Cleaning up Python wrappers

wrappers/python/MANIFEST.in

 include setup.py
 include *.py
 include *.txt
-include doc/*.pdf
-include images/*.bmp
-include images/*.png
 global-include README
 recursive-include simtk     *.txt *.py
 recursive-include OpenMM    *.txt *.py *.so *.dll *.lib *.dylib *.h
-recursive-include examples  *.txt *.py *.pdb *.top *.prmtop *.crd *.sh *.leap
-recursive-include test      *.txt *.py *.pdb *.top *.prmtop *.crd *.sh *.in *log
-recursive-include scripts   *.txt *.py
 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/simtk/chem/element.py

-#!/bin/env python
-
-"""
-element.py: Used for managing elements.
-"""
-__author__ = "Christopher M. Bruns"
-__version__ = "1.0"
-
-
-from simtk.unit import daltons
-
-class Element:
-    elements_by_symbol = {}
-    
-    def __init__(self, number, name, symbol, mass):
-        self.atomic_number = number
-        self.name = name
-        self.symbol = symbol
-        self.mass = mass
-        # Index this element in a global table
-        s = symbol.strip().upper()
-        assert s not in Element.elements_by_symbol
-        Element.elements_by_symbol[s] = self
-
-
-def get_by_symbol(symbol):
-    s = symbol.strip().upper()
-    return Element.elements_by_symbol[s]
-
-
-hydrogen =       Element(  1, "hydrogen", "H", 1.007947*daltons)
-deuterium =      Element(  1, "deuterium", "D", 2.01355321270*daltons)
-helium =         Element(  2, "helium", "He", 4.003*daltons)
-lithium =        Element(  3, "lithium", "Li", 6.9412*daltons)
-beryllium =      Element(  4, "beryllium", "Be", 9.0121823*daltons)
-boron =          Element(  5, "boron", "B", 10.8117*daltons)
-carbon =         Element(  6, "carbon", "C", 12.01078*daltons)
-nitrogen =       Element(  7, "nitrogen", "N", 14.00672*daltons)
-oxygen =         Element(  8, "oxygen", "O", 15.99943*daltons)
-fluorine =       Element(  9, "fluorine", "F", 18.99840325*daltons)
-neon =           Element( 10, "neon", "Ne", 20.17976*daltons)
-sodium =         Element( 11, "sodium", "Na", 22.989769282*daltons)
-magnesium =      Element( 12, "magnesium", "Mg", 24.30506*daltons)
-aluminum =       Element( 13, "aluminum", "Al", 26.98153868*daltons)
-silicon =        Element( 14, "silicon", "Si", 28.08553*daltons)
-phosphorus =     Element( 15, "phosphorus", "P", 30.9737622*daltons)
-sulfur =         Element( 16, "sulfur", "S", 32.0655*daltons)
-chlorine =       Element( 17, "chlorine", "Cl", 35.4532*daltons)
-argon =          Element( 18, "argon", "Ar", 39.9481*daltons)
-potassium =      Element( 19, "potassium", "K", 39.09831*daltons)
-calcium =        Element( 20, "calcium", "Ca", 40.0784*daltons)
-scandium =       Element( 21, "scandium", "Sc", 44.9559126*daltons)
-titanium =       Element( 22, "titanium", "Ti", 47.8671*daltons)
-vanadium =       Element( 23, "vanadium", "V", 50.94151*daltons)
-chromium =       Element( 24, "chromium", "Cr", 51.99616*daltons)
-manganese =      Element( 25, "manganese", "Mn", 54.9380455*daltons)
-iron =           Element( 26, "iron", "Fe", 55.8452*daltons)
-cobalt =         Element( 27, "cobalt", "Co", 58.9331955*daltons)
-nickel =         Element( 28, "nickel", "Ni", 58.69342*daltons)
-copper =         Element( 29, "copper", "Cu", 63.5463*daltons)
-zinc =           Element( 30, "zinc", "Zn", 65.4094*daltons)
-gallium =        Element( 31, "gallium", "Ga", 69.7231*daltons)
-germanium =      Element( 32, "germanium", "Ge", 72.641*daltons)
-arsenic =        Element( 33, "arsenic", "As", 74.921602*daltons)
-selenium =       Element( 34, "selenium", "Se", 78.963*daltons)
-bromine =        Element( 35, "bromine", "Br", 79.9041*daltons)
-krypton =        Element( 36, "krypton", "Kr", 83.7982*daltons)
-rubidium =       Element( 37, "rubidium", "Rb", 85.46783*daltons)
-strontium =      Element( 38, "strontium", "Sr", 87.621*daltons)
-yttrium =        Element( 39, "yttrium", "Y", 88.905852*daltons)
-zirconium =      Element( 40, "zirconium", "Zr", 91.2242*daltons)
-niobium =        Element( 41, "niobium", "Nb", 92.906382*daltons)
-molybdenum =     Element( 42, "molybdenum", "Mo", 95.942*daltons)
-technetium =     Element( 43, "technetium", "Tc", 98*daltons)
-ruthenium =      Element( 44, "ruthenium", "Ru", 101.072*daltons)
-rhodium =        Element( 45, "rhodium", "Rh", 102.905502*daltons)
-palladium =      Element( 46, "palladium", "Pd", 106.421*daltons)
-silver =         Element( 47, "silver", "Ag", 107.86822*daltons)
-cadmium =        Element( 48, "cadmium", "Cd", 112.4118*daltons)
-indium =         Element( 49, "indium", "In", 114.8183*daltons)
-tin =            Element( 50, "tin", "Sn", 118.7107*daltons)
-antimony =       Element( 51, "antimony", "Sb", 121.7601*daltons)
-tellurium =      Element( 52, "tellurium", "Te", 127.603*daltons)
-iodine =         Element( 53, "iodine", "I", 126.904473*daltons)
-xenon =          Element( 54, "xenon", "Xe", 131.2936*daltons)
-cesium =         Element( 55, "cesium", "Cs", 132.90545192*daltons)
-barium =         Element( 56, "barium", "Ba", 137.3277*daltons)
-lanthanum =      Element( 57, "lanthanum", "La", 138.905477*daltons)
-cerium =         Element( 58, "cerium", "Ce", 140.1161*daltons)
-praseodymium =   Element( 59, "praseodymium", "Pr", 140.907652*daltons)
-neodymium =      Element( 60, "neodymium", "Nd", 144.2423*daltons)
-promethium =     Element( 61, "promethium", "Pm", 145*daltons)
-samarium =       Element( 62, "samarium", "Sm", 150.362*daltons)
-europium =       Element( 63, "europium", "Eu", 151.9641*daltons)
-gadolinium =     Element( 64, "gadolinium", "Gd", 157.253*daltons)
-terbium =        Element( 65, "terbium", "Tb", 158.925352*daltons)
-dysprosium =     Element( 66, "dysprosium", "Dy", 162.5001*daltons)
-holmium =        Element( 67, "holmium", "Ho", 164.930322*daltons)
-erbium =         Element( 68, "erbium", "Er", 167.2593*daltons)
-thulium =        Element( 69, "thulium", "Tm", 168.934212*daltons)
-ytterbium =      Element( 70, "ytterbium", "Yb", 173.043*daltons)
-lutetium =       Element( 71, "lutetium", "Lu", 174.9671*daltons)
-hafnium =        Element( 72, "hafnium", "Hf", 178.492*daltons)
-tantalum =       Element( 73, "tantalum", "Ta", 180.947882*daltons)
-tungsten =       Element( 74, "tungsten", "W", 183.841*daltons)
-rhenium =        Element( 75, "rhenium", "Re", 186.2071*daltons)
-osmium =         Element( 76, "osmium", "Os", 190.233*daltons)
-iridium =        Element( 77, "iridium", "Ir", 192.2173*daltons)
-platinum =       Element( 78, "platinum", "Pt", 195.0849*daltons)
-gold =           Element( 79, "gold", "Au", 196.9665694*daltons)
-mercury =        Element( 80, "mercury", "Hg", 200.592*daltons)
-thallium =       Element( 81, "thallium", "Tl", 204.38332*daltons)
-lead =           Element( 82, "lead", "Pb", 207.21*daltons)
-bismuth =        Element( 83, "bismuth", "Bi", 208.980401*daltons)
-polonium =       Element( 84, "polonium", "Po", 209*daltons)
-astatine =       Element( 85, "astatine", "At", 210*daltons)
-radon =          Element( 86, "radon", "Rn", 222.018*daltons)
-francium =       Element( 87, "francium", "Fr", 223*daltons)
-radium =         Element( 88, "radium", "Ra", 226*daltons)
-actinium =       Element( 89, "actinium", "Ac", 227*daltons)
-thorium =        Element( 90, "thorium", "Th", 232.038062*daltons)
-protactinium =   Element( 91, "protactinium", "Pa", 231.035882*daltons)
-uranium =        Element( 92, "uranium", "U", 238.028913*daltons)
-neptunium =      Element( 93, "neptunium", "Np", 237*daltons)
-plutonium =      Element( 94, "plutonium", "Pu", 244*daltons)
-americium =      Element( 95, "americium", "Am", 243*daltons)
-curium =         Element( 96, "curium", "Cm", 247*daltons)
-berkelium =      Element( 97, "berkelium", "Bk", 247*daltons)
-californium =    Element( 98, "californium", "Cf", 251*daltons)
-einsteinium =    Element( 99, "einsteinium", "Es", 252*daltons)
-fermium =        Element(100, "fermium", "Fm", 257*daltons)
-mendelevium =    Element(101, "mendelevium", "Md", 258*daltons)
-nobelium =       Element(102, "nobelium", "No", 259*daltons)
-lawrencium =     Element(103, "lawrencium",     "Lr", 262*daltons)
-rutherfordium =  Element(104, "rutherfordium",  "Rf", 261*daltons)
-dubnium =        Element(105, "dubnium",        "Db", 262*daltons)
-seaborgium =     Element(106, "seaborgium",     "Sg", 266*daltons)
-bohrium =        Element(107, "bohrium",        "Bh", 264*daltons)
-hassium =        Element(108, "hassium",        "Hs", 269*daltons)
-meitnerium =     Element(109, "meitnerium",     "Mt", 268*daltons)
-darmstadtium =   Element(110, "darmstadtium",   "Ds", 281*daltons)
-roentgenium =    Element(111, "roentgenium",    "Rg", 272*daltons)
-ununbium =       Element(112, "ununbium",       "Uub", 285*daltons)
-ununtrium =      Element(113, "ununtrium",      "Uut", 284*daltons)
-ununquadium =    Element(114, "ununquadium",    "Uuq", 289*daltons)
-ununpentium =    Element(115, "ununpentium",    "Uup", 288*daltons)
-ununhexium =     Element(116, "ununhexium",     "Uuh", 292*daltons)

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

@@ -32,33 +32,6 @@ else:
     flags = sys.getdlopenflags()
     sys.setdlopenflags(flags | ctypes.RTLD_GLOBAL)
 
-import simtk.chem
-from simtk.chem.openmm.openmm import *
-
-skipPluginFilenames=["OpenMMFreeEnergy"]
-if len(simtk.chem.__path__) > 1:
-   raise Exception("more than one item in simtk.chem.openmm.__path__")
-pluginPath = os.path.join(simtk.chem.__path__[0],
-                          'openmm',
-                          'OpenMM',
-                          'plugins')
-pluginLoadingErrors={}
-pluginLoadedLibNames=[]
-libFilenames=glob.glob(os.path.join(pluginPath, "*.%s" % (libExt)))
-
-# Load plugins
-for filename in libFilenames:
-    skipPlugin=False
-    for pFilename in skipPluginFilenames:
-        fullFilename = "%s%s.%s" % (libPrefix, pFilename, libExt)
-        if os.path.split(filename)[-1] == fullFilename:
-            skipPlugin=True
-            break
-    if skipPlugin: continue
-    try:
-        Platform.loadPluginLibrary(os.path.join(pluginPath, filename))
-        pluginLoadedLibNames.append(filename)
-    except:
-        pluginLoadingErrors[filename]=sys.exc_info()
-
 
+from simtk.chem.openmm.openmm import Platform
+pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
\ No newline at end of file