``openmm.app`` and returns
     a dictionary with them grouped into three lists, the reporters, the
     classes with the word "File" in the name, and the remainder.
 
@@ -90,7 +90,7 @@ def app_template_variables():
         'fileclasses': [],
         'app_extras': [],
     }
-    app_klasses = inspect.getmembers(simtk.openmm.app, predicate=inspect.isclass)
+    app_klasses = inspect.getmembers(openmm.app, predicate=inspect.isclass)
 
     # gather all Reporters
     for name, klass in app_klasses:
@@ -102,14 +102,14 @@ def app_template_variables():
         if 'File' in name or 'CharmmParameterSet' in name:
             data['fileclasses'].append(fullname(klass))
 
-    # gather all extra subclasses in simtk.openmm.app
-    exclude = ['simtk.openmm.app.topology.Topology',
-               'simtk.openmm.app.topology.Chain',
-               'simtk.openmm.app.topology.Residue',
-               'simtk.openmm.app.topology.Atom',
-               'simtk.openmm.app.modeller.Modeller',
-               'simtk.openmm.app.forcefield.ForceField',
-               'simtk.openmm.app.simulation.Simulation']
+    # gather all extra subclasses in openmm.app
+    exclude = ['openmm.app.topology.Topology',
+               'openmm.app.topology.Chain',
+               'openmm.app.topology.Residue',
+               'openmm.app.topology.Atom',
+               'openmm.app.modeller.Modeller',
+               'openmm.app.forcefield.ForceField',
+               'openmm.app.simulation.Simulation']
     exclude.extend(data['reporters'])
     exclude.extend(data['fileclasses'])
 

docs-source/licenses/Licenses.txt

@@ -126,7 +126,7 @@ freely, subject to the following restrictions:
 OpenMM uses the PDBx/mmCIF parser written by John Westbrook.  It is distributed
 under the Creative Commons Attribution 3.0 Unported license.  For details, see
 https://creativecommons.org/licenses/by/3.0.  This library was modified to move
-it inside the simtk.openmm.app.internal module.
+it inside the openmm.app.internal module.
 
 
 7. irrXML

docs-source/usersguide/application.rst

@@ -95,7 +95,7 @@ CUDA version it was compiled with.
 4. Verify your installation by typing the following command:
 ::
 
-    python -m simtk.testInstallation
+    python -m openmm.testInstallation
 
 This command confirms that OpenMM is installed, checks whether GPU acceleration
 is available (via the OpenCL and/or CUDA platforms), and verifies that all
@@ -121,9 +121,9 @@ steps.
 .. samepage::
     ::
 
-        from simtk.openmm.app import *
-        from simtk.openmm import *
-        from simtk.unit import *
+        from openmm.app import *
+        from openmm import *
+        from openmm.unit import *
         from sys import stdout
 
         pdb = PDBFile('input.pdb')
@@ -164,9 +164,9 @@ You can name your own scripts whatever you want.  Let’s go through the script
 by line and see how it works.
 ::
 
-    from simtk.openmm.app import *
-    from simtk.openmm import *
-    from simtk.unit import *
+    from openmm.app import *
+    from openmm import *
+    from openmm.unit import *
     from sys import stdout
 
 These lines are just telling the Python interpreter about some libraries we will
@@ -299,9 +299,9 @@ found in OpenMM’s :file:`examples` folder with the name :file:`simulateAmber.p
 .. samepage::
     ::
 
-        from simtk.openmm.app import *
-        from simtk.openmm import *
-        from simtk.unit import *
+        from openmm.app import *
+        from openmm import *
+        from openmm.unit import *
         from sys import stdout
 
         prmtop = AmberPrmtopFile('input.prmtop')
@@ -392,9 +392,9 @@ with the name :file:`simulateGromacs.py`.
 .. samepage::
     ::
 
-        from simtk.openmm.app import *
-        from simtk.openmm import *
-        from simtk.unit import *
+        from openmm.app import *
+        from openmm import *
+        from openmm.unit import *
         from sys import stdout
 
         gro = GromacsGroFile('input.gro')
@@ -456,9 +456,9 @@ on the :class:`CharmmPsfFile`.
 .. samepage::
     ::
 
-        from simtk.openmm.app import *
-        from simtk.openmm import *
-        from simtk.unit import *
+        from openmm.app import *
+        from openmm import *
+        from openmm.unit import *
         from sys import stdout, exit, stderr
 
         psf = CharmmPsfFile('input.psf')
@@ -824,7 +824,7 @@ Field Initiative small molecule force fields using the following example:
     from openmmforcefields.generators import SMIRNOFFTemplateGenerator
     smirnoff = SMIRNOFFTemplateGenerator(molecules=molecule)
     # Create an OpenMM ForceField object with AMBER ff14SB and TIP3P with compatible ions
-    from simtk.openmm.app import ForceField
+    from openmm.app import ForceField
     forcefield = ForceField('amber/protein.ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml')
     # Register the SMIRNOFF template generator
     forcefield.registerTemplateGenerator(smirnoff.generator)
@@ -840,14 +840,14 @@ Alternatively, you can use the older `AMBER GAFF small molecule force field <htt
     from openmmforcefields.generators import GAFFTemplateGenerator
     gaff = GAFFTemplateGenerator(molecules=molecule)
     # Create an OpenMM ForceField object with AMBER ff14SB and TIP3P with compatible ions
-    from simtk.openmm.app import ForceField
+    from openmm.app import ForceField
     forcefield = ForceField('amber/protein.ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml')
     # Register the GAFF template generator
     forcefield.registerTemplateGenerator(gaff.generator)
     # You can now parameterize an OpenMM Topology object that contains the specified molecule.
     # forcefield will load the appropriate GAFF parameters when needed, and antechamber
     # will be used to generate small molecule parameters on the fly.
-    from simtk.openmm.app import PDBFile
+    from openmm.app import PDBFile
     pdbfile = PDBFile('t4-lysozyme-L99A-with-benzene.pdb')
     system = forcefield.createSystem(pdbfile.topology)
 
@@ -864,8 +864,8 @@ small molecule force field you want to use:
 ::
 
     # Define the keyword arguments to feed to ForceField
-    from simtk import unit
-    from simtk.openmm import app
+    from openmm import unit
+    from openmm import app
     forcefield_kwargs = { 'constraints' : app.HBonds, 'rigidWater' : True, 'removeCMMotion' : False, 'hydrogenMass' : 4*unit.amu }
     # Initialize a SystemGenerator using the Open Force Field Initiative 1.2.0 force field (openff-1.2.0)
     from openmmforcefields.generators import SystemGenerator
@@ -1787,9 +1787,9 @@ PDB file.
 .. samepage::
     ::
 
-        from simtk.openmm.app import *
-        from simtk.openmm import *
-        from simtk.unit import *
+        from openmm.app import *
+        from openmm import *
+        from openmm.unit import *
 
         print('Loading...')
         pdb = PDBFile('input.pdb')
@@ -3261,9 +3261,9 @@ This :code:`generator` function must conform to the following API:
         """
         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

docs-source/usersguide/library.rst

@@ -2598,14 +2598,14 @@ is set with the :code:`LD_LIBRARY_PATH` environment variable on Linux,
 :code:`DYLD_LIBRARY_PATH` on Mac, or :code:`PATH` on Windows.  See
 Chapter :ref:`installing-openmm` for details.
 
-The Python API is contained in the simtk.openmm package, while the units code is
-contained in the simtk.units package.  (The application layer, described in the
-Application Guide, is contained in the simtk.openmm.app package.)  A program
+The Python API is contained in the openmm package, while the units code is
+contained in the openmm.units package.  (The application layer, described in the
+Application Guide, is contained in the openmm.app package.)  A program
 using it will therefore typically begin
 ::
 
-    import simtk.openmm as mm
-    import simtk.unit as unit
+    import openmm as mm
+    import openmm.unit as unit
 
 Creating and using OpenMM objects is then done exactly as in C++:
 ::
@@ -2675,7 +2675,7 @@ quantity is “0.63 kilograms”.  A Quantity is expressed as a combination of a
 value (e.g., 0.63), and a Unit (e.g., kilogram).  The same Quantity can be
 expressed in different Units.
 
-The set of BaseDimensions defined in the simtk.unit module includes:
+The set of BaseDimensions defined in the openmm.unit module includes:
 
 * mass
 * length
@@ -2687,8 +2687,8 @@ The set of BaseDimensions defined in the simtk.unit module includes:
 
 
 These are not precisely the same list of base dimensions used in the SI unit
-system.  SI defines “current” (charge per time) as a base unit, while simtk.unit
-uses “charge”.  And simtk.unit treats angle as a dimension, even though angle
+system.  SI defines “current” (charge per time) as a base unit, while openmm.unit
+uses “charge”.  And openmm.unit treats angle as a dimension, even though angle
 quantities are often considered dimensionless.  In this case, we choose to err
 on the side of explicitness, particularly because interconversion of degrees and
 radians is a frequent source of unit headaches.
@@ -2696,16 +2696,16 @@ radians is a frequent source of unit headaches.
 Units examples
 --------------
 
-Many common units are defined in the simtk.unit module.
+Many common units are defined in the openmm.unit module.
 ::
 
-    from simtk.unit import nanometer, angstrom, dalton
+    from openmm.unit import nanometer, angstrom, dalton
 
 Sometimes you don’t want to type the full unit name every time, so you can
 assign it a shorter name using the :code:`as` functionality:
 ::
 
-    from simtk.unit import nanometer as nm
+    from openmm.unit import nanometer as nm
 
 New quantities can be created from a value and a unit.  You can use either the
 multiply operator (‘*’) or the explicit Quantity constructor:
@@ -2743,7 +2743,7 @@ Multiplying or dividing two quantities creates a new quantity with a composite
 dimension.  For example, dividing a distance by a time results in a velocity.
 ::
 
-    from simtk.unit import kilogram, meter, second
+    from openmm.unit import kilogram, meter, second
     a = 9.8 * meter / second**2; # acceleration
     m = 0.36 * kilogram; # mass
     F = m * a; # force in kg*m/s**2::
@@ -2754,13 +2754,13 @@ Multiplication or division of two Units results in a composite Unit.
 
     mps = meter / second
 
-Unlike amount (moles), angle (radians) is arguably dimensionless.  But simtk.unit
+Unlike amount (moles), angle (radians) is arguably dimensionless.  But openmm.unit
 treats angle as another dimension.   Use the trigonometric functions from the
-simtk.unit module (not those from the Python math module!) when dealing with
+openmm.unit module (not those from the Python math module!) when dealing with
 Units and Quantities.
 ::
 
-    from simtk.unit import sin, cos, acos
+    from openmm.unit import sin, cos, acos
     x = sin(90.0*degrees)
     angle = acos(0.68); # returns an angle quantity (in radians)
 
@@ -2776,10 +2776,10 @@ Quantities and Units.
 
 The method :code:`sqrt()` is not as built-in as :code:`pow()`\ .  Do not
 use the Python :code:`math.sqrt()` method with Units and Quantities.  Use
-the :code:`simtk.unit.sqrt()` method instead:
+the :code:`openmm.unit.sqrt()` method instead:
 ::
 
-    from simtk.unit import sqrt
+    from openmm.unit import sqrt
     side_length = sqrt(4.0*meter**2)
 
 
@@ -2787,7 +2787,7 @@ Atomic scale mass and energy units are “per amount”
 ---------------------------------------------------
 
 Mass and energy units at the atomic scale are specified “per amount” in the
-simtk.unit module.  Amount (mole) is one of the seven fundamental dimensions in
+openmm.unit module.  Amount (mole) is one of the seven fundamental dimensions in
 the SI unit system.   The atomic scale mass unit, dalton, is defined as grams
 per mole.  The dimension of dalton is therefore mass/amount, instead of simply
 mass.  Similarly, the atomic scale energy unit, kilojoule_per_mole (and
@@ -2812,11 +2812,11 @@ SI prefixes
 -----------
 
 Many units with SI prefixes such as “milligram” (milli) and “kilometer” (kilo)
-are provided in the simtk.unit module.  Others can be created by multiplying a
+are provided in the openmm.unit module.  Others can be created by multiplying a
 prefix symbol by a non-prefixed unit:
 ::
 
-    from simtk.unit import mega, kelvin
+    from openmm.unit import mega, kelvin
     megakelvin = mega * kelvin
     t = 8.3 * megakelvin
 
@@ -2831,13 +2831,13 @@ Use the :code:`Quantity.in_units_of()` method to create a new Quantity with
 different units.
 ::
 
-    from simtk.unit import nanosecond, fortnight
+    from openmm.unit import nanosecond, fortnight
     x = (175000*nanosecond).in_units_of(fortnight)
 
 When you want a plain number out of a Quantity, use the :code:`value_in_unit()` method:
 ::
 
-    from simtk.unit import femtosecond, picosecond
+    from openmm.unit import femtosecond, picosecond
     t = 5.0*femtosecond
     t_just_a_number = t.value_in_unit(picoseconds)
 
@@ -2850,7 +2850,7 @@ Lists, tuples, vectors, numpy arrays, and Units
 -----------------------------------------------
 
 Units can be attached to containers of numbers to create a vector quantity.  The
-simtk.unit module overloads the :code:`__setitem__` and
+openmm.unit module overloads the :code:`__setitem__` and
 :code:`__getitem__` methods for these containers to ensure that Quantities go
 in and out.
 ::

examples/argon-chemical-potential.py

@@ -16,8 +16,8 @@
 # J. Chem. Phys. 129:124105 (2008)  http://dx.doi.org/10.1063/1.2978177
 
 from __future__ import print_function
-from simtk.openmm import *
-from simtk.unit import *
+from openmm import *
+from openmm.unit import *
 import numpy
 
 # =============================================================================

examples/benchmark.py

 from __future__ import print_function
-import simtk.openmm.app as app
-import simtk.openmm as mm
-import simtk.unit as unit
+import openmm.app as app
+import openmm as mm
+import openmm.unit as unit
 import sys
 from datetime import datetime
 import os

examples/simulateAmber.py

-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
 from sys import stdout
 
 prmtop = AmberPrmtopFile('input.prmtop')

examples/simulateCharmm.py

-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
 from sys import stdout, exit, stderr
 
 # Read the PSF

examples/simulateGromacs.py

-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
 from sys import stdout
 
 gro = GromacsGroFile('input.gro')

examples/simulatePdb.py

-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
 from sys import stdout
 
 pdb = PDBFile('input.pdb')

wrappers/python/CMakeLists.txt

@@ -8,6 +8,7 @@ set(OPENMM_PYTHON_STAGING_DIR "${CMAKE_BINARY_DIR}/python"
 mark_as_advanced(OPENMM_PYTHON_STAGING_DIR)
 
 # Create package directory structure
+file(MAKE_DIRECTORY ${OPENMM_PYTHON_STAGING_DIR}/openmm)
 file(MAKE_DIRECTORY ${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm)
 file(MAKE_DIRECTORY ${OPENMM_PYTHON_STAGING_DIR}/simtk/unit)
 file(MAKE_DIRECTORY ${OPENMM_PYTHON_STAGING_DIR}/src/swig_doxygen/swig_lib/python)
@@ -37,14 +38,14 @@ execute_process(
 if(NOT rev_hash_str)
   set(rev_hash_str "Unknown")
 endif()
-file(WRITE "${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm/version.py" "git_revision = '${rev_hash_str}'\n")
+file(WRITE "${OPENMM_PYTHON_STAGING_DIR}/openmm/version.py" "git_revision = '${rev_hash_str}'\n")
 
 # file(GLOB_RECURSE temp RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}/src/*.i")
 # foreach(f ${temp})
 #     set(temp2 "${temp2}\n${f}")
 # endforeach()
 
-set(SUBDIRS src simtk tests)
+set(SUBDIRS src openmm simtk tests)
 foreach(SUBDIR ${SUBDIRS})
     file(GLOB_RECURSE STAGING_INPUT_FILES1 RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*README.txt"
@@ -189,10 +190,10 @@ INSTALL_FILES(/include/swig FILES "${SWIG_OPENMM_DIR}/OpenMMSwigHeaders.i" "${SW
 
 # Run swig
 add_custom_command(
-    OUTPUT "${SWIG_OPENMM_DIR}/OpenMMSwig.cxx" "${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm/openmm.py"
+    OUTPUT "${SWIG_OPENMM_DIR}/OpenMMSwig.cxx" "${OPENMM_PYTHON_STAGING_DIR}/openmm/openmm.py"
     COMMAND ${SWIG_EXECUTABLE}
         -python -c++
-        -outdir "${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm"
+        -outdir "${OPENMM_PYTHON_STAGING_DIR}/openmm"
         -o OpenMMSwig.cxx
         OpenMM.i
     WORKING_DIRECTORY "${SWIG_OPENMM_DIR}"
@@ -204,11 +205,11 @@ add_custom_command(
 )
 add_custom_target(RunSwig DEPENDS
     "${SWIG_OPENMM_DIR}/OpenMMSwig.cxx"
-    "${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm/openmm.py")
+    "${OPENMM_PYTHON_STAGING_DIR}/openmm/openmm.py")
 
 set (STAGING_OUTPUT_FILES ${STAGING_OUTPUT_FILES}
     "${OPENMM_PYTHON_STAGING_DIR}/src/swig_doxygen/OpenMMSwig.cxx"
-    "${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm/openmm.py")
+    "${OPENMM_PYTHON_STAGING_DIR}/openmm/openmm.py")
 
 ##################################################################################################
 ### Make a list of all folders containing include files the wrappers must be compiled against. ###

wrappers/python/MANIFEST.in

@@ -3,7 +3,7 @@ include *.py
 include *.txt
 global-include README
 recursive-include simtk     *.txt *.py
-recursive-include OpenMM    *.txt *.py *.so *.dll *.lib *.dylib *.h
+recursive-include openmm    *.txt *.py *.so *.dll *.lib *.dylib *.h
 recursive-include src       *.txt *.py *.i *.c *.cxx *.h *.sh Doxyfile
 prune src/swig_doxygen/doxygen/html
 prune src/swig_doxygen/doxygen/xml

wrappers/python/openmm/__init__.py

+"""OpenMM is a toolkit for molecular simulation. It can be used either as a
+stand-alone application for running simulations, or as a library you call
+from your own code. It provides a combination of extreme flexibility
+(through custom forces and integrators), openness, and high performance
+(especially on recent GPUs) that make it truly unique among simulation codes.
+"""
+from __future__ import absolute_import
+__author__ = "Peter Eastman"
+
+import os, os.path
+import sys
+from . import version
+
+if sys.platform == 'win32':
+    _path = os.environ['PATH']
+    os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % {
+        'lib': version.openmm_library_path, 'path': _path}
+
+from openmm.openmm import *
+from openmm.vec3 import Vec3
+from openmm.mtsintegrator import MTSIntegrator, MTSLangevinIntegrator
+from openmm.amd import AMDIntegrator, AMDForceGroupIntegrator, DualAMDIntegrator
+
+if os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(version.openmm_library_path):
+    pluginLoadedLibNames = Platform.loadPluginsFromDirectory(os.path.join(version.openmm_library_path, 'plugins'))
+else:
+    pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
+
+if sys.platform == 'win32':
+    os.environ['PATH'] = _path
+    del _path
+__version__ = Platform.getOpenMMVersion()
+
+class OpenMMException(Exception):
+    """This is the class used for all exceptions thrown by the C++ library."""
+    pass