Uni-Mol
Getting Started:
Requirements
Installation
Tutorials:
Quick start
Uni-Mol School
Examples
Uni-Mol tools:
Interface
Data
Models
Task
Utils
Weights
New Features
Uni-Mol
Index
Index
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A
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B
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C
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D
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E
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F
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G
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I
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L
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M
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N
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P
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R
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S
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T
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U
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W
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Y
_
__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)