Index

A

all_but() (in module diurnal.family)

B

Bracket (class in diurnal.evaluate)

BRACKET_TO_ONEHOT (diurnal.structure.Schemes attribute), [1]

C

categorize_matrix() (in module diurnal.train) categorize_vector() (in module diurnal.train) clean_dir_path() (in module diurnal.utils.file_io) clean_matrices() (in module diurnal.train) clean_vectors() (in module diurnal.train) compare_pairings() (in module diurnal.visualize)

confusion_matrix() (diurnal.evaluate.Bracket method) Constants (class in diurnal.structure) ContactMatrix (class in diurnal.evaluate) convert_to_scalars() (diurnal.evaluate.Bracket method) crop() (diurnal.evaluate.Bracket method) (diurnal.evaluate.ContactMatrix method) (diurnal.evaluate.Shadow method)

D

decompress() (in module diurnal.utils.file_io) diurnal module diurnal.database module diurnal.evaluate module diurnal.family module diurnal.models module diurnal.models.baseline module diurnal.models.networks module diurnal.models.networks.cnn module diurnal.models.networks.mlp module

diurnal.structure module diurnal.train module diurnal.utils module diurnal.utils.file_io module diurnal.utils.log module diurnal.utils.rna_data module diurnal.visualize module Dot_Bracket (class in diurnal.models.networks.cnn) download() (in module diurnal.database) (in module diurnal.utils.file_io) download_all() (in module diurnal.database)

E

error() (in module diurnal.utils.log)

F

f1() (diurnal.evaluate.ContactMatrix method) FN() (diurnal.evaluate.ContactMatrix method) (diurnal.evaluate.Shadow method) format_basic() (in module diurnal.database) format_filenames() (in module diurnal.database) format_primary_secondary_structure() (in module diurnal.database) format_primary_structure() (in module diurnal.database) format_secondary_structure() (in module diurnal.database)

forward() (diurnal.models.networks.cnn.Dot_Bracket method) (diurnal.models.networks.cnn.MatrixToMatrixAutoencoder1 method) (diurnal.models.networks.cnn.RNA_CNN method) (diurnal.models.networks.cnn.RNA_CNN_family_aware method) (diurnal.models.networks.cnn.Shadow method) (diurnal.models.networks.mlp.RNA_MLP_classes method) (diurnal.models.networks.mlp.RNA_MLP_classifier method) FP() (diurnal.evaluate.ContactMatrix method) (diurnal.evaluate.Shadow method)

G

get_name() (in module diurnal.family)

H

heatmap() (in module diurnal.visualize)

I

info() (in module diurnal.utils.log) is_downloaded() (in module diurnal.utils.file_io) is_known() (in module diurnal.family)

IUPAC_ONEHOT_PAIRINGS_VECTOR (diurnal.structure.Schemes attribute), [1] IUPAC_PAIRINGS_SCALARS (diurnal.structure.Schemes attribute) IUPAC_PAIRINGS_SCALARS_NEGATIVE_PADDING (diurnal.structure.Schemes attribute) IUPAC_TO_ONEHOT (diurnal.structure.Schemes attribute), [1]

K

k_fold_indices() (in module diurnal.train)

k_fold_split() (in module diurnal.train)

L

lengths() (in module diurnal.visualize) load_data() (in module diurnal.train)

load_families() (in module diurnal.train) LOOP_MIN_DISTANCE (diurnal.structure.Constants attribute), [1]

M

Majority (class in diurnal.models.baseline) MatrixToMatrixAutoencoder1 (class in diurnal.models.networks.cnn) micro_f1() (diurnal.evaluate.Bracket method) module diurnal diurnal.database diurnal.evaluate diurnal.family diurnal.models diurnal.models.baseline diurnal.models.networks diurnal.models.networks.cnn diurnal.models.networks.mlp diurnal.structure diurnal.train diurnal.utils diurnal.utils.file_io diurnal.utils.log diurnal.utils.rna_data diurnal.visualize

N

normalize_distance_matrix() (diurnal.structure.Secondary method)

P

potential_pairings() (in module diurnal.visualize) precision() (diurnal.evaluate.ContactMatrix method) (diurnal.evaluate.Shadow method) prediction() (in module diurnal.visualize)

Primary (class in diurnal.structure) primary_structure() (in module diurnal.visualize) print_contact_matrix() (in module diurnal.visualize) progress_bar() (in module diurnal.utils.log)

Q

quantize() (diurnal.structure.Secondary method) quantize_distance_matrix() (diurnal.structure.Secondary method)

quantize_matrix() (in module diurnal.train) quantize_vector() (diurnal.structure.Secondary method)

R

Random (class in diurnal.models.baseline) read_ct_file() (in module diurnal.utils.rna_data) read_ct_file_length() (in module diurnal.utils.rna_data) recall() (diurnal.evaluate.ContactMatrix method) (diurnal.evaluate.Shadow method)

recall_precision_f1() (diurnal.evaluate.Shadow method) RNA_CNN (class in diurnal.models.networks.cnn) RNA_CNN_family_aware (class in diurnal.models.networks.cnn) RNA_MLP_classes (class in diurnal.models.networks.mlp) RNA_MLP_classifier (class in diurnal.models.networks.mlp)

S

save() (in module diurnal.database) Schemes (class in diurnal.structure) Secondary (class in diurnal.structure) secondary_structure() (in module diurnal.visualize) select() (in module diurnal.family) Shadow (class in diurnal.evaluate) (class in diurnal.models.networks.cnn) shadow() (in module diurnal.visualize)

SHADOW_ENCODING (diurnal.structure.Schemes attribute), [1] shuffle_data() (in module diurnal.train) split() (in module diurnal.family) (in module diurnal.train) split_data() (in module diurnal.train) split_indices() (in module diurnal.train) structure_length_per_family() (in module diurnal.visualize) summarize() (in module diurnal.database) summarize_results() (in module diurnal.evaluate)

T

title() (in module diurnal.utils.log) TN() (diurnal.evaluate.ContactMatrix method) (diurnal.evaluate.Shadow method) to_bracket() (diurnal.structure.Secondary method) to_distance_matrix() (diurnal.structure.Secondary method) to_elements() (diurnal.structure.Secondary method) to_mask() (diurnal.structure.Primary method) to_matrix() (diurnal.structure.Primary method) (diurnal.structure.Secondary method) to_name() (in module diurnal.family)

to_onehot() (diurnal.structure.Primary method) (diurnal.structure.Secondary method) (in module diurnal.family) to_pairings() (diurnal.structure.Secondary method) to_sequence() (diurnal.structure.Primary method) to_shadow() (diurnal.structure.Secondary method) (in module diurnal.evaluate) TP() (diurnal.evaluate.ContactMatrix method) (diurnal.evaluate.Shadow method) trace() (in module diurnal.utils.log)

U

Uniform (class in diurnal.models.baseline)

unpad_matrix() (diurnal.structure.Primary method)

W

warning() (in module diurnal.utils.log)