Index

A

add_args() (in module dscript.commands.extract_3di)

Alphabet (class in dscript.alphabets)

B

batch_size (dscript.commands.train.TrainArguments attribute) batchnorm (dscript.models.contact.FullyConnected attribute)

BlockedPredictionArguments (class in dscript.commands.predict_block) blocks (dscript.commands.predict_block.BlockedPredictionArguments attribute)

C

checkpoint (dscript.commands.train.TrainArguments attribute) cmap() (dscript.models.contact.ContactCNN method) cmd (dscript.commands.embed.EmbeddingArguments attribute) (dscript.commands.evaluate.EvaluateArguments attribute) (dscript.commands.extract_3di.Extract3DiArguments attribute) (dscript.commands.predict_block.BlockedPredictionArguments attribute) (dscript.commands.predict_serial.PredictionArguments attribute) (dscript.commands.train.TrainArguments attribute) collate_paired_sequences() (in module dscript.utils) compute_cw_score() (in module dscript.glider)

compute_cw_score_normalized() (in module dscript.glider) compute_degree_vec() (in module dscript.glider) compute_l3_score_mat() (in module dscript.glider) compute_l3_unweighted_mat() (in module dscript.glider) compute_l3_weighted_mat() (in module dscript.glider) compute_pinverse_diagonal() (in module dscript.glider) compute_X_normalized() (in module dscript.glider) ContactCNN (class in dscript.models.contact) cpred() (dscript.models.interaction.ModelInteraction method) create_edge_dict() (in module dscript.glider) create_neighborhood_dict() (in module dscript.glider)

D

decode() (dscript.alphabets.Alphabet method) densify() (in module dscript.glider) device (dscript.commands.embed.EmbeddingArguments attribute) (dscript.commands.evaluate.EvaluateArguments attribute) (dscript.commands.predict_block.BlockedPredictionArguments attribute) (dscript.commands.predict_serial.PredictionArguments attribute) (dscript.commands.train.TrainArguments attribute) do_pool (dscript.commands.train.TrainArguments attribute) dropout (dscript.commands.train.TrainArguments attribute) dscript.alphabets module dscript.commands.embed module dscript.commands.evaluate module dscript.commands.extract_3di module dscript.commands.predict_block module dscript.commands.predict_serial module dscript.commands.train module

dscript.fasta module dscript.foldseek module dscript.glider module dscript.language_model module dscript.load_worker module dscript.loading module dscript.models.contact module dscript.models.embedding module dscript.models.interaction module dscript.pretrained module dscript.utils module DSCRIPTModel (class in dscript.models.interaction)

E

embed() (dscript.models.interaction.ModelInteraction method) embed_from_directory() (in module dscript.language_model) embed_from_fasta() (in module dscript.language_model) embedding (dscript.commands.evaluate.EvaluateArguments attribute) (dscript.commands.train.TrainArguments attribute)

EmbeddingArguments (class in dscript.commands.embed) embeddings (dscript.commands.predict_block.BlockedPredictionArguments attribute) (dscript.commands.predict_serial.PredictionArguments attribute) encode() (dscript.alphabets.Alphabet method) EvaluateArguments (class in dscript.commands.evaluate) Extract3DiArguments (class in dscript.commands.extract_3di)

F

foldseek_fasta (dscript.commands.predict_block.BlockedPredictionArguments attribute) foldseek_path (dscript.commands.extract_3di.Extract3DiArguments attribute) forward() (dscript.models.contact.ContactCNN method) (dscript.models.contact.FullyConnected method) (dscript.models.embedding.FullyConnectedEmbed method) (dscript.models.embedding.IdentityEmbed method) (dscript.models.interaction.LogisticActivation method)

FullyConnected (class in dscript.models.contact) FullyConnectedEmbed (class in dscript.models.embedding) func (dscript.commands.embed.EmbeddingArguments attribute) (dscript.commands.evaluate.EvaluateArguments attribute) (dscript.commands.extract_3di.Extract3DiArguments attribute) (dscript.commands.predict_block.BlockedPredictionArguments attribute) (dscript.commands.predict_serial.PredictionArguments attribute) (dscript.commands.train.TrainArguments attribute)

G

get_3di_sequences() (in module dscript.foldseek) get_dim() (in module dscript.glider) get_foldseek_onehot() (in module dscript.commands.evaluate) (in module dscript.foldseek) get_kmer() (dscript.alphabets.Alphabet method) get_pretrained() (in module dscript.pretrained)

get_state_dict() (in module dscript.pretrained) get_state_dict_path() (in module dscript.pretrained) glide_compute_map() (in module dscript.glider) glide_predict_links() (in module dscript.glider) glider_score() (in module dscript.glider) glider_thresh (dscript.commands.train.TrainArguments attribute) glider_weight (dscript.commands.train.TrainArguments attribute)

H

hidden_dim (dscript.commands.train.TrainArguments attribute)

I

IdentityEmbed (class in dscript.models.embedding) input_dim (dscript.commands.train.TrainArguments attribute)

interaction_eval() (in module dscript.commands.train) interaction_grad() (in module dscript.commands.train) interaction_weight (dscript.commands.train.TrainArguments attribute)

K

kernel_width (dscript.commands.train.TrainArguments attribute)

L

lm_embed() (in module dscript.language_model) load() (dscript.loading.LoadingPool method) load_hdf5_parallel() (in module dscript.utils) load_once() (dscript.loading.LoadingPool method) load_proc (dscript.commands.predict_block.BlockedPredictionArguments attribute) (dscript.commands.predict_serial.PredictionArguments attribute)

LoadingPool (class in dscript.loading) log() (in module dscript.utils) LogisticActivation (class in dscript.models.interaction) lr (dscript.commands.train.TrainArguments attribute)

M

main() (in module dscript.commands.extract_3di) map_predict() (dscript.models.interaction.ModelInteraction method) model (dscript.commands.evaluate.EvaluateArguments attribute) (dscript.commands.predict_block.BlockedPredictionArguments attribute) (dscript.commands.predict_serial.PredictionArguments attribute) ModelInteraction (class in dscript.models.interaction) module dscript.alphabets dscript.commands.embed dscript.commands.evaluate dscript.commands.extract_3di dscript.commands.predict_block dscript.commands.predict_serial dscript.commands.train dscript.fasta dscript.foldseek dscript.glider dscript.language_model dscript.load_worker dscript.loading dscript.models.contact dscript.models.embedding dscript.models.interaction dscript.pretrained dscript.utils

N

no_augment (dscript.commands.train.TrainArguments attribute) no_sigmoid (dscript.commands.train.TrainArguments attribute)

no_w (dscript.commands.train.TrainArguments attribute) num_epochs (dscript.commands.train.TrainArguments attribute)

O

out_file (dscript.commands.extract_3di.Extract3DiArguments attribute) outfile (dscript.commands.embed.EmbeddingArguments attribute) (dscript.commands.predict_block.BlockedPredictionArguments attribute) (dscript.commands.predict_serial.PredictionArguments attribute) (dscript.commands.train.TrainArguments attribute)

P

PairedDataset (class in dscript.utils) pairs (dscript.commands.predict_block.BlockedPredictionArguments attribute) parse() (in module dscript.fasta) parse_device() (in module dscript.utils) parse_dict() (in module dscript.fasta) parse_directory() (in module dscript.fasta) parse_from_list() (in module dscript.fasta) pdb_directory (dscript.commands.extract_3di.Extract3DiArguments attribute)

plot_eval_predictions() (in module dscript.commands.evaluate) pool_width (dscript.commands.train.TrainArguments attribute) predict() (dscript.models.contact.ContactCNN method) (dscript.models.interaction.ModelInteraction method) predict_cmap_interaction() (in module dscript.commands.train) predict_interaction() (in module dscript.commands.train) PredictionArguments (class in dscript.commands.predict_serial) projection_dim (dscript.commands.train.TrainArguments attribute) protins (dscript.commands.predict_block.BlockedPredictionArguments attribute)

R

RBF() (in module dscript.utils)

retry() (in module dscript.pretrained) run_tt (dscript.commands.train.TrainArguments attribute)

S

save_prefix (dscript.commands.train.TrainArguments attribute) SDM12 (class in dscript.alphabets) seed (dscript.commands.train.TrainArguments attribute) seqs (dscript.commands.embed.EmbeddingArguments attribute) (dscript.commands.predict_serial.PredictionArguments attribute)

setup_logger() (in module dscript.utils) shutdown() (dscript.loading.LoadingPool method) SkipLSTM (class in dscript.models.embedding)

T

test (dscript.commands.evaluate.EvaluateArguments attribute) (dscript.commands.train.TrainArguments attribute) thresh (dscript.commands.predict_block.BlockedPredictionArguments attribute) (dscript.commands.predict_serial.PredictionArguments attribute)

to_one_hot() (dscript.models.embedding.SkipLSTM method) train (dscript.commands.train.TrainArguments attribute) train_model() (in module dscript.commands.train) TrainArguments (class in dscript.commands.train) transform() (dscript.models.embedding.SkipLSTM method)

U

Uniprot21 (class in dscript.alphabets)

unpack() (dscript.alphabets.Alphabet method)

W

weight_decay (dscript.commands.train.TrainArguments attribute)

write() (in module dscript.fasta)