preliminary filename refactoring; may have added some unneccesary fil…

…es produced during testing in the inputs directory

ez_setup.py

@@ -232,7 +232,7 @@ def main(argv, version=DEFAULT_VERSION):
         except ImportError:
             from easy_install import main
         main(list(argv)+[download_setuptools(delay=0)])
-        sys.exit(0) # try to force an exit
+        sys.exit(0) # try to forces an exit
     else:
         if argv:
             from setuptools.command.easy_install import main

intermol/Atom.py

@@ -6,31 +6,26 @@
 Lee <[email protected]>
 """
 import intermol.unit as units
-
-from Converter import convert_units
+from converter import convert_units
 
 
 class Atom(object):
-    __slots__ = ['atomIndex', 'atomName', 'residueIndex', 'residueName',
+    __slots__ = ['index', 'name', 'residue_index', 'residue_name',
             '_position', '_velocity', '_force', '_atomtype', 'bondtype', 'Z',
             'cgnr', '_mass', '_charge', 'ptype', '_sigma', '_epsilon']
-    def __init__(self,
-                atomIndex,
-                atomName=None,
-                residueIndex=-1,
-                residueName=None):
+    def __init__(self, index, name=None, residue_index=-1, residue_name=None):
         """Create an Atom object
 
         Args:
-            atomIndex (int): index of atom in the molecule
-            atomName (str): name of the atom (eg., N, C, H, O)
-            residueIndex (int): index of residue in the molecule
-            residueName (str): name of the residue (eg., THR, CYS)
-        """
-        self.atomIndex = atomIndex
-        self.atomName = atomName
-        self.residueIndex = residueIndex
-        self.residueName = residueName
+            index (int): index of atom in the molecule
+            name (str): name of the atom (eg., N, C, H, O)
+            residue_index (int): index of residue in the molecule
+            residue_name (str): name of the residue (eg., THR, CYS)
+        """
+        self.index = index
+        self.name = name
+        self.residue_index = residue_index
+        self.residue_name = residue_name
         self._position = [0 * units.nanometers,
                             0 * units.nanometers,
                             0 * units.nanometers]
@@ -52,6 +47,31 @@ def __init__(self,
         self._sigma = dict()
         self._epsilon = dict()
 
+    def getAtomType(self, index=None):
+        """Gets the atomtype
+
+        Args:
+            index (str): the value corresponding with type precedence (A Type, B Type)
+
+        Returns:
+            atomtype (list, str): Returns the atomtype list or the value at
+                                  index if index is specified
+        """
+        if index:
+            return self._atomtype[index]
+        return self._atomtype
+
+    def setAtomType(self, index, atomtype):
+        """Sets the atomtype
+
+        Args:
+            atomtype (str): the atomtype of the atom
+            index (str): the value corresponding with type precedence (A Type, B Type)
+        """
+        self._atomtype[index] = atomtype
+
+
+
     def setSigma(self, index, sigma):
         """Sets the sigma
 
@@ -108,28 +128,6 @@ def getCgnr(self, index=None):
             return self._cgnr[index]
         return self._cgnr
 
-    def setAtomType(self, index, atomtype):
-        """Sets the atomtype
-
-        Args:
-            atomtype (str): the atomtype of the atom
-            index (str): the value corresponding with type precedence (A Type, B Type)
-        """
-        self._atomtype[index] = atomtype
-
-    def getAtomType(self, index = None):
-        """Gets the atomtype
-
-        Args:
-            index (str): the value corresponding with type precedence (A Type, B Type)
-
-        Returns:
-            atomtype (list, str): Returns the atomtype list or the value at
-                                  index if index is specified
-        """
-        if index:
-            return self._atomtype[index]
-        return self._atomtype
 
     def setPosition(self, x, y, z):
         """Sets the position of the atom
@@ -242,13 +240,13 @@ def getCharge(self, index=None):
         return self._charge
 
     def __repr__(self):
-        return 'Atom({0}, {1})'.format(self.atomIndex, self.atomName)
+        return 'Atom({0}, {1})'.format(self.index, self.name)
 
     def __cmp__(self, other):
-        return self.atomIndex - other.atomIndex
+        return self.index - other.index
 
     def __eq__(self, other):
-        return self.atomIndex == other.atomIndex
+        return self.index == other.index
 
     def __hash__(self):
-        return hash(self.atomIndex)
+        return hash(self.index)

intermol/Molecule.py

@@ -6,8 +6,8 @@
 Lee <[email protected]>
 """
 
-from Atom import *
-from OrderedSet import OrderedSet
+from atom import *
+from orderedset import OrderedSet
 
 class Molecule(object):
     """An abstract molecule object.

intermol/MoleculeType.py

@@ -1,5 +1,5 @@
-from OrderedSet import OrderedSet
-from HashMap import HashMap
+from orderedset import OrderedSet
+from hashmap import HashMap
 
 
 class MoleculeType(object):
@@ -48,26 +48,26 @@ def getMolecule(self, molecule):
         return get_equivalent(self.moleculeSet, molecule, False)
 
     def addForce(self, force):
-        """Add a force to the moleculeType
+        """Add a forces to the moleculeType
 
         Args:
-            force (AbstractForce): Add a force or contraint to the moleculeType
+            forces (AbstractForce): Add a forces or contraint to the moleculeType
         """
         self.forceSet.add(force)
 
     def removeForce(self, force):
-        """Remove a force from the moleculeType
+        """Remove a forces from the moleculeType
 
         Args:
-            force (AbstractForce): Remove a force from the moleculeType
+            forces (AbstractForce): Remove a forces from the moleculeType
         """
         self.forceSet.remove(force)
 
     def getForce(self, force):
-        """Get a force from the moleculeType
+        """Get a forces from the moleculeType
 
         Args:
-            force (AbstractForce): Retrieve a force from the moleculeType
+            forces (AbstractForce): Retrieve a forces from the moleculeType
         """
         return get_equivalent(self.forceSet, force, False)
 

intermol/System.py

@@ -5,9 +5,9 @@
 from collections import OrderedDict
 import numpy as np
 
-from intermol.MoleculeType import MoleculeType
-from intermol.OrderedSet import OrderedSet
-from intermol.HashMap import HashMap
+from intermol.moleculetype import MoleculeType
+from intermol.orderedset import OrderedSet
+from intermol.hashmap import HashMap
 
 
 class System(object):

intermol/Types/LJ1PairCR1Type.py → intermol/Types/LJ1_pair_CR1_type.py

@@ -1,8 +1,8 @@
 import sys
 sys.path.append('..')
 
-from intermol.Decorators import *
-from AbstractPairType import *
+from intermol.decorators import *
+from abstract_pair_type import *
 
 class LJ1PairCR1Type(AbstractPairType):
     @accepts_compatible_units(None, None, None, units.kilojoules_per_mole * units.nanometers**(6), units.kilojoules_per_mole * units.nanometers**(12))

intermol/Types/LJ1PairCR23Type.py → intermol/Types/LJ1_pair_CR23_type.py

@@ -1,8 +1,8 @@
 import sys
 sys.path.append('..')
 
-from intermol.Decorators import *
-from AbstractPairType import *
+from intermol.decorators import *
+from abstract_pair_type import *
 
 class LJ1PairCR23Type(AbstractPairType):
     @accepts_compatible_units(None, None, None, units.nanometers, units.kilojoules_per_mole)

intermol/Types/LJ2PairCR1Type.py → intermol/Types/LJ2_pair_CR1_type.py

@@ -1,8 +1,8 @@
 
 import sys
 sys.path.append('..')
-from intermol.Decorators import *
-from AbstractPairType import *
+from intermol.decorators import *
+from abstract_pair_type import *
 
 class LJ2PairCR1Type(AbstractPairType):
     @accepts_compatible_units(None, None, None, None, units.elementary_charge, units.elementary_charge, units.kilojoules_per_mole * units.nanometers**(6), units.kilojoules_per_mole * units.nanometers**(12))

intermol/Types/LJ2PairCR23Type.py → intermol/Types/LJ2_pair_CR23_type.py

@@ -1,8 +1,8 @@
 import sys
 sys.path.append('..')
 
-from intermol.Decorators import *
-from AbstractPairType import *
+from intermol.decorators import *
+from abstract_pair_type import *
 
 class LJ2PairCR23Type(AbstractPairType):
     @accepts_compatible_units(None, None, None, None, units.elementary_charge, units.elementary_charge, units.nanometers, units.kilojoules_per_mole)

intermol/Types/LJNBPairCR1Type.py → intermol/Types/LJ_nonbonded_pair_CR1_type.py

@@ -1,8 +1,8 @@
 import sys
 sys.path.append('..')
 
-from intermol.Decorators import *
-from AbstractPairType import *
+from intermol.decorators import *
+from abstract_pair_type import *
 
 class LJNBPairCR1Type(AbstractPairType):
     @accepts_compatible_units(None, None, None, units.elementary_charge, units.elementary_charge, units.kilojoules_per_mole * units.nanometers**(6), units.kilojoules_per_mole * units.nanometers**(12))

intermol/Types/LJNBPairCR23Type.py → intermol/Types/LJ_nonbonded_pair_CR23_type.py

@@ -1,8 +1,8 @@
 import sys
 sys.path.append('..')
 
-from intermol.Decorators import *
-from AbstractPairType import *
+from intermol.decorators import *
+from abstract_pair_type import *
 
 class LJNBPairCR23Type(AbstractPairType):
     @accepts_compatible_units(None, None, None, units.elementary_charge, units.elementary_charge, units.nanometers, units.kilojoules_per_mole)

intermol/Types/RBDihedralType.py → intermol/Types/RB_dihedral_type.py

@@ -1,5 +1,5 @@
-from intermol.Decorators import *
-from AbstractDihedralType import *
+from intermol.decorators import *
+from abstract_dihedral_type import *
 
 class RBDihedralType(AbstractDihedralType):