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CHANGELOG
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CHANGELOG
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SIRE changelog
==============
devel branch:
[2019.3.0] November 2019 - Added functionality to restrict the search space
when finding paths between atoms or searching for rings. Fixed
performance issue in GroTop parser caused by an N^2 loop over
atoms when searching the intrascale matrix. We now loop over
cut-groups, which is far more efficient. Fixed issues with
Python wrapper generation caused by issues with missing define
symbols and a bug in the scanheaders.py script.
[2019.2.1] October 2019 - Updated the Conda recipe to pin the dependencies
of dependencies that are used at run time since Conda doesn't
automatically do this for you. Added instructions detailing the
Azure Pipeline build process and how to create a new release.
[2019.2.0] September 2019 - Updated the Gromacs topology writer to support
perturbable molecules containing a variable number of bonds.
Created a Docker container for building wrappers and updated
to using CastXML. Added support for running background
processes on Windows (@ptosco). Updated SOMD Python wrapper
to write restart files every cycle to simplify system monitoring
in BioSimSpace. Fixed macOS build issue by not linking against
libpython. Made sure that Conda dependencies are pinned
correctly to avoid compatibility issues. Fixed bug that
prevented upload statistics being sent and added support for
tracking BioSimSpace usage.
[2019.1.0] May 2019 - Updates to the Gromacs topology writer to support
free energy perturbation simulations. The MCS matching
functionality has been extended to allow matches between heavy
and light atoms, and the ability to return all current matches,
rather than just the most recent. Temporarily disabled
parallelisation in the AmberPrm parser to avoid a threading
issue. Switched to using Azure Pipelines for continuous
integration to enable a fully automated build, testing, and
deployment pipeline. In addition, we finally have created
a Sire Conda package to simplify the installation and update
process.
[2018.2.0] July 2018 - Improvements to the Gromacs topology reader/writer,
addition of code to improve matching of atoms in proteins,
fixing compile issues on modern Ubuntu, bugfixes for crashes
in the AmberPrm reader, added in text-based searching for
atoms, residues etc. from Systems, MoleculeGroups, Molecules,
etc. based on boost::spirit, updated boost to latest version,
bugfixes for quantomm infinite rotation bug for ions,
general bugfixes.
[2018.1.1] May 2018 - Small bug fixes to allow single-atom solutes
and also to fix small issues with some parsers for BioSimSpace
[2018.1.0] March 2018 - Signficantly improved the Gromacs and Charmm
parser and fixed bugs. Can now write with both :-). Fixed
compilation on Windows 7 and above. Small changes to
the API of AtomProperties to make them easier to work
with from Python. Added a script to automatically color
code swap-based free energies. Fixed localisation
problems for the PDB writer. Improved mbar analysis
code. Added code to track forcefield data of a molecue.
Added code to better manage processes, including redirection
of standard output and error.
[2017.3.0] December 2017 - Added new PDB (PDB2), Mol2, Gro87, and CharmmPSF
parsers, as well as a GroTop parser, all part of the new
MoleculeParser framework. Updated all of the swap-based
methods to use this.
Removed the ViewsOfMol Python wrapper and now have the
code automatically return the correct python object for
the molecule (or part of molecule) that is returned from
the system. This makes simple scripts easier to write.
General bugfixes and optimisations, including fixing
bugs with the way that PropertyMap worked, cleaning
up to/from converters from python objects to automatic
Property wrappers, and fixing Process so that it can
redirect to stdout and that isRunning works without the
user having to call "wait" first!
[2017.2.0] September 2017 - The MoleculeParser framework has
been created to support reading and writing of molecules
in lots of different formats. The first set of formats
that have been completed are Amber Prmtop, Amber Rst7
and Amber Rst/Trj. The parsers work in parallel, with
file formats automatically detected by the parser,
e.g. system = MoleculeParser.read( "file.prm", "file.rst" )
will automatically do the right thing.
Improved automatic compilation on Arch linux.
Fixed temperature checking and general bugfixing for mbar code.
[2017.1.0] April 20 2017 - First 2017 release. Included new
parallel MoleculeParser code for reading molecules,
and moved fully over to C++-14 style coding for new code.
Included AVX-512 vectorisation for Intel KNL and can
now successfully compile and run using GCC 5 and GCC 6,
as well as Intel 2017 compilers and Clang.
[2016.3.1] January 9 2017 - Minor patch release that fixes bugs:
(1) Correctly sets MACOSX_DEPLOYMENT_TARGET to 10.8 so executable works
on OS X 10.8 (Mountain Lion) and above
(2) Fixed a parsing bug in Parameter that prevented integer or float
parameters from being passed to ligandswap, waterswap etc.
(3) Fixed a small bug in MultiDouble that meant it lost precision when
swapping individual values
(4) Fixed a parsing bug in Parameter that meant that windows path names
were not interpreted correctly
(5) Fixed the build scripts so that they placed bundled libraries into
bundled/lib rather than bundled/lib64 (affected SUSE-based distributions)
[2016.3.0] December 22 2016 - Public release containing full LigandSwap. Uses
new optimised forcefields for energy calculations, built on top of Intel Threaded
Building Blocks for parallelisation. New code is significantly faster with better
scaling.
[2016.2.0] June 3 2016 - Semi-private release for the CCP-BioSim workshops. Included
the first version of LigandSwap and general bug fixes
[2016.1.0] April 29 2016 - Merge of Bristol and Edinburgh codes, moved to miniconda
and clean packaging system, including OpenMM fully, added in nautilus, somd etc.,
added optimised forcefields, added a proper unit testing suite.
[OLD] Updated gradient compuation in openmmfreenergst to finite differece gradients
Allow the computation of reduced perturbed energies in openmmfreenergst of all computed lambda values
Separated minimization and equilibration from production run.
Implemented mass repartitioning for hydrogens atoms to allow for larger integration timesteps
Added nautilus scripts