Index

A

allow_zero_length_dataloader_with_multiple_devices (proteinworkshop.models.base.BenchMarkModel attribute)

amino_acid_one_hot() (in module proteinworkshop.features.sequence_features) AstralDataModule (class in proteinworkshop.datasets.astral)

B

BackboneDihedralPredictionTransform (class in proteinworkshop.tasks.backbone_dihedral_angle_prediction) BaseModel (class in proteinworkshop.models.base)

BenchMarkModel (class in proteinworkshop.models.base) BindingSiteTransform (class in proteinworkshop.tasks.binding_site_prediction) (class in proteinworkshop.tasks.ppi_site_prediction)

C

ca_to_bb_repr() (in module proteinworkshop.features.representation) ca_to_bb_sc_repr() (in module proteinworkshop.features.representation) ca_to_ca_sc_repr() (in module proteinworkshop.features.representation) ca_to_fa_repr() (in module proteinworkshop.features.representation) CATHDataModule (class in proteinworkshop.datasets.cath) CDConvModel (class in proteinworkshop.models.graph_encoders.cdconv) coarsen_sidechain() (in module proteinworkshop.features.representation) compose_transforms() (proteinworkshop.datasets.base.ProteinDataModule method) compute_edge_distance() (in module proteinworkshop.features.edge_features) compute_edges() (in module proteinworkshop.features.edges) compute_loss() (proteinworkshop.models.base.BaseModel method)

compute_output() (proteinworkshop.models.base.BenchMarkModel method) compute_scalar_edge_features() (in module proteinworkshop.features.edge_features) compute_scalar_node_features() (in module proteinworkshop.features.node_features) compute_surface_feat() (in module proteinworkshop.features.node_features) compute_vector_node_features() (in module proteinworkshop.features.node_features) config (proteinworkshop.models.base.BaseModel attribute) (proteinworkshop.models.base.BenchMarkModel attribute) configure_losses() (proteinworkshop.models.base.BaseModel method) configure_metrics() (proteinworkshop.models.base.BaseModel method) configure_optimizers() (proteinworkshop.models.base.BaseModel method) create_example_batch() (in module proteinworkshop.datasets.utils)

D

DATA_PATH (in module proteinworkshop.constants) DimeNetPPModel (class in proteinworkshop.models.graph_encoders.dimenetpp) download() (proteinworkshop.datasets.astral.AstralDataModule method) (proteinworkshop.datasets.base.ProteinDataModule method) (proteinworkshop.datasets.base.ProteinDataset method) (proteinworkshop.datasets.cath.CATHDataModule method) (proteinworkshop.datasets.flip_datamodule.FLIPDatamodule method) (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method) (proteinworkshop.datasets.go.GeneOntologyDataset method)

download_data_files() (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method) download_pdb_mmtf() (in module proteinworkshop.datasets.utils) download_structures() (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method)

E

EDGE_FEATURES (in module proteinworkshop.features.edge_features) EdgeDistancePredictionTransform (class in proteinworkshop.tasks.edge_distance_prediction) EGNNModel (class in proteinworkshop.models.graph_encoders.egnn) EMA (class in proteinworkshop.utils) EMAModelCheckpoint (class in proteinworkshop.utils) esm_embed() (proteinworkshop.models.graph_encoders.esm_embeddings.EvolutionaryScaleModeling method)

EvolutionaryScaleModeling (class in proteinworkshop.models.graph_encoders.esm_embeddings) exclude_pdbs() (proteinworkshop.datasets.astral.AstralDataModule method) (proteinworkshop.datasets.base.ProteinDataModule method) (proteinworkshop.datasets.cath.CATHDataModule method) (proteinworkshop.datasets.flip_datamodule.FLIPDatamodule method) (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method) (proteinworkshop.datasets.go.GeneOntologyDataset method)

F

featurise() (proteinworkshop.models.base.BaseModel method) featuriser (proteinworkshop.models.base.BaseModel attribute) (proteinworkshop.models.base.BenchMarkModel attribute) flatten_dir() (in module proteinworkshop.datasets.fold_classification) (in module proteinworkshop.datasets.utils) FLIPDatamodule (class in proteinworkshop.datasets.flip_datamodule) FoldClassificationDataModule (class in proteinworkshop.datasets.fold_classification) FOLDCOMP_DATASET_NAMES (in module proteinworkshop.constants) forward() (proteinworkshop.features.factory.ProteinFeaturiser method) (proteinworkshop.models.base.BaseModel method) (proteinworkshop.models.base.BenchMarkModel method) (proteinworkshop.models.decoders.mlp_decoder.LinearSkipBlock method) (proteinworkshop.models.decoders.mlp_decoder.MLPDecoder method) (proteinworkshop.models.decoders.mlp_decoder.PositionDecoder method) (proteinworkshop.models.graph_encoders.cdconv.CDConvModel method) (proteinworkshop.models.graph_encoders.dimenetpp.DimeNetPPModel method) (proteinworkshop.models.graph_encoders.egnn.EGNNModel method) (proteinworkshop.models.graph_encoders.esm_embeddings.EvolutionaryScaleModeling method) (proteinworkshop.models.graph_encoders.gcpnet.GCPNetModel method) (proteinworkshop.models.graph_encoders.gear_net.GearNet method) (proteinworkshop.models.graph_encoders.gvp.GVPGNNModel method) (proteinworkshop.models.graph_encoders.mace.MACEModel method) (proteinworkshop.models.graph_encoders.schnet.SchNetModel method) (proteinworkshop.models.graph_encoders.tfn.TensorProductModel method)

G

GCPNetModel (class in proteinworkshop.models.graph_encoders.gcpnet) gear_net_edge_features() (proteinworkshop.models.graph_encoders.gear_net.GearNet method) GearNet (class in proteinworkshop.models.graph_encoders.gear_net) GeneOntologyDataset (class in proteinworkshop.datasets.go) get() (proteinworkshop.datasets.base.ProteinDataset method)

get_class_weights() (proteinworkshop.datasets.base.ProteinDataModule method) get_full_atom_coords() (in module proteinworkshop.features.representation) get_labels() (proteinworkshop.models.base.BaseModel method) GOLabeller (class in proteinworkshop.datasets.go) GVPGNNModel (class in proteinworkshop.models.graph_encoders.gvp)

L

len() (proteinworkshop.datasets.base.ProteinDataset method) LinearSkipBlock (class in proteinworkshop.models.decoders.mlp_decoder) load_state_dict() (proteinworkshop.utils.EMA method)

load_weight() (proteinworkshop.models.graph_encoders.esm_embeddings.EvolutionaryScaleModeling method) log_metrics() (proteinworkshop.models.base.BaseModel method) losses (proteinworkshop.models.base.BaseModel attribute) (proteinworkshop.models.base.BenchMarkModel attribute)

M

MACEModel (class in proteinworkshop.models.graph_encoders.mace) max_input_length (proteinworkshop.models.graph_encoders.esm_embeddings.EvolutionaryScaleModeling attribute) md5 (proteinworkshop.models.graph_encoders.esm_embeddings.EvolutionaryScaleModeling attribute) metric_names (proteinworkshop.models.base.BaseModel attribute) (proteinworkshop.models.base.BenchMarkModel attribute) MLPDecoder (class in proteinworkshop.models.decoders.mlp_decoder) model_names (proteinworkshop.models.graph_encoders.esm_embeddings.EvolutionaryScaleModeling attribute) module proteinworkshop.constants proteinworkshop.datasets.astral proteinworkshop.datasets.base proteinworkshop.datasets.cath proteinworkshop.datasets.flip_datamodule proteinworkshop.datasets.fold_classification proteinworkshop.datasets.go proteinworkshop.datasets.utils proteinworkshop.features.edge_features proteinworkshop.features.edges proteinworkshop.features.factory proteinworkshop.features.node_features proteinworkshop.features.representation proteinworkshop.features.sequence_features proteinworkshop.models.base proteinworkshop.models.decoders.mlp_decoder proteinworkshop.models.graph_encoders.cdconv proteinworkshop.models.graph_encoders.dimenetpp proteinworkshop.models.graph_encoders.egnn proteinworkshop.models.graph_encoders.esm_embeddings proteinworkshop.models.graph_encoders.gcpnet proteinworkshop.models.graph_encoders.gear_net proteinworkshop.models.graph_encoders.gvp proteinworkshop.models.graph_encoders.mace proteinworkshop.models.graph_encoders.schnet proteinworkshop.models.graph_encoders.tfn proteinworkshop.tasks.backbone_dihedral_angle_prediction proteinworkshop.tasks.binding_site_prediction proteinworkshop.tasks.edge_distance_prediction proteinworkshop.tasks.ppi_site_prediction proteinworkshop.tasks.remove_missing_ca proteinworkshop.tasks.sequence_denoising proteinworkshop.tasks.structural_denoising proteinworkshop.tasks.torsional_denoising proteinworkshop.train proteinworkshop.types proteinworkshop.utils

N

num_layer (proteinworkshop.models.graph_encoders.esm_embeddings.EvolutionaryScaleModeling attribute)

O

obsolete_pdbs (proteinworkshop.datasets.base.ProteinDataModule property) on_after_batch_transfer() (proteinworkshop.models.base.BaseModel method) on_load_checkpoint() (proteinworkshop.utils.EMA method) on_test_end() (proteinworkshop.utils.EMA method) on_test_start() (proteinworkshop.utils.EMA method)

on_train_batch_end() (proteinworkshop.utils.EMA method) on_train_start() (proteinworkshop.utils.EMA method) on_validation_end() (proteinworkshop.utils.EMA method) on_validation_start() (proteinworkshop.utils.EMA method) orientation() (proteinworkshop.models.graph_encoders.cdconv.CDConvModel static method) output_dim (proteinworkshop.models.graph_encoders.esm_embeddings.EvolutionaryScaleModeling attribute)

P

pair_data() (in module proteinworkshop.datasets.base) parse_class_map() (proteinworkshop.datasets.astral.AstralDataModule method) parse_dataset() (proteinworkshop.datasets.astral.AstralDataModule method) (proteinworkshop.datasets.base.ProteinDataModule method) (proteinworkshop.datasets.cath.CATHDataModule method) (proteinworkshop.datasets.flip_datamodule.FLIPDatamodule method) (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method) (proteinworkshop.datasets.go.GeneOntologyDataset method) parse_labels() (proteinworkshop.datasets.astral.AstralDataModule method) (proteinworkshop.datasets.base.ProteinDataModule method) (proteinworkshop.datasets.cath.CATHDataModule method) (proteinworkshop.datasets.flip_datamodule.FLIPDatamodule method) (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method) (proteinworkshop.datasets.go.GeneOntologyDataset method) PositionDecoder (class in proteinworkshop.models.decoders.mlp_decoder) prepare_data_per_node (proteinworkshop.models.base.BenchMarkModel attribute) process() (proteinworkshop.datasets.base.ProteinDataset method) processed_file_names (proteinworkshop.datasets.base.ProteinDataset property) PROJECT_PATH (in module proteinworkshop.constants) ProteinDataModule (class in proteinworkshop.datasets.base) ProteinDataset (class in proteinworkshop.datasets.base) ProteinFeaturiser (class in proteinworkshop.features.factory) proteinworkshop.constants module proteinworkshop.datasets.astral module proteinworkshop.datasets.base module proteinworkshop.datasets.cath module proteinworkshop.datasets.flip_datamodule module proteinworkshop.datasets.fold_classification module proteinworkshop.datasets.go module proteinworkshop.datasets.utils module proteinworkshop.features.edge_features module proteinworkshop.features.edges module proteinworkshop.features.factory module proteinworkshop.features.node_features module proteinworkshop.features.representation module

proteinworkshop.features.sequence_features module proteinworkshop.models.base module proteinworkshop.models.decoders.mlp_decoder module proteinworkshop.models.graph_encoders.cdconv module proteinworkshop.models.graph_encoders.dimenetpp module proteinworkshop.models.graph_encoders.egnn module proteinworkshop.models.graph_encoders.esm_embeddings module proteinworkshop.models.graph_encoders.gcpnet module proteinworkshop.models.graph_encoders.gear_net module proteinworkshop.models.graph_encoders.gvp module proteinworkshop.models.graph_encoders.mace module proteinworkshop.models.graph_encoders.schnet module proteinworkshop.models.graph_encoders.tfn module proteinworkshop.tasks.backbone_dihedral_angle_prediction module proteinworkshop.tasks.binding_site_prediction module proteinworkshop.tasks.edge_distance_prediction module proteinworkshop.tasks.ppi_site_prediction module proteinworkshop.tasks.remove_missing_ca module proteinworkshop.tasks.sequence_denoising module proteinworkshop.tasks.structural_denoising module proteinworkshop.tasks.torsional_denoising module proteinworkshop.train module proteinworkshop.types module proteinworkshop.utils module

R

raw_dir (proteinworkshop.datasets.base.ProteinDataset property) raw_file_names (proteinworkshop.datasets.base.ProteinDataset property) RemoveMissingCa (class in proteinworkshop.tasks.remove_missing_ca) required_attributes (proteinworkshop.tasks.backbone_dihedral_angle_prediction.BackboneDihedralPredictionTransform property) (proteinworkshop.tasks.binding_site_prediction.BindingSiteTransform property) (proteinworkshop.tasks.sequence_denoising.SequenceNoiseTransform property) (proteinworkshop.tasks.structural_denoising.StructuralNoiseTransform property) required_batch_attributes (proteinworkshop.models.graph_encoders.cdconv.CDConvModel property) (proteinworkshop.models.graph_encoders.dimenetpp.DimeNetPPModel property) (proteinworkshop.models.graph_encoders.egnn.EGNNModel property) (proteinworkshop.models.graph_encoders.esm_embeddings.EvolutionaryScaleModeling property) (proteinworkshop.models.graph_encoders.gcpnet.GCPNetModel property) (proteinworkshop.models.graph_encoders.gear_net.GearNet property) (proteinworkshop.models.graph_encoders.gvp.GVPGNNModel property) (proteinworkshop.models.graph_encoders.mace.MACEModel property) (proteinworkshop.models.graph_encoders.schnet.SchNetModel property) (proteinworkshop.models.graph_encoders.tfn.TensorProductModel property) (proteinworkshop.tasks.edge_distance_prediction.EdgeDistancePredictionTransform property)

S

SchNetModel (class in proteinworkshop.models.graph_encoders.schnet) sequence_edges() (in module proteinworkshop.features.edges) SequenceNoiseTransform (class in proteinworkshop.tasks.sequence_denoising) setup() (proteinworkshop.datasets.astral.AstralDataModule method) (proteinworkshop.datasets.base.ProteinDataModule method) (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method)

SRC_PATH (in module proteinworkshop.constants) state_dict() (proteinworkshop.utils.EMA method) StructuralNoiseTransform (class in proteinworkshop.tasks.structural_denoising)

T

task_transform (proteinworkshop.models.base.BaseModel attribute) (proteinworkshop.models.base.BenchMarkModel attribute) TensorProductModel (class in proteinworkshop.models.graph_encoders.tfn) test_dataloader() (proteinworkshop.datasets.astral.AstralDataModule method) (proteinworkshop.datasets.base.ProteinDataModule method) (proteinworkshop.datasets.cath.CATHDataModule method) (proteinworkshop.datasets.flip_datamodule.FLIPDatamodule method) (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method) (proteinworkshop.datasets.go.GeneOntologyDataset method) test_dataset() (proteinworkshop.datasets.astral.AstralDataModule method) (proteinworkshop.datasets.base.ProteinDataModule method) (proteinworkshop.datasets.cath.CATHDataModule method) (proteinworkshop.datasets.flip_datamodule.FLIPDatamodule method) (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method) (proteinworkshop.datasets.go.GeneOntologyDataset method) test_step() (proteinworkshop.models.base.BaseModel method) (proteinworkshop.models.base.BenchMarkModel method) TorsionalNoiseTransform (class in proteinworkshop.tasks.torsional_denoising) train_dataloader() (proteinworkshop.datasets.astral.AstralDataModule method) (proteinworkshop.datasets.base.ProteinDataModule method) (proteinworkshop.datasets.cath.CATHDataModule method) (proteinworkshop.datasets.flip_datamodule.FLIPDatamodule method) (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method) (proteinworkshop.datasets.go.GeneOntologyDataset method)

train_dataset() (proteinworkshop.datasets.astral.AstralDataModule method) (proteinworkshop.datasets.base.ProteinDataModule method) (proteinworkshop.datasets.cath.CATHDataModule method) (proteinworkshop.datasets.flip_datamodule.FLIPDatamodule method) (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method) (proteinworkshop.datasets.go.GeneOntologyDataset method) train_model() (in module proteinworkshop.train) training (proteinworkshop.models.base.BenchMarkModel attribute) (proteinworkshop.models.decoders.mlp_decoder.LinearSkipBlock attribute) (proteinworkshop.models.decoders.mlp_decoder.MLPDecoder attribute) (proteinworkshop.models.decoders.mlp_decoder.PositionDecoder attribute) (proteinworkshop.models.graph_encoders.cdconv.CDConvModel attribute) (proteinworkshop.models.graph_encoders.dimenetpp.DimeNetPPModel attribute) (proteinworkshop.models.graph_encoders.egnn.EGNNModel attribute) (proteinworkshop.models.graph_encoders.gcpnet.GCPNetModel attribute) (proteinworkshop.models.graph_encoders.gear_net.GearNet attribute) (proteinworkshop.models.graph_encoders.gvp.GVPGNNModel attribute) (proteinworkshop.models.graph_encoders.mace.MACEModel attribute) (proteinworkshop.models.graph_encoders.schnet.SchNetModel attribute) (proteinworkshop.models.graph_encoders.tfn.TensorProductModel attribute) training_step() (proteinworkshop.models.base.BaseModel method) (proteinworkshop.models.base.BenchMarkModel method) transform_encoder_output() (proteinworkshop.models.base.BenchMarkModel method) transform_representation() (in module proteinworkshop.features.representation)

U

url (proteinworkshop.models.graph_encoders.esm_embeddings.EvolutionaryScaleModeling attribute)

V

val_dataloader() (proteinworkshop.datasets.astral.AstralDataModule method) (proteinworkshop.datasets.base.ProteinDataModule method) (proteinworkshop.datasets.cath.CATHDataModule method) (proteinworkshop.datasets.flip_datamodule.FLIPDatamodule method) (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method) (proteinworkshop.datasets.go.GeneOntologyDataset method) val_dataset() (proteinworkshop.datasets.astral.AstralDataModule method) (proteinworkshop.datasets.base.ProteinDataModule method) (proteinworkshop.datasets.cath.CATHDataModule method) (proteinworkshop.datasets.flip_datamodule.FLIPDatamodule method) (proteinworkshop.datasets.fold_classification.FoldClassificationDataModule method) (proteinworkshop.datasets.go.GeneOntologyDataset method)

validation_step() (proteinworkshop.models.base.BaseModel method) (proteinworkshop.models.base.BenchMarkModel method)

W

WANDB_API_KEY (in module proteinworkshop.constants)

WANDB_ENTITY (in module proteinworkshop.constants) WANDB_PROJECT (in module proteinworkshop.constants)

Z

ZENODO_DATASET_NAMES (in module proteinworkshop.constants)