Changelog

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.