Merge branch 'master' of https://github.com/SimTk/openmm

wrappers/python/simtk/unit/baseunit.py

@@ -15,7 +15,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
 Authors: Christopher M. Bruns
 Contributors: Peter Eastman
 
-Permission is hereby granted, free of charge, to any person obtaining a 
+Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
 to deal in the Software without restriction, including without limitation
 the rights to use, copy, modify, merge, publish, distribute, sublicense,
@@ -40,14 +40,14 @@ __version__ = "0.6"
 class BaseUnit(object):
     '''
     Physical unit expressed in exactly one BaseDimension.
-    
+
     For example, meter_base_unit could be a BaseUnit for the length dimension.
     The BaseUnit class is used internally in the more general Unit class.
     '''
 
     def __init__(self, base_dim, name, symbol):
         """Creates a new BaseUnit.
-        
+
         Parameters
          - self: The newly created BaseUnit.
          - base_dim: (BaseDimension) The dimension of the new unit, e.g. 'mass'
@@ -62,7 +62,7 @@ class BaseUnit(object):
         self._conversion_factor_to[self] = 1.0
         self._conversion_factor_to_by_name = {}
         self._conversion_factor_to_by_name[self.name] = 1.0
-    
+
     def __lt__(self, other):
         """
         Comparison function that sorts BaseUnits by BaseDimension
@@ -78,10 +78,10 @@ class BaseUnit(object):
         Returns a dictionary of BaseDimension:exponent pairs, describing the dimension of this unit.
         """
         yield (self.dimension, 1)
-        
+
     def iter_base_units(self):
         yield (self, 1)
-        
+
     def get_dimension_tuple(self):
         """
         Returns a sorted tuple of (BaseDimension, exponent) pairs, that can be used as a dictionary key.
@@ -89,7 +89,7 @@ class BaseUnit(object):
         l = list(self.iter_base_dimensions())
         l.sort()
         return tuple(l)
-        
+
     def __str__(self):
         """Returns a string with the name of this BaseUnit
         """
@@ -97,40 +97,40 @@ class BaseUnit(object):
 
     def __repr__(self):
         return 'BaseUnit(base_dim=%s, name="%s", symbol="%s")' % (self.dimension, self.name, self.symbol)
-        
+
     def define_conversion_factor_to(self, other, factor):
         """
         Defines a conversion factor between two BaseUnits.
-        
+
         self * factor = other
-        
+
         Parameters:
          - self: (BaseUnit) 'From' unit in conversion.
          - other: (BaseUnit) 'To' unit in conversion.
          - factor: (float) Conversion factor.
-        
+
         After calling this method, both self and other will have stored
         conversion factors for one another, plus all other BaseUnits which
         self and other have previously defined.
-        
+
         Both self and other must have the same dimension, otherwise a TypeError
         will be raised.
-        
+
         Returns None.
         """
         if self.dimension != other.dimension:
             raise TypeError('Cannot define conversion for BaseUnits with different dimensions.')
         assert(factor != 0)
-        assert(not self is other)        
+        assert(not self is other)
         # import all transitive conversions
         self._conversion_factor_to[other] = factor
         self._conversion_factor_to_by_name[other.name] = factor
         for (unit, cfac) in other._conversion_factor_to.items():
             if unit is self: continue
             if self._conversion_factor_to.has_key(unit): continue
-            self._conversion_factor_to[unit] = factor * cfac                
+            self._conversion_factor_to[unit] = factor * cfac
             unit._conversion_factor_to[self] = pow(factor * cfac, -1)
-            self._conversion_factor_to_by_name[unit.name] = factor * cfac                
+            self._conversion_factor_to_by_name[unit.name] = factor * cfac
             unit._conversion_factor_to_by_name[self.name] = pow(factor * cfac, -1)
         # and for the other guy
         invFac = pow(factor, -1.0)
@@ -146,13 +146,13 @@ class BaseUnit(object):
 
     def conversion_factor_to(self, other):
         """Returns a conversion factor from this BaseUnit to another BaseUnit.
-        
+
         It does not matter which existing BaseUnit you define the conversion factor to.
         Conversions for all other known BaseUnits will be computed at the same time.
-        
+
         Raises TypeError if dimension does not match.
         Raises LookupError if no conversion has been defined. (see define_conversion_factor_to).
-        
+
         """
         if self is other: return 1.0
         if self.dimension != other.dimension:

wrappers/python/simtk/unit/constants.py

@@ -11,7 +11,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
 Authors: Christopher M. Bruns
 Contributors: Peter Eastman
 
-Permission is hereby granted, free of charge, to any person obtaining a 
+Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
 to deal in the Software without restriction, including without limitation
 the rights to use, copy, modify, merge, publish, distribute, sublicense,

wrappers/python/simtk/unit/mymatrix.py

@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
 Authors: Christopher M. Bruns
 Contributors: Peter Eastman
 
-Permission is hereby granted, free of charge, to any person obtaining a 
+Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
 to deal in the Software without restriction, including without limitation
 the rights to use, copy, modify, merge, publish, distribute, sublicense,
@@ -34,7 +34,7 @@ import sys
 def eye(size):
     """
     Returns identity matrix.
-    
+
     >>> print(eye(3))
     [[1, 0, 0]
      [0, 1, 0]
@@ -50,11 +50,11 @@ def eye(size):
                 r.append(0)
         result.append(r)
     return MyMatrix(result)
-    
+
 def zeros(m, n=None):
     """
     Returns matrix of zeroes
-    
+
     >>> print(zeros(3))
     [[0, 0, 0]
      [0, 0, 0]
@@ -82,7 +82,7 @@ class MyVector(object):
 
     def __str__(self):
         return str(self.data)
-        
+
     def __repr__(self):
         return self.__class__.__name__ + "(" + repr(self.data) + ")"
 
@@ -91,20 +91,20 @@ class MyVector(object):
 
     def __contains__(self, item):
         return item in self.data
-        
+
     def __delitem__(self, key):
         del self.data[key]
-        
+
     def __iter__(self):
         for item in self.data:
             yield item
 
     def __len__(self):
         return len(self.data)
-    
+
     def __setitem__(self, key, value):
         self.data[key] = value
-        
+
     def __rmul__(self, lhs):
         try:
             len(lhs)
@@ -119,7 +119,7 @@ class MyVector(object):
 class MyMatrix(MyVector):
     """
     Pure python linear algebra matrix for internal matrix inversion in UnitSystem.
-    
+
     >>> m = MyMatrix([[1,0,],[0,1,]])
     >>> print(m)
     [[1, 0]
@@ -158,7 +158,7 @@ class MyMatrix(MyVector):
     """
     def numRows(self):
         return len(self.data)
-        
+
     def numCols(self):
         if len(self.data) == 0:
             return 0
@@ -179,13 +179,13 @@ class MyMatrix(MyVector):
             start_char = " "
         result += "]"
         return result
-        
+
     def __repr__(self):
         return 'MyMatrix(' + MyVector.__repr__(self) + ')'
 
     def is_square(self):
         return self.numRows() == self.numCols()
-    
+
     def __iter__(self):
         for item in self.data:
             yield MyVector(item)
@@ -206,7 +206,7 @@ class MyMatrix(MyVector):
     def __mul__(self, rhs):
         """
         Matrix multiplication.
-        
+
         >>> a = MyMatrix([[1,2],[3,4]])
         >>> b = MyMatrix([[5,6],[7,8]])
         >>> print(a)
@@ -218,7 +218,7 @@ class MyMatrix(MyVector):
         >>> print(a*b)
         [[19, 22]
          [43, 50]]
-        
+
         """
         m = self.numRows()
         n = len(rhs[0])
@@ -235,7 +235,7 @@ class MyMatrix(MyVector):
     def __add__(self, rhs):
         """
         Matrix addition.
-        
+
         >>> print(MyMatrix([[1, 2],[3, 4]]) + MyMatrix([[5, 6],[7, 8]]))
         [[6, 8]
          [10, 12]]
@@ -253,7 +253,7 @@ class MyMatrix(MyVector):
     def __sub__(self, rhs):
         """
         Matrix subtraction.
-        
+
         >>> print(MyMatrix([[1, 2],[3, 4]]) - MyMatrix([[5, 6],[7, 8]]))
         [[-4, -4]
          [-4, -4]]
@@ -270,7 +270,7 @@ class MyMatrix(MyVector):
 
     def __pos__(self):
         return self
-        
+
     def __neg__(self):
         m = self.numRows()
         n = self.numCols()
@@ -384,7 +384,7 @@ class MyMatrix(MyVector):
                 for k in range(0,n):
                     temp = a[k][indxr[l]]
                     a[k][indxr[l]] = a[k][indxc[l]]
-                    a[k][indxc[l]] = temp                
+                    a[k][indxc[l]] = temp
             return a
 
     def transpose(self):
@@ -395,13 +395,13 @@ class MyMatrixTranspose(MyMatrix):
 
     def transpose(self):
         return MyMatrix(self.data)
-        
+
     def numRows(self):
         if len(self.data) == 0:
             return 0
         else:
             return len(self.data[0])
-        
+
     def numCols(self):
         return len(self.data)
 
@@ -461,7 +461,7 @@ class MyMatrixTranspose(MyMatrix):
 
 # run module directly for testing
 if __name__=='__main__':
-    
+
     # Test the examples in the docstrings
     import doctest, sys
     doctest.testmod(sys.modules[__name__])

wrappers/python/simtk/unit/prefix.py

@@ -11,7 +11,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
 Authors: Christopher M. Bruns
 Contributors: Peter Eastman
 
-Permission is hereby granted, free of charge, to any person obtaining a 
+Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
 to deal in the Software without restriction, including without limitation
 the rights to use, copy, modify, merge, publish, distribute, sublicense,
@@ -44,14 +44,14 @@ import sys
 class SiPrefix(object):
     """
     Unit prefix that can be multiplied by a unit to yield a new unit.
-    
+
     e.g. millimeter = milli*meter
     """
     def __init__(self, prefix, factor, symbol):
         self.prefix = prefix
         self.factor = factor
         self.symbol = symbol
-        
+
     def __mul__(self, unit):
         """
         SiPrefix * BaseUnit yields new BaseUnit
@@ -136,7 +136,7 @@ si_prefixes = (   yotto
 def define_prefixed_units(base_unit, module = sys.modules[__name__]):
     """
     Create attributes for prefixed units derived from a particular BaseUnit, e.g. "kilometer" from "meter_base_unit"
-    
+
     Parameters
      - base_unit (BaseUnit) existing base unit to use as a basis for prefixed units
      - module (Module) module which will contain the new attributes.  Defaults to simtk.unit module.
@@ -146,7 +146,7 @@ def define_prefixed_units(base_unit, module = sys.modules[__name__]):
         name = new_base_unit.name
         new_unit = Unit({new_base_unit: 1.0})
         # Create base_unit attribute, needed for creating UnitSystems
-        module.__dict__[name + '_base_unit'] = new_base_unit # e.g. "kilometer_base_unit"        
+        module.__dict__[name + '_base_unit'] = new_base_unit # e.g. "kilometer_base_unit"
         # Create attribue in this module
         module.__dict__[name] = new_unit # e.g. "kilometer"
         # And plural version

wrappers/python/simtk/unit/standard_dimensions.py

@@ -13,7 +13,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
 Authors: Christopher M. Bruns
 Contributors: Peter Eastman
 
-Permission is hereby granted, free of charge, to any person obtaining a 
+Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
 to deal in the Software without restriction, including without limitation
 the rights to use, copy, modify, merge, publish, distribute, sublicense,

wrappers/python/simtk/unit/unit_definitions.py

@@ -11,7 +11,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
 Authors: Christopher M. Bruns
 Contributors: Peter Eastman
 
-Permission is hereby granted, free of charge, to any person obtaining a 
+Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
 to deal in the Software without restriction, including without limitation
 the rights to use, copy, modify, merge, publish, distribute, sublicense,

wrappers/python/simtk/unit/unit_math.py

@@ -13,7 +13,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
 Authors: Christopher M. Bruns
 Contributors: Peter Eastman
 
-Permission is hereby granted, free of charge, to any person obtaining a 
+Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
 to deal in the Software without restriction, including without limitation
 the rights to use, copy, modify, merge, publish, distribute, sublicense,
@@ -49,7 +49,7 @@ from unit_definitions import *
 def sin(angle):
     """
     Examples
-    
+
     >>> sin(90*degrees)
     1.0
     """
@@ -67,7 +67,7 @@ def sinh(angle):
 def cos(angle):
     """
     Examples
-    
+
     >>> cos(180*degrees)
     -1.0
     """
@@ -102,10 +102,10 @@ def acos(x):
     0.0 rad
     """
     return math.acos(x) * radians
-    
+
 def acosh(x):
     return math.acosh(x) * radians
-    
+
 def asin(x):
     return math.asin(x) * radians
 
@@ -114,10 +114,10 @@ def asinh(x):
 
 def atan(x):
     return math.atan(x) * radians
-    
+
 def atanh(x):
     return math.atanh(x) * radians
-    
+
 def atan2(x, y):
     return math.atan2(x, y) * radians