DECIMER package

Submodules

DECIMER.decimer module

class DECIMER.decimer.KerasCompatibilityUnpickler(file, *, fix_imports=True, encoding='ASCII', errors='strict', buffers=())

Bases: Unpickler

Custom unpickler to handle Keras 2.x tokenizers in Keras 3 environment.

This handles the module path changes between Keras 2 and Keras 3: - keras.preprocessing.text -> tensorflow.keras.preprocessing.text

find_class(module, name)

Return an object from a specified module.

If necessary, the module will be imported. Subclasses may override this method (e.g. to restrict unpickling of arbitrary classes and functions).

This method is called whenever a class or a function object is needed. Both arguments passed are str objects.

DECIMER.decimer.detokenize_output(predicted_array)

This function takes the predicted tokens from the DECIMER model and returns the decoded SMILES string.

Return type:

str

Args:

predicted_array (int): Predicted tokens from DECIMER

Returns:

(str): SMILES representation of the molecule

DECIMER.decimer.detokenize_output_add_confidence(predicted_array, confidence_array)

This function takes the predicted array of tokens as well as the confidence values returned by the Transformer Decoder and returns a list of tuples that contain each token of the predicted SMILES string and the confidence value.

Return type:

List[Tuple[str, float]]

Args:

predicted_array (tf.Tensor): Transformer Decoder output array (predicted tokens)

Returns:

str: SMILES string

DECIMER.decimer.get_models(model_urls)

Download and load models from the provided URLs.

This function downloads models from the provided URLs to a default location, then loads tokenizers and TensorFlow saved models.

Args:

model_urls (dict): A dictionary containing model names as keys and their corresponding URLs as values.

Returns:

tuple: A tuple containing loaded tokenizer and TensorFlow saved models.

• tokenizer (object): Tokenizer for DECIMER model.

• DECIMER_V2 (tf.saved_model): TensorFlow saved model for DECIMER.

• DECIMER_Hand_drawn (tf.saved_model): TensorFlow saved model for DECIMER HandDrawn.

DECIMER.decimer.load_tokenizer(tokenizer_path)

Load tokenizer with Keras 2/3 compatibility.

Return type:

object

Args:

tokenizer_path (str): Path to the pickled tokenizer file

Returns:

tokenizer: Loaded tokenizer object

DECIMER.decimer.main()

This function take the path of the image as user input and returns the predicted SMILES as output in CLI.

Agrs:

str: image_path

Returns:

str: predicted SMILES

DECIMER.decimer.predict_SMILES(image_input, confidence=False, hand_drawn=False)

Predicts SMILES representation of a molecule depicted in the given image.

Return type:

str

Args:

image_input (str or np.ndarray): Path of chemical structure depiction image or a numpy array representing the image. confidence (bool): Flag to indicate whether to return confidence values along with SMILES prediction. hand_drawn (bool): Flag to indicate whether the molecule in the image is hand-drawn.

Returns:

str: SMILES representation of the molecule in the input image, optionally with confidence values.

DECIMER.config module