"""Custom Tokenization classes.""" import collections import json import os import re from typing import List, Optional, Tuple, Union from transformers.tokenization_utils import PreTrainedTokenizer from transformers.utils import logging logger = logging.get_logger(__name__) VOCAB_FILES_NAMES = {'vocab_file': 'vocab.json'} PRETRAINED_VOCAB_FILES_MAP = { 'qm9': { 'vocab_file': { 'yairschiff/qm9-tokenizer': 'https://huggingface.co/yairschiff/qm9-tokenizer/resolve/main/vocab.json' } }, 'zinc250k': { 'vocab_file': { 'yairschiff/zinc250k-tokenizer': 'https://huggingface.co/yairschiff/zinc250k-tokenizer/resolve/main/vocab.json' } } } class SMILESTokenizer(PreTrainedTokenizer): r""" Construct a tokenizer for SMILES datasets. Based on regex. This tokenizer inherits from [`PreTrainedTokenizer`] which contains most of the main methods. Users should refer to this superclass for more information regarding those methods. Adapted from: https://huggingface.co/ibm/MoLFormer-XL-both-10pct Args: vocab_file (`str`): File containing the vocabulary. unk_token (`str`, *optional*, defaults to `""`): The unknown token. A token not in the vocabulary cannot be converted to an ID and is set to be this token instead. sep_token (`str`, *optional*, defaults to `""`): The separator token, which is used when building a sequence from multiple sequences, e.g., two sequences for sequence classification or for a text and a question for question answering. It is also used as the last token of a sequence built with special tokens. pad_token (`str`, *optional*, defaults to `""`): The token used for padding, for example, when batching sequences of different lengths. cls_token (`str`, *optional*, defaults to `""`): The classifier token which is used when doing sequence classification (classification of the whole sequence instead of per-token classification). It is the first token of the sequence when built with special tokens. mask_token (`str`, *optional*, defaults to `""`): The token used for masking values. This is the token used when training this model with masked language modeling. This is the token, which the model will try to predict. """ vocab_files_names = VOCAB_FILES_NAMES model_input_names = ["input_ids", "attention_mask"] def __init__( self, vocab_file, unk_token='', sep_token='', pad_token='', cls_token='', mask_token='', **kwargs, ): if not os.path.isfile(vocab_file): raise ValueError( "Can't find a vocabulary file at path" f"'{vocab_file}'." ) with open(vocab_file, encoding="utf-8") as vocab_handle: vocab_from_file = json.load(vocab_handle) # Re-index to account for special tokens self.vocab = { cls_token: 0, sep_token: 1, mask_token: 2, pad_token: 3, unk_token: 4, **{k: v + 5 for k, v in vocab_from_file.items()} } self.ids_to_tokens = collections.OrderedDict( [(ids, tok) for tok, ids in self.vocab.items()]) # Regex pattern taken from: # https://github.com/pschwllr/MolecularTransformer self.pattern = ( r"(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|#|-|\+|\\|\/|:|~|@|\?|>|\*|\$|\%[0-9]{2}|[0-9])" ) self.regex_tokenizer = re.compile(self.pattern) super().__init__( unk_token=unk_token, sep_token=sep_token, pad_token=pad_token, cls_token=cls_token, mask_token=mask_token, **kwargs, ) @property def vocab_size(self): return len(self.vocab) def get_vocab(self): return dict(self.vocab, **self.added_tokens_encoder) def _tokenize(self, text, **kwargs): split_tokens = self.regex_tokenizer.findall(text) return split_tokens def _convert_token_to_id(self, token): """Converts token (str) in an id using the vocab.""" return self.vocab.get(token, self.vocab.get(self.unk_token)) def _convert_id_to_token(self, index): """Converts index (integer) in a token (str) using the vocab.""" return self.ids_to_tokens.get(index, self.unk_token) def convert_tokens_to_string(self, tokens): """Converts sequence of tokens (string) in a single string.""" out_string = "".join(tokens).strip() return out_string # Copied from transformers.models.bert.tokenization_bert.BertTokenizer.build_inputs_with_special_tokens def build_inputs_with_special_tokens( self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None ) -> List[int]: """ Build model inputs from a sequence or a pair of sequences for sequence classification tasks by concatenating and adding special tokens. A BERT sequence has the following format: - single sequence: `[CLS] X [SEP]` - pair of sequences: `[CLS] A [SEP] B [SEP]` Args: token_ids_0 (`List[int]`): List of IDs to which the special tokens will be added. token_ids_1 (`List[int]`, *optional*): Optional second list of IDs for sequence pairs. Returns: `List[int]`: List of [input IDs](../glossary#input-ids) with the appropriate special tokens. """ if token_ids_1 is None: return [self.cls_token_id] + token_ids_0 + [self.sep_token_id] cls = [self.cls_token_id] sep = [self.sep_token_id] return cls + token_ids_0 + sep + token_ids_1 + sep # Copied from transformers.models.bert.tokenization_bert.BertTokenizer.get_special_tokens_mask def get_special_tokens_mask( self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None, already_has_special_tokens: bool = False ) -> List[int]: """ Retrieve sequence ids from a token list that has no special tokens added. This method is called when adding special tokens using the tokenizer `prepare_for_model` method. Args: token_ids_0 (`List[int]`): List of IDs. token_ids_1 (`List[int]`, *optional*): Optional second list of IDs for sequence pairs. already_has_special_tokens (`bool`, *optional*, defaults to `False`): Whether the token list is already formatted with special tokens for the model. Returns: `List[int]`: A list of integers in the range [0, 1]: 1 for a special token, 0 for a sequence token. """ if already_has_special_tokens: return super().get_special_tokens_mask( token_ids_0=token_ids_0, token_ids_1=token_ids_1, already_has_special_tokens=True ) if token_ids_1 is not None: return [1] + ([0] * len(token_ids_0)) + [1] + ([0] * len(token_ids_1)) + [1] return [1] + ([0] * len(token_ids_0)) + [1] # Copied from transformers.models.bert.tokenization_bert.BertTokenizer.create_token_type_ids_from_sequences def create_token_type_ids_from_sequences( self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None ) -> List[int]: """ Create a mask from the two sequences passed to be used in a sequence-pair classification task. A BERT sequence pair mask has the following format: ``` 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 | first sequence | second sequence | ``` If `token_ids_1` is `None`, this method only returns the first portion of the mask (0s). Args: token_ids_0 (`List[int]`): List of IDs. token_ids_1 (`List[int]`, *optional*): Optional second list of IDs for sequence pairs. Returns: `List[int]`: List of [token type IDs](../glossary#token-type-ids) according to the given sequence(s). """ sep = [self.sep_token_id] cls = [self.cls_token_id] if token_ids_1 is None: return len(cls + token_ids_0 + sep) * [0] return len(cls + token_ids_0 + sep) * [0] + len(token_ids_1 + sep) * [1] def save_vocabulary( self, save_directory: str, filename_prefix: Optional[str] = None ) -> Union[Tuple[str], None]: if not os.path.isdir(save_directory): logger.error( f"Vocabulary path ({save_directory}) should" "be a directory.") return None vocab_file = os.path.join( save_directory, (filename_prefix + "-" if filename_prefix else "") + VOCAB_FILES_NAMES["vocab_file"] ) with open(vocab_file, "w", encoding="utf-8") as f: f.write( json.dumps( self.vocab, indent=2, sort_keys=True, ensure_ascii=False ) + "\n") return (vocab_file,) class QM9Tokenizer(SMILESTokenizer): pretrained_vocab_files_map = PRETRAINED_VOCAB_FILES_MAP['qm9'] class Zinc250kTokenizer(SMILESTokenizer): pretrained_vocab_files_map = PRETRAINED_VOCAB_FILES_MAP['zinc250k']