The clean PDB API is made available to all Cyrus Engine API customers free of charge. Use of the clean PDB does not count towards yearly request quotas.
The Clean PDB API prepares input PDB files for optimal performance using the Cyrus Engine APIs. When a PDB file is submitted to the API the following changes are made:
All waters are removed
All metal ions are removed
All small molecule ligands are removed
All non-canonical amino acids are converted to the most similar canonical amino acid
Residues are renumbered starting from 1
Cyrus recommends that all PDBs used with the Cyrus Engine API are first passed through this endpoint. prior to use.
Inputs
Input PDB file – a PDB file
CLI argument:
--pdb-file input.pdb
Python submit() argument:
pdb-file="input.pdb"
Command Line Examples
Clean a PDB file:
cyrus submit clean-pdb input_file.pdb
Python Examples
Clean a PDB file:
from engine.clean_pdb.client import CleanPdbClient client = CleanPdbClient() job_id = client.submit(pdb_path="input.pdb")
Outputs
full_structure.pdb – A cleaned PDB file