BioSimSpace is supported by OpenBioSim, a community interest
company supporting open-source development of fostering academic/industrial collaboration
within the biomolecular simulation community. Our software is hosted via the OpenBioSim
Add support for computing trajectory RMSDs using Sire backend (#152).
Add support for setting up systems containing crystal waters (#154).
Fix handling of connectivity changes during molecular perturbations (#157).
Fix issues related to new shared properties in Sire (#160).
Don’t generate velocities when performing a continuation with GROMACS (#169).
Decouple custom parameters and additional commands in
Check for periodic space when updating box information from restart file or trajectory (#173).
Add functionality to allow manual rotation and reduction of triclinic boxes, rather than performing automatically on read (#175).
Allow unit-based protocol options to be passed as strings (#179).
Fix assignment of
gpuconfiguration option for SOMD (#181).
Check for non-periodic cartesian space when setting up vacuum simulations with all engines (#125).
Fixed several issues caught by BioSimSpace tutorials suite (#128).
Fixed import of incorrect
alchemlybextract function for GROMACS (#132).
Handle issues with using certain triclinic box vectors with OpenMM by performing a pre lattice reduction using the internal OpenMM functionality (#135).
Fix use of
totalStepswhen using the OpenMM
alchemlybis imported using
try_importto avoid errors on platforms where it isn’t available (#151).
setup.pyfile to work correctly on Windows (#72).
Fixed bug with missing working directory when using
rmsd_flex_alignscoring function (#75).
openmmsystem to avoid issue parsing triclinic spaces with
Fix parsing of AMBER free-energy perturbation standard output (#79).
Fix bug in
Check molecule numbers in system when caching files to avoid issue when the UID and number of molecules are the same, but the actual molecules are different, e.g. after being edited (#89).
Fix order of imports in
Recenter molecules following vacuum simulation with GROMACS to avoid precision overflow with molecular coordinates on write (#95).
Fix expected angles used in unit test following updates to triclinic box code in Sire (#99).
Avoid streaming issues when reading binary AMBER restart files for a single frame (#105).
Handle updates to Sire parser format naming (#108).
Wrap new Sire units grammar to improve parsing of units from strings (#109).
make_wholeoption in Sire to allow un-wrapping of molecular coordinates on read (#110).
Make sure to call
.value()on objects that now have units (#110).
Handle missing values in AMBER standard output records (#111).
Fix bug in
plumedversion requirement check (#113).
Reinstate temperature control for all GROMACS simulation protocols (#115).
Fix pre-processing selector in test section of
Catch exception when vacuum system has a cartesian space (#120).
Add support for Sire as a trajectory backend (#121).
Rename tests directory to
testsfor compliance with
Fixed parsing of AMBER standard output records (#56).
Re-add pre-minimisation stage to SOMD FEP configuration (#59).
Fixed reference to
plumed.datfile in AMBER configuration input for steered molecular dynamics (#64).
Update GitHub CI for our new release process (#34).
Fixed protocol mixin inheritance (#41).
Update documentation for new development and release process (#43).
Fixed SOMD inverse friction coefficient configuration parameter (#49).
Fixes to the hydration free energy tutorial (#49).
Fixed bug in SOMD test runner that caused it to return prior to assertions (#49).
Make sure that system properties are preserved when creating a new Sire system.
Fixed an issue with the OpenMM minimisation protocol that meant that the number of steps was ignored (#12).
Use native Sire PDB downloading functionality to remove
Fixed an issue with SMILES characters in molecule names causing issues for
Increase default SOMD cut-off since it uses reaction field (#15).
No longer downcast molecules to single residues and atoms when searching (#19).
Remove velocities when combining molecules if the property isn’t present for all molecules (#21).
Set default-valued properties when merging molecules to avoid issues with zero values when units are stripped (#24).
watchdogto avoid non-deterministic parsing of AMBER output (#27).
Improved handling of disulphide bonds in multi-chain PDBs sharing the same residue numbers (#28).
Add mixin classes to allow position restraints to be used with a wider range of protocols (@xiki-tempula) and alchemical simulations for non-production protocols (@msuruzhon). Switch to using
gmx energyto parse GROMACS energy records (@xiki-tempula) (#30).
Switch to using native RDKit conversion throughout to avoid conversion via an intermediate file format.
Expose Sire to OpenMM conversion functionality in
Added Python 3.10 support and now build Python 3.10 packages. This is now the default version of Python for BioSimSpace, and the version we recommend for new workflows. Note that we will drop automatic building of Python 3.8 packages later this year (likely Q3 or Q4). This will be timed to co-incide with when we add Python 3.11 support, and when (we anticipate) conda-forge will drop Python 3.8. Our aim is to only build packages for a maximum of 3 Python versions at a time.
isSamemethod to compare systems using a sub-set of system and molecular properties. This improves our file caching support, allowing a user to exclude properties when comparing cached systems prior to write, e.g. ignoring coordinates and velocities, if those are the only things that differ between the systems (#3).
Fixed several formatting issues with the website documentation.
Minor fixes to website documentation.
Fixed issues with API documentation introduced by pydocstringformatter.
Fixed globbing of GROMACS trajectory files.
Wrapped the new sire.load function to allow loading of URLs.
Add basic file caching support to avoid re-writing files for the same molecular system.
BioSimSpace.IO.globsince globbing is now performed automatically.
Autoformat entire codebase using black.
Fix issues following Sire 2023 API updates.
Update documentation for new OpenBioSim website.
Prior to January 2023,
BioSimSpace was hosted within the michellab
GitHub organisation. The following releases were made during that time.
Improved NAMD restraint implementation for consistency with other engines.
Make sure we wait for
trjconvto finish when calling as a sub-process.
Added wrapper for
Improved interoperability of
BioSimSpace.Sandpitfor experimental features from external collaborators.
Added functionality to check for molecules in a
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
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.
.value()to avoid confusion.
Handle trjconv frame extraction failures within
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).
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.
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.
Pass executable found by
Fixed error in RMSD calculation within
Improved example scripts and notebooks.
2018.1.0 - May 01 2018#
Initial public release of BioSimSpace.