Module ccsfp.informatics.molecules_and_images

Functions

def get_mol_from_inchi(inchi: str, test: bool = False) ‑> rdkit.Chem.rdchem.Mol

Function to make a mol object based on smiles :param inchi: str - SMILES string :param test: True/False - for unit testing

>>> get_mol_from_inchi("InChI=1S/H2O/h1H2", test=True)
1

Expand source code

def get_mol_from_inchi(inchi: str, test: bool = False) -> rdkit.Chem.rdchem.Mol:
    """
    Function to make a mol object based on smiles
    :param inchi: str - SMILES string
    :param test: True/False - for unit testing
    >>> get_mol_from_inchi("InChI=1S/H2O/h1H2", test=True)
    1
    """

    log = logging.getLogger(__name__)

    mol = Chem.MolFromInchi(inchi)
    log.debug("Input inchi: {})".format(inchi))
    Chem.rdmolops.SanitizeMol(mol)
    Chem.rdmolops.Cleanup(mol)

    if test is True:
        return mol.GetNumHeavyAtoms()

    return mol

def get_mol_from_smiles(smiles: str, canonicalize: bool = True, test: bool = False) ‑> rdkit.Chem.rdchem.Mol

Function to make a mol object based on smiles :param smiles: str - SMILES string :param canonicalize: True/False - use RDKit canonicalized smile or the input resprectively :param test: True/False - for unit testing

>>> get_mol_from_smiles("O", test=True)
1

Expand source code

def get_mol_from_smiles(
    smiles: str, canonicalize: bool = True, test: bool = False,
) -> rdkit.Chem.rdchem.Mol:
    """
    Function to make a mol object based on smiles
    :param smiles: str - SMILES string
    :param canonicalize: True/False - use RDKit canonicalized smile or the input resprectively
    :param test: True/False - for unit testing
    >>> get_mol_from_smiles("O", test=True)
    1
    """

    log = logging.getLogger(__name__)

    if canonicalize is True:
        s = Chem.CanonSmiles(smiles, useChiral=1)
    else:
        s = smiles
    mol = Chem.MolFromSmiles(s)
    log.debug(
        "Input smiles: {} RDKit Canonicalized smiles {} (Note RDKit does not use "
        "general canon smiles rules https://github.com/rdkit/rdkit/issues/2747)".format(
            smiles, s,
        ),
    )
    Chem.rdmolops.SanitizeMol(mol)
    Chem.rdmolops.Cleanup(mol)

    if test is True:
        return mol.GetNumHeavyAtoms()

    return mol

def inchi_to_molecule(inchi: str, addH: bool = True, canonicalize: bool = True, threed: bool = True, add_stereo: bool = False, remove_stereo: bool = False, random_seed: int = 10459, verbose: bool = False, test: bool = False) ‑> rdkit.Chem.rdchem.Mol

A function to build a RDKit molecule from an InChI string :param inchi: str - InChI string :param addH: bool - Add Hydrogens or not :param canonicalize: bool - canonicalize molecule rep :param threed: bool - get 3D coordinates of the molecule from smiles :param add_stereo: bool - set stereo chemistry for the molecule :param remove_stereo: bool - remove stereo chemistry for the molecule :param random_seed: int - make the structure generation deterministic :param verbose: bool - provide verbose logging out :param test: bool - for unit test

>>> inchi_to_molecule("InChI=1S/H2O/h1H2", test=True)
3

Expand source code

def inchi_to_molecule(
    inchi: str,
    addH: bool = True,
    canonicalize: bool = True,
    threed: bool = True,
    add_stereo: bool = False,
    remove_stereo: bool = False,
    random_seed: int = 10459,
    verbose: bool = False,
    test: bool = False,
) -> rdkit.Chem.rdchem.Mol:
    """
    A function to build a RDKit molecule from an InChI string
    :param inchi: str - InChI string
    :param addH: bool - Add Hydrogens or not
    :param canonicalize: bool - canonicalize molecule rep
    :param threed: bool - get 3D coordinates of the molecule from smiles
    :param add_stereo: bool - set stereo chemistry for the molecule
    :param remove_stereo: bool - remove stereo chemistry for the molecule
    :param random_seed: int - make the structure generation deterministic
    :param verbose: bool - provide verbose logging out
    :param test: bool - for unit test
    >>> inchi_to_molecule("InChI=1S/H2O/h1H2", test=True)
    3
    """

    log = logging.getLogger(__name__)

    mol = get_mol_from_inchi(inchi)
    Chem.rdmolops.Cleanup(mol)
    Chem.rdmolops.SanitizeMol(mol)

    if remove_stereo is True:
        non_isosmiles = Chem.rdmolfiles.MolToSmiles(
            mol, isomericSmiles=False, allHsExplicit=False,
        )
        mol = get_mol_from_smiles(non_isosmiles, canonicalize=canonicalize)
        Chem.rdmolops.Cleanup(mol)
        Chem.rdmolops.SanitizeMol(mol)

        if verbose is True:
            for atom in mol.GetAtoms():
                log.info(
                    "Atom {} {} in molecule from InChI {} tag will be cleared. "
                    "Set properties {}.".format(
                        atom.GetIdx(),
                        atom.GetSymbol(),
                        inchi,
                        atom.GetPropsAsDict(
                            includePrivate=True, includeComputed=True),
                    ),
                )

    if addH is True:
        mol = Chem.rdmolops.AddHs(mol)

    if add_stereo is True:
        rdCIPLabeler.AssignCIPLabels(mol)

    if threed:
        AllChem.EmbedMolecule(mol, randomSeed=random_seed)

    if test is True:
        return mol.GetNumAtoms()

    return mol

def smiles_to_molecule(s: str, addH: bool = True, canonicalize: bool = True, threed: bool = True, add_stereo: bool = False, remove_stereo: bool = False, random_seed: int = 10459, verbose: bool = False, test: bool = False) ‑> rdkit.Chem.rdchem.Mol

A function to build a RDKit molecule from a smiles string :param s: str - smiles string :param addH: bool - Add Hydrogens or not :param canonicalize: bool - canonicalize molecule rep :param threed: bool - get 3D coordinates of the molecule from smiles :param add_stereo: bool - set stereo chemistry for the molecule :param remove_stereo: bool - remove stereo chemistry for the molecule :param random_seed: int - make the structure generation deterministic :param verbose: bool - provide verbose logging out :param test: True/False - for unit testing

>>> smiles_to_molecule("O", test=True)
3

Expand source code

def smiles_to_molecule(
    s: str,
    addH: bool = True,
    canonicalize: bool = True,
    threed: bool = True,
    add_stereo: bool = False,
    remove_stereo: bool = False,
    random_seed: int = 10459,
    verbose: bool = False,
    test: bool = False,
) -> rdkit.Chem.rdchem.Mol:
    """
    A function to build a RDKit molecule from a smiles string
    :param s: str - smiles string
    :param addH: bool - Add Hydrogens or not
    :param canonicalize: bool - canonicalize molecule rep
    :param threed: bool - get 3D coordinates of the molecule from smiles
    :param add_stereo: bool - set stereo chemistry for the molecule
    :param remove_stereo: bool - remove stereo chemistry for the molecule
    :param random_seed: int - make the structure generation deterministic
    :param verbose: bool - provide verbose logging out
    :param test: True/False - for unit testing
    >>> smiles_to_molecule("O", test=True)
    3
    """

    log = logging.getLogger(__name__)

    mol = get_mol_from_smiles(s, canonicalize=canonicalize)
    Chem.rdmolops.Cleanup(mol)
    Chem.rdmolops.SanitizeMol(mol)

    if remove_stereo is True:
        non_isosmiles = Chem.rdmolfiles.MolToSmiles(
            mol, isomericSmiles=False, allHsExplicit=False,
        )
        mol = get_mol_from_smiles(non_isosmiles, canonicalize=canonicalize)
        Chem.rdmolops.Cleanup(mol)
        Chem.rdmolops.SanitizeMol(mol)

        if verbose is True:
            for atom in mol.GetAtoms():
                log.info(
                    "Atom {} {} in molecule from smiles {} tag will be cleared. "
                    "Set properties {}.".format(
                        atom.GetIdx(),
                        atom.GetSymbol(),
                        s,
                        atom.GetPropsAsDict(
                            includePrivate=True, includeComputed=True),
                    ),
                )

    if addH is True:
        mol = Chem.rdmolops.AddHs(mol)

    if add_stereo is True:
        rdCIPLabeler.AssignCIPLabels(mol)

    if threed:
        AllChem.EmbedMolecule(mol, randomSeed=random_seed)

    if test is True:
        return mol.GetNumAtoms()

    return mol