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Merge pull request #387 from OpenBioSim/release_2024.4.0
Release 2024.4.0
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‎doc/source/changelog.rst

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within the biomolecular simulation community. Our software is hosted via the `OpenBioSim`
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`GitHub <https://github.com/OpenBioSim/biosimspace>`__ organisation.
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`2024.4.0 <https://github.com/openbiosim/biosimspace/compare/2024.3.0...2024.4.0>`_ - Feb 04 2025
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* Improved robustness of restraint search and fixed torsion force constant (`@fjclark <https://github.com/fjclark>`_) (`#360 <https://github.com/OpenBioSim/biosimspace/pull/360>`__).
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* Add support for ``acdoctor`` option for ``Antechamber`` to help with parameterisation of molecules with atypical valence (`#361 <https://github.com/OpenBioSim/biosimspace/pull/361>`__).
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* Added missing AMBER atom mapping pruning options to the :mod:`BioSimSpace.Align` module (`#366 <https://github.com/OpenBioSim/biosimspace/pull/366>`__).
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* 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>`__).
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* 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>`__).
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* Added missing ``._to_default_unit()`` method to the :class:`GeneralUnit <BioSimSpace.Types._GeneralUnit>` class (`#385 <https://github.com/OpenBioSim/biosimspace/pull/385>`__).
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* Clarified the meaning of the ``explicit_dummies`` keyword argument in the :class:`BioSimSpace.Process.Amber` class (`#385 <https://github.com/OpenBioSim/biosimspace/pull/385>`__).
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* Added a new :class:`BioSimSpace.Types.Mass` class to handle atomic masses (`#385 <https://github.com/OpenBioSim/biosimspace/pull/385>`__).
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`2024.3.0 <https://github.com/openbiosim/biosimspace/compare/2024.2.0...2024.3.0>`_ - Oct 24 2024
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‎doc/source/conf.py

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# General information about the project.
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project = "biosimspace"
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copyright = "2017-2024"
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copyright = "2017-2025"
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the

‎doc/source/index.rst

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Citation |DOI for Citing BioSimSpace|
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=====================================
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If you use BioSimSpace in any scientific software, please cite the following paper: ::
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If you use BioSimSpace in any scientific software, please cite the following paper:
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.. code-block:: bibtex
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@article{Hedges2019,
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doi = {10.21105/joss.01831},

‎python/BioSimSpace/Align/__init__.py

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######################################################################
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# BioSimSpace: Making biomolecular simulation a breeze!
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# Copyright: 2017-2024
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# Copyright: 2017-2025
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#
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# Authors: Lester Hedges <lester.hedges@gmail.com>
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#

‎python/BioSimSpace/Align/_align.py

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######################################################################
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# BioSimSpace: Making biomolecular simulation a breeze!
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# Copyright: 2017-2024
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# Authors: Lester Hedges <lester.hedges@gmail.com>
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‎python/BioSimSpace/Align/_merge.py

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

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

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

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

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# BioSimSpace: Making biomolecular simulation a breeze!
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# Copyright: 2017-2025
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# Authors: Lester Hedges <lester.hedges@gmail.com>
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