Update to include SELFIES Tokenizer & Vocabs

[20 Sept 2025]
- Add basic SELFIES tokenizer function
- Upload both core and tailed SELFIES vocab
- Update README to include SELFIES evals

CHANGELOG

@@ -0,0 +1,4 @@
+[20 Sept 2025]
+- Add basic SELFIES tokenizer function
+- Upload both core and tailed SELFIES vocab
+- Update README to include SELFIES evals

FastChemTokenizer.py

@@ -302,6 +302,305 @@ class FastChemTokenizer:
 
         print(f"✅ Tokenizer vocab saved to: {vocab_file}")
 
+    # Load from pretrained directory
+    @classmethod
+    def from_pretrained(cls, pretrained_directory: str, model_max_length=512):
+        """
+        Load tokenizer from directory containing `vocab.json`.
+        """
+        vocab_file = os.path.join(pretrained_directory, "vocab.json")
+
+        if not os.path.exists(vocab_file):
+            raise FileNotFoundError(f"Vocab file not found: {vocab_file}")
+
+        with open(vocab_file, "r", encoding="utf-8") as f:
+            token_to_id = json.load(f)
+
+        # Convert keys to str (JSON loads as str anyway), values to int
+        token_to_id = {str(k): int(v) for k, v in token_to_id.items()}
+
+        return cls(token_to_id=token_to_id, model_max_length=model_max_length)
+
+class FastChemTokenizerSelfies:
+    def __init__(self, token_to_id, model_max_length=512):
+        self.token_to_id = token_to_id
+        self.id_to_token = {v: k for k, v in token_to_id.items()}
+        # No more self.token_set — replaced by trie
+        self.model_max_length = model_max_length
+
+        # Precompute max token length for possible use & clarity
+        self.max_token_len = max(len(t) for t in token_to_id.keys())
+
+        # Build trie for fast longest-match lookup
+        self.trie_root = self._build_trie(token_to_id)
+
+        # Validate required special tokens
+        required_special_tokens = ["<s>", "</s>", "<pad>", "<unk>", "<mask>"]
+        for tok in required_special_tokens:
+            if tok not in token_to_id:
+                raise KeyError(f"Required special token '{tok}' not found in vocab.")
+
+        # Special token IDs
+        self.bos_token_id = token_to_id["<s>"]
+        self.eos_token_id = token_to_id["</s>"]
+        self.pad_token_id = token_to_id["<pad>"]
+        self.unk_token_id = token_to_id["<unk>"]
+        self.mask_token_id = token_to_id["<mask>"]
+
+        # Special tokens for convenience
+        self.bos_token = "<s>"
+        self.eos_token = "</s>"
+        self.pad_token = "<pad>"
+        self.unk_token = "<unk>"
+        self.mask_token = "<mask>"
+
+    def _build_trie(self, token_to_id):
+        root = TrieNode()
+        for token, tid in token_to_id.items():
+            node = root
+            for char in token:
+                if char not in node.children:
+                    node.children[char] = TrieNode()
+                node = node.children[char]
+            node.token_id = tid
+        return root
+
+    def __len__(self):
+        """Return vocab size — REQUIRED for HF compatibility."""
+        return len(self.token_to_id)
+
+    def __call__(self, text: Union[str, List[str]], text_pair: Optional[Union[str, List[str]]] = None, **kwargs) -> BatchEncoding:
+        if isinstance(text, list):
+            batch = [(t, p) if p is not None else t for t, p in zip(text, text_pair)] if text_pair else text
+            return self.batch_encode_plus(batch, **kwargs)
+        else:
+            return self.encode_plus(text=text, text_pair=text_pair, **kwargs)
+
+    @lru_cache(maxsize=10000)
+    def _cached_encode_str(self, s: str) -> Tuple[int, ...]:
+        return tuple(self._encode_core(s))
+
+    def _encode_core(self, text: str) -> List[int]:
+        """Core encoding logic using Trie — skips whitespace if not part of a token."""
+        result_ids = []
+        i = 0
+        n = len(text)
+
+        while i < n:
+            if text[i].isspace():  # ← Skip whitespace unless part of a token
+                i += 1
+                continue
+
+            node = self.trie_root
+            j = i
+            last_match_id = None
+            last_match_end = i
+
+            # Traverse trie while characters match
+            while j < n and text[j] in node.children:
+                node = node.children[text[j]]
+                j += 1
+                if node.token_id is not None:
+                    last_match_id = node.token_id
+                    last_match_end = j
+
+            if last_match_id is not None:
+                result_ids.append(last_match_id)
+                i = last_match_end
+            else:
+                # Fallback: encode single char
+                result_ids.append(self.token_to_id.get(text[i], self.unk_token_id))
+                i += 1
+
+        return result_ids
+
+
+    def encode(self, text: str) -> List[int]:
+        """Public encode method — strips input and uses cache."""
+        return list(self._cached_encode_str(text.strip()))
+
+    def decode(self, token_ids: Union[List[int], torch.Tensor], skip_special_tokens: bool = False) -> str:
+        if isinstance(token_ids, torch.Tensor):
+            token_ids = token_ids.tolist()
+
+        if skip_special_tokens:
+            special_ids = {
+                self.bos_token_id,
+                self.eos_token_id,
+                self.pad_token_id,
+                self.mask_token_id,
+            }
+        else:
+            special_ids = set()
+
+        tokens = []
+        for tid in token_ids:
+            if tid in special_ids:
+                continue
+            token = self.id_to_token.get(tid, self.unk_token)
+            tokens.append(token)
+
+        # ✅ Join with SPACE between tokens — this reconstructs original format
+        return " ".join(tokens)
+
+    def decode_with_trace(self, token_ids: List[int]) -> None:
+        print(f"\n🔍 Decoding {len(token_ids)} tokens:")
+        for i, tid in enumerate(token_ids):
+            token = self.id_to_token.get(tid, self.unk_token)
+            print(f"  [{i:03d}] ID={tid:5d} → '{token}'")
+
+    def convert_ids_to_tokens(self, ids: List[int]) -> List[str]:
+        return [self.id_to_token.get(i, self.unk_token) for i in ids]
+
+    def convert_tokens_to_ids(self, tokens: List[str]) -> List[int]:
+        return [self.token_to_id.get(t, self.unk_token_id) for t in tokens]
+
+    def encode_plus(
+        self,
+        text: str,
+        text_pair: Optional[str] = None,
+        add_special_tokens: bool = True,
+        padding: Union[bool, str] = False,
+        truncation: bool = False,
+        max_length: Optional[int] = None,
+        return_tensors: Optional[str] = None,
+        return_attention_mask: bool = True,
+        return_token_type_ids: bool = True,
+    ) -> BatchEncoding:
+        if max_length is None:
+            max_length = self.model_max_length
+
+        ids_a = self.encode(text)
+
+        if text_pair is not None:
+            ids_b = self.encode(text_pair)
+        else:
+            ids_b = None
+
+        input_ids = []
+        token_type_ids = []
+
+        if add_special_tokens:
+            input_ids.append(self.bos_token_id)
+            token_type_ids.append(0)
+            if ids_b is not None:
+                input_ids.extend(ids_a)
+                token_type_ids.extend([0] * len(ids_a))
+                input_ids.append(self.eos_token_id)
+                token_type_ids.append(0)
+
+                input_ids.extend(ids_b)
+                token_type_ids.extend([1] * len(ids_b))
+                input_ids.append(self.eos_token_id)
+                token_type_ids.append(1)
+            else:
+                input_ids.extend(ids_a)
+                token_type_ids.extend([0] * len(ids_a))
+                input_ids.append(self.eos_token_id)
+                token_type_ids.append(0)
+        else:
+            input_ids = ids_a
+            token_type_ids = [0] * len(input_ids)
+            if ids_b is not None:
+                input_ids.extend(ids_b)
+                token_type_ids.extend([1] * len(ids_b))
+
+        if truncation and len(input_ids) > max_length:
+            input_ids = input_ids[:max_length]
+            token_type_ids = token_type_ids[:max_length]
+
+        if padding:
+            pad_len = max_length - len(input_ids)
+            if pad_len > 0:
+                input_ids.extend([self.pad_token_id] * pad_len)
+                token_type_ids.extend([0] * pad_len)
+
+        attention_mask = [1 if tid != self.pad_token_id else 0 for tid in input_ids]
+
+        encoded_dict = {
+            "input_ids": input_ids,
+            "attention_mask": attention_mask,
+        }
+        if return_token_type_ids:
+            encoded_dict["token_type_ids"] = token_type_ids
+
+        if return_tensors == "pt":
+            output = {}
+            for k, v in encoded_dict.items():
+                tensor = torch.tensor(v, dtype=torch.long)  #  Fixed: use torch.tensor, not as_tensor
+                if tensor.ndim == 1:
+                    tensor = tensor.unsqueeze(0)
+                output[k] = tensor
+        else:
+            output = encoded_dict
+
+        return BatchEncoding(output, tensor_type=return_tensors)
+
+    def batch_encode_plus(
+        self,
+        batch_text_or_text_pairs: List[Union[str, Tuple[str, str]]],
+        **kwargs
+    ) -> BatchEncoding:
+        all_input_ids = []
+        all_attention_masks = []
+        all_token_type_ids = []
+
+        for item in batch_text_or_text_pairs:
+            if isinstance(item, tuple):
+                text, text_pair = item
+            else:
+                text, text_pair = item, None
+
+            encoded = self.encode_plus(
+                text=text,
+                text_pair=text_pair,
+                **kwargs
+            )
+            all_input_ids.append(encoded["input_ids"])
+            all_attention_masks.append(encoded["attention_mask"])
+            if "token_type_ids" in encoded:
+                all_token_type_ids.append(encoded["token_type_ids"])
+
+        batched = {
+            "input_ids": all_input_ids,
+            "attention_mask": all_attention_masks,
+        }
+        if all_token_type_ids:
+            batched["token_type_ids"] = all_token_type_ids
+
+        if kwargs.get("return_tensors") == "pt":
+            def to_tensor_list(lst):
+                # Use torch.tensor for safety — avoids "copy construct from tensor" warning
+                return [torch.tensor(item, dtype=torch.long) for item in lst]
+
+            batched = {
+                k: torch.nn.utils.rnn.pad_sequence(
+                    to_tensor_list(v),
+                    batch_first=True,
+                    padding_value=self.pad_token_id if k == "input_ids" else 0
+                )
+                for k, v in batched.items()
+            }
+
+        return BatchEncoding(batched, tensor_type=kwargs.get("return_tensors"))
+
+    # Save vocab to directory
+    def save_pretrained(self, save_directory: str):
+        """
+        Save tokenizer vocab as `vocab.json` in target directory.
+        Mimics Hugging Face convention.
+        """
+        if not os.path.exists(save_directory):
+            os.makedirs(save_directory)
+
+        vocab_file = os.path.join(save_directory, "vocab.json")
+
+        # Keys are strings, values are ints — JSON-safe
+        with open(vocab_file, "w", encoding="utf-8") as f:
+            json.dump(self.token_to_id, f, ensure_ascii=False, indent=2)
+
+        print(f"✅ Tokenizer vocab saved to: {vocab_file}")
+
     # Load from pretrained directory
     @classmethod
     def from_pretrained(cls, pretrained_directory: str, model_max_length=512):

selftok_core/vocab.json

@@ -0,0 +1,784 @@
+{
+  "<s>": 0,
+  "</s>": 1,
+  "<pad>": 2,
+  "<unk>": 3,
+  "<mask>": 4,
+  "[C] [C] [C@H1] [Branch1] [C] [C] [C@H1] [Branch2]": 5,
+  "[C] [S] [=Branch1] [C] [=O] [=Branch1] [C] [=O]": 6,
+  "[C] [C] [Branch1] [C] [C] [C] [C@H1] [Branch2]": 7,
+  "[C] [O] [C] [=C] [C] [=C] [Branch2] [Branch1]": 8,
+  "[O] [=C] [Branch2] [Ring1] [#Branch1] [N] [C]": 9,
+  "[O] [=C] [Branch1] [C] [O] [C] [Branch1] [C]": 10,
+  "[O] [=C] [Branch2] [Ring1] [Branch1] [N] [C]": 11,
+  "[C] [O] [C] [=C] [C] [=C] [Branch2] [Ring2]": 12,
+  "[C] [C] [Branch1] [C] [C] [Branch1] [C] [C]": 13,
+  "[C] [O] [C] [=C] [C] [=C] [Branch2] [Ring1]": 14,
+  "[O] [=C] [Branch1] [Ring2] [O] [C] [C] [C]": 15,
+  "[O] [=C] [Branch2] [Ring1] [Ring2] [N] [C]": 16,
+  "[C] [C] [Branch1] [C] [C] [C@H1] [Branch2]": 17,
+  "[O] [=C] [Branch1] [Ring1] [O] [C] [C] [C]": 18,
+  "[O] [=C] [Branch2] [Ring1] [Ring1] [N] [C]": 19,
+  "[C] [C] [N] [Branch1] [Ring1] [C] [C] [C]": 20,
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+  "[N] [#C] [C] [=C] [C] [=C] [C] [Branch2]": 23,
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+  "[C] [C] [=C] [C] [Branch1] [C] [C] [=C]": 37,
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+  "[C] [C] [Branch1] [C] [C] [=C] [C] [C]": 50,
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+  "[O] [=C] [Branch1] [#Branch2] [N] [C]": 52,
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+  "[C] [N] [Branch1] [C] [C] [C] [C] [C]": 54,
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+  "[O] [=C] [Branch1] [#C] [N] [C]": 123,
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+}

selftok_wtails/vocab.json

@@ -0,0 +1,1164 @@
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+  "[\\3H]": 1159,
+  "[S-1]": 1160,
+  "[/C@@H1]": 1161
+}