D-SCRIPT
v0.2.4
Installation
Usage
Data
API
D-SCRIPT
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Index
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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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H
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I
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K
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L
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M
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N
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O
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P
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R
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T
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W
A
Alphabet (class in dscript.alphabets)
B
batch_size() (dscript.commands.train.TrainArguments property)
batchnorm (dscript.models.contact.FullyConnected attribute)
C
checkpoint() (dscript.commands.train.TrainArguments property)
cmap() (dscript.models.contact.ContactCNN method)
cmd() (dscript.commands.embed.EmbeddingArguments property)
(dscript.commands.evaluate.EvaluateArguments property)
(dscript.commands.predict.PredictionArguments property)
(dscript.commands.train.TrainArguments property)
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)
count_bins() (in module dscript.fasta)
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 property)
(dscript.commands.evaluate.EvaluateArguments property)
(dscript.commands.predict.PredictionArguments property)
(dscript.commands.train.TrainArguments property)
do_pool() (dscript.commands.train.TrainArguments property)
dropout() (dscript.commands.train.TrainArguments property)
dscript.alphabets
module
dscript.commands.embed
module
dscript.commands.evaluate
module
dscript.commands.predict
module
dscript.commands.train
module
dscript.fasta
module
dscript.glider
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)
embedding() (dscript.commands.evaluate.EvaluateArguments property)
(dscript.commands.train.TrainArguments property)
EmbeddingArguments (class in dscript.commands.embed)
embeddings() (dscript.commands.predict.PredictionArguments property)
encode() (dscript.alphabets.Alphabet method)
EvaluateArguments (class in dscript.commands.evaluate)
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)
func() (dscript.commands.embed.EmbeddingArguments property)
(dscript.commands.evaluate.EvaluateArguments property)
(dscript.commands.predict.PredictionArguments property)
(dscript.commands.train.TrainArguments property)
G
get_dim() (in module dscript.glider)
get_foldseek_onehot() (in module dscript.commands.evaluate)
(in module dscript.commands.train)
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 property)
glider_weight() (dscript.commands.train.TrainArguments property)
H
hidden_dim() (dscript.commands.train.TrainArguments property)
I
IdentityEmbed (class in dscript.models.embedding)
input_dim() (dscript.commands.train.TrainArguments property)
interaction_eval() (in module dscript.commands.train)
interaction_grad() (in module dscript.commands.train)
interaction_weight() (dscript.commands.train.TrainArguments property)
K
kernel_width() (dscript.commands.train.TrainArguments property)
L
lm_embed() (in module dscript.language_model)
load_hdf5_parallel() (in module dscript.utils)
log() (in module dscript.utils)
LogisticActivation (class in dscript.models.interaction)
lr() (dscript.commands.train.TrainArguments property)
M
map_predict() (dscript.models.interaction.ModelInteraction method)
model() (dscript.commands.evaluate.EvaluateArguments property)
(dscript.commands.predict.PredictionArguments property)
ModelInteraction (class in dscript.models.interaction)
module
dscript.alphabets
dscript.commands.embed
dscript.commands.evaluate
dscript.commands.predict
dscript.commands.train
dscript.fasta
dscript.glider
dscript.language_model
dscript.models.contact
dscript.models.embedding
dscript.models.interaction
dscript.pretrained
dscript.utils
N
no_augment() (dscript.commands.train.TrainArguments property)
no_sigmoid() (dscript.commands.train.TrainArguments property)
no_w() (dscript.commands.train.TrainArguments property)
num_epochs() (dscript.commands.train.TrainArguments property)
O
outfile() (dscript.commands.embed.EmbeddingArguments property)
(dscript.commands.predict.PredictionArguments property)
(dscript.commands.train.TrainArguments property)
P
PairedDataset (class in dscript.utils)
parse() (in module dscript.fasta)
parse_directory() (in module dscript.fasta)
plot_eval_predictions() (in module dscript.commands.evaluate)
pool_width() (dscript.commands.train.TrainArguments property)
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)
projection_dim() (dscript.commands.train.TrainArguments property)
R
RBF() (in module dscript.utils)
retry() (in module dscript.pretrained)
run_tt() (dscript.commands.train.TrainArguments property)
S
save_prefix() (dscript.commands.train.TrainArguments property)
SDM12 (class in dscript.alphabets)
seed() (dscript.commands.train.TrainArguments property)
seqs() (dscript.commands.embed.EmbeddingArguments property)
(dscript.commands.predict.PredictionArguments property)
SkipLSTM (class in dscript.models.embedding)
T
test() (dscript.commands.evaluate.EvaluateArguments property)
(dscript.commands.train.TrainArguments property)
thresh() (dscript.commands.predict.PredictionArguments property)
to_one_hot() (dscript.models.embedding.SkipLSTM method)
train() (dscript.commands.train.TrainArguments property)
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 property)
write() (in module dscript.fasta)
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