add smiles canonicalisation, update tokens.txt

chebai/preprocessing/bin/smiles_token/tokens.txt

@@ -819,3 +819,168 @@ p
 [16N]
 [17N]
 [14N]
+[Pb+2]
+[AlH4-]
+[BH4-]
+[Pt-2]
+[Cl+2]
+[I+3]
+[Br+2]
+[Cl+3]
+[Os-2]
+[Cr-2]
+[Hg-2]
+[PH]
+[Br+3]
+[I+2]
+[AsH2]
+[SH]
+[W-2]
+[Cd-2]
+[Ir-2]
+[Ru-2]
+[Rh-2]
+[Ag-2]
+[Be-2]
+[TeH2+]
+[13c]
+[13cH]
+[PH4]
+[AsH4]
+[As-2]
+[SbH3+]
+[SbH4]
+[BiH3]
+[BH3-]
+[GeH3]
+[GeH2]
+[SiH2-]
+[SiH2+]
+[SnH2]
+[SnH3]
+[SnH]
+[PbH]
+[PbH3]
+[Al-2]
+[B+2]
+[N+2]
+[SbH]
+[SbH2]
+[InH2]
+[GaH2]
+[TlH2]
+[Au+2]
+[sH+]
+[Hg+2]
+[Si-2]
+[Sn-2]
+[Pb-2]
+[AsH3]
+[Cr+2]
+[Ag+2]
+[V-2]
+[Ce-2]
+[13C@]
+[*+2]
+[He+2]
+[4He+2]
+[3He+2]
+[Eu+2]
+[Ge+2]
+[Os+2]
+[Y+2]
+[Gd+2]
+[La+2]
+[Se+2]
+[NH-2]
+[TeH2-]
+[AlH3-]
+[SbH3-]
+[AsH3-]
+[BiH3-]
+[PH3-]
+[CH2-2]
+[AsH4+]
+[AlH3+]
+[BiH3+]
+[FH+]
+[CH3+]
+[Te-2]
+[OH]
+[CH3]
+[18OH2]
+[OH3+]
+[OH4+2]
+[SH3]
+[SH3+]
+[SH3-]
+[SH4]
+[SeH2]
+[SeH-]
+[SeH3+]
+[SeH3-]
+[SeH3]
+[SeH+]
+[TeH2]
+[TeH-]
+[TeH3-]
+[TeH3+]
+[TeH+]
+[TeH3]
+[TeH4]
+[PoH2]
+[NH2]
+[NH+2]
+[PH5]
+[PH4+]
+[PH-2]
+[PH4-]
+[PH+2]
+[AsH2+]
+[AsH2-]
+[AsH+2]
+[AsH-2]
+[AsH5]
+[SbH3]
+[SbH4+]
+[SbH5]
+[BiH4+]
+[BiH5]
+[BiH4-]
+[BH2]
+[BH2+]
+[BH2-]
+[BH-2]
+[BH+2]
+[GeH4]
+[GeH3+]
+[GeH3-]
+[SiH3-]
+[SiH3+]
+[SiH+]
+[SiH4]
+[HeH+2]
+[HeH+]
+[AlH]
+[AlH+]
+[SnH4]
+[SnH3-]
+[SnH3+]
+[PbH4]
+[PbH3-]
+[PbH3+]
+[BeH4-2]
+[BeH]
+[BeH+]
+[BeH-]
+[BeH2]
+[AtH]
+[InH3]
+[GaH3]
+[TlH3]
+[IH3]
+[FeH6-4]
+[FH2+]
+[ClH2+]
+[BrH2+]
+[IH2+]

chebai/preprocessing/reader.py

@@ -8,6 +8,7 @@
 import deepsmiles
 import selfies as sf
 from pysmiles.read_smiles import _tokenize
+from rdkit import Chem
 from transformers import RobertaTokenizerFast
 
 from chebai.preprocessing.collate import DefaultCollator, RaggedCollator
@@ -176,21 +177,35 @@ class ChemDataReader(TokenIndexerReader):
 
     COLLATOR = RaggedCollator
 
+    def __init__(self, canonicalize_smiles=True, *args, **kwargs) -> None:
+        super().__init__(*args, **kwargs)
+        self.canonicalize_smiles = canonicalize_smiles
+        print(f"Using SMILES canonicalization: {self.canonicalize_smiles}")
+
     @classmethod
     def name(cls) -> str:
         """Returns the name of the data reader."""
         return "smiles_token"
 
     def _read_data(self, raw_data: str) -> List[int]:
         """
-        Reads and tokenizes raw SMILES data into a list of token indices.
+        Reads and tokenizes raw SMILES data into a list of token indices. Canonicalizes the SMILES string using RDKit.
 
         Args:
             raw_data (str): The raw SMILES string to be tokenized.
 
         Returns:
             List[int]: A list of integers representing the indices of the SMILES tokens.
         """
+        if self.canonicalize_smiles:
+            try:
+                mol = Chem.MolFromSmiles(raw_data.strip())
+                if mol is not None:
+                    raw_data = Chem.MolToSmiles(mol, canonical=True)
+            except Exception as e:
+                print(f"RDKit failed to process {raw_data}")
+                print(f"\t{e}")
+
         return [self._get_token_index(v[1]) for v in _tokenize(raw_data)]