JenkeScheen
JenkeScheen
Recently I've had a few use-cases where it would have been helpful to be able to (within a BSS workflow) convert BSS molecules to RDKit molecules (and back). I worked...
Potentially related to #158 I've been trying to parameterise a protein ( [bace_prep_nowats.pdb.tar.gz](https://github.com/michellab/BioSimSpace/files/5446929/bace_prep_nowats.pdb.tar.gz) ) without much luck using the following lines: ``` protein = BSS.IO.readMolecules("./bace_prep_nowats.pdb")[0] protein_par = BSS.Parameters.ff14SB(protein, work_dir="output") protein_par.getMolecule()...
I'm trying to run solvation free energy calculations (i.e. without vacuum legs) using BSS.FreeEnergy.Solvation() but for the current setup it's much more straightforward to use opencl instead of cuda. I'm...
When running `perses` on a protein-ligand system we've noticed that the `hybrid factory` of edges is huge: ``` 166M P0240-His41(0)-Cys145(0)-His163(0)-3-5/out-hybrid_factory.npy.npz ``` Instead of just serializing out this object we need...
It would be super useful for debugging and explaining `perses` ddG predictions if we would be able to write ligand poses that represent equilibrium during the simulations. This could e.g....
[based on a discussion with `Datryllic` and @jthorton ] ### 1. `status -a` table generation No direct method of getting networks with actioned tasks. Could resolve this by geting individual...
This kind of stuff happens quite often we run MD on weak binders. I suspect that during dataviz there's a step that focusses the view on the ligand, instead we...
This PR enables plotting in `asap-alchemy predict` using categories. This is useful because now we can split a scatterplot (bokeh) by e.g. `MoleculeSet`. Some quick things to resolve (@jthorton let's...
During docking for FECs, _sometimes_, OE does weird things to hydrogens. We should be able to round-trip with RDKit using ``` mol = Chem.rdmolops.RemoveHs(mol) mol = Chem.rdmolops.AddHs(mol, addCoords=True) ``` to...