schrodinger.livedesign.biologics.rdmol_hierarchy module¶

schrodinger.livedesign.biologics.rdmol_hierarchy.add_substance_group(mol: Mol, atoms: list[rdkit.Chem.rdchem.Atom] = None, chains: set[str] = None)¶

Add a substance group to the RDMol. The RDMol is a mol consisting of atoms. The substance group groups these atoms within the mol creating relationships within the mol that denote the heirarchy.

Parameters:

mol – RDMol object
atoms – A list of atoms to include in the substance group. If not supplied, the substance group will contain all the atoms in the mol.
chains – A set of chain IDs to include in the substance group.

schrodinger.livedesign.biologics.rdmol_hierarchy.make_substance_group(mol: Mol, atoms: list[rdkit.Chem.rdchem.Atom])¶

Create a substance group in the RDMol with the given atoms.

Parameters:

mol – RDMol object
atoms – List of atoms to include in the substance group

schrodinger.livedesign.biologics.rdmol_hierarchy.extract_chain(mol: Mol, chain_name: str) → Mol¶

Extract a specific chain from the RDMol.

Parameters:

mol – RDMol object
chain_name – Chain ID to extract

Returns:

RDMol object containing only the specified chain

schrodinger.livedesign.biologics.rdmol_hierarchy.get_chain_atoms(mol: Mol, chain_names: list[str]) → list[rdkit.Chem.rdchem.Atom]¶

Get all atoms in the RDMol that belong to a specific chain.

Parameters:

mol – RDMol object
chain_names – Chain IDs to filter atoms by

Returns:

List of atoms in the specified chain

schrodinger.livedesign.biologics.rdmol_hierarchy.get_group_indices(mol: Mol) → list[set[int]]¶

Get the indices of all the atoms in the substance groups of the RDMol.

Parameters:: mol – RDMol object
Returns:: List of sets, each set contains the indices of atoms in a substance group

schrodinger.livedesign.biologics.rdmol_hierarchy.get_chemical_model(rdmol_binaries: list[tuple[str, int]]) → Mol¶

Given a list of tuples containing rdmol_binary strings and their counts, return the corresponding chemical model.

Parameters:: rdmol_binaries – A list of tuples containing rdmol_binary strings and their counts.
Returns:: The corresponding chemical model.

schrodinger.livedesign.biologics.rdmol_hierarchy.combine_chemical_models(chemical_models: list[rdkit.Chem.rdchem.Mol]) → Mol¶

Given a list of chemical models, combine them into a single chemical model.

The function uses the CombineMols function from RDKit to combine the models. This function combines two molecules into one, and the function reduce from functools is used to apply this function iteratively to the list of chemical models.

Parameters:: chemical_models – A list of chemical models.
Returns:: The combined chemical model.

schrodinger.livedesign.biologics.rdmol_hierarchy.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

schrodinger.livedesign.biologics.rdmol_hierarchy.is_single_chem_monomer(monomer_mol: Mol) → bool¶

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

Parameters:: monomer_mol – Monomeric RDMol object
Returns:: True if the mol is a single CHEM monomer, False otherwise

schrodinger.livedesign.biologics.rdmol_hierarchy.get_sequence_monomers(mol: Mol) → list[rdkit.Chem.rdchem.Atom]¶

Get the monomers to use for sequence generation.

Parameters:: mol – Chemical model
Returns:: List of monomer RDMol objects

schrodinger.livedesign.biologics.rdmol_hierarchy.get_monomer_fasta_sequence(monomers: list[rdkit.Chem.rdchem.Atom]) → str¶

Convert a list of monomer RDMol objects to a monomer string.

Parameters:: monomers – List of monomer RDMol objects
Returns:: Monomer string

schrodinger.livedesign.biologics.rdmol_hierarchy.get_monomer_single_letter_code(monomer: Atom) → str¶

Get the residue name of a monomer RDMol object.

Parameters:: monomer – Monomer RDMol object
Returns:: Residue name

schrodinger.livedesign.biologics.rdmol_hierarchy.get_mol_section_indices(monomers: list[rdkit.Chem.rdchem.Atom], start: int, end: int) → list[int]¶

Get the atom indices corresponding to the given start and end indices in the monomer list.

Parameters:

monomers – List of monomer RDMol objects
start – Start index (inclusive)
end – End index (inclusive)

schrodinger.livedesign.biologics.rdmol_hierarchy.mutate_monomers(mol: Mol, mut_res_by_idx: dict[tuple[str, int], str])¶

Mutate monomers in the RDMol based on the provided mapping of (chain ID, residue number) to new residue names.

Parameters:

mol – RDMol object
mut_res_by_idx – Dictionary mapping (chain ID, residue number) to new residue names

schrodinger.livedesign.biologics.rdmol_hierarchy.remove_non_backbone_connections(mol: Mol) → Mol¶

Remove all non-backbone connections from the given RDMol.

Parameters:: mol – RDMol object
Returns:: RDMol object with only backbone connections