Move charmm package to internal.

wrappers/python/setup.py

@@ -145,7 +145,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                                           "simtk.openmm",
                                           "simtk.openmm.app",
                                           "simtk.openmm.app.internal",
-                                          "simtk.openmm.app.charmm"]
+                                          "simtk.openmm.app.internal.charmm"]
     setupKeywords["data_files"]        = []
     setupKeywords["package_data"]      = {"simtk" : [],
                                           "simtk.unit" : [],

wrappers/python/simtk/openmm/app/__init__.py

@@ -26,8 +26,8 @@ from statedatareporter import StateDataReporter
 from element import Element
 from desmonddmsfile import DesmondDMSFile
 from checkpointreporter import CheckpointReporter
-from charmm.psf import ProteinStructure as CharmmPSF
-from charmm.parameters import ParameterSet as CharmmParameterSet
+from internal.charmm.psf import ProteinStructure as CharmmPSF
+from internal.charmm.parameters import ParameterSet as CharmmParameterSet
 
 # Enumerated values
 

wrappers/python/simtk/openmm/app/charmm/_charmmfile.py → wrappers/python/simtk/openmm/app/internal/charmm/_charmmfile.py

@@ -7,7 +7,7 @@ Author: Jason M. Swails
 Contributors:
 Date: April 9, 2014
 """
-from simtk.openmm.app.charmm.exceptions import CharmmFileError
+from simtk.openmm.app.internal.charmm.exceptions import CharmmFileError
 
 class CharmmFile(object):
     """

wrappers/python/simtk/openmm/app/charmm/parameters.py → wrappers/python/simtk/openmm/app/internal/charmm/parameters.py

@@ -7,11 +7,12 @@ Author: Jason M. Swails
 Contributors:
 Date: April 5, 2014
 """
-from simtk.openmm.app.charmm._charmmfile import CharmmFile, CharmmStreamFile
-from simtk.openmm.app.charmm.topologyobjects import (AtomType, BondType,
-                    AngleType, DihedralType, ImproperType, CmapType,
-                    UreyBradleyType, NoUreyBradley)
-from simtk.openmm.app.charmm.exceptions import CharmmFileError
+from simtk.openmm.app.internal.charmm._charmmfile import (
+            CharmmFile, CharmmStreamFile)
+from simtk.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
 import warnings

wrappers/python/simtk/openmm/app/charmm/psf.py → wrappers/python/simtk/openmm/app/internal/charmm/psf.py

@@ -19,12 +19,14 @@ from simtk.openmm.app.amberprmtopfile import HCT, OBC1, OBC2, GBn, GBn2
 from simtk.openmm.app.internal.customgbforces import (GBSAHCTForce,
                 GBSAOBC1Force, GBSAOBC2Force, GBSAGBnForce, GBSAGBn2Force)
 # CHARMM imports
-from simtk.openmm.app.charmm._charmmfile import CharmmFile
-from simtk.openmm.app.charmm.topologyobjects import (ResidueList, AtomList,
-                TrackedList, Bond, Angle, Dihedral, Improper, AcceptorDonor,
-                Group, Cmap, UreyBradley, NoUreyBradley)
-from simtk.openmm.app.charmm.exceptions import (CharmmPSFError, MoleculeError,
-                CharmmPSFWarning, MissingParameter)
+from simtk.openmm.app.internal.charmm._charmmfile import CharmmFile
+from simtk.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 (
+                CharmmPSFError, MoleculeError, CharmmPSFWarning,
+                MissingParameter)
 import warnings
 
 TINY = 1e-8

wrappers/python/simtk/openmm/app/charmm/topologyobjects.py → wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py

@@ -6,8 +6,9 @@ Author: Jason M. Swails
 Contributors:
 Date: April 9, 2014
 """
-from simtk.openmm.app.charmm.exceptions import (SplitResidueWarning, BondError,
-                ResidueError, CmapError, MissingParameter)
+from simtk.openmm.app.internal.charmm.exceptions import (
+                SplitResidueWarning, BondError, ResidueError, CmapError,
+                MissingParameter)
 import simtk.unit as u
 import warnings