RESP Charges

environment.yml

@@ -8,3 +8,5 @@ dependencies:
   # Include numpy/scipy to reduce the size of the Docker container
   - numpy=2.2.2
   - scipy=1.15.1
+  - openff-toolkit
+  - openff-recharge

requirements.txt

@@ -7,3 +7,9 @@ rdkit==2024.9.4
 --extra-index-url https://pypi.anaconda.org/OpenEye/simple
 openeye-toolkits==2020.2.0
 openmm==8.2.0
+gpu4pyscf-cuda12x
+cutensor-cu12
+Auto3D
+torch
+torchvision
+torchaudio

tests/test_handlers.py

@@ -456,6 +456,34 @@ def test_am1bcc_parameterization():
     # assert vjp_fn(charges_adjoints) == None
 
 
+def test_resp_parameterization():
+    # currently takes no parameters
+    smirks = []
+    params = []
+    props = None
+
+    cache_key = nonbonded.RESP
+    am1h = nonbonded.RESPHandler(smirks, params, props)
+    mol = Chem.AddHs(Chem.MolFromSmiles("C1CNCOC1F"))
+    AllChem.EmbedMolecule(mol)
+
+    assert not mol.HasProp(cache_key)
+
+    charges = am1h.parameterize(mol)
+
+    assert len(charges) == mol.GetNumAtoms()
+    assert mol.HasProp(cache_key)
+
+    cached_charges = am1h.parameterize(mol)
+    np.testing.assert_equal(charges, cached_charges)
+
+    new_charges, vjp_fn = jax.vjp(functools.partial(am1h.partial_parameterize, None, mol))
+
+    # charges_adjoints = np.random.randn(*charges.shape)
+
+    # assert vjp_fn(charges_adjoints) == None
+
+
 def test_am1_ccc():
     patterns = [
         ["[#6X4:1]-[#1:2]", 0.46323257920556493],

tests/test_serialization.py

@@ -281,6 +281,21 @@ def test_am1bcc():
     assert am1.props == am1.props
 
 
+def test_resp():
+    smirks = []
+    params = []
+    props = None
+
+    am1 = nonbonded.RESPHandler(smirks, params, props)
+    obj = am1.serialize()
+    all_handlers, _, _ = deserialize_handlers(bin_to_str(obj))
+
+    am1 = all_handlers[0]
+    np.testing.assert_equal(am1.smirks, am1.smirks)
+    np.testing.assert_equal(am1.params, am1.params)
+    assert am1.props == am1.props
+
+
 def test_am1ccc():
     patterns = [
         ["[#6X4:1]-[#1:2]", 0.46323257920556493],

timemachine/ff/__init__.py

@@ -54,6 +54,7 @@ class Forcefield:
         Union[
             nonbonded.SimpleChargeHandler,
             nonbonded.AM1BCCHandler,
+            nonbonded.RESPHandler,
             nonbonded.AM1CCCHandler,
             nonbonded.AM1BCCCCCHandler,
             nonbonded.PrecomputedChargeHandler,
@@ -252,6 +253,8 @@ def from_handlers(
                 q_handle_intra = nonbonded.AM1CCCIntraHandler(q_handle.smirks, q_handle.params, q_handle.props)
             elif isinstance(q_handle, nonbonded.AM1BCCHandler):
                 q_handle_intra = nonbonded.AM1BCCIntraHandler(q_handle.smirks, q_handle.params, q_handle.props)
+            elif isinstance(q_handle, nonbonded.RESPHandler):
+                q_handle_intra = nonbonded.RESPHandler(q_handle.smirks, q_handle.params, q_handle.props)
             elif isinstance(q_handle, nonbonded.SimpleChargeHandler):
                 q_handle_intra = nonbonded.SimpleChargeIntraHandler(q_handle.smirks, q_handle.params, q_handle.props)
             elif isinstance(q_handle, nonbonded.PrecomputedChargeHandler):