Changelog ========= `2022.3.0 `_ - Sep 28 2022 (Pre-release) ------------------------------------------------------------------------------------------------ * Improved NAMD restraint implementation for consistency with other engines. * Make sure we wait for ``trjconv`` to finish when calling as a sub-process. * Added wrapper for ``Sire.Units.GeneralUnit``. * Improved interoperability of ``BioSimSpace.Trajectory`` sub-package. * Added ``BioSimSpace.Sandpit`` for experimental features from external collaborators. * Added functionality to check for molecules in a ``BioSimSpace.System``. * Added functionality to extract atoms and residues by absolute index. * Allow continuation for GROMACS equilibration simulations. (`@kexul `_) * Update BioSimSpace to work with the new Sire 2023.0.0 Python API. `2022.2.1 `_ - Mar 30 2022 ------------------------------------------------------------------------------------------------ * Fix performance issues when ensuring unique molecule numbering when adding molecules to ``BioSimSpace._SireWrappers.System`` and ``BioSimSpace._SireWrappers.Molecules`` objects. * Fix extraction of box vector magnitudes for triclinic boxes. `2022.2.0 `_ - Mar 24 2022 ------------------------------------------------------------------------------------------------ * Use fast C++ wrappers for updating coordinates and velocities during SOMD simulations. * Fix import issues caused by change in module layout for conda-forge OpenMM package. * Don't check for structural ions when parameterising with GAFF/GAFF2. * Fix errors in funnel correction calculation. * Switch to using conda-forge lomap2 package, removing need to vendor lomap code. * Use py3Dmol to visualise maximum common substructure mappings. * Rename ``.magnitude()`` method on ``BioSimSpace.Type`` objects to ``.value()`` to avoid confusion. * Handle trjconv frame extraction failures within ``BioSimSpace.Process.Gromacs.getSystem()``. * Catch and handle possible GSL error during singular valued decomposition routine used for molecular alignment. `2022.1.0 `_ - Jan 26 2022 ------------------------------------------------------------------------------------------------ * Added basic support for cleaning PDB files with `pdb4amber `_ prior to read. * Added basic support for exporting BioSimSpace Nodes as Common Workflow Language wrappers. * Added support for parameterising molecules using OpenForceField. * Added support for using SMILES strings for input to parameterisation functions. * Added support for funnel metadynamics simulations (`@dlukauskis `_). * Added support for steered molecular dynamics simulations (`@AdeleLip `_). * Added support for generating perturbation networks using LOMAP (`@JenkeScheen `_). * Fixed bug affecting certain improper/dihedral terms in SOMD perturbation file writer. * Numerous performance improvements, particularly involving the manipulation and combination of molecular systems. * Native Python pickling support for wrapped Sire types (`@chryswoods `_). * Numerous free-energy perturbation pipeline fixes and improvements. Thanks to `@kexul `_ and `@msuruzhon `_ for their help testing and debugging. * Switch continuous integration to GitHub actions using conda-forge compliant build and upload to Anaconda cloud. `2020.1.0 `_ - July 28 2020 ------------------------------------------------------------------------------------------------- * Added logo to website and update theme (`@ppxasjsm `_). * Make sure potential terms are sorted when writing to SOMD perturbation files (`@ptosco `_). * Switch to using ipywidgets.FileUpload to eliminate non-conda dependencies. * Added support for single-leg free energy simulations. * Created a KCOMBU mirror to avoid network issues during install. * Allow AMBER simulations when system wasn't loaded from file. * Handle GROMACS simulations with non-periodic boxes. * Run vacuum simulations on a single thread when using GROMACS to avoid domain decomposition. * Make sure BioSimSpace is always built against the latest version of Sire during conda build. `2019.3.0 `_ - Nov 22 2019 ------------------------------------------------------------------------------------------------ * Make FKCOMBU download during conda build resilient to server downtime. * Added support for xtc trajectory files and custom protocols with GROMACS. * Fixed numerous typos in Sphinx documentation. * Added Journal of Open Source Software paper. `2019.2.0 `_ - Sep 11 2019 ------------------------------------------------------------------------------------------------ * Switched to using `RDKit `_ for maximum common substructure (MCS) mappings. * Handle perturbable molecules for non free-energy protocols with SOMD and GROMACS. * Added basic metadynamics functionality with support for distance and torsion collective variables. * Added support for inferring formal charge of molecules. * Numerous MCS mapping fixes and improvements. Thanks to `@maxkuhn `_, `@dlukauskis `_, and `@ptosco `_ for help testing and debugging. * Added Dockerfile to build thirdparty packages required by the BioSimSpace notebook server. * Exposed Sire search functionality. * Added thin-wrappers for several additional Sire objects, e.g. Residue, Atom, and Molecules container. * Performance improvements for searching, indexing, and extracting objects from molecular containers, e.g. System, Molecule. `2019.1.0 `_ - May 02 2019 ------------------------------------------------------------------------------------------------ * Added support for parameterising proteins and ligands. * Added support for solvating molecular systems. * Molecular dynamics drivers updated to support SOMD and GROMACS. * Support free energy perturbation simulations with SOMD and GROMACS. * Added Azure Pipeline to automatically build, test, document, and deploy BioSimSpace. * Created automatic Conda package pipeline. `2018.1.1 `_ - May 02 2018 ------------------------------------------------------------------------------------------------ * Fixed conda NetCDF issue on macOS. Yay for managing `python environments `_\ ! * Install conda `ambertools `_ during `setup `_. * Search for bundled version of ``sander`` when running `AMBER `_ simulation processes. * Pass executable found by ``BioSimSpace.MD`` to ``BioSimSpace.Process`` constructor. * Fixed error in RMSD calculation within ``BioSimSpace.Trajectory`` class. * Improved example scripts and notebooks. 2018.1.0 - May 01 2018 ---------------------- * Initial public release of BioSimSpace.