Andrew Tarzia
Andrew Tarzia
Selecting a new entry refreshes column ordering, which can only be done manually by dragging columns
See title. Low priority as it is frustrating to have to redo each time.
.png or .svg (vector) graphics of a 3D rendering would be great. Opaque or white coloured background for paper figures.
Found issues with the handling of conjugation in stko.GulpUFF.assign_FF(). The method was written based on rdkit code, but the rdkit code also uses the bond order to set bond types,...
``` $write gbsa=true ``` in `_write_detailed_output`.
https://github.com/cclib/cclib
Use the calculate_rmsd tool with the Kabsch algorithm. Actually just use this tool: https://github.com/charnley/rmsd/tree/master/rmsd
for opts and MD? https://notebook.community/open-forcefield-group/openforcefield/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark
This is from a discussion with @lihaoran-001, where on HPC machines it might be useful to be able to specify where the GULP library files are kept directly in stko....
Gulp optimisation and MD can produce odd H atom positions when starting from high energy structures.
I have found many examples of structures after UFF4MOF optimisation or high T MD (using Gulp through stko), where H atoms near binding sites will be pointing the wrong way...