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!_TAG_FILE_FORMAT 2 /extended format; --format=1 will not append ;" to lines/
!_TAG_FILE_SORTED 1 /0=unsorted, 1=sorted, 2=foldcase/
!_TAG_PROGRAM_AUTHOR Darren Hiebert /[email protected]/
!_TAG_PROGRAM_NAME Exuberant Ctags //
!_TAG_PROGRAM_URL http:https://ctags.sourceforge.net /official site/
!_TAG_PROGRAM_VERSION 5.9~svn20110310 //
CharTokenizer MolGen/src/tokenizers/CharTokenizer.py /^class CharTokenizer():$/;" c
RecurrentModel MolGen/src/models/recurrent.py /^class RecurrentModel(nn.Module):$/;" c
SmilesDataset MolGen/src/datasets/dataset.py /^class SmilesDataset(Dataset):$/;" c
Trainer MolGen/src/train/train.py /^class Trainer():$/;" c
__call__ MolGen/src/tokenizers/CharTokenizer.py /^ def __call__(self, smiles, padding=False, max_length=None):$/;" m class:CharTokenizer file:
__getitem__ MolGen/src/datasets/dataset.py /^ def __getitem__(self, idx):$/;" m class:SmilesDataset file:
__init__ MolGen/src/datasets/dataset.py /^ def __init__(self, data_path: str, tokenizer) -> None:$/;" m class:SmilesDataset
__init__ MolGen/src/models/recurrent.py /^ def __init__(self,$/;" m class:RecurrentModel
__init__ MolGen/src/tokenizers/CharTokenizer.py /^ def __init__(self, tokenizer_path: str=None):$/;" m class:CharTokenizer
__init__ MolGen/src/train/train.py /^ def __init__(self, dataset, model, optim, criterion):$/;" m class:Trainer
__len__ MolGen/src/datasets/dataset.py /^ def __len__(self) -> int:$/;" m class:SmilesDataset file:
bos_token MolGen/src/tokenizers/CharTokenizer.py /^ def bos_token(self):$/;" m class:CharTokenizer
bos_token_id MolGen/src/tokenizers/CharTokenizer.py /^ def bos_token_id(self):$/;" m class:CharTokenizer
build_tokenizer MolGen/src/tokenizers/CharTokenizer.py /^ def build_tokenizer(self, tokenizer_path: str, data_path:str) -> Dict[int, str]:$/;" m class:CharTokenizer
calc_diversity MolGen/src/utils/metrics.py /^def calc_diversity(gen_molecules: List[str]) -> float:$/;" f
calc_logp MolGen/src/utils/metrics.py /^def calc_logp(mol: Chem.rdchem.Mol) -> float:$/;" f
calc_novelty MolGen/src/utils/metrics.py /^def calc_novelty(train_set_molecules: List[str], gen_molecules: List[str]) -> float:$/;" f
calc_qed MolGen/src/utils/metrics.py /^def calc_qed(mol: Chem.rdchem.Mol) -> float:$/;" f
calc_sas MolGen/src/utils/metrics.py /^def calc_sas(mol: Chem.rdchem.Mol) -> float:$/;" f
calc_set_stat MolGen/src/train/evaluate.py /^def calc_set_stat(mol_set: List[Chem.rdchem.Mol],$/;" f
calc_valid_molecules MolGen/src/utils/metrics.py /^def calc_valid_molecules(molecules: List[Chem.rdchem.Mol]) -> int:$/;" f
convert_ids_to_tokens MolGen/src/tokenizers/CharTokenizer.py /^ def convert_ids_to_tokens(self, encodings: List[int]) -> List[str]:$/;" m class:CharTokenizer
convert_to_molecules MolGen/src/utils/utils.py /^def convert_to_molecules(smiles_list: List[str]) -> List[Chem.rdchem.Mol]:$/;" f
convert_to_scaffolds MolGen/src/utils/utils.py /^def convert_to_scaffolds(mols: List[Chem.rdchem.Mol]) -> Set[str]:$/;" f
convert_tokens_to_ids MolGen/src/tokenizers/CharTokenizer.py /^ def convert_tokens_to_ids(self, tokens: List[str]) -> List[int]:$/;" m class:CharTokenizer
convert_tokens_to_string MolGen/src/tokenizers/CharTokenizer.py /^ def convert_tokens_to_string(self, tokens: List[str]) -> str:$/;" m class:CharTokenizer
decode MolGen/src/tokenizers/CharTokenizer.py /^ def decode(self, tokens: List[int]) -> str:$/;" m class:CharTokenizer
eos_token MolGen/src/tokenizers/CharTokenizer.py /^ def eos_token(self):$/;" m class:CharTokenizer
eos_token_id MolGen/src/tokenizers/CharTokenizer.py /^ def eos_token_id(self):$/;" m class:CharTokenizer
filter_invalid_molecules MolGen/src/utils/utils.py /^def filter_invalid_molecules(mols: List[Chem.rdchem.Mol]) -> List[Chem.rdchem.Mol]:$/;" f
forward MolGen/src/models/recurrent.py /^ def forward(self, inputs, attention_mask=None, state=None, labels=None):$/;" m class:RecurrentModel
gen_till_train MolGen/src/train/evaluate.py /^def gen_till_train(model, dataset):$/;" f
generate_and_save_plot MolGen/src/utils/utils.py /^def generate_and_save_plot(values,$/;" f
generate_smiles MolGen/src/train/evaluate.py /^def generate_smiles(model, tokenizer, temprature=1, size=1000) -> List[Chem.rdchem.Mol]:$/;" f
get_max_smiles_len MolGen/src/datasets/dataset.py /^ def get_max_smiles_len(self, ) -> int:$/;" m class:SmilesDataset
get_molecule_scaffold MolGen/src/utils/utils.py /^def get_molecule_scaffold(mol: Chem.rdchem.Mol) -> str:$/;" f
get_stats MolGen/src/train/evaluate.py /^def get_stats(train_set, generated_smiles, save_path=None):$/;" f
init_state MolGen/src/models/recurrent.py /^ def init_state(self, sequence_length):$/;" m class:RecurrentModel
load_tokenizer MolGen/src/tokenizers/BPETokenizer.py /^def load_tokenizer(tokenizer_path: str) -> PreTrainedTokenizer:$/;" f
main MolGen/main.py /^def main():$/;" f
main MolGen/src/datasets/dataset.py /^def main():$/;" f
main MolGen/src/models/recurrent.py /^def main():$/;" f
main MolGen/src/tokenizers/BPETokenizer.py /^def main():$/;" f
main MolGen/src/tokenizers/CharTokenizer.py /^def main():$/;" f
main MolGen/src/train/evaluate.py /^def main():$/;" f
numBridgeheadsAndSpiro MolGen/src/utils/metrics.py /^def numBridgeheadsAndSpiro(mol, ri=None):$/;" f
pad_token MolGen/src/tokenizers/CharTokenizer.py /^ def pad_token(self):$/;" m class:CharTokenizer
pad_token_id MolGen/src/tokenizers/CharTokenizer.py /^ def pad_token_id(self):$/;" m class:CharTokenizer
policy_gradients MolGen/src/train/reinforcement.py /^def policy_gradients(model, tokenizer, reward_fn, batch_size=16, epochs=100, discount_factor=0.99):$/;" f
tokenize MolGen/src/tokenizers/CharTokenizer.py /^ def tokenize(self, smiles, padding=None, max_length=None):$/;" m class:CharTokenizer
train MolGen/src/train/train.py /^ def train(self, epochs, batch_size, device):$/;" m class:Trainer
train_tokenizer MolGen/src/tokenizers/BPETokenizer.py /^def train_tokenizer(data_path: str, save_path: str) -> None:$/;" f
vocab_size MolGen/src/tokenizers/CharTokenizer.py /^ def vocab_size(self):$/;" m class:CharTokenizer