deepmol.utils package

Submodules

deepmol.utils.errors module

exception PreConditionViolationException(condition: Optional[str] = None, message: str = 'Pre-condition violation')[source]

Bases: Exception

Exception raised when a pre-condition is violated.

deepmol.utils.utils module

canonicalize_mol_object(mol_object: Mol) → Mol[source]

Canonicalize a molecule object.

Parameters

mol_object (Mol) – Molecule object to canonicalize.

Returns

Canonicalized molecule object.

Return type

Mol

draw_MACCS_Pattern(mol: Mol, smarts_patt_index: int, path: Optional[str] = None)[source]

Draw a molecule with a MACCS key highlighted.

Parameters

  • mol (Mol) – Molecule to draw.

  • smarts_patt_index (int) – Index of the MACCS key to highlight.

  • path (str) – Path to save the image to. If None, the image is not saved.

Returns

im – Image of the molecule with the MACCS key highlighted.

Return type

PIL.Image.Image

draw_morgan_bit_on_molecule(mol: Mol, bit: int, radius: int = 2, nBits: int = 2048, chiral: bool = False, molSize: Tuple[int, int] = (450, 200))[source]

Draw a molecule with a Morgan fingerprint bit highlighted.

Parameters

  • mol (Mol) – Molecule to draw.

  • bit (int) – Bit to highlight.

  • radius (int) – Radius of the Morgan fingerprint.

  • nBits (int) – Number of bits in the Morgan fingerprint.

  • chiral (bool) – If True, the molecule is drawn with chiral information.

  • molSize (Tuple[int, int]) – Size of the molecule.

Returns

The molecule in SVG format.

Return type

SVG

draw_morgan_bits(molecule: Mol, bits: Union[int, str, List[int]], radius: int = 2, nBits: int = 2048)[source]

Draw a molecule with Morgan fingerprint bits highlighted.

Parameters

  • molecule (Mol) – Molecule to draw.

  • bits (Union[int, str, List[int]]) – Bit(s) to highlight. If ‘ON’, all bits that are set to 1 are highlighted.

  • radius (int) – Radius of the Morgan fingerprint.

  • nBits (int) – Number of bits in the Morgan fingerprint.

Returns

Object containing the image of the molecule with the Morgan fingerprint bits highlighted.

Return type

DrawMorganBits

draw_rdk_bit_on_molecule(mol: Mol, bit: int, minPath: int = 1, maxPath: int = 7, fpSize: int = 2048, path_dir: Optional[str] = None, molSize: Tuple[int, int] = (450, 200))[source]

Draw a molecule with a RDK fingerprint bit highlighted.

Parameters

  • mol (Mol) – Molecule to draw.

  • bit (int) – Bit to highlight.

  • minPath (int) – Minimum path length.

  • maxPath (int) – Maximum path length.

  • fpSize (int) – Number of bits in the fingerprint.

  • path_dir (str) – Path to save the image.

  • molSize (Tuple[int, int]) – Size of the molecule.

Returns

The molecule with the fingerprint bit highlighted.

Return type

Images

draw_rdk_bits(mol: Mol, bits: int, minPath: int = 2, maxPath: int = 7, fpSize: int = 2048)[source]

Draw a molecule with a RDK fingerprint bit highlighted.

Parameters

  • mol (Mol) – Molecule to draw.

  • bits (int) – Bit to highlight.

  • minPath (int) – Minimum path length.

  • maxPath (int) – Maximum path length.

  • fpSize (int) – Number of bits in the fingerprint.

Returns

The molecule with the fingerprint bits.

Return type

Draw.DrawRDKitBits

getSubstructDepiction(mol: Mol, atomID: int, radius: int, molSize: Tuple[int, int] = (450, 200))[source]

Get a depiction of a substructure.

Parameters

  • mol (Mol) – Molecule to draw.

  • atomID (int) – ID of the atom to highlight.

  • radius (int) – Radius of the substructure.

  • molSize (Tuple[int, int]) – Size of the molecule.

Returns

The molecule in SVG format.

Return type

SVG

load_from_disk(filename: str) → Any[source]

Load object from file.

Parameters

filename (str) – A filename you want to load.

Returns

A loaded object from file.

Return type

Any

load_pickle_file(input_file: str) → Any[source]

Load from single, possibly gzipped, pickle file.

Parameters

input_file (str) – The filename of pickle file. This function can load from gzipped pickle file like XXXX.pkl.gz.

Returns

The object which is loaded from the pickle file.

Return type

Any

mol_to_smiles(mol: Mol, **kwargs) → Optional[str][source]

Convert SMILES to RDKit molecule object. Parameters ———- mol: Mol

RDKit molecule object to convert.

kwargs:

Keyword arguments for rdkit.Chem.MolToSmiles.

smiles: str

SMILES string.

moltosvg(mol: Mol, molSize: Tuple[int, int] = (450, 200), kekulize: bool = True, drawer: Optional[object] = None, **kwargs)[source]

Convert a molecule to SVG.

Parameters

  • mol (Mol) – Molecule to convert.

  • molSize (Tuple[int, int]) – Size of the molecule.

  • kekulize (bool) – If True, the molecule is kekulized.

  • drawer (object) – Object to draw the molecule.

  • **kwargs – Additional arguments for the drawer.

Returns

The molecule in SVG format.

Return type

SVG

normalize_labels_shape(y_pred: Union[List, ndarray], n_tasks: int) → ndarray[source]

Function to transform output from predict_proba (prob(0) prob(1)) to predict format (0 or 1).

Parameters

  • y_pred (array) – array with predictions

  • n_tasks (int) – number of tasks

Returns

Array of predictions in the format [0, 1, 0, …]/[[0, 1, 0, …], [0, 1, 1, …], …]

Return type

labels

prepareMol(mol: Mol, kekulize: bool)[source]

Prepare a molecule for drawing.

Parameters

  • mol (Mol) – Molecule to prepare.

  • kekulize (bool) – If True, the molecule is kekulized.

Returns

mc – Prepared molecule.

Return type

Mol

smiles_to_mol(smiles: str, **kwargs) → Optional[Mol][source]

Convert SMILES to RDKit molecule object. Parameters ———- smiles: str

SMILES string to convert.

kwargs:

Keyword arguments for rdkit.Chem.MolFromSmiles.

Mol

RDKit molecule object.

Module contents