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

Single py2/3 codebase

.travis.yml

-language: cpp
-compiler:
-  - clang
+language: python
+python:
+  - "2.7_with_system_site_packages"
+  - "3.4"
+
 sudo: false
 addons:
   apt:
@@ -10,16 +12,10 @@ addons:
       - libpcre3
       - libpcre3-dev
       - gromacs
-      - swig
       - doxygen
-      - clang-3.3
-      - llvm-3.3
       - python-numpy
       - python-scipy
-      - python-sphinx
-      - python-yaml
-      - python-pip
-      - python-virtualenv
+
 
 env:
   matrix:
@@ -29,11 +25,14 @@ env:
 before_install:
   - export CC=clang
   - export CXX=clang++
-  - export ASAN_SYMBOLIZER_PATH=/usr/bin/llvm-symbolizer-3.3
+
+  - wget https://anaconda.org/anaconda/swig/3.0.2/download/linux-64/swig-3.0.2-0.tar.bz2
+  - mkdir $HOME/swig
+  - tar -xjvf swig-3.0.2-0.tar.bz2 -C $HOME/swig
+  - export PATH=$HOME/swig/bin:$PATH
+  - export SWIG_LIB=$HOME/swig/share/swig/3.0.2
 
 script:
-  - virtualenv --system-site-packages openmm_env
-  - source openmm_env/bin/activate
   - cmake -DCMAKE_INSTALL_PREFIX=$HOME/OpenMM -DOPENMM_BUILD_STATIC_LIB=$OPENMM_BUILD_STATIC_LIB .
   - make -j2
   - make -j2 install
@@ -43,11 +42,12 @@ script:
   - # run all of the tests, making sure failures at this stage don't cause travis failures
   - ctest -j2 || true
   - # get a list of all of the failed tests into this stupid ctest format
-  - python -c 'fn = "Testing/Temporary/LastTestsFailed.log"; import os; os.path.exists(fn) or exit(0); l = [line.split(":")[0] for line in open(fn)]; triplets = zip(l, l, [","]*len(l)); print "".join(",".join(t) for t in triplets)' > FailedTests.log
+  - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
   - # rerun all of the failed tests
   - if [ -s Testing/Temporary/LastTestsFailed.log ]; then ctest -I FailedTests.log; fi;
   - # run the python tests too
   - cd python/tests  
-  - pip install nose
-  - nosetests -vv --processes=-1 --process-timeout=200
+  - # nosetests -vv --processes=-1 --process-timeout=200
+  - # nosetests -vv
+  - py.test -v *
   - cd -

wrappers/python/setup.py

@@ -122,11 +122,6 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                            build_info=BUILD_INFO):
     from distutils.core import Extension
     setupKeywords = {}
-    try:
-        from distutils.command.build_py import build_py_2to3 as build_py
-    except ImportError:
-        from distutils.command.build_py import build_py
-    setupKeywords["cmdclass"]          = {'build_py': build_py}
     setupKeywords["name"]              = "OpenMM"
     setupKeywords["version"]           = "%s.%s.%s" % (major_version_num,
                                                        minor_version_num,

wrappers/python/simtk/openmm/__init__.py

@@ -4,11 +4,12 @@ from your own code. It provides a combination of extreme flexibility
 (through custom forces and integrators), openness, and high performance
 (especially on recent GPUs) that make it truly unique among simulation codes.
 """
+from __future__ import absolute_import
 __author__ = "Peter Eastman"
 
 import os, os.path
 import sys
-from simtk.openmm import version
+from . import version
 
 if sys.platform == 'win32':
     _path = os.environ['PATH']

wrappers/python/simtk/openmm/amd.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/amberinpcrdfile.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/amberprmtopfile.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"
 
@@ -35,8 +36,8 @@ from math import sqrt
 from simtk.openmm.app import Topology
 from simtk.openmm.app import PDBFile
 from simtk.openmm.app.internal import amber_file_parser
-import forcefield as ff
-import element as elem
+from . import forcefield as ff
+from . import element as elem
 import simtk.unit as unit
 import simtk.openmm as mm
 from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors

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

@@ -33,6 +33,8 @@ 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
 
 from simtk.openmm.app.internal.charmm.exceptions import CharmmFileError
 import simtk.unit as u
@@ -117,7 +119,7 @@ class CharmmCrdFile(object):
                                        len(self.positions))
                 )
 
-        except (ValueError, IndexError), e:
+        except (ValueError, IndexError) as e:
             raise CharmmFileError('Error parsing CHARMM coordinate file')
 
         # Apply units to the positions now. Do it this way to allow for
@@ -197,7 +199,7 @@ class CharmmRstFile(object):
                         self.jhstrt = int(line[5])    # Num total steps?
                         break
                    
-                    except (ValueError, IndexError), e:
+                    except (ValueError, IndexError) as e:
                         raise CharmmFileError('Problem parsing CHARMM restart')
 
         self._scan(crdfile, '!XOLD')
@@ -255,9 +257,9 @@ class CharmmRstFile(object):
 
     def printcoords(self, crds):
         for crd in range(len(crds)):
-            print crds[crd],
+            print(crds[crd], end=' ')
             if not (crd+1) % 3:
-                print '\n',
+                print('\n', end=' ')
 
 if __name__ == '__main__':
     import doctest

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

@@ -33,6 +33,7 @@ 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
 import os
 from simtk.openmm.app.internal.charmm._charmmfile import (
             CharmmFile, CharmmStreamFile)
@@ -428,7 +429,7 @@ class CharmmParameterSet(object):
                     # soldier on
                     if not read_first_nonbonded: continue
                     raise CharmmFileError('Could not parse nonbonded terms.')
-                except CharmmFileError, e:
+                except CharmmFileError as e:
                     if not read_first_nonbonded: continue
                     raise CharmmFileError(str(e))
                 else:
@@ -587,7 +588,7 @@ class CharmmParameterSet(object):
         # multiterm dihedral have to have a DIFFERENT periodicity, we don't have
         # to condense _within_ a single list of torsions assigned to the same
         # key (they're guaranteed to be different)
-        keylist = self.dihedral_types.keys()
+        keylist = list(self.dihedral_types.keys())
         for i in range(len(keylist) - 1):
             key1 = keylist[i]
             for dihedral in self.dihedral_types[key1]:
@@ -606,7 +607,7 @@ class CharmmParameterSet(object):
         Parameter:
             - typedict : Type dictionary to condense
         """
-        keylist = typedict.keys()
+        keylist = list(typedict.keys())
         for i in range(len(keylist) - 1):
             key1 = keylist[i]
             for j in range(i+1, len(keylist)):

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

@@ -33,11 +33,14 @@ 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
+from __future__ import print_function
 
 from functools import wraps
 from math import pi, cos, sin, sqrt
 import os
 import re
+import sys
 import simtk.openmm as mm
 from simtk.openmm.vec3 import Vec3
 import simtk.unit as u
@@ -58,7 +61,8 @@ import warnings
 
 TINY = 1e-8
 WATNAMES = ('WAT', 'HOH', 'TIP3', 'TIP4', 'TIP5', 'SPCE', 'SPC')
-
+if sys.version_info >= (3, 0):
+    xrange = range
 
 def _catchindexerror(func):
     """
@@ -70,7 +74,7 @@ def _catchindexerror(func):
         """ Catch the index error """
         try:
             return func(*args, **kwargs)
-        except IndexError, e:
+        except IndexError as e:
             raise CharmmPSFError('Array is too short: %s' % e)
 
     return newfunc
@@ -386,8 +390,8 @@ class CharmmPsfFile(object):
         """
         try:
             return type(string)
-        except ValueError, e:
-            print e
+        except ValueError as e:
+            print(e)
             raise CharmmPSFError('Could not convert %s' % message)
 
     @staticmethod
@@ -1251,8 +1255,8 @@ class CharmmPsfFile(object):
             elif implicitSolvent is GBn2:
                 gb = GBSAGBn2Force(solventDielectric, soluteDielectric, None,
                                    cutoff, kappa=implicitSolventKappa)
-            for i, atom in enumerate(self.atom_list):
-                gb.addParticle([atom.charge] + list(gb_parms[i]))
+            for atom, gb_parm in zip(self.atom_list, gb_parms):
+                gb.addParticle([atom.charge] + list(gb_parm))
             # Set cutoff method
             if nonbondedMethod is ff.NoCutoff:
                 gb.setNonbondedMethod(mm.NonbondedForce.NoCutoff)

wrappers/python/simtk/openmm/app/checkpointreporter.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__ = "Robert McGibbon"
 __version__ = "1.0"
 
@@ -77,7 +78,7 @@ class CheckpointReporter(object):
         """
 
         self._reportInterval = reportInterval
-        if isinstance(file, basestring):
+        if isinstance(file, str):
             self._own_handle = True
             self._out = open(file, 'w+b', 0)
         else:

wrappers/python/simtk/openmm/app/dcdfile.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/dcdreporter.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/desmonddmsfile.py

@@ -24,6 +24,7 @@ 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
 
 import os
 import math

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

@@ -28,12 +28,18 @@ 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__ = "Christopher M. Bruns"
 __version__ = "1.0"
 
+import sys
 from collections import OrderedDict
 from simtk.unit import daltons, is_quantity
-import copy_reg
+if sys.version_info >= (3, 0):
+    import copyreg
+else:
+    import copy_reg as copyreg
+
 
 class Element(object):
     """An Element represents a chemical element.
@@ -128,7 +134,7 @@ class Element(object):
         diff = mass
         best_guess = None
 
-        for elemmass, element in Element._elements_by_mass.iteritems():
+        for elemmass, element in _iteritems(Element._elements_by_mass):
             massdiff = abs(elemmass - mass)
             if massdiff < diff:
                 best_guess = element
@@ -172,7 +178,7 @@ def get_by_symbol(symbol):
 def _pickle_element(element):
     return (get_by_symbol, (element.symbol,))
 
-copy_reg.pickle(Element, _pickle_element)
+copyreg.pickle(Element, _pickle_element)
 
 # NOTE: getElementByMass assumes all masses are Quantity instances with unit
 # "daltons". All elements need to obey this assumption, or that method will
@@ -299,3 +305,10 @@ ununhexium =     Element(116, "ununhexium",     "Uuh", 292*daltons)
 # relational operators will work with any chosen name
 sulphur = sulfur
 aluminium = aluminum
+
+if sys.version_info >= (3, 0):
+    def _iteritems(dict):
+        return dict.items()
+else:
+    def _iteritems(dict):
+        return dict.iteritems()

wrappers/python/simtk/openmm/app/forcefield.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"
 
@@ -38,7 +40,7 @@ import math
 from math import sqrt, cos
 import simtk.openmm as mm
 import simtk.unit as unit
-import element as elem
+from . import element as elem
 from simtk.openmm.app import Topology
 
 def _convertParameterToNumber(param):
@@ -1883,7 +1885,7 @@ def countConstraint(data):
         if (isConstrained):
             angleCount += 1
 
-    print "Constraints bond=%d angle=%d  total=%d" % (bondCount, angleCount, (bondCount+angleCount))
+    print("Constraints bond=%d angle=%d  total=%d" % (bondCount, angleCount, (bondCount+angleCount)))
 
 ## @private
 class AmoebaBondGenerator:

wrappers/python/simtk/openmm/app/gromacsgrofile.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__ = "Lee-Ping Wang"
 __version__ = "1.0"
 
@@ -36,7 +37,7 @@ import sys
 from simtk.openmm import Vec3
 from re import sub, match
 from simtk.unit import nanometers, angstroms, Quantity
-import element as elem
+from . import element as elem
 try:
     import numpy
 except:

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

@@ -28,14 +28,15 @@ 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"
 
 from simtk.openmm.app import Topology
 from simtk.openmm.app import PDBFile
-import forcefield as ff
-import element as elem
-import amberprmtopfile as prmtop
+from . import forcefield as ff
+from . import element as elem
+from . import amberprmtopfile as prmtop
 import simtk.unit as unit
 import simtk.openmm as mm
 import math
@@ -601,7 +602,7 @@ class GromacsTopFile(object):
         for key in self._dihedralTypes:
             if key[1] == 'X' or key[2] == 'X':
                 wildcardDihedralTypes.append(key)
-                for types in dihedralTypeTable.itervalues():
+                for types in dihedralTypeTable.values():
                     types.append(key)
 
         # Loop over molecules and create the specified number of each type.
@@ -617,7 +618,7 @@ class GromacsTopFile(object):
                 try:
                     bondedTypes = [self._atomTypes[t][1] for t in atomTypes]
                 except KeyError as e:
-                    raise ValueError('Unknown atom type: '+e.message)
+                    raise ValueError('Unknown atom type: ' + e.message)
                 bondedTypes = [b if b is not None else a for a, b in zip(atomTypes, bondedTypes)]
 
                 # Add atoms.

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

@@ -34,6 +34,8 @@ 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
 
 #=============================================================================================
 # GLOBAL IMPORTS
@@ -54,7 +56,7 @@ import simtk.openmm
 from simtk.openmm.app import element as elem
 from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
 from simtk.openmm.vec3 import Vec3
-import customgbforces as customgb
+from . import customgbforces as customgb
 
 #=============================================================================================
 # AMBER parmtop loader (from 'zander', by Randall J. Radmer)
@@ -713,7 +715,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
         raise Exception("Cannot specify both a filename and a loader")
     if prmtop_filename is not None:
         # Load prmtop file.
-        if verbose: print "Reading prmtop file '%s'..." % prmtop_filename
+        if verbose: print("Reading prmtop file '%s'..." % prmtop_filename)
         prmtop = PrmtopLoader(prmtop_filename)
     else:
         prmtop = prmtop_loader
@@ -737,11 +739,11 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
         mm = simtk.openmm
 
     # Create OpenMM System.
-    if verbose: print "Creating OpenMM system..."
+    if verbose: print("Creating OpenMM system...")
     system = mm.System()
 
     # Populate system with atomic masses.
-    if verbose: print "Adding particles..."
+    if verbose: print("Adding particles...")
     for mass in prmtop.getMasses():
         system.addParticle(mass)
 
@@ -759,7 +761,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
                 system.addConstraint(iAtom, jAtom, rMin)
 
     # Add harmonic bonds.
-    if verbose: print "Adding bonds..."
+    if verbose: print("Adding bonds...")
     force = mm.HarmonicBondForce()
     if flexibleConstraints or (shake not in ('h-bonds', 'all-bonds', 'h-angles')):
         for (iAtom, jAtom, k, rMin) in prmtop.getBondsWithH():
@@ -771,7 +773,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
     system.addForce(force)
 
     # Add harmonic angles.
-    if verbose: print "Adding angles..."
+    if verbose: print("Adding angles...")
     force = mm.HarmonicAngleForce()
     if shake == 'h-angles':
         numConstrainedBonds = system.getNumConstraints()
@@ -809,14 +811,14 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
     system.addForce(force)
 
     # Add torsions.
-    if verbose: print "Adding torsions..."
+    if verbose: print("Adding torsions...")
     force = mm.PeriodicTorsionForce()
     for (iAtom, jAtom, kAtom, lAtom, forceConstant, phase, periodicity) in prmtop.getDihedrals():
         force.addTorsion(iAtom, jAtom, kAtom, lAtom, periodicity, phase, forceConstant)
     system.addForce(force)
 
     # Add nonbonded interactions.
-    if verbose: print "Adding nonbonded interactions..."
+    if verbose: print("Adding nonbonded interactions...")
     force = mm.NonbondedForce()
     if (prmtop.getIfBox() == 0):
         # System is non-periodic.
@@ -1044,7 +1046,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
         # Convert implicitSolventKappa to nanometers if it is a unit.
         if units.is_quantity(implicitSolventKappa):
             implicitSolventKappa = implicitSolventKappa.value_in_unit((1/units.nanometers).unit)
-        if verbose: print "Adding GB parameters..."
+        if verbose: print("Adding GB parameters...")
         charges = prmtop.getCharges()
         cutoff = None
         if nonbondedMethod != 'NoCutoff':
@@ -1071,14 +1073,15 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
             gb = customgb.GBSAGBn2Force(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
         else:
             raise Exception("Illegal value specified for implicit solvent model")
-        for iAtom in range(prmtop.getNumAtoms()):
+
+        for charge, gb_parm in zip(charges, gb_parms):
             if gbmodel == 'OBC2' and implicitSolventKappa == 0:
-                gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1])
+                gb.addParticle(charge, gb_parm[0], gb_parm[1])
             elif gbmodel == 'GBn2':
-                gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1],
-                                gb_parms[iAtom][2], gb_parms[iAtom][3], gb_parms[iAtom][4]])
+                gb.addParticle([charge, gb_parm[0], gb_parm[1],
+                                gb_parm[2], gb_parm[3], gb_parm[4]])
             else:
-                gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]])
+                gb.addParticle([charge, gb_parm[0], gb_parm[1]])
         system.addForce(gb)
         if nonbondedMethod == 'NoCutoff':
             gb.setNonbondedMethod(mm.NonbondedForce.NoCutoff)

wrappers/python/simtk/openmm/app/internal/charmm/_charmmfile.py

@@ -33,7 +33,12 @@ 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 simtk.openmm.app.internal.charmm.exceptions import CharmmFileError
+import sys
+if sys.version_info < (3, 0):
+    from codecs import open
+
 
 class CharmmFile(object):
     """
@@ -54,8 +59,8 @@ class CharmmFile(object):
         else:
             self.status = 'NEW'
         try:
-            self._handle = open(fname, mode)
-        except IOError, e:
+            self._handle = open(fname, mode, encoding='utf-8')
+        except IOError as e:
             raise CharmmFileError(str(e))
         self.closed = False
         self.line_number = 0

wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py

@@ -32,6 +32,7 @@ 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
 from simtk.openmm.app.internal.charmm.exceptions import (
                 SplitResidueWarning, BondError, ResidueError, CmapError,
                 MissingParameter)