Index

A

ALLOWED_EXTS (in module pyqmmm.qm.orca_clean_irc) analyze() (in module pyqmmm.md.gbsa_analyzer) analyze_hbonds() (in module pyqmmm.md.hbond_analyzer) (in module pyqmmm.md.hbond_compare)

angles_and_dist_script() (in module pyqmmm.md.amber_toolkit) ask_path() (in module bfactor_chg) (in module bfactor_csv) atom_1 (in module pyqmmm.qm.orca_scan_plotter) atom_pairs (in module pyqmmm.qm.bond_valence)

B

basic_metrics_script() (in module pyqmmm.md.amber_toolkit) bfactor_chg module bfactor_csv module

BLU (in module pyqmmm.md.rmsf_calculator) bond_labels() (in module pyqmmm.md.hbond_analyzer) (in module pyqmmm.md.hbond_compare)

C

calculate_bond_valence() (in module pyqmmm.qm.bond_valence) calculate_hbonds_script() (in module pyqmmm.md.amber_toolkit) calculate_rmsf_per_trajectory() (in module pyqmmm.md.rmsf_calculator) charge_diff() (in module quickcsa) charge_spin_extractor() (in module pyqmmm.qm.charge_spin_extractor) check_exists() (in module pyqmmm.qm.traj_movie_generator) clean_dir() (in module quickcsa) cli() (in module pyqmmm.cli) closest_waters_script() (in module pyqmmm.md.amber_toolkit) cluster_count (in module pyqmmm.md.rmsd_clusters_colorcoder) collect_charges() (in module quickcsa) collect_data() (in module pyqmmm.qm.energy_plotter) (in module pyqmmm.qm.plot_combined_nebs) collect_xyz_data() (in module pyqmmm.md.restraint_plotter)

color_scheme (in module pyqmmm.qm.mechanism_plotter) combine_dssp_files() (in module pyqmmm.md.dssp_plotter) combine_inp() (in module pyqmmm.md.restraint_plotter) combine_trajectories() (in module pyqmmm.qm.combine_nebs) combine_xyz_files() (in module pyqmmm.qm.traj_merger) compare_patch_limits() (in module pyqmmm.md.restraint_plotter) compute_hbonds() (in module pyqmmm.md.hbond_analyzer) condense_numbering() (in module pyqmmm.md.cluster_frame_indexer) config() (in module pyqmmm.md.restraint_plotter) count_nonempty_lines() (in module bfactor_chg) count_occurrences() (in module pyqmmm.md.hbond_analyzer) (in module pyqmmm.md.hbond_compare) create_delete_folder() (in module pyqmmm.qm.orca_neb_restart) create_dir() (in module pyqmmm.qm.traj_movie_generator) create_neb_mep_trj_from_out() (in module pyqmmm.qm.create_mep_trj)

D

dat2df() (in module pyqmmm.md.md_vitals_plotter) (in module pyqmmm.md.rmsd_clusters_colorcoder) (in module pyqmmm.md.rmsd_plotter) dccm_plot_formattor() (in module pyqmmm.md.dccm_plot_formator) delete_pdb_trj_atoms module

delete_xyz_trj_atoms module die() (in module bfactor_chg) (in module bfactor_csv) (in module pyqmmm.md.rmsf_calculator)

E

edia_chain_calculator() (in module pyqmmm.md.edia_chain_calculator) extract() (in module pyqmmm.qm.extract_electronic_energies) (in module pyqmmm.qm.extract_gibbs_free_energies)

extract_energies() (in module pyqmmm.qm.eda_analyze) extract_frames() (in module pyqmmm.qm.combine_nebs) extract_residue_names() (in module pyqmmm.md.residue_lister)

F

figure_formatting() (in module pyqmmm.md.hbond_analyzer) (in module pyqmmm.md.hbond_compare) file_mover() (in module quickcsa) files (in module pyqmmm.md.compare_distances) files_in_directory (in module pyqmmm.qm.orca_neb_restart) find_column() (in module bfactor_csv) find_heavy_atoms() (in module pyqmmm.qm.hydrogen_atom_optimizer) find_leftovers() (in module pyqmmm.qm.orca_clean_irc) format_bfactor() (in module bfactor_csv) format_plot() (in module pyqmmm.md.cc_coupling) (in module pyqmmm.md.compare_distances) (in module pyqmmm.md.dssp_plotter) (in module pyqmmm.md.gbsa_analyzer) (in module pyqmmm.md.rmsd_plotter) (in module pyqmmm.md.rmsf_plotter) (in module pyqmmm.qm.bond_valence) (in module pyqmmm.qm.eda_analyze) (in module pyqmmm.qm.energy_plotter) (in module pyqmmm.qm.mechanism_plotter) (in module pyqmmm.qm.orca_scan_plotter) (in module pyqmmm.qm.plot_combined_nebs) (in module pyqmmm.qm.residue_decomposition) (in module pyqmmm.qm.single-eda-analyze)

G

gbsa_script() (in module pyqmmm.md.amber_toolkit) generate_plot() (in module pyqmmm.qm.mechanism_plotter) generate_tree_structure() (in module repo2markdown) get_atoms() (in module pyqmmm.qm.charge_spin_extractor) get_barplot_plot() (in module pyqmmm.qm.qtaim_analyzer) get_charges() (in module pyqmmm.qm.charge_spin_extractor) get_clusters() (in module pyqmmm.md.cluster_frame_indexer) get_colors() (in module pyqmmm.md.compare_distances) get_dccm() (in module pyqmmm.md.dccm_plot_formator) get_directories() (in module pyqmmm.qm.extract_electronic_energies) (in module pyqmmm.qm.extract_gibbs_free_energies) get_distance() (in module pyqmmm.qm.reaction_coordinate_collector) get_edia() (in module pyqmmm.md.edia_chain_calculator) get_energy() (in module pyqmmm.qm.residue_decomposition) get_files() (in module pyqmmm.qm.charge_spin_extractor) get_frames() (in module pyqmmm.qm.traj_movie_generator) get_gbsa_df() (in module pyqmmm.md.gbsa_analyzer) get_imported_modules() (in module repo2markdown) get_iteration_pairs() (in module pyqmmm.qm.pes_organizer) get_last_frame() (in module pyqmmm.md.amber_toolkit) get_legend_labels() (in module pyqmmm.md.compare_distances) get_mask_res() (in module quickcsa) get_opt_energies() (in module pyqmmm.qm.energy_plotly) (in module pyqmmm.qm.reaction_coordinate_collector) get_pdb_ensemble() (in module pyqmmm.qm.traj_atom_filter)

get_plot() (in module pyqmmm.md.compare_distances) (in module pyqmmm.md.dccm_plot_formator) (in module pyqmmm.md.md_vitals_plotter) (in module pyqmmm.md.rmsd_clusters_colorcoder) (in module pyqmmm.md.rmsd_plotter) get_plot_limits() (in module pyqmmm.md.restraint_plotter) get_reaction_csv() (in module pyqmmm.qm.reaction_coordinate_collector) get_readme_content() (in module repo2markdown) get_relative_energies() (in module pyqmmm.qm.energy_plotly) get_res_diff() (in module quickcsa) get_scan_charges() (in module pyqmmm.qm.pes_organizer) get_scan_spins() (in module pyqmmm.qm.pes_organizer) get_scatter_plot() (in module pyqmmm.qm.energy_plotly) get_selection() (in module pyqmmm.qm.charge_spin_extractor) (in module pyqmmm.qm.traj_atom_filter) get_sorted_xyz_files() (in module pyqmmm.qm.combine_nebs) get_spins() (in module pyqmmm.qm.charge_spin_extractor) get_top_hits_df() (in module pyqmmm.md.gbsa_analyzer) get_trajectory_energies() (in module pyqmmm.qm.energy_plotter) (in module pyqmmm.qm.plot_combined_nebs) get_xy_data() (in module pyqmmm.md.restraint_plotter) get_xyz_file() (in module pyqmmm.qm.hydrogen_atom_optimizer) get_xyz_filenames() (in module pyqmmm.qm.traj_merger) get_xyz_files() (in module pyqmmm.qm.plot_combined_nebs) graph_datasets() (in module pyqmmm.md.restraint_plotter) GRN (in module pyqmmm.md.rmsf_calculator)

H

HARTREE_TO_KCAL (in module pyqmmm.qm.energy_plotter) (in module pyqmmm.qm.mechanism_plotter) (in module pyqmmm.qm.plot_combined_nebs)

HARTREE_TO_KCAL_MOL (in module pyqmmm.qm.orca_scan_plotter) hbond_plotter() (in module pyqmmm.qm.qtaim_analyzer) heatmap() (in module pyqmmm.md.cc_coupling) hydrogen_atom_optimizer() (in module pyqmmm.qm.hydrogen_atom_optimizer)

I

identify_software() (in module pyqmmm.qm.energy_plotter) (in module pyqmmm.qm.plot_combined_nebs) in_files (in module delete_pdb_trj_atoms) (in module delete_xyz_trj_atoms) INCLUDE_EXTENSIONS (in module repo2markdown)

INDENT (in module repo2markdown) input_pdb (in module translate_pdb_to_center) io() (in module pyqmmm.cli) is_atom_record() (in module bfactor_chg) (in module bfactor_csv) is_irc_directory() (in module pyqmmm.qm.orca_clean_irc)

K

keep_file() (in module pyqmmm.qm.orca_neb_restart)

kj_to_kcal (in module pyqmmm.qm.eda_analyze) (in module pyqmmm.qm.single-eda-analyze)

L

list_residues() (in module pyqmmm.md.residue_lister)

load_rmsf_csv_files() (in module pyqmmm.md.rmsf_plotter)

M

main() (in module bfactor_chg) (in module bfactor_csv) (in module delete_pdb_trj_atoms) (in module delete_xyz_trj_atoms) (in module pyqmmm.md.cluster_frame_indexer) (in module pyqmmm.md.rmsf_calculator) (in module pyqmmm.md.rmsf_plotter) (in module pyqmmm.qm.eda_analyze) (in module pyqmmm.qm.neb_doubler) (in module pyqmmm.qm.orca_clean_irc) (in module repo2markdown) (in module submit_clustering) MARKER (in module pyqmmm.qm.orca_clean_irc) mask_maker() (in module quickcsa) md() (in module pyqmmm.cli) md_vitals_plotter() (in module pyqmmm.md.md_vitals_plotter) missing_frame_checkup() (in module pyqmmm.qm.missing_frame_checkup) module bfactor_chg bfactor_csv delete_pdb_trj_atoms delete_xyz_trj_atoms ppm2png_converter pyqmmm pyqmmm.cli pyqmmm.md, [1] pyqmmm.md.amber_toolkit, [1] pyqmmm.md.cc_coupling, [1] pyqmmm.md.cluster_frame_indexer, [1] pyqmmm.md.compare_distances, [1] pyqmmm.md.dccm_plot_formator, [1] pyqmmm.md.dssp_plotter, [1] pyqmmm.md.edia_chain_calculator, [1] pyqmmm.md.gbsa_analyzer, [1] pyqmmm.md.hbond_analyzer, [1] pyqmmm.md.hbond_compare, [1] pyqmmm.md.md_vitals_plotter, [1] pyqmmm.md.pdb_ensemble_generator, [1] pyqmmm.md.residue_lister, [1] pyqmmm.md.restraint_plotter, [1] pyqmmm.md.rmsd_clusters_colorcoder, [1] pyqmmm.md.rmsd_plotter, [1] pyqmmm.md.rmsf_calculator pyqmmm.md.rmsf_plotter, [1] pyqmmm.qm, [1] pyqmmm.qm.bond_valence, [1] pyqmmm.qm.charge_spin_extractor, [1] pyqmmm.qm.combine_nebs, [1] pyqmmm.qm.create_mep_trj, [1] pyqmmm.qm.eda_analyze, [1] pyqmmm.qm.energy_plotly, [1] pyqmmm.qm.energy_plotter, [1] pyqmmm.qm.extract_electronic_energies, [1] pyqmmm.qm.extract_gibbs_free_energies, [1] pyqmmm.qm.hydrogen_atom_optimizer, [1] pyqmmm.qm.mechanism_plotter, [1] pyqmmm.qm.missing_frame_checkup, [1] pyqmmm.qm.neb_doubler, [1] pyqmmm.qm.orca_clean_irc, [1] pyqmmm.qm.orca_neb_restart, [1] pyqmmm.qm.orca_scan_plotter, [1] pyqmmm.qm.pdb_residue_extractor, [1] pyqmmm.qm.pes_organizer, [1] pyqmmm.qm.plot_combined_nebs, [1] pyqmmm.qm.qtaim_analyzer, [1] pyqmmm.qm.reaction_coordinate_collector, [1] pyqmmm.qm.replace_pdb pyqmmm.qm.res_name_format_extractor, [1] pyqmmm.qm.residue_decomposition, [1] pyqmmm.qm.residue_numerator, [1] pyqmmm.qm.single-eda-analyze pyqmmm.qm.traj_atom_filter, [1] pyqmmm.qm.traj_atom_swapper, [1] pyqmmm.qm.traj_merger pyqmmm.qm.traj_movie_generator, [1] pyqmmm.qm.xyz_flipper, [1] quickcsa repo2markdown submit_clustering translate_pdb_to_center xyz2pdb

move_files() (in module pyqmmm.qm.orca_neb_restart) multiframe_xyz_to_list() (in module pyqmmm.qm.traj_merger)

N

natural_sort() (in module pyqmmm.qm.residue_decomposition)

O

OUTPUT_FILE (in module repo2markdown)

P

pair_swapper() (in module pyqmmm.qm.traj_atom_swapper) parse_energy() (in module pyqmmm.qm.energy_plotter) (in module pyqmmm.qm.plot_combined_nebs) parse_final_energy() (in module pyqmmm.qm.extract_electronic_energies) parse_in_file() (in module delete_pdb_trj_atoms) (in module delete_xyz_trj_atoms) parse_orca_out() (in module pyqmmm.qm.extract_gibbs_free_energies) parse_rmsf_input_file() (in module pyqmmm.md.rmsf_calculator) pdb_ensemble_generator() (in module pyqmmm.md.pdb_ensemble_generator) pdb_file_path (in module pyqmmm.qm.replace_pdb) pdb_residue_extractor() (in module pyqmmm.qm.pdb_residue_extractor) (in module pyqmmm.qm.res_name_format_extractor) pes_organizer() (in module pyqmmm.qm.pes_organizer) pes_plotter() (in module pyqmmm.qm.energy_plotly) plot() (in module pyqmmm.md.hbond_analyzer) (in module pyqmmm.md.hbond_compare) plot_all_gbsa() (in module pyqmmm.md.gbsa_analyzer) plot_bond_valence() (in module pyqmmm.qm.bond_valence) plot_clustered_stacked() (in module pyqmmm.md.gbsa_analyzer) plot_data() (in module pyqmmm.md.dssp_plotter) (in module pyqmmm.qm.energy_plotter) (in module pyqmmm.qm.plot_combined_nebs) (in module pyqmmm.qm.residue_decomposition) plot_energies() (in module pyqmmm.qm.energy_plotter) (in module pyqmmm.qm.plot_combined_nebs) (in module pyqmmm.qm.single-eda-analyze) plot_energy() (in module pyqmmm.qm.orca_scan_plotter) plot_group_energies() (in module pyqmmm.qm.mechanism_plotter) plot_multi() (in module pyqmmm.md.hbond_analyzer) (in module pyqmmm.md.hbond_compare) plot_rmsf() (in module pyqmmm.md.rmsf_plotter) plot_single_total_gbsa() (in module pyqmmm.md.gbsa_analyzer) plotly_styling() (in module pyqmmm.qm.energy_plotly) (in module pyqmmm.qm.qtaim_analyzer) ppm2png_converter module ppm2png_converter() (in module ppm2png_converter) print_example_input() (in module pyqmmm.md.rmsf_calculator) process_data() (in module pyqmmm.md.dssp_plotter) (in module pyqmmm.md.hbond_analyzer) (in module pyqmmm.md.hbond_compare) process_directory() (in module pyqmmm.qm.residue_decomposition) process_xyz_files() (in module pyqmmm.qm.mechanism_plotter) protein_id (in module pyqmmm.md.amber_toolkit) pyqmmm module pyqmmm.cli module pyqmmm.md module, [1] pyqmmm.md.amber_toolkit module, [1] pyqmmm.md.cc_coupling module, [1] pyqmmm.md.cluster_frame_indexer module, [1] pyqmmm.md.compare_distances module, [1] pyqmmm.md.dccm_plot_formator module, [1] pyqmmm.md.dssp_plotter module, [1] pyqmmm.md.edia_chain_calculator module, [1] pyqmmm.md.gbsa_analyzer module, [1] pyqmmm.md.hbond_analyzer module, [1] pyqmmm.md.hbond_compare module, [1] pyqmmm.md.md_vitals_plotter module, [1] pyqmmm.md.pdb_ensemble_generator module, [1] pyqmmm.md.residue_lister module, [1]

pyqmmm.md.restraint_plotter module, [1] pyqmmm.md.rmsd_clusters_colorcoder module, [1] pyqmmm.md.rmsd_plotter module, [1] pyqmmm.md.rmsf_calculator module pyqmmm.md.rmsf_plotter module, [1] pyqmmm.qm module, [1] pyqmmm.qm.bond_valence module, [1] pyqmmm.qm.charge_spin_extractor module, [1] pyqmmm.qm.combine_nebs module, [1] pyqmmm.qm.create_mep_trj module, [1] pyqmmm.qm.eda_analyze module, [1] pyqmmm.qm.energy_plotly module, [1] pyqmmm.qm.energy_plotter module, [1] pyqmmm.qm.extract_electronic_energies module, [1] pyqmmm.qm.extract_gibbs_free_energies module, [1] pyqmmm.qm.hydrogen_atom_optimizer module, [1] pyqmmm.qm.mechanism_plotter module, [1] pyqmmm.qm.missing_frame_checkup module, [1] pyqmmm.qm.neb_doubler module, [1] pyqmmm.qm.orca_clean_irc module, [1] pyqmmm.qm.orca_neb_restart module, [1] pyqmmm.qm.orca_scan_plotter module, [1] pyqmmm.qm.pdb_residue_extractor module, [1] pyqmmm.qm.pes_organizer module, [1] pyqmmm.qm.plot_combined_nebs module, [1] pyqmmm.qm.qtaim_analyzer module, [1] pyqmmm.qm.reaction_coordinate_collector module, [1] pyqmmm.qm.replace_pdb module pyqmmm.qm.res_name_format_extractor module, [1] pyqmmm.qm.residue_decomposition module, [1] pyqmmm.qm.residue_numerator module, [1] pyqmmm.qm.single-eda-analyze module pyqmmm.qm.traj_atom_filter module, [1] pyqmmm.qm.traj_atom_swapper module, [1] pyqmmm.qm.traj_merger module pyqmmm.qm.traj_movie_generator module, [1] pyqmmm.qm.xyz_flipper module, [1]

Q

qm() (in module pyqmmm.cli) qmmm() (in module pyqmmm.cli) quick_csa() (in module quickcsa)

quick_csa_intro() (in module quickcsa) quickcsa module

R

reaction_coordinate_collector() (in module pyqmmm.qm.reaction_coordinate_collector) read_charges_from_chg() (in module bfactor_chg) read_data() (in module pyqmmm.md.compare_distances) read_data_from_csv() (in module pyqmmm.qm.single-eda-analyze) read_energy_from_xyz() (in module pyqmmm.qm.mechanism_plotter) read_files() (in module pyqmmm.qm.mechanism_plotter) read_info() (in module pyqmmm.qm.replace_pdb) read_orca_output() (in module pyqmmm.qm.orca_scan_plotter) read_xyz() (in module pyqmmm.qm.xyz_flipper) read_xyz_last_frame() (in module pyqmmm.qm.replace_pdb) RED (in module pyqmmm.md.rmsf_calculator) references() (in module pyqmmm.qm.energy_plotly) remove_atoms() (in module pyqmmm.qm.traj_atom_filter) remove_atoms_from_pdb() (in module delete_pdb_trj_atoms) remove_atoms_from_xyz() (in module delete_xyz_trj_atoms) rename_gbw() (in module pyqmmm.qm.orca_neb_restart)

renumber() (in module pyqmmm.qm.residue_numerator) replace_coordinates_in_pdb() (in module pyqmmm.qm.replace_pdb) repo2markdown module request_frames() (in module pyqmmm.qm.traj_merger) request_rc() (in module pyqmmm.qm.reaction_coordinate_collector) RESET (in module pyqmmm.md.rmsf_calculator) residue_decomposition() (in module pyqmmm.qm.residue_decomposition) residue_key() (in module bfactor_chg) residue_key_from_pdb_line() (in module bfactor_csv) residue_numerator() (in module pyqmmm.qm.residue_numerator) restraint_plots() (in module pyqmmm.md.restraint_plotter) rmsd_clusters_colorcoder() (in module pyqmmm.md.rmsd_clusters_colorcoder) rmsd_plotter() (in module pyqmmm.md.rmsd_plotter) ROOT_DIR (in module repo2markdown) run_cpptraj() (in module pyqmmm.md.amber_toolkit)

S

sanitize_for_filename() (in module bfactor_csv) set_bfactor() (in module bfactor_chg) should_include_file() (in module repo2markdown) SKIP_DIRS (in module repo2markdown) strip_all_script() (in module pyqmmm.md.amber_toolkit)

submit_clustering module submit_script() (in module pyqmmm.md.amber_toolkit) swap_spins() (in module pyqmmm.qm.traj_atom_swapper) swap_xyz() (in module pyqmmm.qm.traj_atom_swapper)

T

three_to_one (in module pyqmmm.md.residue_lister) traj_atom_filter() (in module pyqmmm.qm.traj_atom_filter)

translate_pdb() (in module translate_pdb_to_center) translate_pdb_to_center module

U

update_res_names() (in module pyqmmm.md.gbsa_analyzer)

W

welcome() (in module pyqmmm.cli) write_data() (in module pyqmmm.qm.charge_spin_extractor) write_energies_to_csv() (in module pyqmmm.qm.energy_plotter) (in module pyqmmm.qm.plot_combined_nebs) write_file_contents() (in module repo2markdown)

write_imports_section() (in module repo2markdown) write_residues_to_file() (in module pyqmmm.md.residue_lister) write_scan() (in module pyqmmm.qm.traj_atom_swapper) write_to_csv() (in module pyqmmm.qm.extract_electronic_energies) (in module pyqmmm.qm.extract_gibbs_free_energies) write_xyz() (in module pyqmmm.qm.xyz_flipper)

X

xyz2pdb module xyz2pdb_traj() (in module xyz2pdb)

xyz_flipper() (in module pyqmmm.qm.xyz_flipper) xyz_merger() (in module pyqmmm.qm.traj_merger) xyz_movie_generator() (in module pyqmmm.qm.traj_movie_generator) xyz_traj (in module xyz2pdb)

Y

yaxis_title (in module pyqmmm.md.rmsd_plotter)

YLW (in module pyqmmm.md.rmsf_calculator)