Source code for schrodinger.livedesign.convert

import enum

from rdkit import Chem

from schrodinger.thirdparty import rdkit_adapter


class Format(enum.Enum):
    SDF = enum.auto()
    SMILES = enum.auto()
    CXSMILES = enum.auto()


def convert(data: str, input_format: Format, output_format: Format) -> str:
    """
    :param data: input text string
    :param input_format: expected format for input string
    :param output_format: desired format for output string
    :return: converted text string
    """

    str_to_mol = {
        Format.SDF: sdf_to_rdkit,
        Format.SMILES: Chem.MolFromSmiles,
        Format.CXSMILES: Chem.MolFromSmiles,
    }
    mol_to_str = {
        Format.SDF: rdkit_to_sdf,
        Format.SMILES: Chem.MolToSmiles,
        Format.CXSMILES: rdkit_to_cxsmiles,
    }

    with rdkit_adapter.convert_log_to_exception():
        mol = str_to_mol[input_format](data)
    return mol_to_str[output_format](mol)


def get_sd_reader(molblock: str) -> Chem.SDMolSupplier:
    """
    :param molblock: given SDF molblock
    :return: iterator through each mol in the given SDF data
    """
    reader = Chem.SDMolSupplier()
    reader.SetData(molblock,
                   sanitize=False,
                   removeHs=False,
                   strictParsing=False)
    return reader


def sdf_to_rdkit(molblock: str) -> Chem.rdchem.Mol:
    """
    :param molblock: given SDF molblock
    :return: corresponding RDKit mol
    """
    reader = get_sd_reader(molblock)
    molblock_count = len(reader)
    if molblock_count != 1:
        raise RuntimeError(
            f"Single molblock required; {molblock_count} present")
    with rdkit_adapter.convert_log_to_exception():
        return next(reader)


def rdkit_to_sdf(mol: Chem.rdchem.Mol) -> str:
    """
    :param mol: given RDKit mol
    :return: corresponding SDF molblock
    """
    return Chem.SDWriter.GetText(mol, force_v3000=True)


def rdkit_to_cxsmiles(mol: Chem.rdchem.Mol) -> str:
    """
    :param mol: given RDKit mol
    :return: corresponding CXSMILES stripped of coordinates
    """
    mol.RemoveAllConformers()  # remove coordinates from CXSMILES
    return Chem.MolToCXSmiles(mol)