I am trying to create a workflow that extracts ligands from a PDB file input and finds their coordinates for alter use in docking through Autodock like software that I plan to integrate into the workflow in Python.
One of the key things to keep in mind is that I want to be able to use .pdb files that are not yet registered in the PDB database itself and so the workflow should run without calling the database for anything (hopefully).
Please find the workflow in it’s current state attached:
consensus_docking2.knwf (71.0 KB)
I start by cleaning the PDB file with the pdbfixer library.
I then use the Biopyhon package to separate all the ligands from the file and output a unique .pdb file for each
However, when I try to read these files back into the workflow, both the PDB loader and Load Local PDB Files nodes seem to be able to read the file but I cannot translate them into SDF or SMILES using OpenBabel or any of the other translators available.
Additionally, I would like to ask if there is way to locate the coordinates of a ligand in a PDB file easily and draw the box surrounding the ligand that is ised by software like Autodock
Thanks in advance!