Index

A

Alphabet (class in dscript.alphabets)

B

broadcast() (dscript.models.contact.ContactCNN method)

C

collate_paired_sequences() (in module dscript.utils)

ContactCNN (class in dscript.models.contact) cpred() (dscript.models.interaction.ModelInteraction method)

D

decode() (dscript.alphabets.Alphabet method) dscript.alphabets module dscript.commands.embed module dscript.commands.eval module dscript.commands.predict module dscript.commands.train module dscript.fasta module

dscript.language_model module dscript.models.contact module dscript.models.embedding module dscript.models.interaction module dscript.pretrained module dscript.utils module

E

embed() (dscript.models.interaction.ModelInteraction method) embed_from_directory() (in module dscript.language_model)

embed_from_fasta() (in module dscript.language_model) encode() (dscript.alphabets.Alphabet method)

F

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)

G

get_pretrained() (in module dscript.pretrained)

get_state_dict() (in module dscript.pretrained) gpu_mem() (in module dscript.utils)

I

IdentityEmbed (class in dscript.models.embedding)

interaction_eval() (in module dscript.commands.train) interaction_grad() (in module dscript.commands.train)

L

lm_embed() (in module dscript.language_model)

log() (in module dscript.utils) LogisticActivation (class in dscript.models.interaction)

M

map_predict() (dscript.models.interaction.ModelInteraction method) ModelInteraction (class in dscript.models.interaction) module dscript.alphabets dscript.commands.embed dscript.commands.eval dscript.commands.predict dscript.commands.train dscript.fasta dscript.language_model dscript.models.contact dscript.models.embedding dscript.models.interaction dscript.pretrained dscript.utils

P

PairedDataset (class in dscript.utils) parse() (in module dscript.fasta) parse_directory() (in module dscript.fasta) plot_eval_predictions() (in module dscript.commands.eval) plot_PR_curve() (in module dscript.utils)

plot_ROC_curve() (in module dscript.utils) 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)

R

RBF() (in module dscript.utils)

S

SkipLSTM (class in dscript.models.embedding)

T

to_one_hot() (dscript.models.embedding.SkipLSTM method)

transform() (dscript.models.embedding.SkipLSTM method)

U

Uniprot21 (class in dscript.alphabets)

W

write() (in module dscript.fasta)