Merge pull request #214 from OpenBioSim/backport_210

Backport fixes from PR #210.

doc/source/changelog.rst

@@ -9,6 +9,25 @@ company supporting open-source development of fostering academic/industrial coll
 within the biomolecular simulation community. Our software is hosted via the `OpenBioSim`
 `GitHub <https://github.com/OpenBioSim/biosimspace>`__ organisation.
 
+`2023.4.1 <https://github.com/openbiosim/biosimspace/compare/2023.4.0...2023.4.1>`_ - Dec 14 2023
+-------------------------------------------------------------------------------------------------
+
+* Make sure ``match_water`` keyword argument is passed to specialised solvation functions (`#190 <https://github.com/OpenBioSim/biosimspace/pull/190>`__).
+* Check perturbable molecules for velocities when combining molecules (`#192 <https://github.com/OpenBioSim/biosimspace/pull/192>`__).
+* Make sure velocities are double counted when searching for velocity properties when combining molecules (`#197 <https://github.com/OpenBioSim/biosimspace/pull/197>`__).
+* Remove redundant ``BioSimSpace.Types.Type.__ne__`` operator (`#201 <https://github.com/OpenBioSim/biosimspace/pull/201>`__).
+* Minor internal updates due to Sire API fixes (`#203 <https://github.com/OpenBioSim/biosimspace/pull/203>`__).
+* Fixed bug in the BSS Boresch restraint search code (`@fjclark <https://github.com/fjclark>`_) (`#204 <https://github.com/OpenBioSim/biosimspace/pull/204>`__).
+* Fixed ``renumber`` option in :meth:`extract <BioSimSpace._SireWrappers.Molecule.extract>` method (`#210 <https://github.com/OpenBioSim/biosimspace/pull/210>`__).
+* Add workaround for fixing reconstruction of intrascale matrix in :func:`readPerturbableSystem <BioSimSpace.IO.readPerturbableSystem>` function (`#210 <https://github.com/OpenBioSim/biosimspace/pull/210>`__).
+* Remove incorrect ``try_import`` statement in metadynamics driver script and make sure that global parameters in OpenMM script are unique (`#217 <https://github.com/OpenBioSim/biosimspace/pull/217>`__).
+* Ensure the existing trajectory backend is used when getting the number of trajectory frames from a running process (`#219 <https://github.com/OpenBioSim/biosimspace/pull/219>`__).
+* Fixed setting of ``igb`` config parameter	for PMEMD simulations (`@annamherz <https://github.com/annamherz>`_) (`#220 <https://github.com/OpenBioSim/biosimspace/pull/220>`__).
+* Make sure AMBER restraint mask matches all hydrogen atoms (`#222 <https://github.com/OpenBioSim/biosimspace/pull/222>`__).
+* Ensure all searches for disulphide bonds are convert to a ``SelectorBond`` object (`#224 <https://github.com/OpenBioSim/biosimspace/pull/224>`__).
+* Fix injection of custom commands into ``LEaP`` script (`#226 <https://github.com/OpenBioSim/biosimspace/pull/226>`__).
+
+
 `2023.4.0 <https://github.com/openbiosim/biosimspace/compare/2023.3.1...2023.4.0>`_ - Oct 13 2023
 -------------------------------------------------------------------------------------------------
 

python/BioSimSpace/IO/_io.py

@@ -1100,9 +1100,13 @@ def readPerturbableSystem(top0, coords0, top1, coords1, property_map={}):
     # Flag that the molecule is perturbable.
     mol.setProperty("is_perturbable", _SireBase.wrap(True))
 
+    # Get the two molecules.
+    mol0 = system0[idx]._sire_object
+    mol1 = system1[idx]._sire_object
+
     # Add the molecule0 and molecule1 properties.
-    mol.setProperty("molecule0", system0[idx]._sire_object)
-    mol.setProperty("molecule1", system1[idx]._sire_object)
+    mol.setProperty("molecule0", mol0)
+    mol.setProperty("molecule1", mol1)
 
     # Get the connectivity property name.
     conn_prop = property_map.get("connectivity", "connectivity")
@@ -1121,6 +1125,23 @@ def readPerturbableSystem(top0, coords0, top1, coords1, property_map={}):
         mol = mol.removeProperty(conn_prop + "0").molecule()
         mol = mol.removeProperty(conn_prop + "1").molecule()
 
+    # Reconstruct the intrascale matrices using the GroTop parser.
+    intra0 = (
+        _SireIO.GroTop(_Molecule(mol0).toSystem()._sire_object)
+        .toSystem()[0]
+        .property("intrascale")
+    )
+    intra1 = (
+        _SireIO.GroTop(_Molecule(mol1).toSystem()._sire_object)
+        .toSystem()[0]
+        .property("intrascale")
+    )
+
+    # Set the "intrascale" properties.
+    intrascale_prop = property_map.get("intrascale", "intrascale")
+    mol.setProperty(intrascale_prop + "0", intra0)
+    mol.setProperty(intrascale_prop + "1", intra0)
+
     # Commit the changes.
     mol = _Molecule(mol.commit())
 

python/BioSimSpace/Metadynamics/_aux/metadynamics.py

@@ -28,10 +28,8 @@
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 
-from ..._Utils import _try_import
-
-mm = _try_import("openmm")
-unit = _try_import("openmm.unit", "conda install -c conda-forge openmm")
+import openmm as mm
+from openmm import unit
 
 from collections import namedtuple
 from functools import reduce

python/BioSimSpace/Parameters/_Protocol/_amber.py

@@ -122,8 +122,8 @@ def __init__(
         tolerance=1.2,
         max_distance=_Length(6, "A"),
         water_model=None,
-        custom_parameters=None,
-        leap_commands=None,
+        pre_mol_commands=None,
+        post_mol_commands=None,
         bonds=None,
         ensure_compatible=True,
         property_map={},
@@ -155,14 +155,17 @@ 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.
+        pre_mol_commands : [str]
+            A list of custom LEaP commands to be executed before loading the molecule.
+            This can be used for loading custom parameter files, or sourcing additional
+            scripts. Make sure to use absolute paths when specifying any external 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. When this option is set,
-            we can no longer fall back on GROMACS's pdb2gmx.
+        post_mol_commands : [str]
+            A list of custom LEaP commands to be executed after loading the molecule.
+            This allows the use of additional commands that operate on the molecule,
+            which is named "mol". 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
@@ -218,34 +221,25 @@ 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.")
+        # Validate the additional leap commands.
+        if pre_mol_commands is not None:
+            if not isinstance(pre_mol_commands, (list, tuple)):
+                raise TypeError("'pre_mol_commands must be a 'list' of 'str' types.")
             else:
-                if not all(isinstance(x, str) for x in custom_parameters):
+                if not all(isinstance(x, str) for x in pre_mol_commands):
                     raise TypeError(
-                        "'custom_parameters' must be a 'list' of 'str' types."
+                        "'pre_mol_commands' 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)):
-                raise TypeError("'leap_commands' must be a 'list' of 'str' types.")
+        self._pre_mol_commands = pre_mol_commands
+        if post_mol_commands is not None:
+            if not isinstance(post_mol_commands, (list, tuple)):
+                raise TypeError("'post_mol_commands must be a 'list' of 'str' types.")
             else:
-                if not all(isinstance(x, str) for x in leap_commands):
-                    raise TypeError("'leap_commands' must be a 'list' of 'str' types.")
-        self._leap_commands = leap_commands
+                if not all(isinstance(x, str) for x in post_mol_commands):
+                    raise TypeError(
+                        "'post_mol_commands' must be a 'list' of 'str' types."
+                    )
+        self._post_mol_commands = post_mol_commands
 
         # Validate the bond records.
         if bonds is not None:
@@ -273,7 +267,7 @@ def __init__(
 
         # Set the compatibility flags.
         self._tleap = True
-        if self._custom_parameters is not None or self._leap_commands is not None:
+        if self._pre_mol_commands is not None or self._post_mol_commands is not None:
             self._pdb2gmx = False
 
     def run(self, molecule, work_dir=None, queue=None):
@@ -512,20 +506,20 @@ 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 custom parameters.
-            if self._custom_parameters is not None:
-                for param in self._custom_parameters:
-                    file.write("%s\n" % param)
+            # Write pre-mol user leap commands.
+            if self._pre_mol_commands is not None:
+                for command in self._pre_mol_commands:
+                    file.write("%s\n" % command)
             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:
+            # Write post-mol user leap commands.
+            if self._post_mol_commands is not None:
+                for command in self._post_mol_commands:
                     file.write("%s\n" % command)
             file.write("saveAmberParm mol leap.top leap.crd\n")
             file.write("quit")
@@ -725,7 +719,7 @@ def _get_disulphide_bonds(
 
         # Try searching for disulphide bonds.
         try:
-            disulphides = query(mol, property_map)
+            disulphides = query(mol, property_map).bonds()
         except:
             disulphides = []
 

python/BioSimSpace/Parameters/_parameters.py

@@ -135,8 +135,8 @@ def _parameterise_amber_protein(
     tolerance=1.2,
     max_distance=_Length(6, "A"),
     water_model=None,
-    custom_parameters=None,
-    leap_commands=None,
+    pre_mol_commands=None,
+    post_mol_commands=None,
     bonds=None,
     ensure_compatible=True,
     work_dir=None,
@@ -172,14 +172,17 @@ 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.
+    pre_mol_commands : [str]
+        A list of custom LEaP commands to be executed before loading the molecule.
+        This can be used for loading custom parameter files, or sourcing additional
+        scripts. Make sure to use absolute paths when specifying any external 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. When this option is set,
-        we can no longer fall back on GROMACS's pdb2gmx.
+    post_mol_commands : [str]
+        A list of custom LEaP commands to be executed after loading the molecule.
+        This allows the use of additional commands that operate on the molecule,
+        which is named "mol". 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
@@ -241,8 +244,8 @@ def _parameterise_amber_protein(
         max_distance=max_distance,
         water_model=water_model,
         check_ions=True,
-        custom_parameters=custom_parameters,
-        leap_commands=leap_commands,
+        pre_mol_commands=pre_mol_commands,
+        post_mol_commands=post_mol_commands,
         bonds=bonds,
         ensure_compatible=ensure_compatible,
         property_map=property_map,
@@ -255,8 +258,8 @@ def _parameterise_amber_protein(
         tolerance=tolerance,
         water_model=water_model,
         max_distance=max_distance,
-        custom_parameters=custom_parameters,
-        leap_commands=leap_commands,
+        pre_mol_commands=pre_mol_commands,
+        post_mol_commands=post_mol_commands,
         bonds=bonds,
         ensure_compatible=ensure_compatible,
         property_map=property_map,
@@ -802,8 +805,8 @@ def _validate(
     max_distance=None,
     water_model=None,
     check_ions=False,
-    custom_parameters=None,
-    leap_commands=None,
+    pre_mol_commands=None,
+    post_mol_commands=None,
     bonds=None,
     ensure_compatible=True,
     work_dir=None,
@@ -839,14 +842,17 @@ 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.
+    pre_mol_commands : [str]
+        A list of custom LEaP commands to be executed before loading the molecule.
+        This can be used for loading custom parameter files, or sourcing additional
+        scripts. Make sure to use absolute paths when specifying any external 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. When this option is set,
-        we can no longer fall back on GROMACS's pdb2gmx.
+    post_mol_commands : [str]
+        A list of custom LEaP commands to be executed after loading the molecule.
+        This allows the use of additional commands that operate on the molecule,
+        which is named "mol". 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
@@ -905,22 +911,19 @@ 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.")
+    if pre_mol_commands is not None:
+        if not isinstance(pre_mol_commands, (list, tuple)):
+            raise TypeError("'pre_mol_commands' 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.")
+            if not all(isinstance(x, str) for x in pre_mol_commands):
+                raise TypeError("'pre_mol_commands' must be a 'list' of 'str' types.")
+
+    if post_mol_commands is not None:
+        if not isinstance(post_mol_commands, (list, tuple)):
+            raise TypeError("'post_mol_commands' must be a 'list' of 'str' types.")
         else:
-            if not all(isinstance(x, str) for x in leap_commands):
-                raise TypeError("'leap_commands' must be a 'list' of 'str' types.")
+            if not all(isinstance(x, str) for x in post_mol_commands):
+                raise TypeError("'post_mol_commands' must be a 'list' of 'str' types.")
 
     if bonds is not None:
         if molecule is None:
@@ -981,7 +984,8 @@ def _function(
         tolerance=1.2,
         max_distance=_Length(6, "A"),
         water_model=None,
-        leap_commands=None,
+        pre_mol_commands=None,
+        post_mol_commands=None,
         bonds=None,
         ensure_compatible=True,
         work_dir=None,
@@ -1013,11 +1017,17 @@ def _function(
             or lone oxygen atoms corresponding to structural (crystal) water
             molecules.
 
-        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.
+        pre_mol_commands : [str]
+            A list of custom LEaP commands to be executed before loading the molecule.
+            This can be used for loading custom parameter files, or sourcing additional
+            scripts. Make sure to use absolute paths when specifying any external files.
+            When this option is set, we can no longer fall back on GROMACS's pdb2gmx.
+
+        post_mol_commands : [str]
+            A list of custom LEaP commands to be executed after loading the molecule.
+            This allows the use of additional commands that operate on the molecule,
+            which is named "mol". 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
@@ -1052,7 +1062,8 @@ def _function(
             tolerance=tolerance,
             max_distance=max_distance,
             water_model=water_model,
-            leap_commands=leap_commands,
+            pre_mol_commands=pre_mol_commands,
+            post_mol_commands=post_mol_commands,
             bonds=bonds,
             ensure_compatible=ensure_compatible,
             work_dir=work_dir,