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/amd.py → wrappers/python/openmm/amd.py

@@ -32,8 +32,8 @@ from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
-from simtk.openmm import CustomIntegrator
-from simtk.unit import kilojoules_per_mole, is_quantity
+from openmm import CustomIntegrator
+from openmm.unit import kilojoules_per_mole, is_quantity
 
 class AMDIntegrator(CustomIntegrator):
     """AMDIntegrator implements the aMD integration algorithm.

wrappers/python/openmm/app/__init__.py

+"""
+OpenMM Application
+"""
+from __future__ import absolute_import
+
+__docformat__ = "epytext en"
+
+__author__ = "Peter Eastman"
+__copyright__ = "Copyright 2016-2019, Stanford University and Peter Eastman"
+__credits__ = []
+__license__ = "MIT"
+__maintainer__ = "Peter Eastman"
+__email__ = "peastman@stanford.edu"
+
+from .topology import Topology, Chain, Residue, Atom
+from .pdbfile import PDBFile
+from .pdbxfile import PDBxFile
+from .forcefield import ForceField
+from .simulation import Simulation
+from .pdbreporter import PDBReporter, PDBxReporter
+from .amberprmtopfile import AmberPrmtopFile, HCT, OBC1, OBC2, GBn, GBn2
+from .amberinpcrdfile import AmberInpcrdFile
+from .dcdfile import DCDFile
+from .gromacsgrofile import GromacsGroFile
+from .gromacstopfile import GromacsTopFile
+from .dcdreporter import DCDReporter
+from .modeller import Modeller
+from .statedatareporter import StateDataReporter
+from .element import Element
+from .desmonddmsfile import DesmondDMSFile
+from .checkpointreporter import CheckpointReporter
+from .charmmcrdfiles import CharmmCrdFile, CharmmRstFile
+from .charmmparameterset import CharmmParameterSet
+from .charmmpsffile import CharmmPsfFile, CharmmPSFWarning
+from .simulatedtempering import SimulatedTempering
+from .metadynamics import Metadynamics, BiasVariable
+
+# Enumerated values
+
+NoCutoff = forcefield.NoCutoff
+CutoffNonPeriodic = forcefield.CutoffNonPeriodic
+CutoffPeriodic = forcefield.CutoffPeriodic
+Ewald = forcefield.Ewald
+PME = forcefield.PME
+LJPME = forcefield.LJPME
+
+HBonds = forcefield.HBonds
+AllBonds = forcefield.AllBonds
+HAngles = forcefield.HAngles
+
+Single = topology.Single
+Double = topology.Double
+Triple = topology.Triple
+Aromatic = topology.Aromatic
+Amide = topology.Amide
+

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

@@ -33,8 +33,8 @@ __author__ = "Peter Eastman"
 __version__ = "1.0"
 
 from functools import wraps
-from simtk.openmm.app.internal import amber_file_parser
-from simtk.unit import Quantity, nanometers, picoseconds
+from openmm.app.internal import amber_file_parser
+from openmm.unit import Quantity, nanometers, picoseconds
 import warnings
 try:
     import numpy as np

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

@@ -33,15 +33,15 @@ __author__ = "Peter Eastman"
 __version__ = "1.0"
 
 from math import sqrt
-from simtk.openmm.app import Topology
-from simtk.openmm.app import PDBFile
-from simtk.openmm.app.internal import amber_file_parser
-from simtk.openmm.app.internal.singleton import Singleton
+from openmm.app import Topology
+from openmm.app import PDBFile
+from openmm.app.internal import amber_file_parser
+from openmm.app.internal.singleton import Singleton
 from . import forcefield as ff
 from . import element as elem
-import simtk.unit as u
-import simtk.openmm as mm
-from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
+import openmm.unit as u
+import openmm as mm
+from openmm.app.internal.unitcell import computePeriodicBoxVectors
 
 # Enumerated values for implicit solvent model
 

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

@@ -36,9 +36,9 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 from __future__ import absolute_import
 from __future__ import print_function
 
-from simtk.openmm.app.internal.charmm.exceptions import CharmmFileError
-import simtk.unit as u
-from simtk.openmm.vec3 import Vec3
+from openmm.app.internal.charmm.exceptions import CharmmFileError
+import openmm.unit as u
+from openmm.vec3 import Vec3
 
 CHARMMLEN = 22
 TIMESCALE = 4.888821E-14 * 1e12 # AKMA time units to picoseconds

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

@@ -35,14 +35,14 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 from __future__ import absolute_import
 import os
-from simtk.openmm.app.internal.charmm._charmmfile import (
+from openmm.app.internal.charmm._charmmfile import (
             CharmmFile, CharmmStreamFile)
-from simtk.openmm.app.internal.charmm.topologyobjects import (
+from openmm.app.internal.charmm.topologyobjects import (
             AtomType, BondType, AngleType, DihedralType, ImproperType, CmapType,
             UreyBradleyType, NoUreyBradley)
-from simtk.openmm.app.internal.charmm.exceptions import CharmmFileError
-from simtk.openmm.app.element import Element, get_by_symbol
-import simtk.unit as u
+from openmm.app.internal.charmm.exceptions import CharmmFileError
+from openmm.app.element import Element, get_by_symbol
+import openmm.unit as u
 import warnings
 
 class CharmmParameterSet(object):

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

@@ -38,20 +38,20 @@ from math import pi, cos, sin, sqrt
 import os
 import re
 import sys
-import simtk.openmm as mm
-from simtk.openmm.vec3 import Vec3
-import simtk.unit as u
-from simtk.openmm.app import (forcefield as ff, Topology, element, PDBFile)
-from simtk.openmm.app.amberprmtopfile import HCT, OBC1, OBC2, GBn, GBn2
-from simtk.openmm.app.internal.customgbforces import (GBSAHCTForce,
+import openmm as mm
+from openmm.vec3 import Vec3
+import openmm.unit as u
+from openmm.app import (forcefield as ff, Topology, element, PDBFile)
+from openmm.app.amberprmtopfile import HCT, OBC1, OBC2, GBn, GBn2
+from openmm.app.internal.customgbforces import (GBSAHCTForce,
                 GBSAOBC1Force, GBSAOBC2Force, GBSAGBnForce, GBSAGBn2Force)
-from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
+from openmm.app.internal.unitcell import computePeriodicBoxVectors
 # CHARMM imports
-from simtk.openmm.app.internal.charmm.topologyobjects import (
+from openmm.app.internal.charmm.topologyobjects import (
                 ResidueList, AtomList, TrackedList, Bond, Angle, Dihedral,
                 Improper, AcceptorDonor, Group, Cmap, UreyBradley,
                 NoUreyBradley)
-from simtk.openmm.app.internal.charmm.exceptions import (
+from openmm.app.internal.charmm.exceptions import (
                 CharmmPSFError, MoleculeError, CharmmPSFWarning,
                 MissingParameter, CharmmPsfEOF)
 import warnings

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

@@ -32,7 +32,7 @@ from __future__ import absolute_import
 __author__ = "Robert McGibbon"
 __version__ = "1.0"
 
-import simtk.openmm as mm
+import openmm as mm
 import os
 import os.path
 

wrappers/python/simtk/openmm/app/data/absinth.xml → wrappers/python/openmm/app/data/absinth.xml

@@ -4516,7 +4516,7 @@
   <Atom type="534" charge="-1.0" ljType="22" epsilon="0.29288" radius="2.16" chargeGroup="103" solvGroup="-1" maxSav="1" fos="0" volReduction="1"/>
  </CustomGBForce>
  <Script>
-import simtk.openmm as mm
+import openmm as mm
 gb = [f for f in [sys.getForce(i) for i in range(sys.getNumForces())] if type(f) == mm.CustomGBForce][0]
 
 # Add Lennard-Jones exceptions.