Support Python3 & Python2

chemtools/__init__.py

@@ -23,17 +23,21 @@
 # pragma pylint: disable=wildcard-import
 """The Main ChemTools Package."""
 
+import sys
 
-from chemtools.wrappers import *
 from chemtools.toolbox import *
 from chemtools.conceptual import *
 from chemtools.denstools import *
 from chemtools.utils import *
 from chemtools.outputs import *
-import horton
 
+if sys.version_info.major == 2:
+    from chemtools.wrappers2 import *
+    import horton
+    horton.log.head_banner = ""
+    horton.log.foot_banner = ""
+else:
+    from chemtools.wrappers3 import *
 
-horton.log.head_banner = ""
-horton.log.foot_banner = ""
 
 __version__ = '0.9.0'

chemtools/conceptual/base.py

@@ -402,13 +402,13 @@ def grand_potential_derivative(self, n_elec, order=1):
         else:
             # higher-order derivatives are compute with Faa Di Bruno formula
             # list of hyper-hardneses (derivatives of energy w.r.t. N)
-            e_deriv = [self.energy_derivative(n_elec, i + 1) for i in xrange(1, order)]
-            g_deriv = [self.grand_potential_derivative(n_elec, k + 1) for k in xrange(1, order - 1)]
+            e_deriv = [self.energy_derivative(n_elec, i + 1) for i in range(1, order)]
+            g_deriv = [self.grand_potential_derivative(n_elec, k + 1) for k in range(1, order - 1)]
             if any([item is None for item in e_deriv]) or any([item is None for item in g_deriv]):
                 deriv = None
             else:
                 deriv = 0
-                for k in xrange(1, order - 1):
+                for k in range(1, order - 1):
                     deriv -= g_deriv[k - 1] * sp.bell(order - 1, k, e_deriv[:order - k])
                 deriv /= sp.bell(order - 1, order - 1, [e_deriv[0]])
         return deriv

chemtools/conceptual/general.py

@@ -89,7 +89,7 @@ def __init__(self, expr, n0, n_energies, n_symbol=None, n0_symbol=None, guess=No
                 'the number of electrons.')
         self._n_symb = n_symbol
         # store minimum and maximum number of electrons used for interpolation
-        self._n_min, self._n_max = np.min(n_energies.keys()), np.max(n_energies.keys())
+        self._n_min, self._n_max = np.min(list(n_energies.keys())), np.max(list(n_energies.keys()))
 
         # substitute N0 in energy expression
         if n0_symbol:
@@ -184,7 +184,7 @@ def _solve_parameters(self, expr, n_energies, guess, opts=None):
         # construct system of equations to solve
         system_eqns = []
         d_system_eqns = []
-        for n, energy in n_energies.iteritems():
+        for n, energy in n_energies.items():
             eqn = sp.lambdify((params,), expr.subs(self._n_symb, n) - energy, 'numpy')
             system_eqns.append(eqn)
             d_eqn_row = []
@@ -234,7 +234,6 @@ def _solve_nmax(self, guess):
         d_expr = self._expr.diff(self._n_symb)
         n_max_eqn = sp.lambdify(self._n_symb, d_expr, 'numpy')
         result = root(n_max_eqn, guess)
-        print result
         if result.success:
             n_max = np.asscalar(result.x)
             # n_ceil = math.ceil(n_max)

chemtools/conceptual/leastnorm.py

@@ -26,7 +26,7 @@
 """
 
 import numpy as np
-from scipy.misc import factorial
+from scipy.special import factorial
 
 from chemtools.utils.utils import doc_inherit
 from chemtools.conceptual.base import BaseGlobalTool

chemtools/conceptual/utils.py

@@ -40,15 +40,15 @@ def check_dict_values(dict_values):
     # check length of dictionary & its keys
     if len(dict_values) != 3 or not all([key >= 0 for key in dict_values.keys()]):
         raise ValueError("The energy model requires 3 keys corresponding to positive "
-                         "number of electrons! Given keys={0}".format(dict_values.keys()))
+                         "number of electrons! Given keys={0}".format(list(dict_values.keys())))
     # find reference number of electrons
     n_ref = sorted(dict_values.keys())[1]
     if n_ref < 1:
         raise ValueError("The n_ref cannot be less than one! Given n_ref={0}".format(n_ref))
     # check that number of electrons differ by one
     if sorted(dict_values.keys()) != [n_ref - 1, n_ref, n_ref + 1]:
         raise ValueError("In current implementation, the number of electrons (keys) should "
-                         "differ by one! Given keys={0}".format(dict_values.keys()))
+                         "differ by one! Given keys={0}".format(list(dict_values.keys())))
     # check that all values have the same type
     if not all([isinstance(value, type(dict_values[n_ref])) for value in dict_values.values()]):
         raise ValueError("All values in dictionary should be of the same type!")

chemtools/outputs/vmd.py

@@ -592,7 +592,7 @@ def print_vmd_script_multiple_cube(scriptfile, cubes, isosurfs=None, material='O
         raise TypeError('Each iso-surface value must be a float')
 
     if colors is None:
-        colors = range(len(cubes))
+        colors = list(range(len(cubes)))
     elif not (isinstance(colors, (list, tuple)) and len(colors) == len(cubes)):
         raise TypeError('The colors must be provided as a list or tuple of the same length as the '
                         'number of cube files')

chemtools/scripts/chemtools_mot.py

@@ -25,12 +25,15 @@
 """Molecular Orbital Theory (MOT) Script."""
 
 
+import sys
 import numpy as np
 
-from chemtools.wrappers.molecule import Molecule
 from chemtools.toolbox.motbased import OrbPart
 from chemtools.scripts.common import help_cube, load_molecule_and_grid
 
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+
 
 description_mot = """
 Visualize Molecular Orbitals (MO) using VMD package.

chemtools/scripts/common.py

@@ -24,11 +24,14 @@
 """Common utility for scripts."""
 
 
+import sys
 import numpy as np
 
-from chemtools.wrappers.molecule import Molecule
 from chemtools.utils.cube import UniformGrid
 
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+
 
 help_cube = """
 cubic grid used for evaluation and visualization.

chemtools/toolbox/conceptual.py

@@ -27,11 +27,9 @@
 compute various conceptual density functional theory (DFT) descriptive tools.
 """
 
-
+import sys
 import logging
 
-from chemtools.wrappers.molecule import Molecule
-from chemtools.wrappers.grid import MolecularGrid
 from chemtools.toolbox.utils import check_arg_molecule, get_matching_attr
 from chemtools.toolbox.utils import get_dict_energy, get_dict_density, get_dict_population
 from chemtools.conceptual.linear import LinearGlobalTool, LinearLocalTool, LinearCondensedTool
@@ -40,6 +38,14 @@
 from chemtools.conceptual.exponential import ExponentialGlobalTool
 from chemtools.conceptual.rational import RationalGlobalTool
 from chemtools.conceptual.general import GeneralGlobalTool
+
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+    from chemtools.wrappers2.grid import MolecularGrid
+else:
+    from chemtools.wrappers3.molecule import Molecule
+    from chemtools.wrappers3.grid import MolecularGrid
+
 try:
     from pathlib2 import Path
 except ImportError:

chemtools/toolbox/densbased.py

@@ -23,10 +23,15 @@
 # pragma pylint: disable=invalid-name
 """Density-Based Local Tools."""
 
+import sys
 
-from chemtools.wrappers.molecule import Molecule
 from chemtools.denstools.densbased import DensGradLapKedTool
 
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+else:
+    from chemtools.wrappers3.molecule import Molecule
+
 
 class DensityLocalTool(DensGradLapKedTool):
     """Density Local Tool Class."""

chemtools/toolbox/dftbased.py

@@ -24,11 +24,15 @@
 """Density Functional Theory (DFT) Based Tools."""
 
 
+import sys
 import numpy as np
 
 from scipy.optimize import bisect
 
-from chemtools.wrappers.molecule import Molecule
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+else:
+    from chemtools.wrappers3.molecule import Molecule
 
 
 class DFTBasedTool(object):

chemtools/toolbox/interactions.py

@@ -24,9 +24,9 @@
 """Module for (non)bonding interaction analysis of Quantum Chemistry Output Files."""
 
 
+import sys
 import numpy as np
 
-from chemtools.wrappers.molecule import Molecule
 from chemtools.denstools.densbased import DensGradTool
 from chemtools.utils.utils import doc_inherit
 from chemtools.utils.cube import UniformGrid
@@ -35,6 +35,11 @@
 
 from numpy.ma import masked_less
 
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+else:
+    from chemtools.wrappers3.molecule import Molecule
+
 
 class BaseInteraction(object):
     """Base class for (non)bonding interactions indicators."""

chemtools/toolbox/kinetic.py

@@ -24,12 +24,17 @@
 """Kinetic Energy Density Module."""
 
 
+import sys
 import numpy as np
 
 from chemtools.utils.utils import doc_inherit
-from chemtools.wrappers.molecule import Molecule
 from chemtools.denstools.densbased import DensGradTool, DensGradLapTool, DensGradLapKedTool
 
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+else:
+    from chemtools.wrappers3.molecule import Molecule
+
 
 class KED(object):
     """Kinetic Energy Density Class."""

chemtools/toolbox/motbased.py

@@ -24,11 +24,16 @@
 """Orbital-Based Population Analysis."""
 
 
+import sys
 import numpy as np
 
 from chemtools.utils.utils import doc_inherit
 from chemtools.orbstools.partition import OrbitalPartitionTools
-from chemtools.wrappers.molecule import Molecule, MolecularOrbitals
+
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule, MolecularOrbitals
+else:
+    from chemtools.wrappers3.molecule import Molecule, MolecularOrbitals
 
 
 class OrbPart(object):

chemtools/toolbox/oxidation.py

@@ -23,11 +23,16 @@
 """Module for Oxidation State."""
 
 
+import sys
 import itertools
 import numpy as np
 
-from chemtools.wrappers.molecule import Molecule
-from chemtools.wrappers.part import DensPart
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+    from chemtools.wrappers2.part import DensPart
+else:
+    from chemtools.wrappers3.molecule import Molecule
+    from chemtools.wrappers3.part import DensPart
 
 
 class EOS(object):

chemtools/toolbox/test/test_conceptual_condensed.py

@@ -24,13 +24,20 @@
 """Test chemtools.analysis.conceptual.CondensedConceptualDFT."""
 
 
+import sys
 import numpy as np
 
-from numpy.testing import assert_raises, assert_equal, assert_almost_equal
+from numpy.testing import assert_equal, assert_almost_equal
 
-from chemtools.wrappers.molecule import Molecule
-from chemtools.wrappers.grid import MolecularGrid
 from chemtools.toolbox.conceptual import CondensedConceptualDFT
+
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+    from chemtools.wrappers2.grid import MolecularGrid
+else:
+    from chemtools.wrappers3.molecule import Molecule
+    from chemtools.wrappers3.grid import MolecularGrid
+
 try:
     from importlib_resources import path
 except ImportError:

chemtools/toolbox/test/test_conceptual_global.py

@@ -24,12 +24,18 @@
 """Test chemtools.analysis.conceptual.GlobalConceptualDFT."""
 
 
+import sys
 import numpy as np
 
 from numpy.testing import assert_raises, assert_almost_equal
 
 from chemtools.toolbox.conceptual import GlobalConceptualDFT
-from chemtools.wrappers.molecule import Molecule
+
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+else:
+    from chemtools.wrappers3.molecule import Molecule
+
 try:
     from importlib_resources import path
 except ImportError:

chemtools/toolbox/test/test_conceptual_local.py

@@ -24,13 +24,20 @@
 """Test chemtools.analysis.conceptual.LocalConceptualDFT."""
 
 
+import sys
 import numpy as np
 
 from numpy.testing import assert_raises, assert_equal, assert_almost_equal
 
-from chemtools.wrappers.molecule import Molecule
-from chemtools.wrappers.grid import MolecularGrid
 from chemtools.toolbox.conceptual import LocalConceptualDFT
+
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+    from chemtools.wrappers2.grid import MolecularGrid
+else:
+    from chemtools.wrappers3.molecule import Molecule
+    from chemtools.wrappers3.grid import MolecularGrid
+
 try:
     from importlib_resources import path
 except ImportError:

chemtools/toolbox/test/test_densbased.py

@@ -24,12 +24,18 @@
 """Test chemtools.toolbox.densbased."""
 
 
+import sys
 import numpy as np
 
 from numpy.testing import assert_allclose
 
-from chemtools.wrappers.molecule import Molecule
 from chemtools.toolbox.densbased import DensityLocalTool
+
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+else:
+    from chemtools.wrappers3.molecule import Molecule
+
 try:
     from importlib_resources import path
 except ImportError:

chemtools/toolbox/test/test_dftbased.py

@@ -24,12 +24,18 @@
 """Test chemtools.toolbox.dftbased."""
 
 
+import sys
 import numpy as np
 
 from numpy.testing import assert_raises, assert_array_almost_equal
 
-from chemtools.wrappers.molecule import Molecule
 from chemtools.toolbox.dftbased import DFTBasedTool
+
+if sys.version_info.major == 2:
+    from chemtools.wrappers2.molecule import Molecule
+else:
+    from chemtools.wrappers3.molecule import Molecule
+
 try:
     from importlib_resources import path
 except ImportError:

chemtools/toolbox/test/test_elf.py

@@ -26,6 +26,7 @@
 import numpy as np
 from numpy.testing import assert_allclose, assert_raises
 from chemtools.toolbox.interactions import ELF, LOL
+
 try:
     from importlib_resources import path
 except ImportError: