Optimise by avoiding duplication of water topology check.

[ref #22] [ref #148]
OpenBioSim · Aug 2, 2023 · a702a6b · a702a6b
1 parent 92a815c
commit a702a6b
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Showing 8 changed files with 57 additions and 11 deletions.
diff --git a/python/BioSimSpace/Process/_amber.py b/python/BioSimSpace/Process/_amber.py
@@ -212,7 +212,9 @@ def _setup(self):
         # PRM file (topology).
         try:
             file = _os.path.splitext(self._top_file)[0]
-            _IO.saveMolecules(file, system, "prm7", property_map=self._property_map)
+            _IO.saveMolecules(
+                file, system, "prm7", match_water=False, property_map=self._property_map
+            )
         except Exception as e:
             msg = "Failed to write system to 'PRM7' format."
             if _isVerbose():

diff --git a/python/BioSimSpace/Process/_gromacs.py b/python/BioSimSpace/Process/_gromacs.py
@@ -258,11 +258,15 @@ def _setup(self):
 
         # GRO87 file.
         file = _os.path.splitext(self._gro_file)[0]
-        _IO.saveMolecules(file, system, "gro87", property_map=self._property_map)
+        _IO.saveMolecules(
+            file, system, "gro87", match_water=False, property_map=self._property_map
+        )
 
         # TOP file.
         file = _os.path.splitext(self._top_file)[0]
-        _IO.saveMolecules(file, system, "grotop", property_map=self._property_map)
+        _IO.saveMolecules(
+            file, system, "grotop", match_water=False, property_map=self._property_map
+        )
 
         # Create the binary input file name.
         self._tpr_file = "%s/%s.tpr" % (self._work_dir, self._name)

diff --git a/python/BioSimSpace/Process/_openmm.py b/python/BioSimSpace/Process/_openmm.py
@@ -252,7 +252,9 @@ def _setup(self):
         # PRM file (topology).
         try:
             file = _os.path.splitext(self._top_file)[0]
-            _IO.saveMolecules(file, system, "prm7", property_map=self._property_map)
+            _IO.saveMolecules(
+                file, system, "prm7", match_water=False, property_map=self._property_map
+            )
         except Exception as e:
             msg = "Failed to write system to 'PRM7' format."
             if _isVerbose():

diff --git a/python/BioSimSpace/Process/_somd.py b/python/BioSimSpace/Process/_somd.py
@@ -357,7 +357,9 @@ def _setup(self):
 
         # PRM file (topology).
         try:
-            _IO.saveMolecules(file, system, "prm7", property_map=self._property_map)
+            _IO.saveMolecules(
+                file, system, "prm7", match_water=False, property_map=self._property_map
+            )
         except Exception as e:
             msg = "Failed to write system to 'PRM7' format."
             if _isVerbose():

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
@@ -327,7 +327,13 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if topol_file is not None:
             try:
                 file = _os.path.splitext(topol_file)[0]
-                _IO.saveMolecules(file, system, "prm7", property_map=self._property_map)
+                _IO.saveMolecules(
+                    file,
+                    system,
+                    "prm7",
+                    match_waters=False,
+                    property_map=self._property_map,
+                )
             except Exception as e:
                 msg = "Failed to write system to 'PRM7' format."
                 if _isVerbose():

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py
@@ -347,17 +347,35 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         # GRO87 coordinate files.
         if coord_file is not None:
             file = _os.path.splitext(coord_file)[0]
-            _IO.saveMolecules(file, system, "gro87", property_map=self._property_map)
+            _IO.saveMolecules(
+                file,
+                system,
+                "gro87",
+                match_waters=False,
+                property_map=self._property_map,
+            )
 
         # GRO87 reference files.
         if ref_file is not None:
             file = _os.path.splitext(ref_file)[0]
-            _IO.saveMolecules(file, system, "gro87", property_map=self._property_map)
+            _IO.saveMolecules(
+                file,
+                system,
+                "gro87",
+                match_waters=False,
+                property_map=self._property_map,
+            )
 
         # TOP file.
         if topol_file is not None:
             file = _os.path.splitext(topol_file)[0]
-            _IO.saveMolecules(file, system, "grotop", property_map=self._property_map)
+            _IO.saveMolecules(
+                file,
+                system,
+                "grotop",
+                match_waters=False,
+                property_map=self._property_map,
+            )
 
             # Write the restraint to the topology file
             if self._restraint:

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py
@@ -251,7 +251,13 @@ def _setup(self):
         # PRM file (topology).
         try:
             file = _os.path.splitext(self._top_file)[0]
-            _IO.saveMolecules(file, system, "prm7", property_map=self._property_map)
+            _IO.saveMolecules(
+                file,
+                system,
+                "prm7",
+                match_waters=False,
+                property_map=self._property_map,
+            )
         except Exception as e:
             msg = "Failed to write system to 'PRM7' format."
             if _isVerbose():

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py
@@ -369,7 +369,13 @@ def _setup(self):
         # PRM file (topology).
         try:
             file = _os.path.splitext(self._top_file)[0]
-            _IO.saveMolecules(file, system, "prm7", property_map=self._property_map)
+            _IO.saveMolecules(
+                file,
+                system,
+                "prm7",
+                match_waters=False,
+                property_map=self._property_map,
+            )
         except Exception as e:
             msg = "Failed to write system to 'PRM7' format."
             if _isVerbose():