From dab2834e76b42e95d4829ba549a37667ababd6c6 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 19 Aug 2024 16:19:41 -0500
Subject: [PATCH] ENH: Add `Interchange.to_amber`

---
 docs/using/output.md                          | 14 ++++--
 .../unit_tests/components/test_interchange.py | 13 ++++++
 openff/interchange/components/interchange.py  | 44 ++++++++++++++-----
 3 files changed, 57 insertions(+), 14 deletions(-)

diff --git a/docs/using/output.md b/docs/using/output.md
index 5c25e705..9ae328f8 100644
--- a/docs/using/output.md
+++ b/docs/using/output.md
@@ -74,12 +74,18 @@ openmm_box: openmm.unit.Quantity = interchange.box.to_openmm()
 An `Interchange` object can be written to Amber parameter/topology, coordinate, and SANDER run input files with [`Interchange.to_prmtop()`], [`Interchange.to_inpcrd()`], and [`Interchange.to_sander_input()`]:
 
 ```python
-interchange.to_prmtop("out.prmtop")
-interchange.to_inpcrd("out.inpcrd")
-interchange.to_sander_input("out_pointenergy.in")
+interchange.to_prmtop("mysim.prmtop")
+interchange.to_inpcrd("mysim.inpcrd")
+interchange.to_sander_input("mysim_pointenergy.in")
 ```
 
-Note that the SANDER input file generated is configured for a single-point energy calculation and must be modified to run other simulations. Interchange cannot currently produce PMEMD input files. Amber does not implement a switching function as [commonly used](https://openforcefield.github.io/standards/standards/smirnoff/#vdw) by SMIRNOFF force fields, so these force fields will produce different results in Amber than in OpenMM or GROMACS.
+The [`Interchange.to_amber()`] convenience method produces all three files in one invocation:
+
+```python
+interchange.to_amber("mysim")  # Produces the same three files
+```
+
+Note that the input file generated is configured for a single-point energy calculation with sander and must be modified to run other simulations. Interchange cannot currently produce PMEMD input files. Amber does not implement a switching function as [commonly used](https://openforcefield.github.io/standards/standards/smirnoff/#vdw) by SMIRNOFF force fields, so these force fields will produce different results in Amber than in OpenMM or GROMACS.
 
 <!--
 ## CHARMM
diff --git a/openff/interchange/_tests/unit_tests/components/test_interchange.py b/openff/interchange/_tests/unit_tests/components/test_interchange.py
index cd99dfef..1574d8d8 100644
--- a/openff/interchange/_tests/unit_tests/components/test_interchange.py
+++ b/openff/interchange/_tests/unit_tests/components/test_interchange.py
@@ -1,3 +1,4 @@
+import subprocess
 import numpy
 import pytest
 from openff.toolkit import Molecule, Quantity, Topology, unit
@@ -428,6 +429,18 @@ def test_from_openmm_called(self, monkeypatch, simple_interchange):
             box_vectors=box,
         )
 
+    def test_to_amber(self, simple_interchange):
+        simple_interchange.to_amber(prefix='blargh')
+
+        # Just make sure it returns a non-zero error code
+        subprocess.check_output(
+            "sander -i blargh_pointenergy.in "
+            "-c blargh.inpcrd "
+            "-p blargh.prmtop "
+            "-o out.mdout -O",
+            shell=True,
+        )
+
     def test_from_gromacs_called(self, monkeypatch, simple_interchange):
         monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1")
 
diff --git a/openff/interchange/components/interchange.py b/openff/interchange/components/interchange.py
index e007a4e4..e780209c 100644
--- a/openff/interchange/components/interchange.py
+++ b/openff/interchange/components/interchange.py
@@ -639,16 +639,6 @@ def to_openmm_simulation(
 
         return simulation
 
-    def to_prmtop(self, file_path: Path | str, writer="internal"):
-        """Export this Interchange to an Amber .prmtop file."""
-        if writer == "internal":
-            from openff.interchange.interop.amber import to_prmtop
-
-            to_prmtop(self, file_path)
-
-        else:
-            raise UnsupportedExportError
-
     @requires_package("openmm")
     def to_pdb(self, file_path: Path | str, include_virtual_sites: bool = False):
         """Export this Interchange to a .pdb file."""
@@ -686,6 +676,40 @@ def to_crd(self, file_path: Path | str):
         """Export this Interchange to a CHARMM-style .crd file."""
         raise UnsupportedExportError
 
+    def to_amber(
+        self,
+        prefix: str,
+    ):
+        """
+        Export this Interchange object to Amber files.
+
+        Parameters
+        ----------
+        prefix: str
+            The prefix to use for the Amber parameter/topology, coordinate, and run files, i.e.
+            "foo" will produce "foo.top", "foo.gro", and "foo_pointenergy.in".
+
+        Notes
+        -----
+        The run input file is configured for a single-point energy calculation with sander. It is
+        likely portable to pmemd with little or no work.
+
+        """
+        self.to_prmtop(f"{prefix}.prmtop")
+        self.to_inpcrd(f"{prefix}.inpcrd")
+
+        self.to_sander_input(f"{prefix}_pointenergy.in")
+
+    def to_prmtop(self, file_path: Path | str, writer="internal"):
+        """Export this Interchange to an Amber .prmtop file."""
+        if writer == "internal":
+            from openff.interchange.interop.amber import to_prmtop
+
+            to_prmtop(self, file_path)
+
+        else:
+            raise UnsupportedExportError
+
     def to_inpcrd(self, file_path: Path | str, writer="internal"):
         """Export this Interchange to an Amber .inpcrd file."""
         if writer == "internal":