schrodinger.livedesign.utils module¶

Utility functions used in LiveDesign.

schrodinger.livedesign.utils.convert_to_rdkit_with_seqres(mol_input, st)¶

Convert a Structure to RDKit molecule with SEQRES information attached.

This function extracts SEQRES (sequence records) from a PDB structure and attaches them as a property on the resulting RDKit molecule. This enables downstream conversion to monomeric representation (via toMonomeric()) to produce complete biological sequences even when residues are missing or incomplete in the structure coordinates.

Parameters:

mol_input – String representation of PDB
st (schrodinger.structure.Structure) – Input structure, typically from a PDB file

Returns:

RDKit molecule with SEQRES attached as a “SEQRES” property containing a JSON-encoded dictionary mapping chain IDs to lists of 1-letter amino acid codes (or “X” for unknown residues)

Return type:

rdkit.Chem.rdchem.Mol

Note

The SEQRES property is stored as JSON with the format chain: list[seq]: {"A": ["M", "A", "G", "S", ...], "B": ["V", "L", ...]}

Warning

Non-standard amino acids not in STD_AMINO_ACIDS_THREE_LETTER are mapped to “X”.