Merge pull request #228 from OpenBioSim/release_2023.5.0

Release 2023.5.0

Author: lohedges

.github/workflows/Sandpit_exs.yml

@@ -35,7 +35,7 @@ jobs:
 
       - name: Install dependency
         run: |
-          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.10 ambertools gromacs "sire=2023.3" "alchemlyb>=2.1" pytest openff-interchange pint=0.21 rdkit "jaxlib>0.3.7" tqdm
+          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.10 ambertools gromacs "sire=2023.4" "alchemlyb>=2.1" pytest openff-interchange pint=0.21 rdkit "jaxlib>0.3.7" tqdm
           python -m pip install git+https://github.com/Exscientia/MDRestraintsGenerator.git
           # For the testing of BSS.FreeEnergy.AlchemicalFreeEnergy.analysis
           python -m pip install https://github.com/alchemistry/alchemtest/archive/master.zip

doc/source/changelog.rst

@@ -9,6 +9,12 @@ 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.
 
+`2023.5.0 <https://github.com/openbiosim/biosimspace/compare/2023.4.1...2023.5.0>`_ - Dec 16 2023
+-------------------------------------------------------------------------------------------------
+
+* Add support for detecting nucleic acid backbones (`@fjclark <https://github.com/fjclark>`_) (`#189 <https://github.com/OpenBioSim/biosimspace/pull/189>`__).
+* Added SOMD and GROMACS support for multiple distance restraints for ABFE calculations (`#178 <https://github.com/OpenBioSim/biosimspace/pull/178>`__).
+
 `2023.4.1 <https://github.com/openbiosim/biosimspace/compare/2023.4.0...2023.4.1>`_ - Dec 14 2023
 -------------------------------------------------------------------------------------------------
 
@@ -17,7 +23,7 @@ within the biomolecular simulation community. Our software is hosted via the `Op
 * 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 bug in the 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>`__).

python/BioSimSpace/Parameters/__init__.py

@@ -141,7 +141,7 @@
    # ready to be returned.
    molecule = BSS.Parameters.ff14SB(molecule, water_model="tip3p").getMolecule()
 
-Additional parameters can be loaded by passing the ``leap_commands`` option to
+Additional parameters can be loaded by passing the ``pre_mol_commands`` option to
 any compatible AMBER force field function, e.g.:
 
 .. code-block:: python
@@ -157,7 +157,11 @@
 
    # Initialise the parameterisation process and block until the molecule is
    # ready to be returned.
-   molecule = BSS.Parameters.ff14SB(molecule, leap_commands=leap_commands).getMolecule()
+   molecule = BSS.Parameters.ff14SB(molecule, pre_mol_commands=leap_commands).getMolecule()
+
+If you need to apply any additional operations on the loaded molecule, then this
+can be done using the ``post_mol_commands`` option, using ``mol`` for the name of
+the molecule.
 """
 
 from ._parameters import *

python/BioSimSpace/Sandpit/Exscientia/FreeEnergy/_alchemical_free_energy.py

@@ -258,12 +258,23 @@ def __init__(
                         "Use the 'BioSimSpace.Align' package to map and merge molecules."
                     )
 
-                if self._protocol.getPerturbationType() != "full":
+                pert_type = self._protocol.getPerturbationType()
+                if pert_type not in ["full", "release_restraint"]:
                     raise NotImplementedError(
                         "GROMACS currently only supports the 'full' perturbation "
                         "type. Please use engine='SOMD' when running multistep "
                         "perturbation types."
                     )
+                if pert_type == "release_restraint":
+                    restraint_err = ValueError(
+                        "The 'release_restraint' perturbation type requires a multiple "
+                        "distance restraint restraint type."
+                    )
+                    if not restraint:
+                        raise restraint_err
+                    if restraint._restraint_type != "multiple_distance":
+                        raise restraint_err
+
                 self._exe = _gmx_exe
             elif engine == "AMBER":
                 # Find a molecular dynamics engine and executable.
@@ -354,6 +365,15 @@ def __init__(
                 # Ensure that the system is compatible with the restraint
                 restraint.system = self._system
 
+            # Warn the user about instabilities with multiple distance restraints in SOMD.
+            if restraint._restraint_type == "multiple_distance" and engine == "SOMD":
+                _warnings.warn(
+                    "SOMD simulations with some non-interacting ligands can be unstable. This "
+                    "affects some systems with multiple distance restraints during the release "
+                    "restraint state. If you experience problems, consider using multiple distance "
+                    "restraints with GROMACS instead."
+                )
+
         self._restraint = restraint
 
         # Create fake instance methods for 'analyse' and 'difference'. These