BioSimSpace
BioSimSpace copied to clipboard
michellab
Code and resources for the EPSRC BioSimSpace project.
Hello, Recent changes to ipywidgets have [broken NGLView](https://github.com/nglviewer/nglview/issues/1032) - ensuring version
This is the update of BioSimSpace that is compatible with Sire 2023.0.0. The changes are minimal, i.e. updating to using the new (PEP8) module names of sire (but not the...
Hello! This is the PR relating to the updated analysis in BSS. I have tested this for all three engine outputs via the following, with work_dir being the directory of...
**Is your feature request related to a problem? Please describe.** Hi! I could not find the option to specify the ions to use during system preparation, what in tleap would...
Hi! If possible, it would be helpful to have some extra arguments in "wrapper" functions. For example, while the Process functions `BioSimSpace.Process.Amber(), BioSimSpace.Process.Gromacs(), BioSimSpace.Process.OpenMM(), [...]` support the arguments `name, work_dir,...
**Is your feature request related to a problem? Please describe.** I have tried to prepare a system containing 4 disulfide bridges, however SS-bridge parameters were not in the output parameter...
This PR syncs the EXS/dev to this dev and the major update is the ABFE functionality. Type of change Bug fix (non-breaking change which fixes an issue) - Fix the...
The current sMD implementation allows to use RMSD, Distance and Torsion collective variables. I had a case where I had to use a custom function as one of my CVs...
Hi, this PR adds parameters for the merge function, allowing users select regions of interest to merge, which might be useful for modeling protein mutation and covalent binding. A unit...
As reported by @msuruzhon, pickling/unpickling large BioSimSpace objects has very poor performance on macOS. Using [System.pickle.tar.gz](https://github.com/michellab/BioSimSpace/files/9103247/System.pickle.tar.gz) we see: ```python import BioSimSpace.Sandpit.Exscientia as BSS import pickle import time a = time.time()...
