Improve Amber parsers

openff/interchange/components/interchange.py

@@ -363,7 +363,7 @@ def to_openmm_topology(
     def to_prmtop(self, file_path: Union[Path, str], writer="internal"):
         """Export this Interchange to an Amber .prmtop file."""
         if writer == "internal":
-            from openff.interchange.interop.internal.amber import to_prmtop
+            from openff.interchange.interop.amber.export import to_prmtop
 
             to_prmtop(self, file_path)
 
@@ -403,7 +403,7 @@ def to_crd(self, file_path: Union[Path, str]):
     def to_inpcrd(self, file_path: Union[Path, str], writer="internal"):
         """Export this Interchange to an Amber .inpcrd file."""
         if writer == "internal":
-            from openff.interchange.interop.internal.amber import to_inpcrd
+            from openff.interchange.interop.amber.export import to_inpcrd
 
             to_inpcrd(self, file_path)
 

openff/interchange/drivers/openmm.py

@@ -95,7 +95,7 @@ def _get_openmm_energies(
     positions: openmm.unit.Quantity,
     round_positions: Optional[int],
     platform: str,
-) -> EnergyReport:
+) -> Dict[int, openmm.Force]:
     """Given prepared `openmm` objects, run a single-point energy calculation."""
     for index, force in enumerate(system.getForces()):
         force.setForceGroup(index)

openff/interchange/interop/amber/__init__.py

@@ -0,0 +1 @@
+"""Interoperability with Amber files."""

openff/interchange/interop/amber/_import/__init__.py

@@ -0,0 +1 @@
+"""Interfaces with Amber."""

openff/interchange/interop/amber/_import/_import.py

@@ -0,0 +1,91 @@
+"""Interfaces with Amber."""
+from typing import TYPE_CHECKING, Dict, List
+
+if TYPE_CHECKING:
+    from openff.toolkit import Topology
+
+    from openff.interchange import Interchange
+
+
+def from_prmtop(
+    file: str,
+) -> "Interchange":
+    """Import from a prmtop file."""
+    from openff.interchange import Interchange
+
+    interchange = Interchange()
+
+    data: Dict[str, List[str]] = dict()
+
+    with open(file) as f:
+        for chunk in f.read().split(r"%FLAG"):
+            tag, format, *_data = chunk.strip().split()
+
+            if tag == "%VERSION":
+                continue
+
+            data[tag] = _data
+
+    interchange.topology = _make_topology(data)
+
+    return interchange
+
+
+def _make_topology(data: Dict[str, List[str]]) -> "Topology":
+    """Make a topology from the data."""
+    from openff.toolkit import Topology
+    from openff.toolkit.topology._mm_molecule import _SimpleMolecule
+
+    Topology._add_bond = _add_bond
+
+    topology = Topology()
+
+    start_index = 0
+
+    for molecule_index in range(int(data["POINTERS"][11])):
+        molecule = _SimpleMolecule()
+
+        end_index = start_index + int(data["ATOMS_PER_MOLECULE"][molecule_index])
+
+        for atom_index in range(start_index, end_index):
+            # TODO: Check for isotopes (unsupported) or otherwise botches atomic masses
+            molecule.add_atom(
+                atomic_number=int(data["ATOMIC_NUMBER"][atom_index]),
+                name=data["ATOM_NAME"][atom_index],
+            )
+
+        topology.add_molecule(molecule)
+
+        start_index = end_index
+
+    bonds: List[str] = data["BONDS_INC_HYDROGEN"] + data["BONDS_WITHOUT_HYDROGEN"]
+
+    # third value in each triplet is an index to the bond type
+    for n1, n2 in zip(bonds[::3], bonds[1::3]):
+        # See BONDS_INC_HYDROGEN in https://ambermd.org/prmtop.pdf
+        # For run-time efficiency, the atom indexes are actually indexes into a coordinate array,
+        # so the actual atom index A is calculated from the coordinate array index N by A = N/3 + 1
+
+        a1 = int(int(n1) / 3)
+        a2 = int(int(n2) / 3)
+
+        topology._add_bond(int(a1), int(a2))
+
+    return topology
+
+
+def _add_bond(self, atom1_index: int, atom2_index: int):
+    atom1 = self.atom(atom1_index)
+    atom2 = self.atom(atom2_index)
+
+    if atom1.molecule is not atom2.molecule:
+        raise ValueError(
+            "Cannot add a bond between atoms in different molecules.",
+        )
+
+    molecule = atom1.molecule
+
+    molecule.add_bond(
+        atom1,
+        atom2,
+    )

openff/interchange/interop/amber/export/__init__.py

@@ -0,0 +1,2 @@
+"""Exports to Amber files."""
+from openff.interchange.interop.amber.export.export import to_inpcrd, to_prmtop

openff/interchange/smirnoff/_gbsa.py

@@ -6,6 +6,7 @@
 
 from openff.interchange.components.potentials import Potential
 from openff.interchange.constants import kcal_mol_a2
+from openff.interchange.exceptions import InvalidParameterHandlerError
 from openff.interchange.smirnoff._base import SMIRNOFFCollection
 
 if TYPE_CHECKING:
@@ -70,7 +71,7 @@ def store_potentials(self, parameter_handler: GBSAHandler) -> None:
             self.potentials[potential_key] = potential
 
     @classmethod
-    def create(  # type: ignore[override]
+    def create(
         cls,
         parameter_handler: GBSAHandler,
         topology: "Topology",

setup.cfg

@@ -19,6 +19,7 @@ per-file-ignores =
     openff/interchange/components/*:F821
     openff/interchange/__init__.py:F401
     openff/interchange/tests/data/*:INP001
+    openff/interchange/interop/amber/export/__init__.py:F401
     plugins/*:INP001
 
 [isort]