Index

A

adabmDCA module adabmDCA.dataset module adabmDCA.fasta_utils module adabmDCA.functional module adabmDCA.graph module adabmDCA.io module adabmDCA.parser module adabmDCA.plot module adabmDCA.resampling module

adabmDCA.sampling module adabmDCA.statmech module adabmDCA.stats module adabmDCA.training module adabmDCA.utils module add_args_contacts() (in module adabmDCA.parser) add_args_dca() (in module adabmDCA.parser) add_args_dms() (in module adabmDCA.parser) add_args_eaDCA() (in module adabmDCA.parser) add_args_edDCA() (in module adabmDCA.parser) add_args_energies() (in module adabmDCA.parser) add_args_sample() (in module adabmDCA.parser) add_args_train() (in module adabmDCA.parser)

C

compute_energy() (in module adabmDCA.statmech) compute_entropy() (in module adabmDCA.statmech) compute_log_likelihood() (in module adabmDCA.statmech)

compute_logZ_exact() (in module adabmDCA.statmech) compute_mixing_time() (in module adabmDCA.resampling) compute_weights() (in module adabmDCA.fasta_utils)

D

DatasetDCA (class in adabmDCA.dataset)

decimate_graph() (in module adabmDCA.graph) decode_sequence() (in module adabmDCA.fasta_utils)

E

encode_sequence() (in module adabmDCA.fasta_utils) enumerate_states() (in module adabmDCA.statmech)

extract_Cij_from_freq() (in module adabmDCA.stats) extract_Cij_from_seqs() (in module adabmDCA.stats)

G

generate_unique_triplets() (in module adabmDCA.stats) get_correlation_two_points() (in module adabmDCA.stats) get_covariance_matrix() (in module adabmDCA.stats) get_deltaE() (in module adabmDCA.sampling) get_device() (in module adabmDCA.utils) get_effective_size() (adabmDCA.dataset.DatasetDCA method) get_freq_single_point() (in module adabmDCA.stats) get_freq_three_points() (in module adabmDCA.stats)

get_freq_two_points() (in module adabmDCA.stats) get_mask_save() (in module adabmDCA.utils) get_num_residues() (adabmDCA.dataset.DatasetDCA method) get_num_states() (adabmDCA.dataset.DatasetDCA method) get_sampler() (in module adabmDCA.sampling) get_slope() (in module adabmDCA.stats) get_tokens() (in module adabmDCA.fasta_utils) gibbs_sampling() (in module adabmDCA.sampling)

I

import_clean_dataset() (in module adabmDCA.fasta_utils) import_from_fasta() (in module adabmDCA.fasta_utils)

init_chains() (in module adabmDCA.utils) init_parameters() (in module adabmDCA.utils)

L

load_chains() (in module adabmDCA.io)

load_params() (in module adabmDCA.io) load_params_oldformat() (in module adabmDCA.io)

M

metropolis() (in module adabmDCA.sampling) metropolis_sweep() (in module adabmDCA.sampling) module adabmDCA adabmDCA.dataset adabmDCA.fasta_utils adabmDCA.functional adabmDCA.graph adabmDCA.io adabmDCA.parser adabmDCA.plot adabmDCA.resampling adabmDCA.sampling adabmDCA.statmech adabmDCA.stats adabmDCA.training adabmDCA.utils

O

one_hot() (in module adabmDCA.functional)

P

plot_autocorrelation() (in module adabmDCA.plot) plot_hist() (in module adabmDCA.plot) plot_PCA() (in module adabmDCA.plot)

plot_pearson_sampling() (in module adabmDCA.plot) plot_scatter_correlations() (in module adabmDCA.plot) plot_scatter_labels() (in module adabmDCA.plot)

R

resample_sequences() (in module adabmDCA.utils)

S

save_chains() (in module adabmDCA.io) save_params() (in module adabmDCA.io)

save_params_oldformat() (in module adabmDCA.io) set_zerosum_gauge() (in module adabmDCA.utils) shuffle() (adabmDCA.dataset.DatasetDCA method)

T

train_graph() (in module adabmDCA.training)

U

update() (in module adabmDCA.training)

update_mask() (in module adabmDCA.graph) update_weights_AIS() (in module adabmDCA.statmech)

V

validate_alphabet() (in module adabmDCA.fasta_utils)

W

write_fasta() (in module adabmDCA.fasta_utils)