Merge branch 'devel' into feature_reduce

python/BioSimSpace/Parameters/_Protocol/_amber.py

@@ -122,6 +122,7 @@ def __init__(
         tolerance=1.2,
         max_distance=_Length(6, "A"),
         water_model=None,
+        custom_parameters=None,
         leap_commands=None,
         bonds=None,
         ensure_compatible=True,
@@ -154,11 +155,14 @@ def __init__(
             Run 'BioSimSpace.Solvent.waterModels()' to see the supported
             water models.
 
+        custom_parameters: [str]
+            A list of paths to custom parameter files. When this option is set,
+            we can no longer fall back on GROMACS's pdb2gmx.
+
         leap_commands : [str]
             An optional list of extra commands for the LEaP program. These
-            will be added after any default commands and can be used to, e.g.,
-            load additional parameter files. When this option is set, we can no
-            longer fall back on GROMACS's pdb2gmx.
+            will be added after any default commands. When this option is set,
+            we can no longer fall back on GROMACS's pdb2gmx.
 
         bonds : ((class:`Atom <BioSimSpace._SireWrappers.Atom>`, class:`Atom <BioSimSpace._SireWrappers.Atom>`))
             An optional tuple of atom pairs to specify additional atoms that
@@ -214,6 +218,26 @@ def __init__(
         else:
             self._water_model = water_model
 
+        # Validate the custom parameter file list.
+        if custom_parameters is not None:
+            if not isinstance(custom_parameters, (list, tuple)):
+                raise TypeError("'custom_parameters' must be a 'list' of 'str' types.")
+            else:
+                if not all(isinstance(x, str) for x in custom_parameters):
+                    raise TypeError(
+                        "'custom_parameters' must be a 'list' of 'str' types."
+                    )
+                for x in custom_parameters:
+                    if not os.path.isfile(x):
+                        raise ValueError(f"Custom parameter file does not exist: '{x}'")
+
+            # Convert to absolute paths.
+            self._custom_parameters = []
+            for x in enumerate(custom_parameters):
+                self._custom_parameters.append(_os.path.abspath(x))
+        else:
+            self._custom_parameters = None
+
         # Validate the additional leap commands.
         if leap_commands is not None:
             if not isinstance(leap_commands, (list, tuple)):
@@ -249,7 +273,7 @@ def __init__(
 
         # Set the compatibility flags.
         self._tleap = True
-        if self._leap_commands is not None:
+        if self._custom_parameters is not None or self._leap_commands is not None:
             self._pdb2gmx = False
 
     def run(self, molecule, work_dir=None, queue=None):
@@ -488,17 +512,21 @@ def _run_tleap(self, molecule, work_dir):
                     file.write("source leaprc.water.tip4pew\n")
                 else:
                     file.write("source leaprc.water.%s\n" % self._water_model)
-            # Write extra user commands.
-            if self._leap_commands is not None:
-                for command in self._leap_commands:
-                    file.write("%s\n" % command)
+            # Write custom parameters.
+            if self._custom_parameters is not None:
+                for param in self._custom_parameters:
+                    file.write("%s\n" % param)
             file.write("mol = loadPdb leap.pdb\n")
             # Add any disulphide bond records.
             for bond in disulphide_bonds:
                 file.write("%s\n" % bond)
             # Add any additional bond records.
             for bond in pruned_bond_records:
                 file.write("%s\n" % bond)
+            # Write user leap commands.
+            if self._leap_commands is not None:
+                for command in self._leap_commands:
+                    file.write("%s\n" % command)
             file.write("saveAmberParm mol leap.top leap.crd\n")
             file.write("quit")
 

python/BioSimSpace/Parameters/_parameters.py

@@ -135,6 +135,7 @@ def _parameterise_amber_protein(
     tolerance=1.2,
     max_distance=_Length(6, "A"),
     water_model=None,
+    custom_parameters=None,
     leap_commands=None,
     bonds=None,
     ensure_compatible=True,
@@ -171,11 +172,14 @@ def _parameterise_amber_protein(
         or lone oxygen atoms corresponding to structural (crystal) water
         molecules.
 
+    custom_parameters: [str]
+        A list of paths to custom parameter files. When this option is set,
+        we can no longer fall back on GROMACS's pdb2gmx.
+
     leap_commands : [str]
         An optional list of extra commands for the LEaP program. These
-        will be added after any default commands and can be used to, e.g.,
-        load additional parameter files. When this option is set, we can no
-        longer fall back on GROMACS's pdb2gmx.
+        will be added after any default commands. When this option is set,
+        we can no longer fall back on GROMACS's pdb2gmx.
 
     bonds : ((class:`Atom <BioSimSpace._SireWrappers.Atom>`, class:`Atom <BioSimSpace._SireWrappers.Atom>`))
         An optional tuple of atom pairs to specify additional atoms that
@@ -237,6 +241,7 @@ def _parameterise_amber_protein(
         max_distance=max_distance,
         water_model=water_model,
         check_ions=True,
+        custom_parameters=custom_parameters,
         leap_commands=leap_commands,
         bonds=bonds,
         ensure_compatible=ensure_compatible,
@@ -250,6 +255,7 @@ def _parameterise_amber_protein(
         tolerance=tolerance,
         water_model=water_model,
         max_distance=max_distance,
+        custom_parameters=custom_parameters,
         leap_commands=leap_commands,
         bonds=bonds,
         ensure_compatible=ensure_compatible,
@@ -796,6 +802,7 @@ def _validate(
     max_distance=None,
     water_model=None,
     check_ions=False,
+    custom_parameters=None,
     leap_commands=None,
     bonds=None,
     ensure_compatible=True,
@@ -832,11 +839,14 @@ def _validate(
         Whether to check for the presence of structural ions. This is only
         required when parameterising with protein force fields.
 
+    custom_parameters: [str]
+        A list of paths to custom parameter files. When this option is set,
+        we can no longer fall back on GROMACS's pdb2gmx.
+
     leap_commands : [str]
         An optional list of extra commands for the LEaP program. These
-        will be added after any default commands and can be used to, e.g.,
-        load additional parameter files. When this option is set, we can no
-        longer fall back on GROMACS's pdb2gmx.
+        will be added after any default commands. When this option is set,
+        we can no longer fall back on GROMACS's pdb2gmx.
 
     bonds : ((class:`Atom <BioSimSpace._SireWrappers.Atom>`, class:`Atom <BioSimSpace._SireWrappers.Atom>`))
         An optional tuple of atom pairs to specify additional atoms that
@@ -895,6 +905,16 @@ def _validate(
                 "Please choose a 'water_model' for the ion parameters."
             )
 
+    if custom_parameters is not None:
+        if not isinstance(custom_parameters, (list, tuple)):
+            raise TypeError("'custom_parameters' must be a 'list' of 'str' types.")
+        else:
+            if not all(isinstance(x, str) for x in custom_parameters):
+                raise TypeError("'custom_parameters' must be a 'list' of 'str' types.")
+            for x in custom_parameters:
+                if not os.path.isfile(x):
+                    raise ValueError(f"Custom parameter file does not exist: '{x}'")
+
     if leap_commands is not None:
         if not isinstance(leap_commands, (list, tuple)):
             raise TypeError("'leap_commands' must be a 'list' of 'str' types.")

python/BioSimSpace/Process/_amber.py

@@ -442,9 +442,10 @@ def getSystem(self, block="AUTO"):
             # Update the box information in the original system.
             if "space" in new_system._sire_object.propertyKeys():
                 box = new_system._sire_object.property("space")
-                old_system._sire_object.setProperty(
-                    self._property_map.get("space", "space"), box
-                )
+                if box.isPeriodic():
+                    old_system._sire_object.setProperty(
+                        self._property_map.get("space", "space"), box
+                    )
 
             return old_system
 

python/BioSimSpace/Process/_gromacs.py

@@ -2537,9 +2537,10 @@ def _getFrame(self, time):
                     and space_prop in new_system._sire_object.propertyKeys()
                 ):
                     box = new_system._sire_object.property("space")
-                    old_system._sire_object.setProperty(
-                        self._property_map.get("space", "space"), box
-                    )
+                    if box.isPeriodic():
+                        old_system._sire_object.setProperty(
+                            self._property_map.get("space", "space"), box
+                        )
 
                 # If this is a vacuum simulation, then translate the centre of mass
                 # of the system back to the origin.

python/BioSimSpace/Process/_namd.py

@@ -789,9 +789,10 @@ def getSystem(self, block="AUTO"):
                 # Update the box information in the original system.
                 if "space" in new_system._sire_object.propertyKeys():
                     box = new_system._sire_object.property("space")
-                    old_system._sire_object.setProperty(
-                        self._property_map.get("space", "space"), box
-                    )
+                    if box.isPeriodic():
+                        old_system._sire_object.setProperty(
+                            self._property_map.get("space", "space"), box
+                        )
 
                 return old_system
 

python/BioSimSpace/Process/_openmm.py

@@ -1318,9 +1318,10 @@ def getSystem(self, block="AUTO"):
                 # Update the box information in the original system.
                 if "space" in new_system._sire_object.propertyKeys():
                     box = new_system._sire_object.property("space")
-                    old_system._sire_object.setProperty(
-                        self._property_map.get("space", "space"), box
-                    )
+                    if box.isPeriodic():
+                        old_system._sire_object.setProperty(
+                            self._property_map.get("space", "space"), box
+                        )
 
                 return old_system
 

python/BioSimSpace/Process/_somd.py

@@ -540,6 +540,13 @@ def getSystem(self, block="AUTO"):
 
             new_system = _IO.readMolecules(self._restart_file)
 
+            # Try loading the trajectory file to get the box information.
+            try:
+                frame = self.getTrajectory().getFrames(-1)
+                box = frame._sire_object.property("space")
+            except:
+                box = None
+
             # Since SOMD requires specific residue and water naming we copy the
             # coordinates back into the original system.
             old_system = self._system.copy()
@@ -564,8 +571,7 @@ def getSystem(self, block="AUTO"):
             self._mapping = mapping
 
             # Update the box information in the original system.
-            if "space" in new_system._sire_object.propertyKeys():
-                box = new_system._sire_object.property("space")
+            if box and box.isPeriodic():
                 old_system._sire_object.setProperty(
                     self._property_map.get("space", "space"), box
                 )

python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_amber.py

@@ -122,6 +122,7 @@ def __init__(
         tolerance=1.2,
         max_distance=_Length(6, "A"),
         water_model=None,
+        custom_parameters=None,
         leap_commands=None,
         bonds=None,
         ensure_compatible=True,
@@ -154,11 +155,14 @@ def __init__(
             Run 'BioSimSpace.Solvent.waterModels()' to see the supported
             water models.
 
+        custom_parameters: [str]
+            A list of paths to custom parameter files. When this option is set,
+            we can no longer fall back on GROMACS's pdb2gmx.
+
         leap_commands : [str]
             An optional list of extra commands for the LEaP program. These
-            will be added after any default commands and can be used to, e.g.,
-            load additional parameter files. When this option is set, we can no
-            longer fall back on GROMACS's pdb2gmx.
+            will be added after any default commands. When this option is set,
+            we can no longer fall back on GROMACS's pdb2gmx.
 
         bonds : ((class:`Atom <BioSimSpace._SireWrappers.Atom>`, class:`Atom <BioSimSpace._SireWrappers.Atom>`))
             An optional tuple of atom pairs to specify additional atoms that
@@ -214,6 +218,26 @@ def __init__(
         else:
             self._water_model = water_model
 
+        # Validate the custom parameter file list.
+        if custom_parameters is not None:
+            if not isinstance(custom_parameters, (list, tuple)):
+                raise TypeError("'custom_parameters' must be a 'list' of 'str' types.")
+            else:
+                if not all(isinstance(x, str) for x in custom_parameters):
+                    raise TypeError(
+                        "'custom_parameters' must be a 'list' of 'str' types."
+                    )
+                for x in custom_parameters:
+                    if not os.path.isfile(x):
+                        raise ValueError(f"Custom parameter file does not exist: '{x}'")
+
+            # Convert to absolute paths.
+            self._custom_parameters = []
+            for x in enumerate(custom_parameters):
+                self._custom_parameters.append(_os.path.abspath(x))
+        else:
+            self._custom_parameters = None
+
         # Validate the additional leap commands.
         if leap_commands is not None:
             if not isinstance(leap_commands, (list, tuple)):
@@ -249,7 +273,7 @@ def __init__(
 
         # Set the compatibility flags.
         self._tleap = True
-        if self._leap_commands is not None:
+        if self._custom_parameters is not None or self._leap_commands is not None:
             self._pdb2gmx = False
 
     def run(self, molecule, work_dir=None, queue=None):
@@ -488,17 +512,21 @@ def _run_tleap(self, molecule, work_dir):
                     file.write("source leaprc.water.tip4pew\n")
                 else:
                     file.write("source leaprc.water.%s\n" % self._water_model)
-            # Write extra user commands.
-            if self._leap_commands is not None:
-                for command in self._leap_commands:
-                    file.write("%s\n" % command)
+            # Write custom parameters.
+            if self._custom_parameters is not None:
+                for param in self._custom_parameters:
+                    file.write("%s\n" % param)
             file.write("mol = loadPdb leap.pdb\n")
             # Add any disulphide bond records.
             for bond in disulphide_bonds:
                 file.write("%s\n" % bond)
             # Add any additional bond records.
             for bond in pruned_bond_records:
                 file.write("%s\n" % bond)
+            # Write user leap commands.
+            if self._leap_commands is not None:
+                for command in self._leap_commands:
+                    file.write("%s\n" % command)
             file.write("saveAmberParm mol leap.top leap.crd\n")
             file.write("quit")