Merge pull request #1083 from rmcgibbo/wip-single-23-codebase

Single py2/3 codebase

wrappers/python/simtk/openmm/app/internal/customgbforces.py

@@ -30,6 +30,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 
 from __future__ import division
+from __future__ import absolute_import
 
 from simtk.openmm import CustomGBForce, Continuous2DFunction
 
@@ -369,13 +370,13 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
 
 def convertParameters(params, gbmodel):
     """Convert the GB parameters from the file into the values expected by the appropriate CustomGBForce."""
-    newparams = [None]*len(params)
     if gbmodel == 'GBn2':
         offset = 0.0195141
     else:
         offset = 0.009
-    for i in range(len(params)):
-        newparams[i] = list(params[i])
-        newparams[i][0] -= offset
-        newparams[i][1] *= newparams[i][0]
-    return newparams
+
+    for p in params:
+        newParam = list(p)
+        newParam[0] -= offset
+        newParam[1] *= newParam[0]
+        yield newParam

wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxContainers.py

@@ -36,6 +36,7 @@ The DataCategory class provides base storage container for instance
 data and definition meta data.
 
 """
+from __future__ import absolute_import
 
 __docformat__ = "restructuredtext en"
 __author__    = "John Westbrook"
@@ -99,13 +100,13 @@ class ContainerBase(object):
         self.__name=name
 
     def exists(self,name):
-        if self.__objCatalog.has_key(name):
+        if name in self.__objCatalog:
             return True
         else:
             return False
         
     def getObj(self,name):
-        if self.__objCatalog.has_key(name):
+        if name in self.__objCatalog:
             return self.__objCatalog[name]
         else:
             return None
@@ -118,7 +119,7 @@ class ContainerBase(object):
             of the same name will be overwritten.
         """
         if obj.getName() is not None:
-            if not self.__objCatalog.has_key(obj.getName()):
+            if obj.getName() not in self.__objCatalog:
                 # self.__objNameList is keeping track of object order here -- 
                 self.__objNameList.append(obj.getName())
             self.__objCatalog[obj.getName()]=obj
@@ -126,7 +127,7 @@ class ContainerBase(object):
     def replace(self,obj):
         """ Replace an existing object with the input object
         """
-        if ((obj.getName() is not None) and (self.__objCatalog.has_key(obj.getName())) ):
+        if ((obj.getName() is not None) and (obj.getName() in self.__objCatalog) ):
             self.__objCatalog[obj.getName()]=obj
         
 
@@ -158,7 +159,7 @@ class ContainerBase(object):
         """ Revmove object by name.  Return True on success or False otherwise.
         """
         try:
-            if self.__objCatalog.has_key(curName):
+            if curName in self.__objCatalog:
                 del self.__objCatalog[curName]
                 i=self.__objNameList.index(curName)
                 del self.__objNameList[i]
@@ -217,7 +218,7 @@ class DataContainer(ContainerBase):
         
     def invokeDataBlockMethod(self,type,method,db):
         self.__currentRow = 1
-        exec method.getInline()
+        exec(method.getInline())
 
     def setGlobal(self):
         self.__globalFlag=True
@@ -328,7 +329,7 @@ class DataCategory(DataCategoryBase):
                 return self._rowList[0][ii]
             except (IndexError, KeyError):
                 raise KeyError
-        raise TypeError, x
+        raise TypeError(x)
         
     
     def getCurrentAttribute(self):
@@ -464,7 +465,7 @@ class DataCategory(DataCategoryBase):
                 return self._rowList[rowI][self._attributeNameList.index(attribute)]
             except (IndexError):
                 raise IndexError        
-        raise IndexError, attribute
+        raise IndexError(attribute)
 
     def setValue(self,value,attributeName=None,rowIndex=None):
         if attributeName is None:
@@ -544,13 +545,13 @@ class DataCategory(DataCategoryBase):
             if (ind >= ll):
                 row.extend([None for ii in xrange(2*ind-ll)])
                 row[ind]=None
-            exec method.getInline()
+            exec(method.getInline())
             self.__currentRowIndex+=1
             currentRowIndex=self.__currentRowIndex
 
     def invokeCategoryMethod(self,type,method,db):
         self.__currentRowIndex = 0
-        exec method.getInline()
+        exec(method.getInline())
 
     def getAttributeLengthMaximumList(self):
         mList=[0 for i in len(self._attributeNameList)]
@@ -750,7 +751,7 @@ class DataCategory(DataCategoryBase):
             except (IndexError):
                 self.__lfh.write("attributeName %s rowI %r rowdata %r\n" % (attributeName,rowI,self._rowList[rowI]))
                 raise IndexError        
-        raise TypeError, attribute
+        raise TypeError(attribute)
         
 
     def getValueFormattedByIndex(self,attributeIndex,rowIndex):

wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxParser.py

@@ -27,6 +27,7 @@ Acknowledgements:
  See:  http://pymmlib.sourceforge.net/
 
 """
+from __future__ import absolute_import
 
 __docformat__ = "restructuredtext en"
 __author__    = "John Westbrook"
@@ -137,7 +138,7 @@ class PdbxReader(object):
         # Find the first reserved word and begin capturing data.
         #
         while True:
-            curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
+            curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
             if curWord is None:
                 continue
             reservedWord, state  = self.__getState(curWord)
@@ -194,7 +195,7 @@ class PdbxReader(object):
 
 
                 # Get the data for this attribute from the next token
-                tCat, tAtt, curQuotedString, curWord = tokenizer.next()
+                tCat, tAtt, curQuotedString, curWord = next(tokenizer)
 
                 if tCat is not None or (curQuotedString is None and curWord is None):
                     self.__syntaxError("Missing data for item _%s.%s" % (curCatName,curAttName))
@@ -215,7 +216,7 @@ class PdbxReader(object):
                 else:
                     self.__syntaxError("Missing value in item-value pair")
 
-                curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
+                curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
                 continue
 
             #
@@ -225,14 +226,14 @@ class PdbxReader(object):
 
                 # The category name in the next curCatName,curAttName pair
                 #    defines the name of the category container.
-                curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
+                curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
                 if curCatName is None or curAttName is None:
                     self.__syntaxError("Unexpected token in loop_ declaration")
                     return
 
                 # Check for a previous category declaration.
-                if categoryIndex.has_key(curCatName):
+                if curCatName in categoryIndex:
                     self.__syntaxError("Duplicate category declaration in loop_")
                     return
 
@@ -248,7 +249,7 @@ class PdbxReader(object):
 
                 # Read the rest of the loop_ declaration 
                 while True:
-                    curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
+                    curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
                     
                     if curCatName is None:
                         break
@@ -280,7 +281,7 @@ class PdbxReader(object):
                         elif curQuotedString is not None:
                             curRow.append(curQuotedString)
 
-                        curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
+                        curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
                     # loop_ data processing ends if - 
 
@@ -306,7 +307,7 @@ class PdbxReader(object):
                     categoryIndex = {}
                     curCategory = None
 
-                curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
+                curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
             elif state == "ST_DATA_CONTAINER":
                 #
@@ -317,7 +318,7 @@ class PdbxReader(object):
                 containerList.append(curContainer)
                 categoryIndex = {}
                 curCategory = None
-                curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
+                curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
             elif state == "ST_STOP":
                 return
@@ -327,7 +328,7 @@ class PdbxReader(object):
                 containerList.append(curContainer)
                 categoryIndex = {}
                 curCategory = None
-                curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
+                curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
             elif state == "ST_UNKNOWN":
                 self.__syntaxError("Unrecogized syntax element: " + str(curWord))
@@ -366,7 +367,7 @@ class PdbxReader(object):
 
         ## Tokenizer loop begins here ---
         while True:
-            line = fileIter.next()
+            line = next(fileIter)
             self.__curLineNumber += 1
 
             # Dump comments
@@ -379,7 +380,7 @@ class PdbxReader(object):
             if line.startswith(";"):
                 mlString = [line[1:]]
                 while True:
-                    line = fileIter.next()
+                    line = next(fileIter)
                     self.__curLineNumber += 1
                     if line.startswith(";"):
                         break
@@ -451,7 +452,7 @@ class PdbxReader(object):
 
         ## Tokenizer loop begins here ---
         while True:
-            line = fileIter.next()
+            line = next(fileIter)
             self.__curLineNumber += 1
 
             # Dump comments
@@ -464,7 +465,7 @@ class PdbxReader(object):
             if line.startswith(";"):
                 mlString = [line[1:]]
                 while True:
-                    line = fileIter.next()
+                    line = next(fileIter)
                     self.__curLineNumber += 1
                     if line.startswith(";"):
                         break

wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxReadWriteTests.py

@@ -10,6 +10,7 @@
 ##
 """  Various tests caess for PDBx/mmCIF data file and dictionary reader and writer. 
 """
+from __future__ import absolute_import
 
 __docformat__ = "restructuredtext en"
 __author__    = "John Westbrook"

wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxReader.py

@@ -22,6 +22,7 @@ Acknowledgements:
  See:  http://pymmlib.sourceforge.net/
 
 """
+from __future__ import absolute_import
 
 import re,sys
 from simtk.openmm.app.internal.pdbx.reader.PdbxContainers import *
@@ -126,7 +127,7 @@ class PdbxReader(object):
         # Find the first reserved word and begin capturing data.
         #
         while True:
-            curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
+            curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
             if curWord is None:
                 continue
             reservedWord, state  = self.__getState(curWord)
@@ -183,7 +184,7 @@ class PdbxReader(object):
 
 
                 # Get the data for this attribute from the next token
-                tCat, tAtt, curQuotedString, curWord = tokenizer.next()
+                tCat, tAtt, curQuotedString, curWord = next(tokenizer)
 
                 if tCat is not None or (curQuotedString is None and curWord is None):
                     self.__syntaxError("Missing data for item _%s.%s" % (curCatName,curAttName))
@@ -204,7 +205,7 @@ class PdbxReader(object):
                 else:
                     self.__syntaxError("Missing value in item-value pair")
 
-                curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
+                curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
                 continue
 
             #
@@ -214,14 +215,14 @@ class PdbxReader(object):
 
                 # The category name in the next curCatName,curAttName pair
                 #    defines the name of the category container.
-                curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
+                curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
                 if curCatName is None or curAttName is None:
                     self.__syntaxError("Unexpected token in loop_ declaration")
                     return
 
                 # Check for a previous category declaration.
-                if categoryIndex.has_key(curCatName):
+                if curCatName in categoryIndex:
                     self.__syntaxError("Duplicate category declaration in loop_")
                     return
 
@@ -237,7 +238,7 @@ class PdbxReader(object):
 
                 # Read the rest of the loop_ declaration 
                 while True:
-                    curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
+                    curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
                     
                     if curCatName is None:
                         break
@@ -269,7 +270,7 @@ class PdbxReader(object):
                         elif curQuotedString is not None:
                             curRow.append(curQuotedString)
 
-                        curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
+                        curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
                     # loop_ data processing ends if - 
 
@@ -295,7 +296,7 @@ class PdbxReader(object):
                     categoryIndex = {}
                     curCategory = None
 
-                curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
+                curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
             elif state == "ST_DATA_CONTAINER":
                 #
@@ -306,7 +307,7 @@ class PdbxReader(object):
                 containerList.append(curContainer)
                 categoryIndex = {}
                 curCategory = None
-                curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
+                curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
             elif state == "ST_STOP":
                 return
@@ -316,7 +317,7 @@ class PdbxReader(object):
                 containerList.append(curContainer)
                 categoryIndex = {}
                 curCategory = None
-                curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
+                curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
 
             elif state == "ST_UNKNOWN":
                 self.__syntaxError("Unrecogized syntax element: " + str(curWord))
@@ -355,7 +356,7 @@ class PdbxReader(object):
 
         ## Tokenizer loop begins here ---
         while True:
-            line = fileIter.next()
+            line = next(fileIter)
             self.__curLineNumber += 1
 
             # Dump comments
@@ -368,7 +369,7 @@ class PdbxReader(object):
             if line.startswith(";"):
                 mlString = [line[1:]]
                 while True:
-                    line = fileIter.next()
+                    line = next(fileIter)
                     self.__curLineNumber += 1
                     if line.startswith(";"):
                         break
@@ -426,7 +427,7 @@ class PdbxReader(object):
 
         ## Tokenizer loop begins here ---
         while True:
-            line = fileIter.next()
+            line = next(fileIter)
             self.__curLineNumber += 1
 
             # Dump comments
@@ -439,7 +440,7 @@ class PdbxReader(object):
             if line.startswith(";"):
                 mlString = [line[1:]]
                 while True:
-                    line = fileIter.next()
+                    line = next(fileIter)
                     self.__curLineNumber += 1
                     if line.startswith(";"):
                         break

wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxReaderTests.py

@@ -12,6 +12,7 @@
 Test cases for reading PDBx/mmCIF data files PdbxReader class -
 
 """
+from __future__ import absolute_import
 import sys, unittest, traceback
 import sys, time, os, os.path, shutil
 

wrappers/python/simtk/openmm/app/internal/pdbx/writer/PdbxWriter.py

@@ -11,6 +11,7 @@
 Classes for writing data and dictionary containers in PDBx/mmCIF format.
 
 """
+from __future__ import absolute_import
 __docformat__ = "restructuredtext en"
 __author__    = "John Westbrook"
 __email__     = "jwest@rcsb.rutgers.edu"

wrappers/python/simtk/openmm/app/internal/pdbx/writer/PdbxWriterTests.py

@@ -12,6 +12,7 @@
 Test implementing PDBx/mmCIF write and formatting operations.
 
 """
+from __future__ import absolute_import
 __docformat__ = "restructuredtext en"
 __author__    = "John Westbrook"
 __email__     = "jwest@rcsb.rutgers.edu"

wrappers/python/simtk/openmm/app/internal/unitcell.py

@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 

wrappers/python/simtk/openmm/app/modeller.py

@@ -29,6 +29,7 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 from __future__ import division
+from __future__ import absolute_import
 
 __author__ = "Peter Eastman"
 __version__ = "1.0"
@@ -40,7 +41,7 @@ from simtk.openmm.vec3 import Vec3
 from simtk.openmm import System, Context, NonbondedForce, CustomNonbondedForce, HarmonicBondForce, HarmonicAngleForce, VerletIntegrator, LocalEnergyMinimizer
 from simtk.unit import nanometer, molar, elementary_charge, amu, gram, liter, degree, sqrt, acos, is_quantity, dot, norm
 import simtk.unit as unit
-import element as elem
+from . import element as elem
 import os
 import random
 import xml.etree.ElementTree as etree
@@ -877,7 +878,7 @@ class Modeller(object):
         # Create copies of all residue templates that have had all extra points removed.
 
         templatesNoEP = {}
-        for resName, template in forcefield._templates.iteritems():
+        for resName, template  in forcefield._templates.items():
             if any(atom.element is None for atom in template.atoms):
                 index = 0
                 newIndex = {}

wrappers/python/simtk/openmm/app/pdbreporter.py

@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 

wrappers/python/simtk/openmm/app/simulation.py

@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
@@ -133,7 +134,7 @@ class Simulation(object):
         
     def _simulate(self, endStep=None, endTime=None):
         if endStep is None:
-            endStep = sys.maxint
+            endStep = sys.maxsize
         nextReport = [None]*len(self.reporters)
         while self.currentStep < endStep and (endTime is None or datetime.now() < endTime):
             nextSteps = endStep-self.currentStep

wrappers/python/simtk/openmm/app/statedatareporter.py

@@ -28,6 +28,8 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
+from __future__ import print_function
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
@@ -146,7 +148,7 @@ class StateDataReporter(object):
         if not self._hasInitialized:
             self._initializeConstants(simulation)
             headers = self._constructHeaders()
-            print >>self._out, '#"%s"' % ('"'+self._separator+'"').join(headers)
+            print('#"%s"' % ('"'+self._separator+'"').join(headers), file=self._out)
             try:
                 self._out.flush()
             except AttributeError:
@@ -163,7 +165,7 @@ class StateDataReporter(object):
         values = self._constructReportValues(simulation, state)
 
         # Write the values.
-        print >>self._out, self._separator.join(str(v) for v in values)
+        print(self._separator.join(str(v) for v in values), file=self._out)
         try:
             self._out.flush()
         except AttributeError:

wrappers/python/simtk/openmm/app/topology.py

@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 

wrappers/python/simtk/openmm/mtsintegrator.py

@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 

wrappers/python/simtk/openmm/vec3.py

@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 

wrappers/python/simtk/testInstallation.py

 from __future__ import print_function
+from __future__ import absolute_import
 from functools import wraps
 import os
 import sys

wrappers/python/simtk/unit/__init__.py

-"""
-Physical quantities with units for dimensional analysis and automatic unit conversion.
-"""
-__docformat__ = "epytext en"
-
-__author__ = "Christopher M. Bruns"
-__copyright__ = "Copyright 2010, Stanford University and Christopher M. Bruns"
-__credits__ = []
-__license__ = "MIT"
-__maintainer__ = "Christopher M. Bruns"
-__email__ = "cmbruns@stanford.edu"
-
-from unit import Unit, is_unit
-from quantity import Quantity, is_quantity
-from unit_math import *
-from unit_definitions import *
-from constants import *
+"""
+Physical quantities with units for dimensional analysis and automatic unit conversion.
+"""
+from __future__ import absolute_import
+
+__docformat__ = "epytext en"
+__author__ = "Christopher M. Bruns"
+__copyright__ = "Copyright 2010, Stanford University and Christopher M. Bruns"
+__credits__ = []
+__license__ = "MIT"
+__maintainer__ = "Christopher M. Bruns"
+__email__ = "cmbruns@stanford.edu"
+
+from .unit import Unit, is_unit
+from .quantity import Quantity, is_quantity
+from .unit_math import *
+from .unit_definitions import *
+from .constants import *

wrappers/python/simtk/unit/quantity.py

@@ -807,8 +807,8 @@ def _is_string(x):
      if isinstance(x, str):
          return True
      try:
-         first_item = iter(x).next()
-         inner_item = iter(first_item).next()
+         first_item = next(iter(x))
+         inner_item = next(iter(first_item))
          if first_item is inner_item:
              return True
          else: