deepmol.datasets package

Submodules

deepmol.datasets.datasets module

class Dataset[source]

Bases: ABC

Abstract base class for datasets Subclasses need to implement their own methods based on this class.

abstract property X: ndarray

Get the features in the dataset.

Returns:

X – The features in the dataset.

Return type:

np.ndarray

clear_cached_properties()[source]

Clears the cached properties of the class.

abstract property feature_names: ndarray

Get the feature labels of the molecules in the dataset.

Returns:

feature_names – Feature names of the molecules.

Return type:

np.ndarray

abstract get_shape() → tuple[source]

Get the shape of molecules, features and labels in the dataset.

Returns:

shape – The shape of molecules, features and labels.

Return type:

tuple

abstract property ids: ndarray

Get the ids in the dataset.

Returns:

ids – The ids in the dataset.

Return type:

np.ndarray

abstract property label_names: ndarray

Get the labels names of the dataset. If you have a single task this will be a list of length 1 with the name of the label. If you have a multi-task dataset this will be a list of length n_tasks with the names of the labels.

Returns:

label_names – Label names of the molecules.

Return type:

np.ndarray

abstract property mode: str | List[str]

Get the mode of the dataset.

Returns:

mode – The mode of the dataset.

Return type:

Union[str, List[str]]

abstract property mols: ndarray

Get the molecules in the dataset.

Returns:

mols – Molecules in the dataset.

Return type:

np.ndarray

abstract property n_tasks: int

Get the number of tasks in the dataset.

Returns:

n_tasks – The number of tasks in the dataset.

Return type:

int

abstract remove_elements(indexes: List) → None[source]

Remove the elements from the dataset.

Parameters:

indexes (List[int]) – The indexes of the elements to remove.

abstract remove_nan(axis: int = 0) → None[source]

Remove the nan values from the dataset.

Parameters:

axis (int) – The axis to remove the nan values.

abstract property removed_elements: ndarray

Get the molecules in the dataset.

Returns:

mols – Removed molecules in the dataset.

Return type:

np.ndarray

abstract select(indexes: List[int], axis: int = 0) → None[source]

Select the elements from the dataset.

Parameters:

  • indexes (List[int]) – The indexes of the elements to select.

  • axis (int) – The axis to select the elements.

abstract select_features_by_index(indexes: List[int]) → Dataset[source]

Select the features from the dataset. :param indexes: The indexes of the features to select. :type indexes: List[int]

abstract select_features_by_name(names: List[str]) → None[source]

Select features with specific names from the dataset :param names: The names of the features to select from the dataset. :type names: List[str]

abstract select_to_split(indexes: ndarray | List[int]) → Dataset[source]

Select the elements from the dataset to split.

Parameters:

indexes (Union[np.ndarray, List[int]]) – The indexes of the elements to select.

abstract property smiles: ndarray

Get the smiles in the dataset. :returns: mols – Molecule smiles in the dataset. :rtype: np.ndarray

abstract property y: ndarray

Get the labels in the dataset.

Returns:

y – The labels in the dataset.

Return type:

np.ndarray

class SmilesDataset(smiles: ndarray | List[str], mols: ndarray | List[Mol] | None = None, ids: List | ndarray | None = None, X: List | ndarray | None = None, feature_names: List | ndarray | None = None, y: List | ndarray | None = None, label_names: List | ndarray | None = None, mode: str | List[str] = 'auto')[source]

Bases: Dataset

A Dataset defined by in-memory numpy arrays. This subclass of ‘Dataset’ stores arrays for smiles strings, Mol objects, features X, labels y, and molecule ids in memory as numpy arrays.

X

Get the features of the molecules in the dataset. :returns: Features of the molecules in the dataset. :rtype: np.ndarray

property feature_names: ndarray

Get the feature labels of the molecules in the dataset. :returns: Feature names of the molecules in the dataset. :rtype: np.ndarray

classmethod from_mols(mols: ndarray | List[Mol], ids: List | ndarray | None = None, X: List | ndarray | None = None, feature_names: List | ndarray | None = None, y: List | ndarray | None = None, label_names: List | ndarray | None = None, mode: str = 'auto') → SmilesDataset[source]

Initialize a dataset from RDKit Mol objects.

Parameters:

  • mols (Union[np.ndarray, List[Mol]]) – RDKit Mol objects of the molecules.

  • ids (Union[List, np.ndarray]) – IDs of the molecules.

  • X (Union[List, np.ndarray]) – Features of the molecules.

  • feature_names (Union[List, np.ndarray]) – Names of the features.

  • y (Union[List, np.ndarray]) – Labels of the molecules.

  • label_names (Union[List, np.ndarray]) – Names of the labels. If you have a single task this will be a list of length 1 with the name of the label. If you have a multi-task dataset this will be a list of length n_tasks with the names of the labels.

  • mode (str) – The mode of the dataset. If ‘auto’, the mode is inferred from the labels. If ‘classification’, the dataset is treated as a classification dataset. If ‘regression’, the dataset is treated as a regression dataset. If ‘multitask’, the dataset is treated as a multitask dataset.

Returns:

The dataset instance.

Return type:

SmilesDataset

get_shape() → Tuple[Tuple, Tuple | None, Tuple | None][source]

Get the shape of the dataset. Returns three tuples, giving the shape of the smiles, X and y arrays.

Returns:

  • smiles_shape (Tuple) – The shape of the mols array.

  • X_shape (Union[Tuple, None]) – The shape of the X array.

  • y_shape (Union[Tuple, None]) – The shape of the y array.

property ids: ndarray

Get the IDs of the molecules in the dataset. :returns: IDs of the molecules in the dataset. :rtype: np.ndarray

property label_names: ndarray

Get the label names of the molecules in the dataset. If you have a single task this will be a list of length 1 with the name of the label. If you have a multi-task dataset this will be a list of length n_tasks with the names of the labels.

Returns:

Label names in the dataset.

Return type:

np.ndarray

load_features(*args, inplace=False, **kwargs)

Method to make inplace.

Parameters:

  • self (object) – Object to apply the method to.

  • args (list) – Arguments to pass to the method.

  • inplace (bool) – Whether to apply the method inplace.

  • kwargs (dict) – Keyword arguments to pass to the method.

Returns:

result – Result of the method.

Return type:

object

merge(datasets: List[Dataset]) → SmilesDataset[source]

Merges provided datasets with the self dataset. :param datasets: List of datasets to merge. :type datasets: List[Dataset]

Returns:

A merged NumpyDataset.

Return type:

NumpyDataset

property mode: str | List[str]

Get the mode of the dataset. :returns: mode – The mode of the dataset. :rtype: Union[str, List[str]]

property mols: ndarray

Get the RDKit Mol objects of the molecules in the dataset. :returns: RDKit molecules of the molecules in the dataset. :rtype: np.ndarray

property n_tasks: int

Get the number of tasks in the dataset.

Returns:

n_tasks – The number of tasks in the dataset.

Return type:

int

remove_duplicates(*args, inplace=False, **kwargs)

Method to make inplace.

Parameters:

  • self (object) – Object to apply the method to.

  • args (list) – Arguments to pass to the method.

  • inplace (bool) – Whether to apply the method inplace.

  • kwargs (dict) – Keyword arguments to pass to the method.

Returns:

result – Result of the method.

Return type:

object

remove_elements(*args, inplace=False, **kwargs)

Method to make inplace.

Parameters:

  • self (object) – Object to apply the method to.

  • args (list) – Arguments to pass to the method.

  • inplace (bool) – Whether to apply the method inplace.

  • kwargs (dict) – Keyword arguments to pass to the method.

Returns:

result – Result of the method.

Return type:

object

remove_elements_by_index(*args, inplace=False, **kwargs)

Method to make inplace.

Parameters:

  • self (object) – Object to apply the method to.

  • args (list) – Arguments to pass to the method.

  • inplace (bool) – Whether to apply the method inplace.

  • kwargs (dict) – Keyword arguments to pass to the method.

Returns:

result – Result of the method.

Return type:

object

remove_nan(*args, inplace=False, **kwargs)

Method to make inplace.

Parameters:

  • self (object) – Object to apply the method to.

  • args (list) – Arguments to pass to the method.

  • inplace (bool) – Whether to apply the method inplace.

  • kwargs (dict) – Keyword arguments to pass to the method.

Returns:

result – Result of the method.

Return type:

object

property removed_elements: ndarray

Get the molecules in the dataset.

Returns:

mols – Removed molecules in the dataset.

Return type:

np.ndarray

save_features(path: str = 'features.csv') → None[source]

Save the features to a csv file. :param path: Path to save the csv file. :type path: str

select(*args, inplace=False, **kwargs)

Method to make inplace.

Parameters:

  • self (object) – Object to apply the method to.

  • args (list) – Arguments to pass to the method.

  • inplace (bool) – Whether to apply the method inplace.

  • kwargs (dict) – Keyword arguments to pass to the method.

Returns:

result – Result of the method.

Return type:

object

select_features_by_index(*args, inplace=False, **kwargs)

Method to make inplace.

Parameters:

  • self (object) – Object to apply the method to.

  • args (list) – Arguments to pass to the method.

  • inplace (bool) – Whether to apply the method inplace.

  • kwargs (dict) – Keyword arguments to pass to the method.

Returns:

result – Result of the method.

Return type:

object

select_features_by_name(*args, inplace=False, **kwargs)

Method to make inplace.

Parameters:

  • self (object) – Object to apply the method to.

  • args (list) – Arguments to pass to the method.

  • inplace (bool) – Whether to apply the method inplace.

  • kwargs (dict) – Keyword arguments to pass to the method.

Returns:

result – Result of the method.

Return type:

object

select_to_split(indexes: ndarray | List[int]) → SmilesDataset[source]

Select elements with specific indexes to split the dataset :param indexes: The indexes of the elements to split the dataset. :type indexes: Union[np.ndarray, List[int]]

Returns:

The dataset with the selected elements.

Return type:

SmilesDataset

property smiles: ndarray

Get the SMILES strings of the molecules in the dataset. :returns: SMILES strings of the molecules in the dataset. :rtype: np.ndarray

to_csv(path: str, **kwargs) → None[source]

Save the dataset to a csv file. :param path: Path to save the csv file. :type path: str

to_dataframe()[source]

Convert data into dataframe

to_sdf(path: str) → None[source]

Save the dataset to a sdf file. :param path: Path to save the sdf file. :type path: str

property y: ndarray

Get the labels of the molecules in the dataset. :returns: Labels of the molecules in the dataset. :rtype: np.ndarray

Module contents