fast_conformation package

Subpackages

• fast_conformation.ensemble_analysis package
  • Submodules
  • fast_conformation.ensemble_analysis.analysis_utils module
    • auto_select_2d_references()
    • create_directory()
    • load_config()
    • load_frames()
    • load_pdb_files_as_universe()
    • load_predictions()
    • load_predictions_json()
    • parabola()
    • reorder_frames_by()
    • save_traj()
  • fast_conformation.ensemble_analysis.pca module
    • pca_from_ensemble()
  • fast_conformation.ensemble_analysis.rmsd module
    • build_dataset_rmsd_modes()
    • calculate_rmsd()
    • rmsd_kde()
    • rmsd_mode_analysis()
  • fast_conformation.ensemble_analysis.rmsf module
    • build_dataset_rmsf_peaks()
    • calculate_rmsf_and_call_peaks()
    • calculate_rmsf_multiple()
    • plot_plddt_line()
    • plot_plddt_rmsf_corr()
  • fast_conformation.ensemble_analysis.tmscore module
    • build_dataset_tmscore_modes()
    • run_tmscore()
    • slice_models()
    • tmscore_kde()
    • tmscore_mode_analysis()
    • tmscore_wrapper()
  • fast_conformation.ensemble_analysis.traj module
    • save_trajs()
  • fast_conformation.ensemble_analysis.twodrmsd module
    • TwodRMSD
      • TwodRMSD.calculate_2d_rmsd()
      • TwodRMSD.cluster_2d_data()
      • TwodRMSD.fit_and_filter_data()
      • TwodRMSD.get_2d_rmsd()
      • TwodRMSD.plot_and_save_2d_data()
      • TwodRMSD.plot_filtering_data()
      • TwodRMSD.show_filt_data()
  • fast_conformation.ensemble_analysis.twotmscore module
    • TwoTMScore
      • TwoTMScore.calculate_2d_tmscore()
      • TwoTMScore.cluster_2d_data()
      • TwoTMScore.fit_and_filter_data()
      • TwoTMScore.get_2d_tmscore()
      • TwoTMScore.plot_and_save_2d_data()
      • TwoTMScore.plot_filtering_data()
      • TwoTMScore.run_tmscore()
      • TwoTMScore.slice_models()
      • TwoTMScore.tmscore_wrapper()
  • Module contents
• fast_conformation.gui package
  • Submodules
  • fast_conformation.gui.analysis_config module
    • AnalysisCategory
      • AnalysisCategory.widget
      • AnalysisCategory.tool_tip
      • AnalysisCategory.tool_tip
      • AnalysisCategory.widget
    • AnalysisConfigWidget
      • AnalysisConfigWidget.job_manager
      • AnalysisConfigWidget.show_plot()
    • GeneralAnalysisWidget
      • GeneralAnalysisWidget.clear_seq_pairs()
      • GeneralAnalysisWidget.select_output_path()
      • GeneralAnalysisWidget.select_predictions_path()
      • GeneralAnalysisWidget.auto_detect_sequence_pairs()
      • GeneralAnalysisWidget.get_general_options()
      • GeneralAnalysisWidget.add_seq_pair()
      • GeneralAnalysisWidget.remove_seq_pair()
      • GeneralAnalysisWidget.add_seq_pair()
      • GeneralAnalysisWidget.auto_detect_sequence_pairs()
      • GeneralAnalysisWidget.clear_seq_pairs()
      • GeneralAnalysisWidget.get_general_options()
      • GeneralAnalysisWidget.remove_seq_pair()
      • GeneralAnalysisWidget.select_output_path()
      • GeneralAnalysisWidget.select_predictions_path()
    • PCAWidget
      • PCAWidget.validate_inputs()
      • PCAWidget.get_specific_options()
      • PCAWidget.run_specific_analysis()
      • PCAWidget.get_specific_options()
      • PCAWidget.run_specific_analysis()
      • PCAWidget.validate_inputs()
    • RMSD2DWidget
      • RMSD2DWidget.validate_inputs()
      • RMSD2DWidget.get_specific_options()
      • RMSD2DWidget.run_specific_analysis()
      • RMSD2DWidget.get_specific_options()
      • RMSD2DWidget.run_specific_analysis()
      • RMSD2DWidget.validate_inputs()
    • RMSDAnalysisWidget
      • RMSDAnalysisWidget.validate_inputs()
      • RMSDAnalysisWidget.get_specific_options()
      • RMSDAnalysisWidget.run_specific_analysis()
      • RMSDAnalysisWidget.get_specific_options()
      • RMSDAnalysisWidget.run_specific_analysis()
      • RMSDAnalysisWidget.validate_inputs()
    • RMSFAnalysisWidget
      • RMSFAnalysisWidget.validate_inputs()
      • RMSFAnalysisWidget.get_specific_options()
      • RMSFAnalysisWidget.run_specific_analysis()
      • RMSFAnalysisWidget.get_specific_options()
      • RMSFAnalysisWidget.run_specific_analysis()
      • RMSFAnalysisWidget.validate_inputs()
    • TMSCOREWidget
      • TMSCOREWidget.validate_inputs()
      • TMSCOREWidget.get_specific_options()
      • TMSCOREWidget.run_specific_analysis()
      • TMSCOREWidget.get_specific_options()
      • TMSCOREWidget.run_specific_analysis()
      • TMSCOREWidget.validate_inputs()
    • TrajectorySavingWidget
      • TrajectorySavingWidget.validate_inputs()
      • TrajectorySavingWidget.get_specific_options()
      • TrajectorySavingWidget.run_specific_analysis()
      • TrajectorySavingWidget.get_specific_options()
      • TrajectorySavingWidget.run_specific_analysis()
      • TrajectorySavingWidget.validate_inputs()
    • TwoTMScoreWidget
      • TwoTMScoreWidget.validate_inputs()
      • TwoTMScoreWidget.get_specific_options()
      • TwoTMScoreWidget.run_specific_analysis()
      • TwoTMScoreWidget.get_specific_options()
      • TwoTMScoreWidget.run_specific_analysis()
      • TwoTMScoreWidget.validate_inputs()
  • fast_conformation.gui.build_msa module
    • MSAOptionsWidget
      • MSAOptionsWidget.init_ui()
      • MSAOptionsWidget.select_sequence_path()
      • MSAOptionsWidget.select_output_path()
      • MSAOptionsWidget.toggle_additional_options()
      • MSAOptionsWidget.validate_inputs()
      • MSAOptionsWidget.get_specific_options()
      • MSAOptionsWidget.run_specific_analysis()
      • MSAOptionsWidget.run_analysis()
      • MSAOptionsWidget.get_specific_options()
      • MSAOptionsWidget.init_ui()
      • MSAOptionsWidget.run_analysis()
      • MSAOptionsWidget.run_specific_analysis()
      • MSAOptionsWidget.select_output_path()
      • MSAOptionsWidget.select_sequence_path()
      • MSAOptionsWidget.toggle_additional_options()
      • MSAOptionsWidget.validate_inputs()
    • run_msa_job()
  • fast_conformation.gui.dock_widget module
    • Category
      • Category.widget
      • Category.tool_tip
      • Category.tool_tip
      • Category.widget
    • MainWidget
      • MainWidget.create_dock_widget()
      • MainWidget.create_new_job_widget()
      • MainWidget.wrap_with_border()
      • MainWidget._on_item_clicked()
      • MainWidget.clear_dock_widget()
      • MainWidget.show_job_status_page()
      • MainWidget.show_new_job_page()
      • MainWidget.clear_layout()
      • MainWidget.clear_dock_widget()
      • MainWidget.clear_layout()
      • MainWidget.create_dock_widget()
      • MainWidget.create_new_job_widget()
      • MainWidget.show_job_status_page()
      • MainWidget.show_new_job_page()
      • MainWidget.wrap_with_border()
  • fast_conformation.gui.icons module
    • Icons
      • Icons.addItem()
      • Icons.addItems()
      • Icons.addItem()
      • Icons.addItems()
  • fast_conformation.gui.job_manager module
    • JobItemWidget
      • JobItemWidget.update_status()
      • JobItemWidget.show_log()
      • JobItemWidget.show_log()
      • JobItemWidget.update_status()
    • JobManager
      • JobManager.job_finished
      • JobManager.job_started
      • JobManager.get_job_log()
      • JobManager.get_job_name()
      • JobManager.get_job_status()
      • JobManager.job_finished
      • JobManager.job_started
      • JobManager.monitor_queue()
      • JobManager.run_job()
      • JobManager.stop()
      • JobManager.update_job_status()
    • JobManagerBackend
      • JobManagerBackend.jobs
      • JobManagerBackend.manager
      • JobManagerBackend.queue
      • JobManagerBackend.get_job_log()
      • JobManagerBackend.get_job_name()
      • JobManagerBackend.get_job_status()
      • JobManagerBackend.run_job()
      • JobManagerBackend.update_job_status()
    • JobStatusPage
      • JobStatusPage.refresh_job_statuses()
      • JobStatusPage.update_job_status()
      • JobStatusPage.add_job_item()
      • JobStatusPage.add_job_item()
      • JobStatusPage.refresh_job_statuses()
      • JobStatusPage.update_job_status()
    • job_wrapper()
  • fast_conformation.gui.make_predictions module
    • MakePredictionsWidget
      • MakePredictionsWidget.init_ui()
      • MakePredictionsWidget.select_msa_path()
      • MakePredictionsWidget.select_output_path()
      • MakePredictionsWidget.add_seq_pair()
      • MakePredictionsWidget.remove_seq_pair()
      • MakePredictionsWidget.validate_inputs()
      • MakePredictionsWidget.get_specific_options()
      • MakePredictionsWidget.run_analysis()
      • MakePredictionsWidget.get_seq_pairs()
      • MakePredictionsWidget.add_seq_pair()
      • MakePredictionsWidget.get_seq_pairs()
      • MakePredictionsWidget.get_specific_options()
      • MakePredictionsWidget.init_ui()
      • MakePredictionsWidget.remove_seq_pair()
      • MakePredictionsWidget.run_analysis()
      • MakePredictionsWidget.select_msa_path()
      • MakePredictionsWidget.select_output_path()
      • MakePredictionsWidget.validate_inputs()
  • fast_conformation.gui.plot_widget module
    • PlotWidget
      • PlotWidget.add_plot()
      • PlotWidget.add_borders()
      • PlotWidget.add_scatter()
      • PlotWidget.add_line()
      • PlotWidget.add_colorbar()
      • PlotWidget.add_borders()
      • PlotWidget.add_colorbar()
      • PlotWidget.add_line()
      • PlotWidget.add_plot()
      • PlotWidget.add_scatter()
  • fast_conformation.gui.run_gui module
    • BackgroundWidget
      • BackgroundWidget.paintEvent()
      • BackgroundWidget.paintEvent()
    • MainFrame
      • MainFrame.create_terminal_dock()
      • MainFrame.show_terminal()
      • MainFrame.apply_styles()
      • MainFrame.show_home_page()
      • MainFrame.show_new_job_page()
      • MainFrame.show_job_status_page()
      • MainFrame.show_plot()
      • MainFrame.show_dock_widget()
      • MainFrame.hide_all_dock_widgets()
      • MainFrame.set_initial_window_size()
      • MainFrame.apply_styles()
      • MainFrame.create_terminal_dock()
      • MainFrame.hide_all_dock_widgets()
      • MainFrame.set_initial_window_size()
      • MainFrame.show_dock_widget()
      • MainFrame.show_home_page()
      • MainFrame.show_job_status_page()
      • MainFrame.show_new_job_page()
      • MainFrame.show_plot()
      • MainFrame.show_terminal()
    • QPlainTextEditLogger
      • QPlainTextEditLogger.write()
      • QPlainTextEditLogger.flush()
      • QPlainTextEditLogger.flush()
      • QPlainTextEditLogger.write()
    • handle_sigint()
    • main()
  • fast_conformation.gui.widget_base module
    • AnalysisWidgetBase
      • AnalysisWidgetBase.job_manager
      • AnalysisWidgetBase.timer
      • AnalysisWidgetBase.validate_inputs()
      • AnalysisWidgetBase.run_analysis()
      • AnalysisWidgetBase.get_specific_options()
      • AnalysisWidgetBase.run_specific_analysis()
      • AnalysisWidgetBase.show_error_message()
      • AnalysisWidgetBase.show_info_message()
      • AnalysisWidgetBase.on_job_finished()
      • AnalysisWidgetBase.check_job_manager_queue()
      • AnalysisWidgetBase.check_job_manager_queue()
      • AnalysisWidgetBase.get_specific_options()
      • AnalysisWidgetBase.on_job_finished()
      • AnalysisWidgetBase.run_analysis()
      • AnalysisWidgetBase.run_specific_analysis()
      • AnalysisWidgetBase.show_error_message()
      • AnalysisWidgetBase.show_info_message()
      • AnalysisWidgetBase.validate_inputs()
    • merge_configs()
  • Module contents
• fast_conformation.msa_generation package
  • Submodules
  • fast_conformation.msa_generation.colabfold module
    • chain_break()
    • get_hash()
    • homooligomerize()
    • homooligomerize_heterooligomer()
    • homooliomerize()
    • plot_confidence()
    • plot_msas()
    • plot_plddt_legend()
    • plot_ticks()
  • fast_conformation.msa_generation.get_msa_jackhmmer module
    • prep_inputs()
    • prep_msa()
    • run_jackhmmer()
  • fast_conformation.msa_generation.jackhmmer module
    • Jackhmmer
      • Jackhmmer.query()
  • fast_conformation.msa_generation.msa_utils module
    • create_directory()
    • create_ram_disk()
    • read_fasta()
    • save_dict_to_fasta()
    • timing()
    • tmpdir_manager()
  • fast_conformation.msa_generation.pairmsa module
    • get_uni_jackhmmer()
    • hash_it()
    • map_retrieve()
    • parse_a3m()
    • stitch()
    • uni_num()
  • fast_conformation.msa_generation.parsers module
    • TemplateHit
      • TemplateHit.aligned_cols
      • TemplateHit.hit_sequence
      • TemplateHit.index
      • TemplateHit.indices_hit
      • TemplateHit.indices_query
      • TemplateHit.name
      • TemplateHit.query
      • TemplateHit.sum_probs
    • convert_stockholm_to_a3m()
    • parse_a3m()
    • parse_e_values_from_tblout()
    • parse_fasta()
    • parse_hhr()
    • parse_stockholm()
  • Module contents

Submodules

fast_conformation.fast_conformation module

fast_conformation.fast_conf_init module

fast_conformation.fast_conformation_init.main()

fast_conformation.jackhmmer_msa module

fast_conformation.jackhmmer_msa.build_jackhmmer_msa(config)

Build the MSA using jackhmmer for the target sequence based on the provided configuration.

Parameters:

config (dict) – Configuration dictionary containing all necessary parameters.

fast_conformation.jackhmmer_msa.build_msa(sequence, jobname, complete_output_dir, homooligomer, tmp_dir, use_ramdisk)

Build the MSA using jackhmmer for the target sequence.

Parameters:

• sequence (str) – The target sequence for MSA.

• jobname (str) – The job name.

• complete_output_dir (str) – The output directory path.

• homooligomer (int) – The number of copies of the protein.

• tmp_dir (str) – Temporary directory path.

• use_ramdisk (bool) – Whether to use a RAM disk for the process.

fast_conformation.jackhmmer_msa.convert_msa(filename)

Convert the MSA pickle file to a formatted sequence list.

Parameters:

filename (str) – Path to the MSA pickle file.

Returns:

Converted and formatted sequences from the MSA.

Return type:

list

fast_conformation.jackhmmer_msa.load_config(file_path)

Load the configuration file in JSON format.

Parameters:

file_path (str) – Path to the configuration file.

Returns:

Configuration dictionary with default values if the file is not found or if there’s an error in reading the file.

Return type:

dict

fast_conformation.jackhmmer_msa.main()

Main function that handles command-line arguments and initiates the MSA building process.

fast_conformation.jackhmmer_msa.prepare_os()

Prepare the operating system environment by creating a RAM disk.

fast_conformation.jackhmmer_msa.reformat_sequences(input_msa)

Reformat sequences from MSA for use in colabfold_batch.

Parameters:

input_msa (list) – List of sequences from the MSA.

Returns:

Formatted sequences in FASTA format.

Return type:

list

fast_conformation.jackhmmer_msa.save_formatted_sequences_to_file(formatted_sequences, output_file)

Save the formatted sequences to a file.

Parameters:

• formatted_sequences (list) – List of formatted sequences.

• output_file (str) – Path to save the formatted sequences.

fast_conformation.mmseqs2_msa module

fast_conformation.mmseqs2_msa.copy_msa_and_clean(src_file_path, dest_dir_path)

Clean up and copy the MSA file to the destination directory.

Parameters:

• src_file_path (str) – Path to the source MSA file.

• dest_dir_path (str) – Path to the destination directory.

Raises:

OSError – If the source directory cannot be deleted.

fast_conformation.mmseqs2_msa.get_mmseqs_msa(sequence_file_path, output_path, jobname, env)

Run mmseqs2 to generate the MSA (Multiple Sequence Alignment) for the target sequence.

Parameters:

• sequence_file_path (str) – Path to the file containing the target sequence.

• output_path (str) – Directory path to save the output results.

• jobname (str) – Name of the job.

• env (dict) – Environment variables for the subprocess.

Raises:

RuntimeError – If the subprocess fails to execute.

fast_conformation.mmseqs2_msa.load_config(config_file)

Load the configuration from a JSON file.

Parameters:

config_file (str) – Path to the configuration file.

Returns:

Configuration dictionary with default values if the file is not found or if there’s an error in reading the file.

Return type:

dict

fast_conformation.mmseqs2_msa.main()

Main function to parse command-line arguments and execute the MSA pipeline.

fast_conformation.mmseqs2_msa.remove_duplicate_sequences(input_file)

Remove duplicate sequences from a FASTA file.

Parameters:

input_file (str) – Path to the FASTA file containing sequences.

fast_conformation.mmseqs2_msa.remove_first_line(file_path)

Remove the first line from a file.

Parameters:

file_path (str) – Path to the file to modify.

fast_conformation.mmseqs2_msa.run_mmseqs2_msa(config)

Run the full MSA pipeline using mmseqs2.

Parameters:

config (dict) – Configuration dictionary containing necessary parameters.

fast_conformation.mmseqs2_msa.save_config(config, file_path)

Save the configuration to a JSON file.

Parameters:

• config (dict) – Configuration dictionary to save.

• file_path (str) – Path to save the configuration file.

fast_conformation.mmseqs2_msa.validate_inputs(fasta_path, output_path, jobname)

Validate the inputs to ensure they are correct.

Parameters:

• fasta_path (str) – Path to the FASTA file containing the target sequence.

• output_path (str) – Directory path to save the output results.

• jobname (str) – Name of the job.

Raises:

ValueError – If the FASTA path is not a valid file, the output path is not a valid directory, or the jobname is not a string.

fast_conformation.pca_clustering module

fast_conformation.pca_clustering.main()

Main function to parse arguments and run PCA analysis.

fast_conformation.pca_clustering.run_pca_analysis(config, widget=None)

Run PCA analysis based on the provided configuration.

Parameters: config (dict): Configuration dictionary containing parameters for the analysis. widget (object, optional): Widget for displaying results (default is None).

Raises: NotADirectoryError: If the specified output path is not a directory.

fast_conformation.predict_conformation module

fast_conformation.rmsd_mode1d module

fast_conformation.rmsd_mode1d.main()

Main function to parse arguments and run RMSD analysis.

fast_conformation.rmsd_mode1d.run_rmsd_analysis(config, plot_widget=None)

Run RMSD analysis based on the provided configuration.

Parameters: config (dict): Configuration dictionary containing parameters for the analysis. plot_widget (object, optional): Plot widget for displaying results (default is None).

Raises: NotADirectoryError: If the specified output path is not a directory.

fast_conformation.rmsd_mode2d module

fast_conformation.rmsd_mode2d.main()

Main function to parse arguments and run 2D RMSD analysis.

fast_conformation.rmsd_mode2d.run_2d_rmsd_analysis(config, widget=None)

Run 2D RMSD analysis based on the provided configuration.

Parameters: config (dict): Configuration dictionary containing parameters for the analysis. widget (object, optional): Widget for displaying results (default is None).

Raises: NotADirectoryError: If the specified output path is not a directory.

fast_conformation.rmsf_plddt module

fast_conformation.rmsf_plddt.main()

Main function to parse arguments and run RMSF analysis.

fast_conformation.rmsf_plddt.run_rmsf_analysis(config, widget=None)

Run RMSF analysis based on the provided configuration.

Parameters: config (dict): Configuration dictionary containing parameters for the analysis. widget (object, optional): Widget for displaying results (default is None).

Raises: NotADirectoryError: If the specified output path is not a directory.

fast_conformation.save_traj module

fast_conformation.save_traj.run_trajectory_saving(config)

Run the process of saving ensemble predictions as trajectories.

Parameters:

config (dict) –

Configuration dictionary containing the following keys: - output_path (str): Path to save the output trajectories. - predictions_path (str, optional): Path to the predictions directory. If not provided, it defaults to the

predictions directory within the output path.

• seq_pairs (list): List of sequence pairs for the analysis.

• jobname (str): Name of the job.

• analysis_range (tuple): The range of residues or frames to analyze.

• analysis_range_name (str): The name associated with the analysis range.

• reorder (str, optional): Reordering method to use (e.g., RMSD, TMSCORE, PCA).

• traj_format (str): Format to save the trajectory (e.g., PDB, DCD).

• engine (str): The molecular dynamics engine used (e.g., AlphaFold, Rosetta).

• starting_residue (int, optional): The starting residue number for the trajectory.

Raises:

NotADirectoryError – If the specified output path is not a directory.

fast_conformation.tmscore_mode1d module

fast_conformation.tmscore_mode1d.main()

Main function to parse arguments and run TM-Score analysis.

fast_conformation.tmscore_mode1d.run_tmscore_analysis(config, plot_widget=None)

Run TM-Score analysis based on the provided configuration.

Parameters: config (dict): Configuration dictionary containing parameters for the analysis. plot_widget (object, optional): Widget for displaying results (default is None).

Raises: NotADirectoryError: If the specified output path is not a directory.

fast_conformation.tmscore_mode2d module

fast_conformation.tmscore_mode2d.main()

Main function to parse arguments and run 2D TM-Score analysis.

fast_conformation.tmscore_mode2d.run_2d_tmscore_analysis(config, widget=None)

Run 2D TM-Score analysis based on the provided configuration.

Parameters: config (dict): Configuration dictionary containing parameters for the analysis. widget (object, optional): Widget for displaying results (default is None).

Raises: NotADirectoryError: If the specified output path is not a directory.

Module contents