Sire
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michellab
Sire Molecular Simulations Framework
In reference to [this](https://github.com/michellab/BioSimSpace/issues/97) BioSimSpace issue: How do you actually load and use the streamed Sire system? I've followed what's done in [OpenMMMD.py](https://github.com/michellab/Sire/blob/devel/wrapper/Tools/OpenMMMD.py), but get errors whenever I try to...
I'm not sure if this is an issue with [DCDFile.py](https://github.com/michellab/Sire/blob/devel/wrapper/Tools/DCDFile.py), or the `dcdplugin` used by `MDTraj`, which is what BioSImSpace uses to read trajectories. When I attempt to read a...
I'm seeing this failure occasionally during the Azure Pipeline on macOS. ```sh ====================================================================== FAIL: test_amberparams.test_params ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/vsts/sire.app/lib/python3.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/Users/vsts/sire.app/share/Sire/test/SireUnitTests/unittests/SireIO/test_amberparams.py",...
It would be nice if sire could support amber style input file for charmm style forcefield formats, containing CMAP corrections, currently amber.cpp throughs an error when reading the attached input...
The 'old' SireIO:Amber() object that implements readCrdTop() is still needed because the new parser doesn't create a SIreMol::AmberParameters object for each loaded molecule. This object is needed for initialising an...
Hello! I hope you are doing well! We are a security research team. Our tool automatically detected a vulnerability in this repository. We want to disclose it responsibly. GitHub has...
Dear Sire developers: The new website has three color themes, but the light color theme does not seem to work. 
WaterSwap seems to be broken in the current development version of Flare and it also throws a `SireError` when running it from Sire release version 2023.0.0 The command I used...
