Index

_

__init__() (unimol_tools.data.conformer.ConformerGen method) (unimol_tools.data.conformer.UniMolV2Feature method) (unimol_tools.data.datahub.DataHub method) (unimol_tools.data.datascaler.TargetScaler method) (unimol_tools.data.split.Splitter method) (unimol_tools.models.loss.GHM_Loss method) (unimol_tools.models.loss.GHMC_Loss method) (unimol_tools.models.loss.GHMR_Loss method) (unimol_tools.models.nnmodel.NNModel method) (unimol_tools.models.nnmodel.TorchDataset method) (unimol_tools.models.transformers.SelfMultiheadAttention method) (unimol_tools.models.transformers.TransformerEncoderLayer method) (unimol_tools.models.transformers.TransformerEncoderWithPair method) (unimol_tools.models.unimol.ClassificationHead method) (unimol_tools.models.unimol.GaussianLayer method) (unimol_tools.models.unimol.NonLinearHead method) (unimol_tools.models.unimol.NumericalEmbed method) (unimol_tools.models.unimol.UniMolModel method) (unimol_tools.predict.MolPredict method) (unimol_tools.predictor.MolDataset method) (unimol_tools.predictor.UniMolRepr method) (unimol_tools.tasks.trainer.Trainer method) (unimol_tools.train.MolTrain method) (unimol_tools.utils.base_logger.Logger method) (unimol_tools.utils.config_handler.YamlHandler method) (unimol_tools.utils.metrics.Metrics method)

_custom_loss() (unimol_tools.models.loss.GHM_Loss method) (unimol_tools.models.loss.GHMC_Loss method) (unimol_tools.models.loss.GHMR_Loss method) _custom_loss_grad() (unimol_tools.models.loss.GHM_Loss method) (unimol_tools.models.loss.GHMC_Loss method) (unimol_tools.models.loss.GHMR_Loss method) _early_stop_choice() (unimol_tools.tasks.trainer.Trainer method) _g2bin() (unimol_tools.models.loss.GHM_Loss method) _init_data() (unimol_tools.data.datahub.DataHub method) _init_features() (unimol_tools.data.conformer.ConformerGen method) (unimol_tools.data.conformer.UniMolV2Feature method) _init_model() (unimol_tools.models.nnmodel.NNModel method) _init_split() (unimol_tools.data.split.Splitter method) _init_trainer() (unimol_tools.tasks.trainer.Trainer method) _judge_early_stop_loss() (unimol_tools.tasks.trainer.Trainer method)

A

addict2dict() (in module unimol_tools.utils.config_handler) anomaly_clean() (unimol_tools.data.datareader.MolDataReader method)

anomaly_clean_regression() (unimol_tools.data.datareader.MolDataReader method) atom_to_feature_vector() (in module unimol_tools.data.conformer)

B

batch_collate_fn() (unimol_tools.models.unimol.UniMolModel method)

bond_to_feature_vector() (in module unimol_tools.data.conformer) build_model() (unimol_tools.models.unimol.UniMolModel class method)

C

cal_classification_metric() (unimol_tools.utils.metrics.Metrics method) cal_multiclass_metric() (unimol_tools.utils.metrics.Metrics method) cal_reg_metric() (unimol_tools.utils.metrics.Metrics method) check_smiles() (unimol_tools.data.datareader.MolDataReader method) ClassificationHead (class in unimol_tools.models.unimol)

collect_data() (unimol_tools.models.nnmodel.NNModel method) ConformerGen (class in unimol_tools.data.conformer) coords2unimol() (in module unimol_tools.data.conformer) count_parameters() (unimol_tools.models.nnmodel.NNModel method) create_mol_from_atoms_and_coords() (in module unimol_tools.data.conformer)

D

DataHub (class in unimol_tools.data.datahub) decorate_batch() (unimol_tools.tasks.trainer.Trainer method) decorate_graph_batch() (unimol_tools.tasks.trainer.Trainer method)

decorate_torch_batch() (unimol_tools.tasks.trainer.Trainer method) download_all_weights() (in module unimol_tools.weights.weighthub) dump() (unimol_tools.models.nnmodel.NNModel method)

E

evaluate() (unimol_tools.models.nnmodel.NNModel method)

F

filter() (unimol_tools.utils.base_logger.PackagePathFilter method) fit() (unimol_tools.data.datascaler.TargetScaler method) (unimol_tools.train.MolTrain method) fit_predict() (unimol_tools.tasks.trainer.Trainer method) FocalLoss() (in module unimol_tools.models.loss) FocalLossWithLogits() (in module unimol_tools.models.loss) forward() (unimol_tools.models.loss.GHM_Loss method) (unimol_tools.models.transformers.TransformerEncoderLayer method) (unimol_tools.models.transformers.TransformerEncoderWithPair method) (unimol_tools.models.unimol.ClassificationHead method) (unimol_tools.models.unimol.GaussianLayer method) (unimol_tools.models.unimol.NonLinearHead method) (unimol_tools.models.unimol.NumericalEmbed method) (unimol_tools.models.unimol.UniMolModel method)

G

gaussian() (in module unimol_tools.models.unimol) GaussianLayer (class in unimol_tools.models.unimol) get_activation_fn() (in module unimol_tools.models.transformers) (in module unimol_tools.models.unimol) get_graph() (in module unimol_tools.data.conformer)

get_linear_schedule_with_warmup() (in module unimol_tools.tasks.trainer) get_logger() (unimol_tools.utils.base_logger.Logger method) get_repr() (unimol_tools.predictor.UniMolRepr method) GHM_Loss (class in unimol_tools.models.loss) GHMC_Loss (class in unimol_tools.models.loss) GHMR_Loss (class in unimol_tools.models.loss)

I

inference() (unimol_tools.tasks.trainer.Trainer method) inner_coords() (in module unimol_tools.data.conformer)

inner_smi2coords() (in module unimol_tools.data.conformer) inverse_transform() (unimol_tools.data.datascaler.TargetScaler method) is_skewed() (unimol_tools.data.datascaler.TargetScaler method)

L

load_pretrained_weights() (unimol_tools.models.unimol.UniMolModel method)

Logger (class in unimol_tools.utils.base_logger)

M

MAEwithNan() (in module unimol_tools.models.loss) Metrics (class in unimol_tools.utils.metrics) module unimol_tools.data.conformer unimol_tools.data.datahub unimol_tools.data.datareader unimol_tools.data.datascaler unimol_tools.data.split unimol_tools.models.loss unimol_tools.models.nnmodel unimol_tools.models.transformers unimol_tools.models.unimol unimol_tools.predict unimol_tools.predictor unimol_tools.tasks.trainer unimol_tools.train unimol_tools.utils.base_logger unimol_tools.utils.config_handler unimol_tools.utils.metrics unimol_tools.utils.util unimol_tools.weights.weighthub

mol2unimolv2() (in module unimol_tools.data.conformer) MolDataReader (class in unimol_tools.data.datareader) MolDataset (class in unimol_tools.predictor) MolPredict (class in unimol_tools.predict) MolTrain (class in unimol_tools.train) myCrossEntropyLoss() (in module unimol_tools.models.loss)

N

NNDataLoader() (in module unimol_tools.tasks.trainer) NNDataset() (in module unimol_tools.models.nnmodel)

NNModel (class in unimol_tools.models.nnmodel) NonLinearHead (class in unimol_tools.models.unimol) NumericalEmbed (class in unimol_tools.models.unimol)

P

PackagePathFilter (class in unimol_tools.utils.base_logger) pad_1d_tokens() (in module unimol_tools.utils.util) pad_2d() (in module unimol_tools.utils.util)

pad_coords() (in module unimol_tools.utils.util) predict() (unimol_tools.predict.MolPredict method) (unimol_tools.tasks.trainer.Trainer method)

R

read_data() (unimol_tools.data.datareader.MolDataReader method)

read_yaml() (unimol_tools.utils.config_handler.YamlHandler method) run() (unimol_tools.models.nnmodel.NNModel method)

S

safe_index() (in module unimol_tools.data.conformer) save_predict() (unimol_tools.predict.MolPredict method) scaler_choose() (unimol_tools.data.datascaler.TargetScaler method) SelfMultiheadAttention (class in unimol_tools.models.transformers) set_seed() (unimol_tools.tasks.trainer.Trainer method)

single_process() (unimol_tools.data.conformer.ConformerGen method) (unimol_tools.data.conformer.UniMolV2Feature method) smi2scaffold() (unimol_tools.data.datareader.MolDataReader method) softmax_dropout() (in module unimol_tools.models.transformers) split() (unimol_tools.data.split.Splitter method) Splitter (class in unimol_tools.data.split)

T

TargetScaler (class in unimol_tools.data.datascaler) TorchDataset (class in unimol_tools.models.nnmodel) Trainer (class in unimol_tools.tasks.trainer)

transform() (unimol_tools.data.datascaler.TargetScaler method) TransformerEncoderLayer (class in unimol_tools.models.transformers) TransformerEncoderWithPair (class in unimol_tools.models.transformers)

U

unimol_tools.data.conformer module unimol_tools.data.datahub module unimol_tools.data.datareader module unimol_tools.data.datascaler module unimol_tools.data.split module unimol_tools.models.loss module unimol_tools.models.nnmodel module unimol_tools.models.transformers module unimol_tools.models.unimol module unimol_tools.predict module

unimol_tools.predictor module unimol_tools.tasks.trainer module unimol_tools.train module unimol_tools.utils.base_logger module unimol_tools.utils.config_handler module unimol_tools.utils.metrics module unimol_tools.utils.util module unimol_tools.weights.weighthub module UniMolModel (class in unimol_tools.models.unimol) UniMolRepr (class in unimol_tools.predictor) UniMolV2Feature (class in unimol_tools.data.conformer) update_and_save_config() (unimol_tools.train.MolTrain method)

W

weight_download() (in module unimol_tools.weights.weighthub)

weight_download_v2() (in module unimol_tools.weights.weighthub) write_yaml() (unimol_tools.utils.config_handler.YamlHandler method)

Y

YamlHandler (class in unimol_tools.utils.config_handler)