hjxdl 0.0.1__py3-none-any.whl

hdl/features/utils/utils.py

@@ -0,0 +1,111 @@
+import csv
+import os
+import pickle
+from typing import List
+
+import numpy as np
+import pandas as pd
+from rdkit.Chem import PandasTools
+
+
+SMI_REGEX_PATTERN = \
+    r"""(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.\|=|#|-|\+|\\|\/|:|~|@|\?|>>?|\*|\$|\%[0-9]{2}|[0-9])"""
+
+
+def save_features(path: str, features: List[np.ndarray]) -> None:
+    """
+    Saves features to a compressed :code:`.npz` file with array name "features".
+
+    :param path: Path to a :code:`.npz` file where the features will be saved.
+    :param features: A list of 1D numpy arrays containing the features for molecules.
+    """
+    np.savez_compressed(path, features=features)
+
+
+def load_features(path: str) -> np.ndarray:
+    """
+    Loads features saved in a variety of formats.
+
+    Supported formats:
+
+    * :code:`.npz` compressed (assumes features are saved with name "features")
+    * .npy
+    * :code:`.csv` / :code:`.txt` (assumes comma-separated features with a header and with one line per molecule)
+    * :code:`.pkl` / :code:`.pckl` / :code:`.pickle` containing a sparse numpy array
+
+    .. note::
+
+       All formats assume that the SMILES loaded elsewhere in the code are in the same
+       order as the features loaded here.
+
+    :param path: Path to a file containing features.
+    :return: A 2D numpy array of size :code:`(num_molecules, features_size)` containing the features.
+    """
+    extension = os.path.splitext(path)[1]
+
+    if extension == '.npz':
+        features = np.load(path)['features']
+    elif extension == '.npy':
+        features = np.load(path)
+    elif extension in ['.csv', '.txt']:
+        with open(path) as f:
+            reader = csv.reader(f)
+            next(reader)  # skip header
+            features = np.array([[float(value) for value in row] for row in reader])
+    elif extension in ['.pkl', '.pckl', '.pickle']:
+        with open(path, 'rb') as f:
+            features = np.array([np.squeeze(np.array(feat.todense())) for feat in pickle.load(f)])
+    else:
+        raise ValueError(f'Features path extension {extension} not supported.')
+
+    return features
+
+
+def load_valid_atom_or_bond_features(path: str, smiles: List[str]) -> List[np.ndarray]:
+    """
+    Loads features saved in a variety of formats.
+
+    Supported formats:
+
+    * :code:`.npz` descriptors are saved as 2D array for each molecule in the order of that in the data.csv
+    * :code:`.pkl` / :code:`.pckl` / :code:`.pickle` containing a pandas dataframe with smiles as index and numpy array of descriptors as columns
+    * :code:'.sdf' containing all mol blocks with descriptors as entries
+
+    :param path: Path to file containing atomwise features.
+    :return: A list of 2D array.
+    """
+
+    extension = os.path.splitext(path)[1]
+
+    if extension == '.npz':
+        container = np.load(path)
+        features = [container[key] for key in container]
+
+    elif extension in ['.pkl', '.pckl', '.pickle']:
+        features_df = pd.read_pickle(path)
+        if features_df.iloc[0, 0].ndim == 1:
+            features = features_df.apply(lambda x: np.stack(x.tolist(), axis=1), axis=1).tolist()
+        elif features_df.iloc[0, 0].ndim == 2:
+            features = features_df.apply(lambda x: np.concatenate(x.tolist(), axis=1), axis=1).tolist()
+        else:
+            raise ValueError(f'Atom/bond descriptors input {path} format not supported')
+
+    elif extension == '.sdf':
+        features_df = PandasTools.LoadSDF(path).drop(['ID', 'ROMol'], axis=1).set_index('SMILES')
+
+        features_df = features_df[~features_df.index.duplicated()]
+
+        # locate atomic descriptors columns
+        features_df = features_df.iloc[:, features_df.iloc[0, :].apply(lambda x: isinstance(x, str) and ',' in x).to_list()]
+        features_df = features_df.reindex(smiles)
+        if features_df.isnull().any().any():
+            raise ValueError('Invalid custom atomic descriptors file, Nan found in data')
+
+        features_df = features_df.applymap(lambda x: np.array(x.replace('\r', '').replace('\n', '').split(',')).astype(float))
+
+        features = features_df.apply(lambda x: np.stack(x.tolist(), axis=1), axis=1).tolist()
+
+    else:
+        raise ValueError(f'Extension "{extension}" is not supported.')
+
+    return features

hdl/layers/general/gp.py

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+# import torch
+import gpytorch
+
+
+class ExactGPModel(gpytorch.models.ExactGP):
+    def __init__(self, train_x, train_y, likelihood):
+        super(ExactGPModel, self).__init__(train_x, train_y, likelihood)
+        self.mean_module = gpytorch.means.ConstantMean()
+        self.covar_module = gpytorch.kernels.ScaleKernel(gpytorch.kernels.RBFKernel())
+
+    def forward(self, x):
+        mean_x = self.mean_module(x)
+        covar_x = self.covar_module(x)
+        return gpytorch.distributions.MultivariateNormal(mean_x, covar_x)