Merge pull request #255 from choderalab/update/assigncharges

Updates for OEAssignCharges to allow use of new, improved OE charging method

.travis.yml

@@ -45,7 +45,7 @@ script:
   - conda install --yes --use-local ${PACKAGENAME}-dev
   # Install testing dependencies
   - conda install --yes --quiet nose nose-timer
-  - conda install --yes --quiet openmmtools  
+  - conda install --yes --quiet openmmtools
   - conda install --yes --quiet packmol
   - conda install --yes --quiet rdkit
   # Test the package

openmoltools/openeye.py

@@ -10,7 +10,8 @@
 
 # Note: We recommend having every function return *copies* of input, to avoid headaches associated with in-place changes
 
-def get_charges(molecule, max_confs=800, strictStereo=True, normalize=True, keep_confs=None):
+def get_charges(molecule, max_confs=800, strictStereo=True,
+                normalize=True, keep_confs=None, legacy=True):
     """Generate charges for an OpenEye OEMol molecule.
 
     Parameters
@@ -34,6 +35,9 @@ def get_charges(molecule, max_confs=800, strictStereo=True, normalize=True, keep
         Otherwise, keep_confs = N will return an OEMol with up to N
         generated conformations.  Multiple conformations are still used to
         *determine* the charges.
+    legacy : bool, default=True
+        If False, uses the new OpenEye charging engine.
+        See https://docs.eyesopen.com/toolkits/python/quacpactk/OEProtonFunctions/OEAssignCharges.html#
 
     Returns
     -------
@@ -62,10 +66,16 @@ def get_charges(molecule, max_confs=800, strictStereo=True, normalize=True, keep
 
     charged_copy = generate_conformers(molecule, max_confs=max_confs, strictStereo=strictStereo)  # Generate up to max_confs conformers
 
-    status = oequacpac.OEAssignPartialCharges(charged_copy, oequacpac.OECharges_AM1BCCSym)  # AM1BCCSym recommended by Chris Bayly to KAB+JDC, Oct. 20 2014.
+    if not legacy:
+        # 2017.2.1 OEToolkits new charging function
+        status = oequacpac.OEAssignCharges(charged_copy, oequacpac.OEAM1BCCCharges())
+        if not status: raise(RuntimeError("OEAssignCharges failed."))
+    else:
+        # AM1BCCSym recommended by Chris Bayly to KAB+JDC, Oct. 20 2014.
+        status = oequacpac.OEAssignPartialCharges(charged_copy, oequacpac.OECharges_AM1BCCSym)
+        if not status: raise(RuntimeError("OEAssignPartialCharges returned error code %d" % status))
+
 
-    if not status:
-        raise(RuntimeError("OEAssignPartialCharges returned error code %d" % status))
 
     #Determine conformations to return
     if keep_confs == None:
@@ -78,6 +88,8 @@ def get_charges(molecule, max_confs=800, strictStereo=True, normalize=True, keep
         #Copy coordinates to single conformer
         charged_copy.SetCoords( original )
     elif keep_confs > 0:
+        logger.debug("keep_confs was set to %s. Molecule positions will be reset." % keep_confs)
+
         #Otherwise if a number is provided, return this many confs if available
         for k, conf in enumerate( charged_copy.GetConfs() ):
             if k > keep_confs - 1:

openmoltools/tests/test_openeye.py

@@ -50,7 +50,7 @@ def test_butanol_unnormalized():
     m0 = openmoltools.openeye.iupac_to_oemol("butanol")
     m0.SetTitle("MyCustomTitle")
     m1 = openmoltools.openeye.get_charges(m0, normalize=False, keep_confs=1)
-    eq(m0.NumAtoms(), m1.NumAtoms()) 
+    eq(m0.NumAtoms(), m1.NumAtoms())
     assert m1.NumConfs() == 1, "This OEMol was created to have a single conformation."
     assert m1.NumAtoms() == 15, "Butanol should have 15 atoms"
     assert m0.GetTitle() == m1.GetTitle(), "The title of the molecule should not be changed by normalization."
@@ -91,19 +91,19 @@ def test_butanol():
     eq(m0.NumAtoms(), m1.NumAtoms())
     assert m1.NumConfs() >= 2, "Butanol should have multiple conformers."
     assert m1.NumAtoms() == 15, "Butanol should have 15 atoms"
-    
+
     all_data = {}
     for k, molecule in enumerate(m1.GetConfs()):
         names_to_charges, str_repr = openmoltools.openeye.get_names_to_charges(molecule)
         all_data[k] = names_to_charges
         eq(sum(names_to_charges.values()), 0.0, decimal=7)  # Net charge should be zero
-    
+
     # Build a table of charges indexed by conformer number and atom name
     all_data = pd.DataFrame(all_data)
-    
+
     # The standard deviation along the conformer axis should be zero if all conformers have same charges
     eq(all_data.std(1).values, np.zeros(m1.NumAtoms()), decimal=7)
-    
+
     with utils.enter_temp_directory():
         # Try saving to disk as mol2
         openmoltools.openeye.molecule_to_mol2(m1, "out.mol2")
@@ -128,10 +128,10 @@ def test_benzene():
     print(m1.NumConfs())
     assert m1.NumConfs() == 1, "Benezene should have 1 conformer"
     assert m1.NumAtoms() == 12, "Benezene should have 12 atoms"
-    
+
     names_to_charges, str_repr = openmoltools.openeye.get_names_to_charges(m1)
     eq(sum(names_to_charges.values()), 0.0, decimal=7)  # Net charge should be zero
-    
+
     with utils.enter_temp_directory():
         # Try saving to disk as mol2
         openmoltools.openeye.molecule_to_mol2(m1, "out.mol2")
@@ -149,7 +149,7 @@ def test_benzene():
 
 
 @skipIf(not HAVE_OE, "Cannot test openeye module without OpenEye tools.")
-def test_link_in_utils():    
+def test_link_in_utils():
     m0 = openmoltools.openeye.iupac_to_oemol("benzene")
     m1 = openmoltools.openeye.get_charges(m0)
     with utils.enter_temp_directory():
@@ -170,7 +170,7 @@ def test_smiles():
 
 @skipIf(not HAVE_OE, "Cannot test openeye module without OpenEye tools.")
 def test_ffxml():
-    with utils.enter_temp_directory():    
+    with utils.enter_temp_directory():
         m0 = openmoltools.openeye.smiles_to_oemol("CCCCO")
         charged0 = openmoltools.openeye.get_charges(m0)
         m1 = openmoltools.openeye.smiles_to_oemol("ClC(Cl)(Cl)Cl")
@@ -182,7 +182,7 @@ def test_ffxml():
 @skipIf(not HAVE_OE, "Cannot test openeye module without OpenEye tools.")
 def test_ffxml_simulation():
     """Test converting toluene and benzene smiles to oemol to ffxml to openmm simulation."""
-    with utils.enter_temp_directory():    
+    with utils.enter_temp_directory():
         m0 = openmoltools.openeye.smiles_to_oemol("Cc1ccccc1")
         charged0 = openmoltools.openeye.get_charges(m0)
         m1 = openmoltools.openeye.smiles_to_oemol("c1ccccc1")
@@ -208,11 +208,11 @@ def test_ffxml_simulation():
         for k, ligand in enumerate(ligands):
             ligand_traj = trajectories[k]
             ligand_traj.center_coordinates()
-        
+
             eq(ligand_traj.n_atoms, n_atoms[k])
             eq(ligand_traj.n_frames, 1)
 
-            #Move the pre-centered ligand sufficiently far away from the protein to avoid a clash.  
+            #Move the pre-centered ligand sufficiently far away from the protein to avoid a clash.
             min_atom_pair_distance = ((ligand_traj.xyz[0] ** 2.).sum(1) ** 0.5).max() + ((protein_traj.xyz[0] ** 2.).sum(1) ** 0.5).max() + 0.3
             ligand_traj.xyz += np.array([1.0, 0.0, 0.0]) * min_atom_pair_distance
 
@@ -252,7 +252,7 @@ def test_charge_fail2():
 
 @skipIf(not HAVE_OE, "Cannot test openeye module without OpenEye tools.")
 def test_charge_success1():
-    with utils.enter_temp_directory():    
+    with utils.enter_temp_directory():
         openmoltools.openeye.smiles_to_antechamber(smiles_fails_with_strictStereo, "test.mol2",  "test.frcmod", strictStereo=False)
 
 
@@ -261,6 +261,18 @@ def test_charge_success2():
     m = openmoltools.openeye.smiles_to_oemol(smiles_fails_with_strictStereo)
     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)
+
+@skipIf(not HAVE_OE, "Cannot test openeye module without OpenEye tools.")
+def test_oeassigncharges_success():
+    # Success test for OEToolkits (2017.2.1) new charging function
+    m = openmoltools.openeye.iupac_to_oemol("butanol")
+    m = openmoltools.openeye.get_charges(m, legacy=False)
 
 @skipIf(not HAVE_OE, "Cannot test openeye module without OpenEye tools.")
 @skipIf(not HAVE_PARMED, "Cannot test without Parmed Chemistry.")