Remove duplicate definition (#1144)

* Remove duplicate definition

* Fix akma unit system and update units package to latest

* Remove unnecessary module

parmed/topologyobjects.py

@@ -25,15 +25,6 @@
            'ThreeParticleExtraPointFrame', 'OutOfPlaneExtraPointFrame', 'RBTorsionType',
            'UnassignedAtomType', 'Link', 'DrudeAtom', 'DrudeAnisotropy']
 
-# Create the AKMA unit system which is the unit system used by Amber and CHARMM
-scale_factor = u.sqrt(1/u.kilocalories_per_mole * (u.daltons * u.angstroms**2))
-scale_factor = scale_factor.value_in_unit(u.picoseconds)
-akma_time_unit = u.BaseUnit(u.picosecond_base_unit.dimension, 'akma time', symbol='aks')
-akma_time_unit.define_conversion_factor_to(u.picosecond_base_unit, scale_factor)
-akma_unit_system = u.UnitSystem([u.angstrom_base_unit, u.dalton_base_unit, akma_time_unit,
-                                 u.elementary_charge_base_unit, u.kelvin_base_unit,
-                                 u.mole_base_unit, u.radian_base_unit])
-
 def _strip_units(value, unit=None):
     """
     Strips any units from the given value by casting them into the AKMA unit
@@ -44,7 +35,7 @@ def _strip_units(value, unit=None):
         if unit is None:
             if value.unit.is_compatible(u.degrees):
                 return value.value_in_unit(u.degrees)
-            return value.value_in_unit_system(akma_unit_system)
+            return value.value_in_unit_system(u.akma_unit_system)
         else:
             return value.value_in_unit(unit)
     return value

parmed/unit/__init__.py

@@ -34,7 +34,7 @@
 
 _time_scale = (daltons * angstroms**2 / kilocalories_per_mole).conversion_factor_to(picoseconds**2)
 akma_time_base_unit = BaseUnit(time_dimension, "akma_time_unit", "akma-s")
-akma_time_base_unit.define_conversion_factor_to(picosecond_base_unit, 1 / sqrt(_time_scale))
+akma_time_base_unit.define_conversion_factor_to(picosecond_base_unit, sqrt(_time_scale))
 del _time_scale
 
 akma_unit_system = UnitSystem([

parmed/unit/basedimension.py

@@ -1,6 +1,6 @@
 #!/bin/env python
 """
-Module simtk.unit.basedimension
+Module openmm.unit.basedimension
 
 BaseDimension class for use by units and quantities.
 BaseDimensions are things like "length" and "mass".
@@ -61,8 +61,7 @@ def __init__(self, name):
         """Create a new BaseDimension.
 
         Each new BaseDimension is assumed to be independent of all other BaseDimensions.
-        Use the existing BaseDimensions in simtk.dimension instead of creating
-        new ones.
+        Use the existing BaseDimensions instead of creating new ones.
         """
         self.name = name
         if not self.name in BaseDimension._index_by_name.keys():
@@ -80,6 +79,15 @@ def __lt__(self, other):
         """
         return self._index < other._index
 
+    def __le__(self, other):
+        return self._index <= other._index
+
+    def __gt__(self, other):
+        return self._index > other._index
+
+    def __ge__(self, other):
+        return self._index >= other._index
+
     def __hash__(self):
         """
         Needed for using BaseDimensions as hash keys.

parmed/unit/baseunit.py

@@ -2,7 +2,7 @@
 
 
 """
-Module simtk.unit.baseunit
+Module openmm.unit.baseunit
 
 Contains BaseUnit class, which is a component of the Unit class.
 

parmed/unit/constants.py

@@ -1,13 +1,13 @@
 #!/bin/env python
 """
-Module simtk.unit.constants
+Module openmm.unit.constants
 
 This is part of the OpenMM molecular simulation toolkit originating from
 Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012 Stanford University and the Authors.
+Portions copyright (c) 2012-2020 Stanford University and the Authors.
 Authors: Christopher M. Bruns
 Contributors: Peter Eastman
 
@@ -40,14 +40,12 @@
 ### CONSTANTS ###
 #################
 
-# codata 2006
-AVOGADRO_CONSTANT_NA = 6.02214179e23 / mole
-BOLTZMANN_CONSTANT_kB = 1.3806504e-23 * joule / kelvin
+# codata 2018
+AVOGADRO_CONSTANT_NA = 6.02214076e23 / mole
+BOLTZMANN_CONSTANT_kB = 1.380649e-23 * joule / kelvin
 MOLAR_GAS_CONSTANT_R = AVOGADRO_CONSTANT_NA * BOLTZMANN_CONSTANT_kB
-
-# From simtkcommon
 SPEED_OF_LIGHT_C = 2.99792458e8 * meter / second
-GRAVITATIONAL_CONSTANT_G = 6.6742e-11 * newton * meter**2 / kilogram**2
+GRAVITATIONAL_CONSTANT_G = 6.6743e-11 * newton * meter**2 / kilogram**2
 
 # run module directly for testing
 if __name__=='__main__':

parmed/unit/prefix.py

@@ -1,6 +1,6 @@
 #!/bin/env python
 """
-Module simtk.unit.prefix
+Module openmm.unit.prefix
 
 This is part of the OpenMM molecular simulation toolkit originating from
 Simbios, the NIH National Center for Physics-Based Simulation of
@@ -140,7 +140,7 @@ def define_prefixed_units(base_unit, module = sys.modules[__name__]):
 
     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.
+     - module (Module) module which will contain the new attributes.  Defaults to openmm.unit module.
     """
     for prefix in si_prefixes:
         new_base_unit = prefix * base_unit

parmed/unit/quantity.py

@@ -1,6 +1,6 @@
 #!/bin/env python
 """
-Module simtk.unit.quantity
+Module openmm.unit.quantity
 
 Physical quantities with units, intended to produce similar functionality
 to Boost.Units package in C++ (but with a runtime cost).
@@ -9,14 +9,14 @@
 In particular, there is no underlying set of 'canonical' base
 units, whereas in Scientific.Physics.PhysicalQuantities all
 units are secretly in terms of SI units.  Also, it is easier
-to add new fundamental dimensions to simtk.dimensions.  You
+to add new fundamental dimensions to basedimension.  You
 might want to make new dimensions for, say, "currency" or
 "information".
 
 Some features of this implementation:
   * Quantities are a combination of a value and a unit.  The value
     part can be any python type, including numbers, lists, numpy
-    arrays, and anything else.  The unit part must be a simtk.unit.Unit.
+    arrays, and anything else.  The unit part must be a openmm.unit.Unit.
   * Operations like adding incompatible units raises an error.
   * Multiplying or dividing units/quantities creates new units.
   * Users can create new Units and Dimensions, but most of the useful
@@ -100,7 +100,7 @@ def __init__(self, value=None, unit=None):
 
         Parameters
          - value: (any type, usually a number) Measure of this quantity
-         - unit: (Unit) the physical unit, e.g. simtk.unit.meters.
+         - unit: (Unit) the physical unit, e.g. openmm.unit.meters.
         """
         # When no unit is specified, bend over backwards to handle all one-argument possibilities
         if unit is None: # one argument version, copied from UList
@@ -112,13 +112,13 @@ def __init__(self, value=None, unit=None):
                 # Ulist of a Quantity is just the Quantity itself
                 unit = value.unit
                 value = value._value
-            elif isinstance(value, str):
+            elif _is_string(value):
                 unit = dimensionless
             else:
                 # Is value a container?
                 is_container = True
                 try:
-                    i = iter(value)
+                    _ = iter(value)
                 except TypeError:
                     is_container = False
                 if is_container:
@@ -267,7 +267,7 @@ def __eq__(self, other):
     def __ne__(self, other):
         """
         """
-        return not self.__eq__(other)
+        return not self == other
 
     def __lt__(self, other):
         """Compares two quantities.
@@ -287,6 +287,8 @@ def __le__(self, other):
     def __lt__(self, other):
         return self._value < (other.value_in_unit(self.unit))
 
+    __hash__ = None
+
     _reduce_cache = {}
 
     def reduce_unit(self, guide_unit=None):
@@ -597,6 +599,11 @@ def __neg__(self):
         """
         return Quantity(-(self._value), self.unit)
 
+    def __nonzero__(self):
+        """Returns True if value underlying Quantity is zero, False otherwise.
+        """
+        return bool(self._value)
+
     def __bool__(self):
         return bool(self._value)
 
@@ -732,8 +739,8 @@ def __setitem__(self, key, value):
         # Delegate slices to one-at-a time ___setitem___
         if isinstance(key, slice): # slice
             indices = key.indices(len(self))
-            for i in range(*indices):
-                self[i] = value[i]
+            for value_idx, self_idx in enumerate(range(*indices)):
+                self[self_idx] = value[value_idx]
         else: # single index
             # Check unit compatibility
             if self.unit.is_dimensionless() and is_dimensionless(value):
@@ -776,6 +783,7 @@ def pop(self, *args):
     # list.sort with no arguments will delegate correctly
     # list.sort with a comparison function cannot be done correctly
 
+
 def is_quantity(x):
     """
     Returns True if x is a Quantity, False otherwise.
@@ -793,6 +801,25 @@ def is_dimensionless(x):
         # everything else in the universe is dimensionless
         return True
 
+# Strings can cause trouble
+# as can any container that has infinite levels of containment
+def _is_string(x):
+     # step 1) String is always a container
+     # and its contents are themselves containers.
+     if isinstance(x, str):
+         return True
+     try:
+         first_item = next(iter(x))
+         inner_item = next(iter(first_item))
+         if first_item is inner_item:
+             return True
+         else:
+             return False
+     except TypeError:
+         return False
+     except StopIteration:
+         return False
+
 # run module directly for testing
 if __name__=='__main__':
     # Test the examples in the docstrings

parmed/unit/standard_dimensions.py

@@ -1,6 +1,6 @@
 #!/bin/env python
 """
-Module simtk.unit.standard_dimensions
+Module openmm.unit.standard_dimensions
 
 Definition of principal dimensions: mass, length, time, etc.