schrodinger.livedesign.standardizer module

Does a standardization procedure given an RDKit MonomerMol.

Currently a place holder, initial version to be implemented in BIOLUM-5697

schrodinger.livedesign.standardizer.standardize(mol: Mol, options: RegistrationOptions)

Standardize the given RDKit mol that may be atomistic or monomeric. This should always be a leaf node of customer provided data.

NOTE: this is a placeholder for BIOLUM-5697

Parameters:

rdmol – RDKit mol to standardize

Returns:

standardized RDKit mol

schrodinger.livedesign.standardizer.determine_monomeric_state(mol: Mol)

Converts the given mol to monomeric or atomistic based on its composition and feature flags that are set (TODO: should be based on standardization options not feature flags)

schrodinger.livedesign.standardizer.has_smiles_representation(monomer_mol: Mol) → bool

Check if a single monomer has a SMILES representation available, either because it’s SMILES-based or because it’s in the database.

Parameters:

monomer_mol – Monomeric RDMol object

Returns:

True if the monomer has a SMILES representation, False otherwise

schrodinger.livedesign.standardizer.convert_single_monomer_to_atomistic(monomer_mol: Mol) → bool

Determine if a single monomer should be converted to atomistic representation.

Parameters:

monomer_mol – Monomeric RDMol object

Returns:

True if the monomer has CHEM based chain and has a smiles representation

schrodinger.livedesign.standardizer.is_single_smiles_monomer(monomer_mol: Mol) → bool

Check if the given monomer mol is a single SMILES monomer.

Parameters:

monomer_mol – Monomeric RDMol object

Returns:

True if the mol is a single SMILES monomer, False otherwise