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

2018.1.0 - May 01 2018

  • Initial public release of BioSimSpace.