Merge pull request #263 from choderalab/iupac_fix

Make OEIUPAC optional for normalize_molecule, cut release

.travis.yml

@@ -36,6 +36,10 @@ script:
   - conda config --add channels ${ORGNAME}
   # Add omnia dev channels
   - conda config --add channels https://conda.anaconda.org/omnia/label/dev
+  # Add the conda-forge channel
+  - conda config --add channels conda-forge
+  # Update everything
+  - conda update --quiet --yes --all
   # Install OpenEye toolkit
   - conda install --yes --quiet pip
   - pip install $OPENEYE_CHANNEL openeye-toolkits && python -c "import openeye; print(openeye.__version__)"
@@ -55,12 +59,12 @@ env:
   matrix:
     # OpenEye production
     - CONDA_PY=27 python=2.7 OPENEYE_CHANNEL="-i https://pypi.anaconda.org/OpenEye/simple/"
-    - CONDA_PY=34 python=3.4 OPENEYE_CHANNEL="-i https://pypi.anaconda.org/OpenEye/simple/"
     - CONDA_PY=35 python=3.5 OPENEYE_CHANNEL="-i https://pypi.anaconda.org/OpenEye/simple/"
+    - CONDA_PY=36 python=3.6 OPENEYE_CHANNEL="-i https://pypi.anaconda.org/OpenEye/simple/"
     # OpenEye beta
     - CONDA_PY=27 python=2.7 OPENEYE_CHANNEL="--pre -i https://pypi.anaconda.org/OpenEye/simple/"
-    - CONDA_PY=34 python=3.4 OPENEYE_CHANNEL="--pre -i https://pypi.anaconda.org/OpenEye/simple/"
     - CONDA_PY=35 python=3.5 OPENEYE_CHANNEL="--pre -i https://pypi.anaconda.org/OpenEye/simple/"
+    - CONDA_PY=36 python=3.6 OPENEYE_CHANNEL="--pre -i https://pypi.anaconda.org/OpenEye/simple/"
 
   global:
     - ORGNAME="omnia"

devtools/travis-ci/install.sh

@@ -9,5 +9,5 @@ bash $MINICONDA -b -p $HOME/miniconda
 PIP_ARGS="-U"
 
 export PATH=$HOME/miniconda/bin:$PATH
-
-conda install --yes conda-build=2.1.5 jinja2 anaconda-client pip
+conda update --yes conda
+conda install --yes conda-build=2.1.7 jinja2 anaconda-client pip

openmoltools/openeye.py

@@ -105,7 +105,9 @@ def get_charges(molecule, max_confs=800, strictStereo=True,
 
 
 def normalize_molecule(molecule):
-    """Normalize a copy of the molecule by checking aromaticity, adding explicit hydrogens, and renaming by IUPAC name.
+    """
+    Normalize a copy of the molecule by checking aromaticity, adding explicit hydrogens, and
+    (if possible) renaming by IUPAC name.
 
     Parameters
     ----------
@@ -119,9 +121,10 @@ def normalize_molecule(molecule):
 
     """
     oechem = import_("openeye.oechem")
-    if not oechem.OEChemIsLicensed(): raise(ImportError("Need License for OEChem!"))
+    if not oechem.OEChemIsLicensed():
+        raise(ImportError("Need License for OEChem!"))
     oeiupac = import_("openeye.oeiupac")
-    if not oeiupac.OEIUPACIsLicensed(): raise(ImportError("Need License for OEOmega!"))
+    has_iupac = oeiupac.OEIUPACIsLicensed()
 
     molcopy = oechem.OEMol(molecule)
 
@@ -132,15 +135,17 @@ def normalize_molecule(molecule):
     oechem.OEAddExplicitHydrogens(molcopy)
 
     # Set title to IUPAC name.
-    name = oeiupac.OECreateIUPACName(molcopy)
-    molcopy.SetTitle(name)
+    if has_iupac:
+        name = oeiupac.OECreateIUPACName(molcopy)
+        molcopy.SetTitle(name)
 
     # Check for any missing atom names, if found reassign all of them.
     if any([atom.GetName() == '' for atom in molcopy.GetAtoms()]):
         oechem.OETriposAtomNames(molcopy)
 
     return molcopy
 
+
 def iupac_to_oemol(iupac_name):
     """Create a OEMolBuilder from a iupac name.
 
@@ -156,9 +161,11 @@ def iupac_to_oemol(iupac_name):
 
     """
     oechem = import_("openeye.oechem")
-    if not oechem.OEChemIsLicensed(): raise(ImportError("Need License for OEChem!"))
+    if not oechem.OEChemIsLicensed():
+        raise(ImportError("Need License for OEChem!"))
     oeiupac = import_("openeye.oeiupac")
-    if not oeiupac.OEIUPACIsLicensed(): raise(ImportError("Need License for OEOmega!"))
+    if not oeiupac.OEIUPACIsLicensed():
+        raise(ImportError("Need License for OEIupac!"))
 
     # Create an OEMol molecule from IUPAC name.
     molecule = oechem.OEMol()  # create a molecule
@@ -171,6 +178,7 @@ def iupac_to_oemol(iupac_name):
 
     return molecule
 
+
 def smiles_to_oemol(smiles):
     """Create a OEMolBuilder from a smiles string.
 

openmoltools/tests/test_openeye.py

@@ -11,7 +11,7 @@
 import openmoltools.openeye
 import pandas as pd
 import mdtraj as md
-from mdtraj.testing import raises
+from numpy.testing import assert_raises
 
 smiles_fails_with_strictStereo = "CN1CCN(CC1)CCCOc2cc3c(cc2OC)C(=[NH+]c4cc(c(cc4Cl)Cl)OC)C(=C=[N-])C=[NH+]3"
 
@@ -237,17 +237,17 @@ def test_ffxml_simulation():
 
 
 @skipIf(not HAVE_OE, "Cannot test openeye module without OpenEye tools.")
-@raises(RuntimeError)
 def test_charge_fail1():
-    with utils.enter_temp_directory():
-        openmoltools.openeye.smiles_to_antechamber(smiles_fails_with_strictStereo, "test.mol2",  "test.frcmod", strictStereo=True)
+    with assert_raises(RuntimeError):
+        with utils.enter_temp_directory():
+            openmoltools.openeye.smiles_to_antechamber(smiles_fails_with_strictStereo, "test.mol2",  "test.frcmod", strictStereo=True)
 
 
 @skipIf(not HAVE_OE, "Cannot test openeye module without OpenEye tools.")
-@raises(RuntimeError)
 def test_charge_fail2():
-    m = openmoltools.openeye.smiles_to_oemol(smiles_fails_with_strictStereo)
-    m = openmoltools.openeye.get_charges(m, strictStereo=True, keep_confs=1)
+    with assert_raises(RuntimeError):
+        m = openmoltools.openeye.smiles_to_oemol(smiles_fails_with_strictStereo)
+        m = openmoltools.openeye.get_charges(m, strictStereo=True, keep_confs=1)
 
 
 @skipIf(not HAVE_OE, "Cannot test openeye module without OpenEye tools.")
@@ -262,11 +262,11 @@ def test_charge_success2():
     m = openmoltools.openeye.get_charges(m, strictStereo=False)
 
 @skipIf(not HAVE_OE, "Cannot test openeye module without OpenEye tools.")
-@raises(RuntimeError)
 def test_oeassigncharges_fail():
-    # Fail test for OEToolkits (2017.2.1) new charging function
-    m = openmoltools.openeye.smiles_to_oemol(smiles_fails_with_strictStereo)
-    m = openmoltools.openeye.get_charges(m,  strictStereo=False, legacy=False)
+    with assert_raises(RuntimeError):
+        # Fail test for OEToolkits (2017.2.1) new charging function
+        m = openmoltools.openeye.smiles_to_oemol(smiles_fails_with_strictStereo)
+        m = openmoltools.openeye.get_charges(m,  strictStereo=False, legacy=False)
 
 @skipIf(not HAVE_OE, "Cannot test openeye module without OpenEye tools.")
 def test_oeassigncharges_success():

setup.py

@@ -21,11 +21,9 @@
     setup_kwargs = {}
     cython_extension = 'c'
 
-
-
 ##########################
-VERSION = "0.8.2dev0"
-ISRELEASED = False
+VERSION = "0.8.2"
+ISRELEASED = True
 __version__ = VERSION
 ##########################