Index A | B | C | D | E | F | G | I | L | M | P | R | S | T | U | W A Alphabet (class in dscript.alphabets) B batchnorm (dscript.models.contact.FullyConnected attribute) C cmap() (dscript.models.contact.ContactCNN method) 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) dscript.alphabets 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) 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_3di_sequences() (in module dscript.foldseek) get_dim() (in module dscript.glider) get_foldseek_onehot() (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) I IdentityEmbed (class in dscript.models.embedding) 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) LoadingPool (class in dscript.loading) 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.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 P PairedDataset (class in dscript.utils) 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) predict() (dscript.models.contact.ContactCNN method) (dscript.models.interaction.ModelInteraction method) R RBF() (in module dscript.utils) retry() (in module dscript.pretrained) S SDM12 (class in dscript.alphabets) setup_logger() (in module dscript.utils) shutdown() (dscript.loading.LoadingPool method) 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) unpack() (dscript.alphabets.Alphabet method) W write() (in module dscript.fasta)