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Commit dc4d96fa authored by Peter Eastman's avatar Peter Eastman
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Cleaning up Python wrappers

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wrappers/python/MANIFEST.in
View file @ dc4d96fa
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 deleted 100644 → 0
View file @ 65b9d0b6
#!/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
View file @ dc4d96fa
......@@ -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
wrappers/python/simtk/chem/pdbstructure.py deleted 100644 → 0
View file @ 65b9d0b6
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