Hello,
I would like to ask if MolSnapper can do scaffold decoration, and if yes, how please.
The parameters state
sdf_path = 'Path to the SDF file representing ligands or reference points with atom positions and types.'
use_pharma = 'Boolean parameter indicating whether to extract pharmacophore points from the SDF file or use the SDF as reference points.'
Let's assume the same setup as in #4
After preparing the pocket from the separate protein pdb and ligand sdf, I also extracted a fragment from the ligand into another sdf.
I run sample_single_pocket.py with --use_pharma False, taking as inputs pocket.pkl and the fragment sdf. I also set mol_size to more atoms than the extracted fragment, e.g. the same number of atoms as in the full ligand.
To my surprise, I did not get the error from #4 although I set --use_pharma False.
Is it the correct way to decorate my fragment sdf or shall I provide reference atoms in another format or with other parameters please?
Hello,
I would like to ask if MolSnapper can do scaffold decoration, and if yes, how please.
The parameters state
sdf_path = 'Path to the SDF file representing ligands or reference points with atom positions and types.'
use_pharma = 'Boolean parameter indicating whether to extract pharmacophore points from the SDF file or use the SDF as reference points.'
Let's assume the same setup as in #4
After preparing the pocket from the separate protein pdb and ligand sdf, I also extracted a fragment from the ligand into another sdf.
I run
sample_single_pocket.pywith--use_pharma False, taking as inputspocket.pkland the fragment sdf. I also setmol_sizeto more atoms than the extracted fragment, e.g. the same number of atoms as in the full ligand.To my surprise, I did not get the error from #4 although I set
--use_pharma False.Is it the correct way to decorate my fragment sdf or shall I provide reference atoms in another format or with other parameters please?