Index

_

_log_open (ringtail.OutputManager attribute) (ringtail.outputmanager.OutputManager attribute)

_run_mode (ringtail.RingtailCore attribute) (ringtail.ringtailcore.RingtailCore attribute)

A

add_interactions (ringtail.DockingFileReader attribute) (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) (ringtail.mpreaderwriter.DockingFileReader attribute)

add_results_from_files() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) add_results_from_vina_string() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method)

B

blob2str() (ringtail.ReceptorManager static method) (ringtail.receptormanager.ReceptorManager static method) bookmark_has_rows() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method)

bookmark_name (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute)

C

check_passing_bookmark_exists() (ringtail.StorageManager method) (ringtail.storagemanager.StorageManager method) check_ringtaildb_version() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) check_storage_compatibility() (ringtail.StorageManager method) (ringtail.storagemanager.StorageManager method) check_storage_ready() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) checks() (ringtail.Filters method) (ringtail.ringtailoptions.Filters method) (ringtail.ringtailoptions.GeneralOptions method) (ringtail.ringtailoptions.InputFiles method) (ringtail.ringtailoptions.InputStrings method) (ringtail.ringtailoptions.OutputOptions method) (ringtail.ringtailoptions.ReadOptions method) (ringtail.ringtailoptions.ResultsProcessingOptions method) (ringtail.ringtailoptions.StorageOptions method) chunk_size (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) clone() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method)

CLOptionParser (class in ringtail) (class in ringtail.cloptionparser) close_logfile() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) close_storage() (ringtail.StorageManager method) (ringtail.storagemanager.StorageManager method) cmdline_parser() (in module ringtail.cloptionparser) conn (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute) count_receptors_in_db() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) create_bookmark() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) create_bookmark_from_temp_table() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) create_temp_table_from_bookmark() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) crossref_filter() (ringtail.StorageManager method) (ringtail.storagemanager.StorageManager method) current_bookmark_name (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute)

D

data_from_bookmark (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) DatabaseConnectionError, [1] DatabaseInsertionError, [1] DatabaseQueryError, [1] DatabaseTableCreationError, [1] DatabaseViewCreationError, [1] db_file (ringtail.RingtailCore attribute) (ringtail.ringtailcore.RingtailCore attribute) (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute) default_dict() (ringtail.RingtailCore static method) (ringtail.ringtailcore.RingtailCore static method) display_pymol() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method)

docking_mode (ringtail.DockingFileReader attribute) (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) (ringtail.mpreaderwriter.DockingFileReader attribute) (ringtail.RingtailCore attribute) (ringtail.RingtailCore property) (ringtail.ringtailcore.RingtailCore attribute) (ringtail.ringtailcore.RingtailCore property) DockingFileReader (class in ringtail) (class in ringtail.mpreaderwriter) drop_bookmark() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) duplicate_handling (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute)

E

export_bookmark_db (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) export_bookmark_db() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) export_csv() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method)

export_receptor (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) export_receptors() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) export_sdf_path (ringtail.OutputManager attribute) (ringtail.outputmanager.OutputManager attribute)

F

fetch_bookmark() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_clustered_similars() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_data_for_passing_results() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_filters_from_bookmark() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_flexres_info() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_interaction_info_by_index() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_nonpassing_pose_properties() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_passing_ligand_output_info() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_passing_pose_properties() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_pose_interactions() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_receptor_object_by_name() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_receptor_objects() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_single_ligand_output_info() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_single_pose_properties() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) fetch_summary_data() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) field_to_column_name (ringtail.StorageManager attribute) (ringtail.storagemanager.StorageManager attribute) (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute)

file_pattern (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) file_sources (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) FileParsingError, [1] filter() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) filter_bookmark (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute) filter_results() (ringtail.StorageManager method) (ringtail.storagemanager.StorageManager method) filtering (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) filtering_window (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute) Filters (class in ringtail) (class in ringtail.ringtailoptions) filters (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) (ringtail.RingtailCore attribute) (ringtail.ringtailcore.RingtailCore attribute) finalize_database_write() (ringtail.StorageManager method) (ringtail.storagemanager.StorageManager method) finalize_write() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) find_pose_interactions() (ringtail.InteractionFinder method) (ringtail.interactions.InteractionFinder method) find_similar_ligands() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) format_for_storage() (ringtail.storagemanager.StorageManagerSQLite class method) (ringtail.StorageManagerSQLite class method)

G

GeneralOptions (class in ringtail.ringtailoptions) generate_config_file_template() (ringtail.RingtailCore static method) (ringtail.ringtailcore.RingtailCore static method) get_all_bookmark_names() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) get_bookmark_names() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) get_current_bookmark_name() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) get_filter_keys() (ringtail.Filters class method) (ringtail.ringtailoptions.Filters class method)

get_maxmiss_union() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) get_options_info() (ringtail.RingtailCore static method) (ringtail.ringtailcore.RingtailCore static method) get_plot_data() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) (ringtail.StorageManager method) (ringtail.storagemanager.StorageManager method) get_previous_filter_data() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method)

I

index_columns (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute) initialize_from_dict() (ringtail.ringtailoptions.RTOptions method) InputFiles (class in ringtail.ringtailoptions) InputStrings (class in ringtail.ringtailoptions) insert_data() (ringtail.StorageManager method) (ringtail.storagemanager.StorageManager method) insert_interactions() (ringtail.StorageManager method) (ringtail.storagemanager.StorageManager method) insert_receptor_blob() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) interaction_cluster (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute)

interaction_cutoff_radii (ringtail.InteractionFinder attribute) (ringtail.interactions.InteractionFinder attribute) interaction_cutoffs (ringtail.DockingFileReader attribute) (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) (ringtail.mpreaderwriter.DockingFileReader attribute) interaction_tolerance (ringtail.DockingFileReader attribute) (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) (ringtail.mpreaderwriter.DockingFileReader attribute) InteractionFinder (class in ringtail) (class in ringtail.interactions) is_valid_path() (ringtail.ringtailoptions.RTOptions class method)

L

ligands_rdkit_mol() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) log_file (ringtail.OutputManager attribute) (ringtail.outputmanager.OutputManager attribute)

log_num_passing_ligands() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method)

M

make_receptor_blobs() (ringtail.ReceptorManager static method) (ringtail.receptormanager.ReceptorManager static method) max_poses (ringtail.DockingFileReader attribute) (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) (ringtail.mpreaderwriter.DockingFileReader attribute) max_proc (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) mfpt_cluster (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute) module ringtail ringtail.cloptionparser ringtail.exceptions ringtail.interactions ringtail.mpmanager ringtail.mpreaderwriter ringtail.outputmanager ringtail.parsers ringtail.receptormanager ringtail.resultsmanager ringtail.ringtailcore ringtail.ringtailoptions ringtail.storagemanager

MPManager (class in ringtail) (class in ringtail.mpmanager) MultiprocessingError, [1]

N

NoInputError

num_files (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute)

O

open_cursors (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute) open_logfile() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) OptionError, [1] options (ringtail.Filters attribute) (ringtail.ringtailoptions.Filters attribute) (ringtail.ringtailoptions.GeneralOptions attribute) (ringtail.ringtailoptions.InputFiles attribute) (ringtail.ringtailoptions.InputStrings attribute) (ringtail.ringtailoptions.OutputOptions attribute) (ringtail.ringtailoptions.ReadOptions attribute) (ringtail.ringtailoptions.ResultsProcessingOptions attribute) (ringtail.ringtailoptions.StorageOptions attribute) order_options (ringtail.ringtailoptions.StorageOptions attribute) order_results (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute)

outfields (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute) output_all_poses (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute) OutputError, [1] outputman (ringtail.RingtailCore attribute) (ringtail.ringtailcore.RingtailCore attribute) OutputManager (class in ringtail) (class in ringtail.outputmanager) OutputOptions (class in ringtail.ringtailoptions) outputopts (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) overwrite (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute) overwrite_storage() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method)

P

parse_single_dlg() (in module ringtail) (in module ringtail.parsers) parse_vina_result() (in module ringtail) (in module ringtail.parsers) pipe_conn (ringtail.DockingFileReader attribute) (ringtail.mpreaderwriter.DockingFileReader attribute) plot (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) plot() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) plot_all_data() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) plot_single_points() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) print_summary (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute)

process_data() (ringtail.mpreaderwriter.Writer method) (ringtail.Writer method) process_docking_data() (ringtail.ResultsManager method) (ringtail.resultsmanager.ResultsManager method) process_mode (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) process_options() (ringtail.CLOptionParser method) (ringtail.cloptionparser.CLOptionParser method) process_results() (ringtail.MPManager method) (ringtail.mpmanager.MPManager method) produce_summary() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) prune() (ringtail.StorageManager method) (ringtail.storagemanager.StorageManager method) pymol (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute)

Q

queueIn (ringtail.DockingFileReader attribute) (ringtail.mpreaderwriter.DockingFileReader attribute)

queueOut (ringtail.DockingFileReader attribute) (ringtail.mpreaderwriter.DockingFileReader attribute)

R

ReadOptions (class in ringtail.ringtailoptions) rec_string (ringtail.InteractionFinder attribute) (ringtail.interactions.InteractionFinder attribute) receptor_file (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) receptor_pdbqt_parser() (in module ringtail.parsers) ReceptorManager (class in ringtail) (class in ringtail.receptormanager) resultsman (ringtail.RingtailCore attribute) (ringtail.ringtailcore.RingtailCore attribute) ResultsManager (class in ringtail) (class in ringtail.resultsmanager) ResultsProcessingError, [1] ResultsProcessingOptions (class in ringtail.ringtailoptions) ringtail module ringtail.cloptionparser module ringtail.exceptions module ringtail.interactions module ringtail.mpmanager module ringtail.mpreaderwriter module

ringtail.outputmanager module ringtail.parsers module ringtail.receptormanager module ringtail.resultsmanager module ringtail.ringtailcore module ringtail.ringtailoptions module ringtail.storagemanager module RingtailCore (class in ringtail) (class in ringtail.ringtailcore) rtcore (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) RTCoreError, [1] RTOptions (class in ringtail.ringtailoptions) run() (ringtail.DockingFileReader method) (ringtail.mpreaderwriter.DockingFileReader method) (ringtail.mpreaderwriter.Writer method) (ringtail.Writer method)

S

save_receptor() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) save_scatterplot() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) scatter_hist() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) set_bookmark_suffix() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) set_filters() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) set_output_options() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) set_resultsman_attributes() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) set_storageman_attributes() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) StorageError, [1] storageman (ringtail.DockingFileReader attribute) (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) (ringtail.mpreaderwriter.DockingFileReader attribute) (ringtail.RingtailCore attribute) (ringtail.ringtailcore.RingtailCore attribute)

storageman_class (ringtail.DockingFileReader attribute) (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) (ringtail.mpreaderwriter.DockingFileReader attribute) StorageManager (class in ringtail) (class in ringtail.storagemanager) StorageManagerSQLite (class in ringtail) (class in ringtail.storagemanager) StorageOptions (class in ringtail.ringtailoptions) storageopts (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) store_all_poses (ringtail.DockingFileReader attribute) (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) (ringtail.mpreaderwriter.DockingFileReader attribute) string_sources (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute)

T

target (ringtail.DockingFileReader attribute) (ringtail.MPManager attribute) (ringtail.mpmanager.MPManager attribute) (ringtail.mpreaderwriter.DockingFileReader attribute) temptable_suffix (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute)

to_dataframe() (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method) todict() (ringtail.ringtailoptions.RTOptions method) TypeSafe (class in ringtail.ringtailoptions)

U

update_database_version() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) (ringtail.storagemanager.StorageManagerSQLite method) (ringtail.StorageManagerSQLite method)

V

valid_bookmark_name() (ringtail.ringtailoptions.RTOptions static method)

view_suffix (ringtail.storagemanager.StorageManagerSQLite attribute) (ringtail.StorageManagerSQLite attribute)

W

write_filter_log() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) write_filters_to_log() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) write_find_similar_header() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) write_flexres_pdb() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method) write_maxmiss_union_header() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) write_molecule_sdfs() (ringtail.RingtailCore method) (ringtail.ringtailcore.RingtailCore method)

write_out_mol() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) write_receptor_pdbqt() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) write_results_bookmark_to_log() (ringtail.OutputManager method) (ringtail.outputmanager.OutputManager method) write_to_storage() (ringtail.mpreaderwriter.Writer method) (ringtail.Writer method) writeopts (ringtail.CLOptionParser attribute) (ringtail.cloptionparser.CLOptionParser attribute) Writer (class in ringtail) (class in ringtail.mpreaderwriter) WriteToStorageError, [1]