Changelog#
OpenBioSim#
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
GitHub organisation.
2023.1.2 - Feb 24 2023#
Refactor code to use a unified
WorkDir
class to simplify the creation of working directories.Added
isSame
method 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.Added the initial version of
BioSimSpace.Convert
, which provides support for converting between nativeBioSimSpace
, Sire, and RDKit objects.Fixed several formatting issues with the website documentation.
2023.1.1 - Feb 07 2023#
Minor fixes to website documentation.
Fixed issues with API documentation introduced by pydocstringformatter.
Fix globbing of GROMACS trajectory files.
2023.1.0 - Feb 03 2023#
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.
Added
BioSimSpace._Config
sub-package to simplify the generation of configuration files for molecular dynamics engines and improve flexiblity. (Adapted from code written by @msuruzhon.)Deprecated
BioSimSpace.IO.glob
since globbing is now performed automatically.Autoformat entire codebase using black.
Fix issues following Sire 2023 API updates.
Update documentation for new OpenBioSim website.
Michellab#
Prior to January 2023, BioSimSpace
was hosted within the michellab
GitHub organisation. The following releases were made during that time.
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.
2022.2.1 - Mar 30 2022#
Fix performance issues when ensuring unique molecule numbering when adding molecules to
BioSimSpace._SireWrappers.System
andBioSimSpace._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 onBioSimSpace.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
toBioSimSpace.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.