Maciej Wójcikowski
Maciej Wójcikowski
Hi Michel, Thanks for reporting the issue. May you please share how you prepared the molecules in PDBQT format? Reading back PDBQT files is many times not the best idea,...
`oddt_vina_sescriptor` scores the representation of molecule in the toolkit, Openbabel or RDKit. If you produce PDBQT with ODDT I would expect the scores to be identical. In your case, the...
Hi @parkc23, Could you please provide the code and file to reproduce the issue?
Hi Thomas, In oddt we have created additional module for such operations in RDKit in `oddt.toolkits.extras.rdkit.fixer`. Note it requires `Chem.Mol`, not `oddt.Molecule`. ```python from oddt.toolkits.extras.rdkit.fixer import ExtractPocketAndLigand mol = Chem.MolFromPDBFile("complex_forscoring_frm.1.min.pdb",...
@tevang It looks like you need to sanitize the molecule first. Or at least generate rings with `Chem.FastFindRings(...)`
@tevang I would say that sanitization is highly recommended. That said being consistent is the key for most use cases, so you might get away with it. Keep in mind...
Pdb format does not always include charges, which is particular problem for ligands, I would suggest using another format better suited for small molecules such as sdf or mol2. Additionally...
Can you upload a sample file I will try to look a at it next week to figure it out
Hi Tim, I think I was procrastinating a release long enough indeed. I will prepare a new release shortly.
Just to let you know - I'm fixing some of the silent-failing tests. Move to azure didn't go so well...