Index

_

_on_item_clicked() (fast_conformation.gui.dock_widget.MainWidget method)

A

add_borders() (fast_conformation.gui.plot_widget.PlotWidget method), [1] add_colorbar() (fast_conformation.gui.plot_widget.PlotWidget method), [1] add_job_item() (fast_conformation.gui.job_manager.JobStatusPage method), [1] add_line() (fast_conformation.gui.plot_widget.PlotWidget method), [1] add_plot() (fast_conformation.gui.plot_widget.PlotWidget method), [1] add_scatter() (fast_conformation.gui.plot_widget.PlotWidget method), [1] add_seq_pair() (fast_conformation.gui.analysis_config.GeneralAnalysisWidget method), [1] (fast_conformation.gui.make_predictions.MakePredictionsWidget method), [1]

addItem() (fast_conformation.gui.icons.Icons method), [1] addItems() (fast_conformation.gui.icons.Icons method), [1] aligned_cols (fast_conformation.msa_generation.parsers.TemplateHit attribute) AnalysisCategory (class in fast_conformation.gui.analysis_config) AnalysisConfigWidget (class in fast_conformation.gui.analysis_config) AnalysisWidgetBase (class in fast_conformation.gui.widget_base) apply_styles() (fast_conformation.gui.run_gui.MainFrame method), [1] auto_detect_sequence_pairs() (fast_conformation.gui.analysis_config.GeneralAnalysisWidget method), [1] auto_select_2d_references() (in module fast_conformation.ensemble_analysis.analysis_utils)

B

BackgroundWidget (class in fast_conformation.gui.run_gui) build_dataset_rmsd_modes() (in module fast_conformation.ensemble_analysis.rmsd) build_dataset_rmsf_peaks() (in module fast_conformation.ensemble_analysis.rmsf)

build_dataset_tmscore_modes() (in module fast_conformation.ensemble_analysis.tmscore) build_jackhmmer_msa() (in module fast_conformation.jackhmmer_msa) build_msa() (in module fast_conformation.jackhmmer_msa)

C

calculate_2d_rmsd() (fast_conformation.ensemble_analysis.twodrmsd.TwodRMSD method) calculate_2d_tmscore() (fast_conformation.ensemble_analysis.twotmscore.TwoTMScore method) calculate_rmsd() (in module fast_conformation.ensemble_analysis.rmsd) calculate_rmsf_and_call_peaks() (in module fast_conformation.ensemble_analysis.rmsf) calculate_rmsf_multiple() (in module fast_conformation.ensemble_analysis.rmsf) Category (class in fast_conformation.gui.dock_widget) chain_break() (in module fast_conformation.msa_generation.colabfold) check_job_manager_queue() (fast_conformation.gui.widget_base.AnalysisWidgetBase method), [1] clear_dock_widget() (fast_conformation.gui.dock_widget.MainWidget method), [1] clear_layout() (fast_conformation.gui.dock_widget.MainWidget method), [1] clear_seq_pairs() (fast_conformation.gui.analysis_config.GeneralAnalysisWidget method), [1]

cluster_2d_data() (fast_conformation.ensemble_analysis.twodrmsd.TwodRMSD method) (fast_conformation.ensemble_analysis.twotmscore.TwoTMScore method) convert_msa() (in module fast_conformation.jackhmmer_msa) convert_stockholm_to_a3m() (in module fast_conformation.msa_generation.parsers) copy_msa_and_clean() (in module fast_conformation.mmseqs2_msa) create_directory() (in module fast_conformation.ensemble_analysis.analysis_utils) (in module fast_conformation.msa_generation.msa_utils) create_dock_widget() (fast_conformation.gui.dock_widget.MainWidget method), [1] create_new_job_widget() (fast_conformation.gui.dock_widget.MainWidget method), [1] create_ram_disk() (in module fast_conformation.msa_generation.msa_utils) create_terminal_dock() (fast_conformation.gui.run_gui.MainFrame method), [1]

F

fast_conformation module fast_conformation.ensemble_analysis module fast_conformation.ensemble_analysis.analysis_utils module fast_conformation.ensemble_analysis.pca module fast_conformation.ensemble_analysis.rmsd module fast_conformation.ensemble_analysis.rmsf module fast_conformation.ensemble_analysis.tmscore module fast_conformation.ensemble_analysis.traj module fast_conformation.ensemble_analysis.twodrmsd module fast_conformation.ensemble_analysis.twotmscore module fast_conformation.fast_conformation module fast_conformation.fast_conformation_init module fast_conformation.gui module fast_conformation.gui.analysis_config module fast_conformation.gui.build_msa module fast_conformation.gui.dock_widget module fast_conformation.gui.icons module fast_conformation.gui.job_manager module fast_conformation.gui.make_predictions module fast_conformation.gui.plot_widget module

fast_conformation.gui.run_gui module fast_conformation.gui.widget_base module fast_conformation.jackhmmer_msa module fast_conformation.mmseqs2_msa module fast_conformation.msa_generation module fast_conformation.msa_generation.colabfold module fast_conformation.msa_generation.get_msa_jackhmmer module fast_conformation.msa_generation.jackhmmer module fast_conformation.msa_generation.msa_utils module fast_conformation.msa_generation.pairmsa module fast_conformation.msa_generation.parsers module fast_conformation.pca_clustering module fast_conformation.rmsd_mode1d module fast_conformation.rmsd_mode2d module fast_conformation.rmsf_plddt module fast_conformation.save_traj module fast_conformation.tmscore_mode1d module fast_conformation.tmscore_mode2d module fit_and_filter_data() (fast_conformation.ensemble_analysis.twodrmsd.TwodRMSD method) (fast_conformation.ensemble_analysis.twotmscore.TwoTMScore method) flush() (fast_conformation.gui.run_gui.QPlainTextEditLogger method), [1]

G

GeneralAnalysisWidget (class in fast_conformation.gui.analysis_config) get_2d_rmsd() (fast_conformation.ensemble_analysis.twodrmsd.TwodRMSD method) get_2d_tmscore() (fast_conformation.ensemble_analysis.twotmscore.TwoTMScore method) get_general_options() (fast_conformation.gui.analysis_config.GeneralAnalysisWidget method), [1] get_hash() (in module fast_conformation.msa_generation.colabfold) get_job_log() (fast_conformation.gui.job_manager.JobManager method) (fast_conformation.gui.job_manager.JobManagerBackend method) get_job_name() (fast_conformation.gui.job_manager.JobManager method) (fast_conformation.gui.job_manager.JobManagerBackend method) get_job_status() (fast_conformation.gui.job_manager.JobManager method) (fast_conformation.gui.job_manager.JobManagerBackend method) get_mmseqs_msa() (in module fast_conformation.mmseqs2_msa)

get_seq_pairs() (fast_conformation.gui.make_predictions.MakePredictionsWidget method), [1] get_specific_options() (fast_conformation.gui.analysis_config.PCAWidget method), [1] (fast_conformation.gui.analysis_config.RMSD2DWidget method), [1] (fast_conformation.gui.analysis_config.RMSDAnalysisWidget method), [1] (fast_conformation.gui.analysis_config.RMSFAnalysisWidget method), [1] (fast_conformation.gui.analysis_config.TMSCOREWidget method), [1] (fast_conformation.gui.analysis_config.TrajectorySavingWidget method), [1] (fast_conformation.gui.analysis_config.TwoTMScoreWidget method), [1] (fast_conformation.gui.build_msa.MSAOptionsWidget method), [1] (fast_conformation.gui.make_predictions.MakePredictionsWidget method), [1] (fast_conformation.gui.widget_base.AnalysisWidgetBase method), [1] get_uni_jackhmmer() (in module fast_conformation.msa_generation.pairmsa)

H

handle_sigint() (in module fast_conformation.gui.run_gui) hash_it() (in module fast_conformation.msa_generation.pairmsa) hide_all_dock_widgets() (fast_conformation.gui.run_gui.MainFrame method), [1]

hit_sequence (fast_conformation.msa_generation.parsers.TemplateHit attribute) homooligomerize() (in module fast_conformation.msa_generation.colabfold) homooligomerize_heterooligomer() (in module fast_conformation.msa_generation.colabfold) homooliomerize() (in module fast_conformation.msa_generation.colabfold)

I

Icons (class in fast_conformation.gui.icons) index (fast_conformation.msa_generation.parsers.TemplateHit attribute) indices_hit (fast_conformation.msa_generation.parsers.TemplateHit attribute)

indices_query (fast_conformation.msa_generation.parsers.TemplateHit attribute) init_ui() (fast_conformation.gui.build_msa.MSAOptionsWidget method), [1] (fast_conformation.gui.make_predictions.MakePredictionsWidget method), [1]

J

Jackhmmer (class in fast_conformation.msa_generation.jackhmmer) job_finished (fast_conformation.gui.job_manager.JobManager attribute), [1] job_manager (fast_conformation.gui.analysis_config.AnalysisConfigWidget attribute) (fast_conformation.gui.widget_base.AnalysisWidgetBase attribute) job_started (fast_conformation.gui.job_manager.JobManager attribute), [1]

job_wrapper() (in module fast_conformation.gui.job_manager) JobItemWidget (class in fast_conformation.gui.job_manager) JobManager (class in fast_conformation.gui.job_manager) JobManagerBackend (class in fast_conformation.gui.job_manager) jobs (fast_conformation.gui.job_manager.JobManagerBackend attribute) JobStatusPage (class in fast_conformation.gui.job_manager)

L

load_config() (in module fast_conformation.ensemble_analysis.analysis_utils) (in module fast_conformation.jackhmmer_msa) (in module fast_conformation.mmseqs2_msa)

load_frames() (in module fast_conformation.ensemble_analysis.analysis_utils) load_pdb_files_as_universe() (in module fast_conformation.ensemble_analysis.analysis_utils) load_predictions() (in module fast_conformation.ensemble_analysis.analysis_utils) load_predictions_json() (in module fast_conformation.ensemble_analysis.analysis_utils)

M

main() (in module fast_conformation.fast_conformation_init) (in module fast_conformation.gui.run_gui) (in module fast_conformation.jackhmmer_msa) (in module fast_conformation.mmseqs2_msa) (in module fast_conformation.pca_clustering) (in module fast_conformation.rmsd_mode1d) (in module fast_conformation.rmsd_mode2d) (in module fast_conformation.rmsf_plddt) (in module fast_conformation.tmscore_mode1d) (in module fast_conformation.tmscore_mode2d) MainFrame (class in fast_conformation.gui.run_gui) MainWidget (class in fast_conformation.gui.dock_widget) MakePredictionsWidget (class in fast_conformation.gui.make_predictions) manager (fast_conformation.gui.job_manager.JobManagerBackend attribute) map_retrieve() (in module fast_conformation.msa_generation.pairmsa) merge_configs() (in module fast_conformation.gui.widget_base) module fast_conformation fast_conformation.ensemble_analysis fast_conformation.ensemble_analysis.analysis_utils fast_conformation.ensemble_analysis.pca fast_conformation.ensemble_analysis.rmsd fast_conformation.ensemble_analysis.rmsf fast_conformation.ensemble_analysis.tmscore fast_conformation.ensemble_analysis.traj fast_conformation.ensemble_analysis.twodrmsd fast_conformation.ensemble_analysis.twotmscore fast_conformation.fast_conformation fast_conformation.fast_conformation_init fast_conformation.gui fast_conformation.gui.analysis_config fast_conformation.gui.build_msa fast_conformation.gui.dock_widget fast_conformation.gui.icons fast_conformation.gui.job_manager fast_conformation.gui.make_predictions fast_conformation.gui.plot_widget fast_conformation.gui.run_gui fast_conformation.gui.widget_base fast_conformation.jackhmmer_msa fast_conformation.mmseqs2_msa fast_conformation.msa_generation fast_conformation.msa_generation.colabfold fast_conformation.msa_generation.get_msa_jackhmmer fast_conformation.msa_generation.jackhmmer fast_conformation.msa_generation.msa_utils fast_conformation.msa_generation.pairmsa fast_conformation.msa_generation.parsers fast_conformation.pca_clustering fast_conformation.rmsd_mode1d fast_conformation.rmsd_mode2d fast_conformation.rmsf_plddt fast_conformation.save_traj fast_conformation.tmscore_mode1d fast_conformation.tmscore_mode2d

monitor_queue() (fast_conformation.gui.job_manager.JobManager method) MSAOptionsWidget (class in fast_conformation.gui.build_msa)

N

name (fast_conformation.msa_generation.parsers.TemplateHit attribute)

O

on_job_finished() (fast_conformation.gui.widget_base.AnalysisWidgetBase method), [1]

P

paintEvent() (fast_conformation.gui.run_gui.BackgroundWidget method), [1] parabola() (in module fast_conformation.ensemble_analysis.analysis_utils) parse_a3m() (in module fast_conformation.msa_generation.pairmsa) (in module fast_conformation.msa_generation.parsers) parse_e_values_from_tblout() (in module fast_conformation.msa_generation.parsers) parse_fasta() (in module fast_conformation.msa_generation.parsers) parse_hhr() (in module fast_conformation.msa_generation.parsers) parse_stockholm() (in module fast_conformation.msa_generation.parsers) pca_from_ensemble() (in module fast_conformation.ensemble_analysis.pca) PCAWidget (class in fast_conformation.gui.analysis_config) plot_and_save_2d_data() (fast_conformation.ensemble_analysis.twodrmsd.TwodRMSD method) (fast_conformation.ensemble_analysis.twotmscore.TwoTMScore method)

plot_confidence() (in module fast_conformation.msa_generation.colabfold) plot_filtering_data() (fast_conformation.ensemble_analysis.twodrmsd.TwodRMSD method) (fast_conformation.ensemble_analysis.twotmscore.TwoTMScore method) plot_msas() (in module fast_conformation.msa_generation.colabfold) plot_plddt_legend() (in module fast_conformation.msa_generation.colabfold) plot_plddt_line() (in module fast_conformation.ensemble_analysis.rmsf) plot_plddt_rmsf_corr() (in module fast_conformation.ensemble_analysis.rmsf) plot_ticks() (in module fast_conformation.msa_generation.colabfold) PlotWidget (class in fast_conformation.gui.plot_widget) prep_inputs() (in module fast_conformation.msa_generation.get_msa_jackhmmer) prep_msa() (in module fast_conformation.msa_generation.get_msa_jackhmmer) prepare_os() (in module fast_conformation.jackhmmer_msa)

Q

QPlainTextEditLogger (class in fast_conformation.gui.run_gui) query (fast_conformation.msa_generation.parsers.TemplateHit attribute)

query() (fast_conformation.msa_generation.jackhmmer.Jackhmmer method) queue (fast_conformation.gui.job_manager.JobManagerBackend attribute)

R

read_fasta() (in module fast_conformation.msa_generation.msa_utils) reformat_sequences() (in module fast_conformation.jackhmmer_msa) refresh_job_statuses() (fast_conformation.gui.job_manager.JobStatusPage method), [1] remove_duplicate_sequences() (in module fast_conformation.mmseqs2_msa) remove_first_line() (in module fast_conformation.mmseqs2_msa) remove_seq_pair() (fast_conformation.gui.analysis_config.GeneralAnalysisWidget method), [1] (fast_conformation.gui.make_predictions.MakePredictionsWidget method), [1] reorder_frames_by() (in module fast_conformation.ensemble_analysis.analysis_utils) RMSD2DWidget (class in fast_conformation.gui.analysis_config) rmsd_kde() (in module fast_conformation.ensemble_analysis.rmsd) rmsd_mode_analysis() (in module fast_conformation.ensemble_analysis.rmsd) RMSDAnalysisWidget (class in fast_conformation.gui.analysis_config) RMSFAnalysisWidget (class in fast_conformation.gui.analysis_config) run_2d_rmsd_analysis() (in module fast_conformation.rmsd_mode2d) run_2d_tmscore_analysis() (in module fast_conformation.tmscore_mode2d) run_analysis() (fast_conformation.gui.build_msa.MSAOptionsWidget method), [1] (fast_conformation.gui.make_predictions.MakePredictionsWidget method), [1] (fast_conformation.gui.widget_base.AnalysisWidgetBase method), [1] run_jackhmmer() (in module fast_conformation.msa_generation.get_msa_jackhmmer)

run_job() (fast_conformation.gui.job_manager.JobManager method) (fast_conformation.gui.job_manager.JobManagerBackend method) run_mmseqs2_msa() (in module fast_conformation.mmseqs2_msa) run_msa_job() (in module fast_conformation.gui.build_msa) run_pca_analysis() (in module fast_conformation.pca_clustering) run_rmsd_analysis() (in module fast_conformation.rmsd_mode1d) run_rmsf_analysis() (in module fast_conformation.rmsf_plddt) run_specific_analysis() (fast_conformation.gui.analysis_config.PCAWidget method), [1] (fast_conformation.gui.analysis_config.RMSD2DWidget method), [1] (fast_conformation.gui.analysis_config.RMSDAnalysisWidget method), [1] (fast_conformation.gui.analysis_config.RMSFAnalysisWidget method), [1] (fast_conformation.gui.analysis_config.TMSCOREWidget method), [1] (fast_conformation.gui.analysis_config.TrajectorySavingWidget method), [1] (fast_conformation.gui.analysis_config.TwoTMScoreWidget method), [1] (fast_conformation.gui.build_msa.MSAOptionsWidget method), [1] (fast_conformation.gui.widget_base.AnalysisWidgetBase method), [1] run_tmscore() (fast_conformation.ensemble_analysis.twotmscore.TwoTMScore method) (in module fast_conformation.ensemble_analysis.tmscore) run_tmscore_analysis() (in module fast_conformation.tmscore_mode1d) run_trajectory_saving() (in module fast_conformation.save_traj)

S

save_config() (in module fast_conformation.mmseqs2_msa) save_dict_to_fasta() (in module fast_conformation.msa_generation.msa_utils) save_formatted_sequences_to_file() (in module fast_conformation.jackhmmer_msa) save_traj() (in module fast_conformation.ensemble_analysis.analysis_utils) save_trajs() (in module fast_conformation.ensemble_analysis.traj) select_msa_path() (fast_conformation.gui.make_predictions.MakePredictionsWidget method), [1] select_output_path() (fast_conformation.gui.analysis_config.GeneralAnalysisWidget method), [1] (fast_conformation.gui.build_msa.MSAOptionsWidget method), [1] (fast_conformation.gui.make_predictions.MakePredictionsWidget method), [1] select_predictions_path() (fast_conformation.gui.analysis_config.GeneralAnalysisWidget method), [1] select_sequence_path() (fast_conformation.gui.build_msa.MSAOptionsWidget method), [1] set_initial_window_size() (fast_conformation.gui.run_gui.MainFrame method), [1] show_dock_widget() (fast_conformation.gui.run_gui.MainFrame method), [1] show_error_message() (fast_conformation.gui.widget_base.AnalysisWidgetBase method), [1] show_filt_data() (fast_conformation.ensemble_analysis.twodrmsd.TwodRMSD method)

show_home_page() (fast_conformation.gui.run_gui.MainFrame method), [1] show_info_message() (fast_conformation.gui.widget_base.AnalysisWidgetBase method), [1] show_job_status_page() (fast_conformation.gui.dock_widget.MainWidget method), [1] (fast_conformation.gui.run_gui.MainFrame method), [1] show_log() (fast_conformation.gui.job_manager.JobItemWidget method), [1] show_new_job_page() (fast_conformation.gui.dock_widget.MainWidget method), [1] (fast_conformation.gui.run_gui.MainFrame method), [1] show_plot() (fast_conformation.gui.analysis_config.AnalysisConfigWidget method) (fast_conformation.gui.run_gui.MainFrame method), [1] show_terminal() (fast_conformation.gui.run_gui.MainFrame method), [1] slice_models() (fast_conformation.ensemble_analysis.twotmscore.TwoTMScore static method) (in module fast_conformation.ensemble_analysis.tmscore) stitch() (in module fast_conformation.msa_generation.pairmsa) stop() (fast_conformation.gui.job_manager.JobManager method) sum_probs (fast_conformation.msa_generation.parsers.TemplateHit attribute)

T

TemplateHit (class in fast_conformation.msa_generation.parsers) timer (fast_conformation.gui.widget_base.AnalysisWidgetBase attribute) timing() (in module fast_conformation.msa_generation.msa_utils) tmpdir_manager() (in module fast_conformation.msa_generation.msa_utils) tmscore_kde() (in module fast_conformation.ensemble_analysis.tmscore) tmscore_mode_analysis() (in module fast_conformation.ensemble_analysis.tmscore) tmscore_wrapper() (fast_conformation.ensemble_analysis.twotmscore.TwoTMScore static method) (in module fast_conformation.ensemble_analysis.tmscore)

TMSCOREWidget (class in fast_conformation.gui.analysis_config) toggle_additional_options() (fast_conformation.gui.build_msa.MSAOptionsWidget method), [1] tool_tip (fast_conformation.gui.analysis_config.AnalysisCategory attribute), [1] (fast_conformation.gui.dock_widget.Category attribute), [1] TrajectorySavingWidget (class in fast_conformation.gui.analysis_config) TwodRMSD (class in fast_conformation.ensemble_analysis.twodrmsd) TwoTMScore (class in fast_conformation.ensemble_analysis.twotmscore) TwoTMScoreWidget (class in fast_conformation.gui.analysis_config)

U

uni_num() (in module fast_conformation.msa_generation.pairmsa) update_job_status() (fast_conformation.gui.job_manager.JobManager method) (fast_conformation.gui.job_manager.JobManagerBackend method) (fast_conformation.gui.job_manager.JobStatusPage method), [1]

update_status() (fast_conformation.gui.job_manager.JobItemWidget method), [1]

V

validate_inputs() (fast_conformation.gui.analysis_config.PCAWidget method), [1] (fast_conformation.gui.analysis_config.RMSD2DWidget method), [1] (fast_conformation.gui.analysis_config.RMSDAnalysisWidget method), [1] (fast_conformation.gui.analysis_config.RMSFAnalysisWidget method), [1] (fast_conformation.gui.analysis_config.TMSCOREWidget method), [1] (fast_conformation.gui.analysis_config.TrajectorySavingWidget method), [1] (fast_conformation.gui.analysis_config.TwoTMScoreWidget method), [1] (fast_conformation.gui.build_msa.MSAOptionsWidget method), [1] (fast_conformation.gui.make_predictions.MakePredictionsWidget method), [1] (fast_conformation.gui.widget_base.AnalysisWidgetBase method), [1] (in module fast_conformation.mmseqs2_msa)

W

widget (fast_conformation.gui.analysis_config.AnalysisCategory attribute), [1] (fast_conformation.gui.dock_widget.Category attribute), [1]

wrap_with_border() (fast_conformation.gui.dock_widget.MainWidget method), [1] write() (fast_conformation.gui.run_gui.QPlainTextEditLogger method), [1]