qp.protonate.get_protoss

Add hydrogens using Protoss

Usage

1. Submitting existing or custom PDB file:

   >>> from qp.protonate import get_protoss
   >>> pid = get_protoss.upload("path/to/PDB.pdb")
   >>> job = get_protoss.submit(pid)
   >>> get_protoss.download(job, "path/to/OUT.pdb")
   

2. Submitting PDB code:

   >>> from qp.protonate import get_protoss
   >>> pdb = "1dry"
   >>> job = get_protoss.submit(pdb)
   >>> get_protoss.download(job, "path/to/OUT.pdb")
   >>> get_protoss.download(job, "path/to/OUT.sdf", "ligands")
   

Protoss automatically removes alternative conformations and overlapping entries. Download the log file (key="log" in get_protoss.download) to see affected atoms.

Some metal-coordinating residues may be incorrectly protonated. Use get_protoss.adjust_activesites(path, metals) with the metal IDs to deprotonate these residues.

Functions

download	Download a Protoss output file.
repair_ligands	Repair ligands that Protoss renamed to MOL.
submit	Submit a PDB code or ProteinsPlus ID to the Protoss web API.
upload	Upload a PDB file to the ProteinsPlus web server.