Have amber process write binary RST file instead of text rst7 file (#22)

Co-authored-by: William (Zhiyi) Wu <zwu@exscientia.co.uk>

python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py

@@ -27,6 +27,7 @@
 __all__ = ["Amber"]
 
 import os
+import shutil
 from pathlib import Path as _Path
 
 from .._Utils import _try_import
@@ -303,9 +304,11 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if coord_file is not None:
             try:
                 file = _os.path.splitext(coord_file)[0]
-                _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
+                _IO.saveMolecules(file, system, "rst", property_map=self._property_map)
+                # To keep the file extension the same.
+                shutil.move(f"{file}.rst", f"{file}.rst7")
             except Exception as e:
-                msg = "Failed to write system to 'RST7' format."
+                msg = "Failed to write system to 'rst7' format."
                 if _isVerbose():
                     raise IOError(msg) from e
                 else:
@@ -315,9 +318,11 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if ref_file is not None:
             try:
                 file = _os.path.splitext(ref_file)[0]
-                _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
+                _IO.saveMolecules(file, system, "rst", property_map=self._property_map)
+                # To keep the file extension the same.
+                shutil.move(f"{file}.rst", f"{file}.rst7")
             except Exception as e:
-                msg = "Failed to write system to 'RST7' format."
+                msg = "Failed to write system to 'rst7' format."
                 if _isVerbose():
                     raise IOError(msg) from e
                 else:

tests/Sandpit/Exscientia/Process/test_position_restraint.py

@@ -5,6 +5,7 @@
 
 import pandas as pd
 import pytest
+from sire.legacy.IO import AmberRst
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 from BioSimSpace.Sandpit.Exscientia.Units.Energy import kj_per_mol
@@ -121,8 +122,8 @@ def test_gromacs(protocol, system, ref_system, tmp_path):
 
 
 @pytest.mark.skipif(
-    has_gromacs is False or has_openff is False,
-    reason="Requires AMBER and openff to be installed",
+    has_openff is False,
+    reason="Requires openff to be installed",
 )
 def test_amber(protocol, system, ref_system, tmp_path):
     proc = BSS.Process.Amber(
@@ -137,12 +138,11 @@ def test_amber(protocol, system, ref_system, tmp_path):
 
     # We have generated a separate restraint reference
     assert os.path.exists(proc._ref_file)
-    contents_ref, contents_rst = (
-        open(proc._ref_file).readlines(),
-        open(proc._rst_file).readlines(),
-    )
-    diff = list(unified_diff(contents_ref, contents_rst))
-    assert len(diff)
+
+    ref = AmberRst(proc._ref_file).getFrame(0)
+    rst = AmberRst(proc._rst_file).getFrame(0)
+
+    assert ref != rst
 
     # We are pointing the reference to the correct file
     assert f"{proc._work_dir}/{proc.getArgs()['-ref']}" == proc._ref_file