schrodinger.protein.helm.monomer_db_converter module

Script to convert an existing monomer database into a database that’s supported by the coarse grain apis.

Use $SCHRODINGER/run python3 -m schrodinger.protein.helm.monomer_db_converter [OPTIONS] to invoke this script.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.protein.helm.monomer_db_converter.assign_pdb_names_to_residues(mol: Mol)

Assigns PDB residue name and atom names to the given RDKit molecule, assuming the structure is a single residue. Searches RESIDUE_PATTERNS for an exact match, and if that fails, a basic check for a peptidic structure is done to label core atoms.

Parameters:

mol (rdkit.Chem.rdchem.Mol) – The RDKit molecule to assign PDB residue name to.

Returns:

The PDB residue name.

schrodinger.protein.helm.monomer_db_converter.main()