diff --git a/.gitattributes b/.gitattributes index 4d914157d4ba0f48ef8d60869c341e01f414eca5..4455eabc3b9fb9a392f501ea2147f75a01eb7d41 100644 --- a/.gitattributes +++ b/.gitattributes @@ -33,6 +33,7 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text *.xz filter=lfs diff=lfs merge=lfs -text *.zip filter=lfs diff=lfs merge=lfs -text *.zst filter=lfs diff=lfs merge=lfs -text +*.zstd filter=lfs diff=lfs merge=lfs -text *tfevents* filter=lfs diff=lfs merge=lfs -text # Audio files - uncompressed *.pcm filter=lfs diff=lfs merge=lfs -text diff --git a/Kaggle/SMILES_Big_Data_Set.parquet b/Kaggle/SMILES_Big_Data_Set.parquet new file mode 100644 index 0000000000000000000000000000000000000000..46f5114796a981997060205c86705e8bc18d4d1b --- /dev/null +++ b/Kaggle/SMILES_Big_Data_Set.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7e541cbcfee7bae68bfebc29d9f80cb1e13198da193c79b73c9214e1a2388349 +size 415328 diff --git a/Kaggle/SMILES_Big_Data_Set.smi b/Kaggle/SMILES_Big_Data_Set.smi deleted file mode 100644 index 6160354d144026adfe9a14d361172f7bd00caf86..0000000000000000000000000000000000000000 --- a/Kaggle/SMILES_Big_Data_Set.smi +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:44a5ff2dbed46be2e4fd12685d7521a0805cff0854d1291829b946250c8254ba -size 536980 diff --git a/Kaggle/chembl_22_clean_1576904_sorted_std_final.parquet b/Kaggle/chembl_22_clean_1576904_sorted_std_final.parquet new file mode 100644 index 0000000000000000000000000000000000000000..b53493bf7c11e34a3fe7f32b8c860f637c929d0f --- /dev/null +++ b/Kaggle/chembl_22_clean_1576904_sorted_std_final.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3c5db30612a3fbbf288c2d5c139fe7df7ce3d9ee906abb8e2a52fdbf459aa88a +size 60982380 diff --git a/Kaggle/chembl_22_clean_1576904_sorted_std_final.smi b/Kaggle/chembl_22_clean_1576904_sorted_std_final.smi deleted file mode 100644 index ddd44dc9b99830d0394264c42340b979acef99b8..0000000000000000000000000000000000000000 --- a/Kaggle/chembl_22_clean_1576904_sorted_std_final.smi +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:015f3edc65f0deff98b98b576bf69eacf5a619b63a2b62fbff0567ff4fe3be6d -size 81204947 diff --git a/Tokenizer.md b/Tokenizer.md new file mode 100644 index 0000000000000000000000000000000000000000..156ed4975f9906caea76352d7cd0b70b93516f6b --- /dev/null +++ b/Tokenizer.md @@ -0,0 +1,107 @@ +# SELFIES Tokenizer Documentation + +## Overview +This tokenizer is designed specifically for SELFIES (Self-Referencing Embedded Strings) chemical structure notation. It provides a simple mapping between SELFIES tokens and their corresponding IDs for machine learning applications. + +## File Format +The tokenizer configuration is stored in a JSON file with the following structure: +```json +{ + "vocab": { + "[UNK]": 0, + "[CLS]": 1, + "[SEP]": 2, + "[PAD]": 3, + "[MASK]": 4, + // ... chemical tokens ... + }, + "special_tokens": { + "unk_token": "[UNK]", + "cls_token": "[CLS]", + "sep_token": "[SEP]", + "pad_token": "[PAD]", + "mask_token": "[MASK]" + }, + "model_max_length": 512 +} +``` + +## Special Tokens +- `[UNK]`: Used for unknown tokens (ID: 0) +- `[CLS]`: Classification token, added at start of sequence (ID: 1) +- `[SEP]`: Separator token, added at end of sequence (ID: 2) +- `[PAD]`: Padding token (ID: 3) +- `[MASK]`: Masking token for masked language modeling (ID: 4) + +## Tokenization Process +Since SELFIES strings are already tokenized by design, the process is straightforward: + +1. Split the SELFIES string into tokens (they are naturally delimited by `[]`) +2. Convert each token to its corresponding ID using the vocab mapping +3. Add special tokens as needed ([CLS] at start, [SEP] at end) +4. Pad/truncate to model_max_length if necessary + +Example implementation: +```python +import re + +class SelfiesTokenizer: + def __init__(self, tokenizer_path): + with open(tokenizer_path, 'r') as f: + config = json.load(f) + self.vocab = config['vocab'] + self.special_tokens = config['special_tokens'] + self.max_length = config['model_max_length'] + # Create reverse mapping (id -> token) for decoding + self.id2token = {v: k for k, v in self.vocab.items()} + + def tokenize(self, selfies_string): + """Split SELFIES string into tokens""" + return re.findall(r'\[.*?\]', selfies_string) + + def convert_tokens_to_ids(self, tokens): + """Convert tokens to their IDs""" + return [self.vocab.get(token, self.vocab['[UNK]']) for token in tokens] + + def encode(self, selfies_string, add_special_tokens=True): + """Full encoding process""" + tokens = self.tokenize(selfies_string) + ids = self.convert_tokens_to_ids(tokens) + + if add_special_tokens: + ids = [self.vocab['[CLS]']] + ids + [self.vocab['[SEP]']] + + # Truncate or pad as needed + if len(ids) > self.max_length: + ids = ids[:self.max_length] + else: + ids.extend([self.vocab['[PAD]']] * (self.max_length - len(ids))) + + return ids + + def decode(self, ids): + """Convert IDs back to SELFIES string""" + tokens = [self.id2token[id] for id in ids] + # Remove special tokens + tokens = [t for t in tokens if t not in self.special_tokens.values()] + return ''.join(tokens) +``` + +## Usage Example +```python +# Initialize tokenizer +tokenizer = SelfiesTokenizer('tokenizer.json') + +# Encode a SELFIES string +selfies = '[C][=C][C][=C][O][H]' +ids = tokenizer.encode(selfies) + +# Decode back to SELFIES +decoded = tokenizer.decode(ids) +``` + +## Notes +- The tokenizer assumes well-formed SELFIES strings as input +- No additional preprocessing is needed since SELFIES tokens are already well-defined +- The vocab mapping preserves IDs from the original tokenizer where possible +- Maximum sequence length is set to 512 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+[\CH0] +[CH0] +[#CH1] +[/C@@H1] +[/C@H1] +[=CH1] +[\C@@H1] +[\C@H1] +[\CH1] +[C@@H1] +[C@H1] +[CH1] +[/CH1-1] +[=CH1+1] +[=CH1-1] +[CH1+1] +[CH1-1] +[=CH1-2] +[/CH2] +[=CH2] +[CH2] +[\CH2-1] +[CH2+1] +[CH2-1] +[CH2-2] +[CH3] +[CH3-1] +[CH4] +[/Cl] +[=Cl] +[\Cl] +[Cl] +[=Cl+1] +[=Cl-1] +[Cl+1] +[Cl-1] +[Cl+2] +[Cl-2] +[Cl+3] +[Cl-3] +[Cl-4] +[=ClH0] +[ClH0] +[ClH1] +[ClH1-2] +[ClH2] +[ClH2-3] +[ClH3-2] +[=Co] +[Co] +[Co+1] +[Co+10] +[Co+2] +[Co-2] +[Co+3] +[Co-3] +[Co+4] +[Co+5] +[Co+6] +[Co+7] +[Co+8] +[Co+9] +[CoH1+2] +[CoH2] +[CoH2+2] +[CoH2+3] +[CoH4] +[CoH4+2] +[CoH4+6] +[CoH4+7] +[CoH5] +[CoH5+8] +[CoH6] +[CoH6+9] +[#Cr] +[=Cr] +[Cr] +[Cr+1] +[Cr+2] +[Cr+3] +[Cr-3] +[Cr+4] +[Cr+5] +[Cr+6] +[Cr+7] +[Cr+9] +[CrH1] +[CrH2] +[CrH3] +[CrH3+2] +[CrH4] +[CrH4+3] +[CrH4+6] +[CrH5] +[CrH6] +[CrH6+4] +[CrH8] +[Cs] +[Cs+1] +[Cs+3] +[CsH1] +[/Cu] +[=Cu] +[Cu] +[=Cu+1] +[Cu+1] +[Cu-1] +[Cu+2] +[=Cu-3] +[Cu+3] +[Cu+4] +[Cu+5] +[Cu+6] +[Cu+7] +[Cu+8] +[=CuH1] +[CuH1] +[CuH1+1] +[CuH2] +[CuH2+1] +[CuH2+2] +[CuH2+3] +[CuH2+4] +[CuH2+6] +[CuH3] +[CuH3+4] +[CuH3+5] +[CuH4] +[CuH4+1] +[CuH4+2] +[CuH4+4] +[CuH4+5] +[CuH4+6] +[CuH5] +[CuH6] +[CuH6+8] +[=Dy] +[Dy] +[Dy+11] +[Dy+2] +[Dy+3] +[Dy+9] +[DyH3] +[DyH6+9] +[=Er] +[Er] +[Er+1] +[Er+2] +[Er+3] +[ErH3] +[Es] +[=Eu] +[Eu] +[Eu+1] +[Eu+10] +[Eu+2] +[Eu+3] +[Eu+6] +[Eu+9] +[EuH3] +[EuH6+9] +[EuH7+10] +[/F] +[\F] +[F] +[=F+1] +[=F-1] +[F+1] +[F-1] +[F+2] +[F-2] +[\Fe] +[Fe] +[=Fe+1] +[Fe+1] +[Fe-1] +[Fe+2] +[Fe-2] +[Fe+3] +[Fe-3] +[Fe+4] +[Fe-4] +[Fe+5] +[Fe+6] +[Fe+7] +[Fe+8] +[Fe+9] +[FeH1] +[FeH2] +[FeH2+2] +[FeH2+3] +[FeH2+4] +[FeH3] +[FeH3+2] +[FeH3+3] +[FeH4] +[FeH4+2] +[FeH4+3] +[FeH4+4] +[FeH4+6] +[FeH4+7] +[FeH5] +[FeH6+3] +[FeH6+8] +[FeH6+9] +[FeH8] +[=FH0] +[FH0] +[=Ga] +[Ga] +[Ga+1] +[Ga+2] +[Ga+3] +[Ga+7] +[Ga+9] +[=GaH1] +[GaH1] +[GaH1+1] +[GaH2] +[GaH3] +[=Gd] +[Gd] +[Gd+1] +[Gd+10] +[Gd+11] +[Gd+2] +[Gd+3] +[Gd+4] +[Gd+7] +[Gd+8] +[Gd+9] +[GdH3] +[GdH8+11] +[=Ge] +[Ge] +[Ge+1] +[Ge+2] +[Ge+3] +[Ge+4] +[#GeH1] +[=GeH1] +[GeH1] +[GeH1+3] +[=GeH2] +[GeH2] +[GeH3] +[GeH4] +[GeH4+3] +[/H] +[\H] +[H] +[H+1] +[H-1] +[H-2] +[#Hf] +[=Hf] +[Hf] +[#Hf+1] +[Hf+1] +[Hf+12] +[Hf+2] +[Hf+3] +[Hf+4] +[Hf+6] +[HfH2] +[HfH3] +[HfH4] +[Hg] +[Hg+1] +[Hg+2] +[=Ho] +[Ho] +[Ho+1] +[Ho+2] +[Ho+3] +[Ho+9] +[/I] +[=I] +[\I] +[I@@] +[I@] +[I] +[=I+1] +[I+1] +[I-1] +[=I+2] +[I+2] +[I-2] +[I+3] +[I-3] +[I+5] +[=IH0] +[\IH0] +[IH0] +[IH1] +[IH1+1] +[=IH2] +[IH2] +[IH2+1] +[IH2-2] +[IH3] +[#In] +[=In] +[In] +[In+1] +[In+2] +[In+3] +[In+9] +[=InH1] +[InH1] +[InH2] +[InH3] +[=Ir] +[Ir] +[=Ir+1] +[Ir+1] +[Ir+2] +[Ir+3] +[Ir-3] +[Ir+4] +[Ir+5] +[Ir+6] +[Ir+7] +[Ir+9] +[=IrH1] +[IrH1] +[IrH2] +[IrH2+1] +[IrH2+2] +[IrH2+3] +[IrH3] +[IrH3+6] +[IrH4] +[IrH4+1] +[IrH4+5] +[IrH5] +[IrH6] +[IrH6+3] +[K] +[K+1] +[K-1] +[K+2] +[K+3] +[KH1] +[KH1+1] +[KH2] +[KH6] +[=La] +[La] +[La+1] +[La+2] +[La+3] +[La+6] +[La+9] +[LaH3] +[Li] +[Li+1] +[LiH1] +[LiH1+1] +[=Lu] +[Lu] +[Lu+2] +[Lu+3] +[Lu+6] +[LuH3] +[=Mg] +[Mg] +[Mg+1] +[Mg+2] +[Mg-2] +[Mg+3] +[Mg+4] +[Mg+5] +[Mg+6] +[Mg+8] +[MgH1] +[MgH1+1] +[MgH2] +[MgH2+1] +[MgH2+2] +[MgH3+3] +[MgH3+5] +[MgH4] +[MgH4+2] +[MgH4+6] +[MgH6+8] +[=Mn] +[Mn] +[Mn+1] +[Mn+2] +[Mn+3] +[Mn+4] +[Mn+5] +[Mn+6] +[Mn+7] +[Mn+8] +[Mn+9] +[=MnH1] +[MnH2] +[MnH2+2] +[MnH2+3] +[MnH3] +[MnH4+5] +[MnH4+6] +[MnH4+7] +[MnH5] +[MnH5+8] +[MnH6] +[MnH6+8] +[MnH7+9] +[#Mo] +[=Mo] +[Mo] +[#Mo+1] +[=Mo+1] +[Mo+1] +[Mo+2] +[=Mo+3] +[Mo+3] +[Mo+4] +[=Mo+5] +[Mo+5] +[Mo+6] +[Mo+7] +[Mo+8] +[#MoH1] +[MoH2] +[MoH3] +[MoH4] +[MoH4+2] +[MoH6] +[MoH6+4] +[MoH8] +[MoH8+2] +[#N] +[/N@@] +[/N@] +[/N] +[=N] +[\N] +[N@@] +[N@] +[N] +[#N+1] +[#N-1] +[/N+1] +[/N-1] +[=N+1] +[=N-1] +[\N+1] +[\N-1] +[N+1] +[N-1] +[N@+1] +[N@@+1] +[/N-2] +[=N+2] +[=N-2] +[\N-2] +[N+2] +[N-2] +[N-3] +[Na] +[Na+1] +[NaH1] +[NaH1+1] +[NaH1+2] +[NaH2] +[Nb] +[Nb+1] +[Nb+2] +[Nb+3] +[Nb+4] +[Nb+5] +[Nb+7] +[NbH3] +[NbH5] +[NbH5+3] +[NbH8] +[Nd] +[Nd+1] +[Nd+2] +[Nd+3] +[Nd+5] +[NdH3] +[NdH3+6] +[#NH0] +[/NH0] +[=NH0] +[\NH0] +[NH0] +[#NH1] +[/NH1] +[=NH1] +[\NH1] +[N@H1] +[NH1] +[/NH1+1] +[/NH1-1] +[=NH1+1] +[=NH1-1] +[\NH1+1] +[\NH1-1] +[N@@H1+1] +[N@H1+1] +[NH1+1] +[NH1-1] +[NH1-2] +[=NH2] +[NH2] +[/NH2+1] +[/NH2-1] +[=NH2+1] +[=NH2-1] +[\NH2+1] +[\NH2-1] +[NH2+1] +[NH2-1] +[NH3] +[/NH3+1] +[\NH3+1] +[NH3+1] +[NH3-1] +[NH4] +[NH4+1] +[NH4-1] +[=Ni] +[Ni] +[=Ni+1] +[Ni+1] +[=Ni+2] +[Ni+2] +[Ni-2] +[Ni+3] +[Ni+4] +[Ni+5] +[Ni+6] +[Ni+7] +[Ni+8] +[NiH1] +[NiH2] +[NiH2+2] +[NiH3] +[NiH3+2] +[NiH3+5] +[NiH4] +[NiH4+2] +[NiH4+3] +[NiH4+4] +[NiH4+5] +[NiH4+6] +[NiH4+7] +[NiH6] +[NiH6+2] +[NiH8] +[=No] +[/O] +[=O] +[\O] +[O] +[#O+1] +[#O-1] +[/O+1] +[/O-1] +[=O+1] +[=O-1] +[\O+1] +[\O-1] +[O+1] +[O-1] +[O-2] +[=O-3] +[O-3] +[O-4] +[O-5] +[O-7] +[#OH0] +[/OH0] +[=OH0] +[\OH0] +[OH0] +[=OH1] +[OH1] +[=OH1+1] +[=OH1-1] +[OH1+1] +[OH1-1] +[OH1-2] +[OH2] +[/OH2+1] +[OH2+1] +[OH2-1] +[OH2-2] +[OH3] +[OH3+1] +[OH3-1] +[OH3-2] +[OH3-3] +[OH3-5] +[OH4-4] +[Os] +[Os+2] +[Os+3] +[Os+4] +[Os+5] +[Os+6] +[Os+8] +[OsH4] +[OsH6] +[OsH6+4] +[OsH8] +[#P] +[/P] +[=P@@] +[=P@] +[=P] +[\P] +[P@@] +[P@] +[P] +[/P+1] +[=P+1] +[=P-1] +[\P+1] +[P+1] +[P-1] +[P@+1] +[P@-1] +[P@@+1] +[P@@-1] +[P-19] +[P-2] +[P-3] +[P+5] +[Pb] +[Pb+2] +[Pb+3] +[Pb+4] +[Pb+6] +[PbH1] +[PbH1+1] +[PbH1+3] +[PbH2] +[PbH3] +[PbH4] +[PbH6] +[=Pd] +[Pd] +[=Pd+1] +[\Pd+1] +[Pd+1] +[Pd-1] +[=Pd+2] +[Pd+2] +[Pd-2] +[=Pd+3] +[Pd+3] +[Pd+4] +[Pd+5] +[Pd+6] +[=Pd+7] +[=PdH1] +[\PdH1] +[PdH1] +[PdH1+2] +[=PdH2] +[PdH2] +[PdH2+2] +[=PdH3] +[PdH3] +[PdH3+2] +[PdH3+5] +[PdH4] +[PdH4+2] +[PdH4+6] +[PdH6] +[PdH6+4] +[=PH0] +[PH0] +[=P@@H1] +[=P@H1] +[=PH1] +[P@@H1] +[P@H1] +[PH1] +[PH1+1] +[PH1-1] +[PH1-2] +[PH2] +[PH2-1] +[PH3+1] +[PH4] +[Pm+3] +[Pr] +[Pr+1] +[Pr+2] +[Pr+3] +[Pr+4] +[Pr+5] +[Pr+9] +[PrH6] +[Pt] +[Pt+1] +[Pt+10] +[Pt+2] +[Pt-2] +[=Pt+3] +[Pt+3] +[Pt+4] +[Pt+5] +[Pt+6] +[PtH1] +[PtH2] +[PtH2+2] +[PtH3] +[PtH3+5] +[PtH4] +[PtH4+2] +[PtH4+6] +[PtH4+8] +[PtH6] +[PtH6+10] +[PtH6+4] +[Rb] +[Rb+1] +[RbH1] +[Re] +[Re+1] +[Re+2] +[Re+3] +[Re+4] +[Re+5] +[Re+6] +[Re+7] +[ReH1] +[ReH4] +[ReH5] +[ReH6] +[ReH7] +[ReH7+4] +[ReH8+3] +[Rh] +[=Rh+1] +[Rh+1] +[Rh-1] +[Rh+2] +[Rh-2] +[Rh+3] +[Rh+4] +[Rh+5] +[Rh+6] +[Rh+7] +[Rh+8] +[Rh+9] +[RhH1] +[RhH2] +[RhH2+3] +[RhH3] +[RhH4] +[RhH4+2] +[RhH4+6] +[RhH5] +[RhH5+2] +[RhH5+7] +[RhH6+3] +[#Ring1] +[-/Ring1] +[-\Ring1] +[=Ring1] +[Ring1] +[#Ring2] +[-/Ring2] +[-\Ring2] +[=Ring2] +[Ring2] +[=Ring3] +[Ring3] +[=Ru] +[Ru] +[=Ru+1] +[\Ru+1] +[Ru+1] +[Ru-1] +[Ru+10] +[=Ru+2] +[\Ru+2] +[Ru+2] +[=Ru+3] +[\Ru+3] +[Ru+3] +[=Ru+4] +[\Ru+4] +[Ru+4] +[Ru-4] +[Ru+5] +[Ru+6] +[Ru+7] +[Ru+8] +[Ru+9] +[=RuH1] +[RuH1] +[=RuH1+1] +[RuH1+1] +[RuH1+2] +[=RuH2] +[RuH2] +[RuH2+4] +[=RuH3] +[\RuH3] +[RuH3] +[\RuH3+3] +[RuH3+4] +[=RuH4] +[RuH4] +[RuH5] +[RuH6] +[RuH6+2] +[RuH6+4] +[RuH6+8] +[RuH7+4] +[RuH8+3] +[#S] +[/S@@] +[/S@] +[/S] +[=S@@] +[=S@] +[=S] +[\S@@] +[\S@] +[\S] +[S@@] +[S@] +[S] +[/S+1] +[/S-1] +[=S+1] +[=S-1] +[=S@+1] +[=S@@+1] +[\S+1] +[\S-1] +[\S@+1] +[\S@@+1] +[S+1] +[S-1] +[S@+1] +[S@@+1] +[/S-2] +[\S-2] +[S-2] +[#Sb] +[\Sb] +[Sb] +[Sb+11] +[\Sb+2] +[Sb+2] +[Sb+3] +[Sb-3] +[Sb+5] +[Sb+6] +[Sb+7] +[SbH1+1] +[SbH1+3] +[SbH1+4] +[SbH2] +[SbH2+3] +[SbH3] +[SbH4] +[SbH4+1] +[SbH4+3] +[SbH4+4] +[SbH4+7] +[SbH5] +[SbH5+5] +[SbH6] +[SbH6+5] +[=Sc] +[Sc] +[Sc+1] +[Sc+2] +[Sc+3] +[Sc+6] +[ScH3] +[/Se] +[=Se] +[\Se] +[Se] +[=Se+1] +[Se+1] +[Se-1] +[Se-2] +[SeH1] +[SeH1-1] +[=SeH2] +[SeH2] +[SeH3] +[SeH6] +[#SH0] +[=SH0] +[SH0] +[/SH1] +[=SH1] +[S@@H1] +[SH1] +[=SH1-1] +[SH1+1] +[SH1-1] +[/SH1-2] +[SH1-2] +[=SH2] +[SH2] +[SH2-2] +[SH3] +[#Si] +[/Si] +[=Si] +[\Si] +[Si@@] +[Si@] +[Si] +[#Si+1] +[#Si-1] +[Si+1] +[Si-1] +[=Si-2] +[Si+2] +[Si-2] +[Si+4] +[Si-4] +[#SiH1] +[=SiH1] +[\SiH1] +[Si@@H1] +[Si@H1] +[SiH1] +[SiH1-1] +[=SiH2] +[SiH2] +[SiH2-1] +[SiH2-2] +[SiH3] +[SiH3-1] +[SiH4] +[SiH4+4] +[Sm] +[Sm+2] +[Sm+3] +[SmH3] +[/Sn] +[=Sn] +[\Sn] +[Sn@@] +[Sn@] +[Sn] +[Sn+1] +[Sn+10] +[Sn+2] +[Sn+3] +[Sn+4] +[Sn+6] +[SnH1] +[SnH1+1] +[SnH1+3] +[SnH2] +[SnH3] +[SnH3+1] +[SnH4] +[SnH4+3] +[SnH4+6] +[SnH4+8] +[SnH6] +[Sr] +[Sr+1] +[Sr+2] +[Sr+4] +[SrH1] +[SrH1+1] +[SrH2] +[SrH9] +[Ta] +[#Ta+1] +[Ta+1] +[Ta+11] +[Ta+2] +[Ta+3] +[Ta+4] +[Ta+5] +[TaH5] +[TaH5+3] +[TaH6+11] +[TaH7+5] +[Tb] +[Tb+11] +[Tb+2] +[Tb+3] +[TbH3] +[=Te] +[Te] +[Te+1] +[Te+2] +[Te-2] +[Te+4] +[TeH1] +[TeH1-1] +[=TeH2] +[TeH2] +[TeH3] +[Th] +[Th+4] +[#Ti] +[Ti] +[Ti+1] +[Ti+10] +[Ti+12] +[Ti+2] +[Ti+3] +[Ti+4] +[Ti+5] +[Ti+6] +[Ti+7] +[TiH2] +[TiH3] +[TiH3+7] +[TiH4] +[TiH4+3] +[TiH6] +[TiH6+10] +[TiH6+4] +[TiH6+7] +[Tl] +[Tl+1] +[Tl+3] +[TlH1] +[TlH1+1] +[TlH3] +[Tm] +[Tm+2] +[Tm+3] +[TmH3] +[=U] +[U] +[U+1] +[U+6] +[V] +[#V+1] +[V+1] +[V+10] +[V+2] +[V+3] +[V+4] +[V+5] +[V+7] +[V+8] +[VH2] +[VH2+1] +[VH3] +[VH3+4] +[VH4] +[VH5] +[VH5+3] +[VH5+4] +[VH6] +[VH6+7] +[VH6+8] +[VH6+9] +[VH7+8] +[VH8+10] +[#W] +[=W] +[W] +[#W+1] +[W+1] +[W-1] +[W+10] +[W+2] +[W-2] +[#W+3] +[W+3] +[W+4] +[W+5] +[W+6] +[W-60] +[WH2] +[WH3] +[WH4] +[WH4+6] +[WH5] +[WH6] +[WH6+3] +[WH6+4] +[WH7] +[Xe] +[=Y] +[Y] +[Y+1] +[Y+2] +[Y+3] +[Y+6] +[=Yb] +[Yb] +[Yb+1] +[Yb+2] +[Yb+3] +[Yb+6] +[YbH3] +[=YH1] +[YH2] +[YH3] +[Zn] +[Zn+1] +[Zn+2] +[Zn+3] +[Zn+4] +[Zn+5] +[Zn+6] +[Zn+8] +[ZnH1] +[ZnH2] +[ZnH2+1] +[ZnH2+2] +[ZnH3+2] +[ZnH3+5] +[ZnH4] +[ZnH4+2] +[ZnH4+6] +[ZnH6] +[ZnH6+8] +[Zr] +[#Zr+1] +[Zr+1] +[Zr+10] +[Zr+2] +[Zr+3] +[Zr+4] +[Zr+5] +[Zr+6] +[Zr+7] +[Zr+9] +[ZrH2] +[ZrH2+3] +[ZrH2+4] +[ZrH4] +[ZrH4+3] +[ZrH5+9] +[ZrH6+10] +[ZrH7+11] diff --git a/parquet_converter.py b/parquet_converter.py new file mode 100644 index 0000000000000000000000000000000000000000..2e1d7c65c9b6deed95b62032e94bccc49420afa0 --- /dev/null +++ b/parquet_converter.py @@ -0,0 +1,146 @@ +import json +import re +from pathlib import Path +import pandas as pd +import pyarrow as pa +import pyarrow.parquet as pq +from tqdm import tqdm +import concurrent.futures +from typing import List, Dict +import argparse + +class SelfiesTokenizer: + def __init__(self, tokenizer_path: str): + with open(tokenizer_path, 'r') as f: + config = json.load(f) + self.vocab = config['vocab'] + self.special_tokens = config['special_tokens'] + self.max_length = config['model_max_length'] + self.id2token = {v: k for k, v in self.vocab.items()} + + def tokenize(self, selfies_string: str) -> List[str]: + """Split SELFIES string into tokens""" + return re.findall(r'\[.*?\]', selfies_string) + + def convert_tokens_to_ids(self, tokens: List[str]) -> List[int]: + """Convert tokens to their IDs""" + return [self.vocab.get(token, self.vocab['[UNK]']) for token in tokens] + + def encode(self, selfies_string: str, add_special_tokens: bool = True) -> List[int]: + """Full encoding process""" + tokens = self.tokenize(selfies_string) + ids = self.convert_tokens_to_ids(tokens) + + if add_special_tokens: + ids = [self.vocab['[CLS]']] + ids + [self.vocab['[SEP]']] + + if len(ids) > self.max_length: + ids = ids[:self.max_length] + else: + ids.extend([self.vocab['[PAD]']] * (self.max_length - len(ids))) + + return ids + +def process_chunk(chunk: List[str], tokenizer: SelfiesTokenizer) -> Dict[str, List]: + """Process a chunk of SELFIES strings""" + sequences = [seq.strip() for seq in chunk] + tokenized = [tokenizer.encode(seq) for seq in sequences] + return { + 'sequence': sequences, + 'tokenized_sequence': tokenized + } + +def convert_to_parquet(input_files: List[str], output_file: str, tokenizer_path: str, + chunk_size: int = 10000, num_workers: int = 4): + """Convert SELFIES files to parquet with optimized settings""" + + tokenizer = SelfiesTokenizer(tokenizer_path) + + # Create schema for the parquet file + schema = pa.schema([ + ('sequence', pa.string()), + ('tokenized_sequence', pa.list_(pa.int16())) + ]) + + # Set up parquet writer with optimized settings + writer = pq.ParquetWriter( + output_file, + schema, + compression='zstd', + compression_level=9, # Maximum ZSTD compression + use_dictionary=True, + write_statistics=True + ) + + # Process each input file + for input_file in input_files: + print(f"Processing {input_file}...") + + # Count total lines for progress bar + total_lines = sum(1 for _ in open(input_file, 'r')) + + with open(input_file, 'r') as f: + # Process file in chunks + for chunk_start in tqdm(range(0, total_lines, chunk_size)): + chunk = [] + for _ in range(chunk_size): + line = f.readline() + if not line: + break + chunk.append(line) + + if not chunk: + break + + # Process chunks in parallel + with concurrent.futures.ThreadPoolExecutor(max_workers=num_workers) as executor: + chunk_size_per_worker = len(chunk) // num_workers + futures = [] + + for i in range(0, len(chunk), chunk_size_per_worker): + chunk_part = chunk[i:i + chunk_size_per_worker] + futures.append( + executor.submit(process_chunk, chunk_part, tokenizer) + ) + + # Combine results + results = { + 'sequence': [], + 'tokenized_sequence': [] + } + + for future in concurrent.futures.as_completed(futures): + chunk_results = future.result() + results['sequence'].extend(chunk_results['sequence']) + results['tokenized_sequence'].extend(chunk_results['tokenized_sequence']) + + # Convert to PyArrow table and write + table = pa.Table.from_pydict(results, schema=schema) + writer.write_table(table) + + writer.close() + + # Print final statistics + parquet_file = pq.ParquetFile(output_file) + print(f"\nParquet file statistics:") + print(f"Number of row groups: {parquet_file.num_row_groups}") + print(f"Number of rows: {parquet_file.metadata.num_rows}") + print(f"File size: {Path(output_file).stat().st_size / (1024*1024):.2f} MB") + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='Convert SELFIES files to parquet dataset') + parser.add_argument('input_files', nargs='+', help='Input SELFIES files') + parser.add_argument('output_file', help='Output parquet file') + parser.add_argument('tokenizer_path', help='Path to tokenizer config JSON') + parser.add_argument('--chunk-size', type=int, default=10000, help='Chunk size for processing') + parser.add_argument('--num-workers', type=int, default=4, help='Number of worker threads') + + args = parser.parse_args() + + convert_to_parquet( + args.input_files, + args.output_file, + args.tokenizer_path, + args.chunk_size, + args.num_workers + ) diff --git a/tokenizer.json b/tokenizer.json new file mode 100644 index 0000000000000000000000000000000000000000..fcdd7f4bcc5185256e4b6cd5652ae1003d9ce1cd --- /dev/null +++ b/tokenizer.json @@ -0,0 +1,1470 @@ +{ + "vocab": { + "[UNK]": 0, + "[CLS]": 1, + "[SEP]": 2, + "[PAD]": 3, + "[MASK]": 4, + ".": 5, + "[#13CH1]": 6, + "[#13C]": 7, + "[#15N]": 8, + "[#2H]": 9, + "[#Al]": 10, + "[#B]": 11, + "[#Bi]": 12, + "[#Branch1]": 13, + "[#Branch2]": 14, + "[#C+1]": 15, + "[#C-1]": 16, + "[#CH0]": 17, + "[#CH1]": 18, + "[#C]": 19, + "[#Cr]": 20, + "[#Hf+1]": 21, + "[#Mo+1]": 22, + "[#N+1]": 23, + "[#N-1]": 24, + "[#NH0]": 25, + "[#NH1]": 26, + "[#N]": 27, + "[#O+1]": 28, + "[#OH0]": 29, + "[#P]": 30, + "[#S]": 31, + "[#Sb]": 32, + "[#Si+1]": 33, + 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