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.
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.
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.
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.
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.
Fixed conda NetCDF issue on macOS. Yay for managing python environments!
Search for bundled version of
sanderwhen running AMBER simulation processes.
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.