Closed kexul closed 3 years ago
The code for this class is a bit convoluted and probably needs a more thorough refactoring, although I don't have the time to do so. In any case, I just pushed a commit that should take care of this behaviour. Let me know if there are any issues with it.
Thanks, the new version worked like a charm.
Here is the code to reproduce:
Here is the sdf file I used, which is 2D structure. test1.zip
The generated inpcrd file and mol2 file is 2D, though minimise is set to True (3D structure was expected).
In
Ligand.py
, theparametrise
function only take effect onself.protonated_filename
. It may be better ifself.molecule
is parametrised.