OpenBioSim · lohedges · Feb 5, 2025 · Oct 24, 2024 · Oct 24, 2024 · Oct 24, 2024
diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst
@@ -9,6 +9,18 @@ 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.
 
+`2024.4.0 <https://github.com/openbiosim/biosimspace/compare/2024.3.0...2024.4.0>`_ - Feb 04 2025
+-------------------------------------------------------------------------------------------------
+
+* Improved robustness of restraint search and fixed torsion force constant (`@fjclark <https://github.com/fjclark>`_) (`#360 <https://github.com/OpenBioSim/biosimspace/pull/360>`__).
+* Add support for ``acdoctor`` option for ``Antechamber`` to help with parameterisation of molecules with atypical valence (`#361 <https://github.com/OpenBioSim/biosimspace/pull/361>`__).
+* Added missing AMBER atom mapping pruning options to the :mod:`BioSimSpace.Align` module (`#366 <https://github.com/OpenBioSim/biosimspace/pull/366>`__).
+* Improved error messages when no lambda windows are found during alchemical free-energy analysis (`@fjclark <https://github.com/fjclark>`_) (`#368 <https://github.com/OpenBioSim/biosimspace/pull/368>`__).
+* Decouple the selection used for aligment and RMSD for the :class:`RMSD <BioSimSpace.Metadynamics.CollectiveVariable.RMSD>` collective variable (`#379 <https://github.com/OpenBioSim/biosimspace/pull/379>`__).
+* Added missing ``._to_default_unit()`` method to the :class:`GeneralUnit <BioSimSpace.Types._GeneralUnit>` class (`#385 <https://github.com/OpenBioSim/biosimspace/pull/385>`__).
+* Clarified the meaning of the ``explicit_dummies`` keyword argument in the :class:`BioSimSpace.Process.Amber` class (`#385 <https://github.com/OpenBioSim/biosimspace/pull/385>`__).
+* Added a new :class:`BioSimSpace.Types.Mass` class to handle atomic masses (`#385 <https://github.com/OpenBioSim/biosimspace/pull/385>`__).
+
 `2024.3.0 <https://github.com/openbiosim/biosimspace/compare/2024.2.0...2024.3.0>`_ - Oct 24 2024
 -------------------------------------------------------------------------------------------------
 

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -43,7 +43,7 @@
 
 # General information about the project.
 project = "biosimspace"
-copyright = "2017-2024"
+copyright = "2017-2025"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -30,7 +30,9 @@ BioSimSpace is distributed and supported as an open source community project by
 Citation |DOI for Citing BioSimSpace|
 =====================================
 
-If you use BioSimSpace in any scientific software, please cite the following paper: ::
+If you use BioSimSpace in any scientific software, please cite the following paper:
+
+.. code-block:: bibtex
 
     @article{Hedges2019,
       doi = {10.21105/joss.01831},

diff --git a/python/BioSimSpace/Align/__init__.py b/python/BioSimSpace/Align/__init__.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #

diff --git a/python/BioSimSpace/Align/_align.py b/python/BioSimSpace/Align/_align.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #

diff --git a/python/BioSimSpace/Align/_merge.py b/python/BioSimSpace/Align/_merge.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #

diff --git a/python/BioSimSpace/Box/__init__.py b/python/BioSimSpace/Box/__init__.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #

diff --git a/python/BioSimSpace/Box/_box.py b/python/BioSimSpace/Box/_box.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #

diff --git a/python/BioSimSpace/Convert/__init__.py b/python/BioSimSpace/Convert/__init__.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #

diff --git a/python/BioSimSpace/Convert/_convert.py b/python/BioSimSpace/Convert/_convert.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #

diff --git a/python/BioSimSpace/FreeEnergy/__init__.py b/python/BioSimSpace/FreeEnergy/__init__.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #

diff --git a/python/BioSimSpace/FreeEnergy/_atm.py b/python/BioSimSpace/FreeEnergy/_atm.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #          Matthew Burman <matthew@openbiosim.org>

diff --git a/python/BioSimSpace/FreeEnergy/_ddg.py b/python/BioSimSpace/FreeEnergy/_ddg.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #          Matthew Burman <matthew@openbiosim.org>

diff --git a/python/BioSimSpace/FreeEnergy/_relative.py b/python/BioSimSpace/FreeEnergy/_relative.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #

diff --git a/python/BioSimSpace/FreeEnergy/_utils.py b/python/BioSimSpace/FreeEnergy/_utils.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #

diff --git a/python/BioSimSpace/Gateway/__init__.py b/python/BioSimSpace/Gateway/__init__.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #

diff --git a/python/BioSimSpace/Gateway/_node.py b/python/BioSimSpace/Gateway/_node.py
@@ -1,7 +1,7 @@
 ######################################################################
 # BioSimSpace: Making biomolecular simulation a breeze!
 #
-# Copyright: 2017-2024
+# Copyright: 2017-2025
 #
 # Authors: Lester Hedges <lester.hedges@gmail.com>
 #
@@ -60,6 +60,7 @@
 from ._requirements import Energy as _Energy
 from ._requirements import Integer as _Integer
 from ._requirements import Length as _Length
+from ._requirements import Mass as _Mass
 from ._requirements import Pressure as _Pressure
 from ._requirements import Requirement as _Requirement
 from ._requirements import String as _String
@@ -74,6 +75,7 @@
     _Energy,
     _Pressure,
     _Length,
+    _Mass,
     _Area,
     _Volume,
     _Temperature,
@@ -86,6 +88,7 @@
     _Energy,
     _Pressure,
     _Length,
+    _Mass,
     _Area,
     _Volume,
     _Temperature,