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.

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.

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.

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.

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.

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.

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.