Index

_

__call__() (kinactive.model.EarlyStoppingCallback method) (kinactive.model.EvalSetSupplier method) (kinactive.model.ObjectiveFn method) __init__() (kinactive.config.DBConfig method) (kinactive.config.MatrixConfig method) (kinactive.db.DB method) (kinactive.distances.DistanceMatrix method) (kinactive.features.DefaultFeatures method) (kinactive.model.DFGClassifier method) (kinactive.model.EarlyStoppingCallback method) (kinactive.model.EvalSetSupplier method) (kinactive.model.KinactiveModel method) (kinactive.model.ModelT method) (kinactive.model.ObjectiveFn method)

A

ac_helix (kinactive.features.DefaultFeatures attribute)

al (kinactive.features.DefaultFeatures attribute) asp_atoms (kinactive.config.MatrixConfig attribute)

B

b3_sheet (kinactive.features.DefaultFeatures attribute) bb_atoms (kinactive.config.MatrixConfig attribute)

build() (kinactive.db.DB method) (kinactive.distances.DistanceMatrix class method)

C

ca_pos_per_str() (in module kinactive.distances) calculate() (in module kinactive.features) calculate_all_vs() (kinactive.features.DefaultFeatures method) calculate_lig_vs() (kinactive.features.DefaultFeatures method) calculate_seq_vs() (kinactive.features.DefaultFeatures method) calculate_str_vs() (kinactive.features.DefaultFeatures method) chains (kinactive.db.DB property) chunksize (kinactive.config.MatrixConfig attribute)

closest_to() (kinactive.distances.DistanceMatrix method) covered_pos() (in module kinactive.distances) cv() (kinactive.model.DFGClassifier method) (kinactive.model.KinactiveModel method) (kinactive.model.ModelBase method) cv_col (kinactive.model.KinactiveModel attribute) cv_pred() (kinactive.model.DFGClassifier method) (kinactive.model.KinactiveModel method)

D

DB (class in kinactive.db) DBConfig (class in kinactive.config) DefaultFeatures (class in kinactive.features) df (kinactive.distances.DistanceMatrix attribute) df_pos (kinactive.config.MatrixConfig attribute)

dfg_features (kinactive.model.DFGClassifier property) DFGClassifier (class in kinactive.model) DFGModels (class in kinactive.model) dir (kinactive.config.MatrixConfig attribute) discover_domains() (kinactive.db.DB method) DistanceMatrix (class in kinactive.distances)

E

EarlyStoppingCallback (class in kinactive.model)

EvalSetSupplier (class in kinactive.model)

F

features (kinactive.model.DFGClassifier property) (kinactive.model.KinactiveModel property) (kinactive.model.ModelBase property)

fetch() (kinactive.distances.DistanceMatrix method) fit() (kinactive.model.ModelT method)

G

generate_fold_idx() (kinactive.model.DFGClassifier method) (kinactive.model.EvalSetSupplier method) (kinactive.model.KinactiveClassifier method) (kinactive.model.KinactiveRegressor method) (kinactive.model.ModelBase method)

H

hrd (kinactive.features.DefaultFeatures attribute)

I

in_ (kinactive.model.DFGModels attribute) init_add_structure_cpus (kinactive.config.DBConfig attribute) init_cpus (kinactive.config.DBConfig attribute)

init_map_numbering_cpus (kinactive.config.DBConfig attribute) init_tolerate_failures (kinactive.config.DBConfig attribute) init_vs() (in module kinactive.features) io_cpus (kinactive.config.DBConfig attribute)

K

kinactive.base module kinactive.config module kinactive.db module kinactive.distances module kinactive.features module

kinactive.io module kinactive.model module kinactive.resources module KinactiveClassifier (class in kinactive.model) KinactiveModel (class in kinactive.model) KinactiveRegressor (class in kinactive.model)

L

lig_vs (kinactive.features.Results attribute) load() (in module kinactive.io) (kinactive.db.DB method) (kinactive.distances.DistanceMatrix class method) load_data_links() (in module kinactive.config) load_dfg() (in module kinactive.io) load_json() (in module kinactive.io) load_kinactive() (in module kinactive.io)

load_seq_model_features() (in module kinactive.features) load_seq_models() (in module kinactive.io) load_sklearn() (in module kinactive.io) load_str_model_features() (in module kinactive.features) load_str_models() (in module kinactive.io) load_txt_lines() (in module kinactive.io) load_xgb() (in module kinactive.io) lr_objective() (in module kinactive.model)

M

make() (in module kinactive.model) make_lig_vs() (kinactive.features.DefaultFeatures method) make_seq_vs() (kinactive.features.DefaultFeatures method) make_str_vs() (kinactive.features.DefaultFeatures method) matrix_ids() (kinactive.distances.DistanceMatrix method) MatrixConfig (class in kinactive.config) max_fetch_trials (kinactive.config.DBConfig attribute) max_seq_size (kinactive.config.DBConfig attribute) meta (kinactive.model.DFGModels attribute) meta_features (kinactive.model.DFGClassifier property) min_seq_size (kinactive.config.DBConfig attribute)

model (kinactive.model.KinactiveModel property) ModelBase (class in kinactive.model) ModelT (class in kinactive.model) module kinactive.base kinactive.config kinactive.db kinactive.distances kinactive.features kinactive.io kinactive.model kinactive.resources

N

n_proc (kinactive.config.MatrixConfig attribute)

n_super_pos (kinactive.config.MatrixConfig attribute)

O

ObjectiveFn (class in kinactive.model) obtain_sifts_seqs() (kinactive.db.DB method)

other (kinactive.model.DFGModels attribute) out (kinactive.model.DFGModels attribute)

P

params (kinactive.model.KinactiveModel attribute) pdb_dir (kinactive.config.DBConfig attribute) pdb_dir_info (kinactive.config.DBConfig attribute) pdb_fmt (kinactive.config.DBConfig attribute) pdb_num_fetch_threads (kinactive.config.DBConfig attribute) pdb_str_min_size (kinactive.config.DBConfig attribute) phe_atoms (kinactive.config.MatrixConfig attribute) pk_map_name (kinactive.config.DBConfig attribute) (kinactive.config.MatrixConfig attribute) pk_min_cov_hmm (kinactive.config.DBConfig attribute) pk_min_cov_seq (kinactive.config.DBConfig attribute) pk_min_score (kinactive.config.DBConfig attribute) pk_min_seq_domain_size (kinactive.config.DBConfig attribute)

pk_min_str_domain_size (kinactive.config.DBConfig attribute) pk_min_str_seq_match (kinactive.config.DBConfig attribute) pocket (kinactive.features.DefaultFeatures attribute) pos_sup (kinactive.distances.DistanceMatrix attribute) predict() (kinactive.model.DFGClassifier method) (kinactive.model.KinactiveModel method) (kinactive.model.ModelBase method) (kinactive.model.ModelT method) predict_full() (kinactive.model.DFGClassifier method) predict_proba() (kinactive.model.KinactiveClassifier method) (kinactive.model.ModelT method) proba_names (kinactive.model.DFGClassifier property) profile (kinactive.config.DBConfig attribute) profile_pos (kinactive.features.DefaultFeatures attribute)

R

rank_features() (kinactive.model.KinactiveModel method) reinit_model() (kinactive.model.DFGClassifier method) (kinactive.model.KinactiveModel method) (kinactive.model.ModelBase method)

Results (class in kinactive.features) rf_objective() (in module kinactive.model)

S

save() (in module kinactive.io) (kinactive.db.DB method) (kinactive.distances.DistanceMatrix method) save_dfg() (in module kinactive.io) save_json() (in module kinactive.io) save_sklearn() (in module kinactive.io) save_txt_lines() (in module kinactive.io) save_xgb() (in module kinactive.io) score() (kinactive.model.DFGClassifier method) (kinactive.model.KinactiveClassifier method) (kinactive.model.KinactiveRegressor method) (kinactive.model.ModelBase method)

score_fn (kinactive.model.KinactiveModel attribute) select_features() (kinactive.model.KinactiveModel method) select_params() (kinactive.model.KinactiveModel method) selector (kinactive.model.KinactiveModel attribute) seq_dir (kinactive.config.DBConfig attribute) seq_vs (kinactive.features.Results attribute) str_seq_vs (kinactive.features.Results attribute) str_vs (kinactive.features.Results attribute) super_pos() (in module kinactive.distances) superpose() (kinactive.distances.DistanceMatrix method)

T

target_dir (kinactive.config.DBConfig attribute) targets (kinactive.model.DFGClassifier property) (kinactive.model.KinactiveModel property) (kinactive.model.ModelBase property)

tk2pk (kinactive.config.DBConfig attribute) train() (kinactive.model.DFGClassifier method) (kinactive.model.KinactiveModel method) (kinactive.model.ModelBase method)

U

uniprot_chunk_size (kinactive.config.DBConfig attribute)

uniprot_num_fetch_threads (kinactive.config.DBConfig attribute) use_early_stopping (kinactive.model.KinactiveModel attribute)

V

verbose (kinactive.config.DBConfig attribute)

W

weight_col (kinactive.model.KinactiveModel attribute)

X

xdfgx (kinactive.features.DefaultFeatures attribute)

xgb_objective() (in module kinactive.model)