Index

B

build_pairpro() (in module pairpro.preprocessing)

build_sample_l2t() (in module pairpro.dev_tools)

C

calculate_jaccard_similarity() (in module pairpro.hmmer) calculate_similarity_API() (in module pairpro.hmmer) calculate_similarity_user() (in module pairpro.hmmer) check_input_nans() (in module pairpro.evaluate_input_cleaning) (in module pairpro.train_val_input_cleaning) check_input_type() (in module pairpro.evaluate_input_cleaning) (in module pairpro.train_val_input_cleaning)

clean_input_columns() (in module pairpro.evaluate_input_cleaning) (in module pairpro.train_val_input_cleaning) clean_new_dataframe() (in module pairpro.train_val_featuregen) compare_fatcat() (in module pairpro.structures) connect_db() (in module pairpro.preprocessing) create_new_dataframe() (in module pairpro.train_val_featuregen)

D

download_af() (in module pairpro.structures) download_aff() (in module pairpro.structures)

download_pdb() (in module pairpro.structures) download_structure() (in module pairpro.structures)

E

evaluate_model() (in module pairpro.evaluate_model)

F

find_jaccard_similarity_API() (in module pairpro.hmmer)

G

gap_compressed_percent_id() (in module pairpro.user_blast) get_fasta_from_dataframe() (in module pairpro.train_val_featuregen) get_file_pairs_API() (in module pairpro.hmmer)

get_file_pairs_user() (in module pairpro.hmmer) get_matches_gaps() (in module pairpro.user_blast) get_protein_descriptors() (in module pairpro.train_val_featuregen)

H

hmmerscanner() (in module pairpro.hmmer)

hmmpress_hmms() (in module pairpro.hmmer)

I

input_cleaning_wrapper() (in module pairpro.evaluate_input_cleaning) (in module pairpro.train_val_input_cleaning)

L

local_hmmer_wrapper() (in module pairpro.hmmer)

local_hmmer_wrapper_example() (in module pairpro.hmmer)

M

make_blast_df() (in module pairpro.user_blast) make_pairs() (in module pairpro.utils) module pairpro.dev_tools pairpro.evaluate_input_cleaning pairpro.evaluate_model pairpro.hmmer pairpro.preprocessing pairpro.structures pairpro.train_val_classification pairpro.train_val_featuregen pairpro.train_val_input_cleaning pairpro.train_val_wrapper pairpro.user_blast pairpro.utils

N

normalize_bit_scores() (in module pairpro.evaluate_input_cleaning) (in module pairpro.train_val_input_cleaning)

P

pairpro.dev_tools module pairpro.evaluate_input_cleaning module pairpro.evaluate_model module pairpro.hmmer module pairpro.preprocessing module pairpro.structures module pairpro.train_val_classification module pairpro.train_val_featuregen module pairpro.train_val_input_cleaning module

pairpro.train_val_wrapper module pairpro.user_blast module pairpro.utils module parse_function_csv_API() (in module pairpro.hmmer) parse_function_csv_user() (in module pairpro.hmmer) parse_pyhmmer() (in module pairpro.hmmer) parse_pyhmmer_user() (in module pairpro.hmmer) plot_model() (in module pairpro.train_val_classification) prefetch_targets() (in module pairpro.hmmer) preprocess_accessions() (in module pairpro.hmmer) process_pairs_table() (in module pairpro.hmmer) process_response() (in module pairpro.hmmer) process_row() (in module pairpro.structures)

R

rf_wrapper() (in module pairpro.train_val_classification) run_download_af_all() (in module pairpro.structures)

run_fatcat_dict_job() (in module pairpro.structures) run_hmmerscanner() (in module pairpro.hmmer) run_pyhmmer() (in module pairpro.hmmer)

S

save_to_digital_sequences() (in module pairpro.hmmer) save_to_digital_sequences_user_query() (in module pairpro.hmmer) save_to_digital_sequences_user_subject() (in module pairpro.hmmer)

send_request() (in module pairpro.hmmer) sequence_validate() (in module pairpro.user_blast) start_logger_if_necessary() (in module pairpro.utils)

T

train_model() (in module pairpro.train_val_classification)

train_model_structure() (in module pairpro.train_val_classification) train_val_wrapper() (in module pairpro.train_val_wrapper)

U

user_local_hmmer_wrapper_query() (in module pairpro.hmmer)

user_local_hmmer_wrapper_subject() (in module pairpro.hmmer)

V

validate_model() (in module pairpro.train_val_classification) verify_input_columns() (in module pairpro.evaluate_input_cleaning) (in module pairpro.train_val_input_cleaning)

verify_protein_pairs() (in module pairpro.evaluate_input_cleaning) (in module pairpro.train_val_input_cleaning)

W

write_function_output_API() (in module pairpro.hmmer)