Index

A

active_passive_to_ambig() (in module haddock.libs.librestraints) actpass_to_ambig() (in module haddock.clis.restraints.active_passive_to_ambig) add() (haddock.libs.libontology.ModuleIO method) add_actpass_to_ambig_arguments() (in module haddock.clis.restraints.active_passive_to_ambig) add_calc_accessibility_arguments() (in module haddock.clis.restraints.calc_accessibility) add_chain_from_segid() (haddock.modules.analysis.caprieval.capri.CAPRI static method) add_charges_to_ions() (in module haddock.gear.preprocessing) add_chordchart_legends() (in module haddock.modules.analysis.contactmap.contmap) add_cluster_info() (in module haddock.libs.libclust) add_clustfcc_arguments() (in module haddock.clis.re.clustfcc) add_clustrmsd_arguments() (in module haddock.clis.re.clustrmsd) add_delta_to_bfactor() (in module haddock.modules.analysis.alascan.scan) add_extend_run() (in module haddock.gear.extend_run) add_handler() (in module haddock.libs.liblog) add_log_for_CLI() (in module haddock.libs.liblog) add_logfile_handler() (in module haddock.libs.liblog) add_loglevel_arg() (in module haddock.libs.liblog) add_ncores_arg() (in module haddock.libs.libcli) add_output_dir_arg() (in module haddock.libs.libcli) add_parent_to_paths() (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method), [1] add_pass_from_act_arguments() (in module haddock.clis.restraints.passive_from_active) add_rescore_arguments() (in module haddock.clis.re.score)

add_restart_arg() (in module haddock.gear.restart_run) add_restrain_bodies_arguments() (in module haddock.clis.restraints.restrain_bodies) add_rundir_arg() (in module haddock.libs.libcli) add_stringio_handler() (in module haddock.libs.liblog) add_suffix_to_files() (in module haddock.libs.libio) add_syserr_handler() (in module haddock.libs.liblog) add_sysout_handler() (in module haddock.libs.liblog) add_validate_tbl_arguments() (in module haddock.clis.restraints.validate_tbl) add_version_arg() (in module haddock.libs.libcli) add_zscores() (in module haddock.modules.analysis.alascan.scan) aggregate_contacts() (haddock.modules.analysis.contactmap.contmap.ClusteredContactMap static method) alascan_cluster_analysis() (in module haddock.modules.analysis.alascan.scan) align_seq() (in module haddock.libs.libalign) align_strct() (in module haddock.libs.libalign) ALIGNError ambig2dic() (in module haddock.modules.sampling.gdock) analyse_step() (in module haddock.clis.cli_analyse) AnyT (class in haddock.core.typing) apply_cutoff() (in module haddock.clis.restraints.calc_accessibility) apply_min_population() (in module haddock.modules.analysis.clustrmsd.clustrmsd) archive_files_ext() (in module haddock.libs.libio) atoms (haddock.core.supported_molecules.CNSTopologyResidue property) AtomsDict (in module haddock.core.typing)

B

BaseCNSModule (class in haddock.modules.base_cns_module), [1] BaseHaddockModule (class in haddock.modules), [1] BaseJob (class in haddock.libs.libsubprocess) belongs_to_multiple_index() (in module haddock.gear.expandable_parameters)

belongs_to_single_index() (in module haddock.gear.expandable_parameters) box_plot_data() (in module haddock.libs.libplots) box_plot_handler() (in module haddock.libs.libplots) box_plot_plotly() (in module haddock.libs.libplots) build_restraints() (in module haddock.libs.librestraints)

C

calc_accessibility() (in module haddock.clis.restraints.calc_accessibility) calc_dockq() (haddock.modules.analysis.caprieval.capri.CAPRI method) calc_euclidean() (in module haddock.libs.librestraints) calc_fnat() (haddock.modules.analysis.caprieval.capri.CAPRI method) calc_haddock_score() (haddock.gear.haddockmodel.HaddockModel method) calc_ilrmsd() (haddock.modules.analysis.caprieval.capri.CAPRI method) calc_irmsd() (haddock.modules.analysis.caprieval.capri.CAPRI method) calc_lrmsd() (haddock.modules.analysis.caprieval.capri.CAPRI method) calc_rmsd() (in module haddock.libs.libalign) calc_score() (in module haddock.modules.analysis.alascan.scan) calc_size() (in module haddock.clis.cli_dmn) calc_stats() (in module haddock.modules.analysis.caprieval.capri) cancel() (haddock.libs.libhpc.HPCWorker method) CAPRI (class in haddock.modules.analysis.caprieval.capri) capri_cluster_analysis() (in module haddock.modules.analysis.caprieval.capri) CAPRIError centroid() (in module haddock.libs.libalign) chainf() (in module haddock.libs.libfunc) chainfs() (in module haddock.libs.libfunc) charge (haddock.core.supported_molecules.CNSTopologyResidue property) check_chains() (haddock.modules.analysis.caprieval.capri.CAPRI method) check_common_atoms() (in module haddock.libs.libalign) check_faulty() (haddock.libs.libontology.ModuleIO method) check_if_modules_are_installed() (in module haddock.gear.prepare_run) check_if_path_exists() (in module haddock.gear.prepare_run) check_mandatory_argments_are_present() (in module haddock.gear.prepare_run) check_parenthesis() (in module haddock.libs.librestraints) check_run_dir_exists() (in module haddock.gear.prepare_run) check_specific_validations() (in module haddock.gear.prepare_run) check_square_matrix() (in module haddock.modules.analysis.contactmap.contmap) clean() (haddock.gear.extend_run.WorkflowManagerExtend method) (haddock.libs.libworkflow.Step method) (haddock.libs.libworkflow.WorkflowManager method) clean_capri_table() (in module haddock.libs.libplots) clean_output() (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method), [1] (in module haddock.gear.clean_steps) clean_suffix() (in module haddock.libs.libio) cli() (in module haddock.clis.cli) (in module haddock.clis.cli_analyse) (in module haddock.clis.cli_bm) (in module haddock.clis.cli_cfg) (in module haddock.clis.cli_clean) (in module haddock.clis.cli_cp) (in module haddock.clis.cli_dmn) (in module haddock.clis.cli_mpi) (in module haddock.clis.cli_pp) (in module haddock.clis.cli_score) (in module haddock.clis.cli_traceback) (in module haddock.clis.cli_unpack) ClRank (in module haddock.libs.libplots) clt_table_handler() (in module haddock.libs.libplots) ClusteredContactMap (class in haddock.modules.analysis.contactmap.contmap) clustrmsd_tolerance_params() (in module haddock.libs.libclust) cns_exec (haddock.libs.libsubprocess.CNSJob property) CNS_INPUT (haddock.libs.libontology.Format attribute) CNS_MODULES (in module haddock.core.defaults) CNS_OUTPUT (haddock.libs.libontology.Format attribute) CNSJob (class in haddock.libs.libsubprocess)

CNSRunningError CNSScoringModule (class in haddock.modules.scoring) CNSTopologyResidue (class in haddock.core.supported_molecules) compress_files_ext() (in module haddock.libs.libio) compute_distance_matrix() (in module haddock.modules.analysis.contactmap.contmap) cond_index() (in module haddock.modules.analysis.clustrmsd.clustrmsd) config_key_error() (in module haddock.gear.prepare_run) ConfigFormatError ConfigurationError confirm_installation() (haddock.modules.analysis.alascan.HaddockModule class method) (haddock.modules.analysis.caprieval.HaddockModule class method) (haddock.modules.analysis.clustfcc.HaddockModule class method) (haddock.modules.analysis.clustrmsd.HaddockModule class method) (haddock.modules.analysis.contactmap.HaddockModule class method) (haddock.modules.analysis.ilrmsdmatrix.HaddockModule class method) (haddock.modules.analysis.rmsdmatrix.HaddockModule class method) (haddock.modules.analysis.seletop.HaddockModule class method) (haddock.modules.analysis.seletopclusts.HaddockModule class method) (haddock.modules.base_cns_module.BaseCNSModule class method) (haddock.modules.BaseHaddockModule class method), [1] (haddock.modules.extras.exit.HaddockModule class method) (haddock.modules.refinement.emref.HaddockModule class method) (haddock.modules.refinement.flexref.HaddockModule class method) (haddock.modules.refinement.mdref.HaddockModule class method) (haddock.modules.sampling.gdock.HaddockModule class method) (haddock.modules.sampling.lightdock.HaddockModule class method) (haddock.modules.sampling.rigidbody.HaddockModule class method) (haddock.modules.scoring.emscoring.HaddockModule class method) (haddock.modules.scoring.mdscoring.HaddockModule class method) (haddock.modules.topology.topoaa.HaddockModule class method) confirm_resdic_chainid_length() (in module haddock.modules.analysis) Contact (class in haddock.modules.analysis.ilrmsdmatrix.ilrmsd) ContactJob (class in haddock.modules.analysis.ilrmsdmatrix.ilrmsd) contacts_to_connect_matrix() (in module haddock.modules.analysis.contactmap.contmap) ContactsMap (class in haddock.modules.analysis.contactmap.contmap) ContactsMapJob (class in haddock.modules.analysis.contactmap.contmap) control_pts() (in module haddock.modules.analysis.contactmap.contmap) convert_ATOM_to_HETATM() (in module haddock.gear.preprocessing) convert_HETATM_to_ATOM() (in module haddock.gear.preprocessing) convert_record() (in module haddock.gear.preprocessing) convert_seconds_to_min_sec() (in module haddock.libs.libtimer) convert_to_path() (in module haddock.gear.config) convert_variables_to_paths() (in module haddock.gear.config) copy_files_to_dir() (in module haddock.libs.libutil) copy_input_files_to_data_dir() (in module haddock.gear.prepare_run) copy_molecules_to_data_dir() (in module haddock.gear.prepare_run) copy_molecules_to_topology() (in module haddock.gear.prepare_run) copy_renum_step_folders() (in module haddock.gear.extend_run) correct_equal_chain_segids() (in module haddock.gear.preprocessing) create_alascan_plots() (in module haddock.modules.analysis.alascan.scan) create_cfg_test_daemon() (in module haddock.clis.cli_bm) create_cfg_ti() (in module haddock.clis.cli_bm) create_CNS_export_envvars() (in module haddock.libs.libhpc) create_data_dir() (in module haddock.gear.prepare_run) create_html() (in module haddock.libs.libplots) create_job() (in module haddock.clis.cli_bm) create_other_cluster() (in module haddock.libs.libplots) create_slurm_header() (in module haddock.libs.libhpc) create_torque_header() (in module haddock.libs.libhpc) ctrl_rib_chords() (in module haddock.modules.analysis.contactmap.contmap)

D

datakey_to_colorscale() (in module haddock.modules.analysis.contactmap.contmap) default_envvars() (haddock.modules.base_cns_module.BaseCNSModule method), [1]

dot_suffix() (in module haddock.libs.libio) dump_as_izone() (in module haddock.libs.libalign)

E

elements (haddock.core.supported_molecules.CNSTopologyResidue property) EmptyPath (class in haddock) envvars (haddock.libs.libsubprocess.CNSJob property) execute() (haddock.libs.libworkflow.Step method) ExpertLevel (in module haddock.core.typing) export_io_models() (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method), [1] export_passive() (in module haddock.clis.restraints.calc_accessibility)

export_plotly_figure() (in module haddock.libs.libplots) extract_heavyatom_contacts() (in module haddock.modules.analysis.contactmap.contmap) extract_keys_recursive() (in module haddock.libs.libutil) extract_multiple_index_params() (in module haddock.gear.expandable_parameters) extract_pdb_coords() (in module haddock.modules.analysis.contactmap.contmap) extract_pdb_dt() (in module haddock.modules.analysis.contactmap.contmap) extract_single_index_params() (in module haddock.gear.expandable_parameters) extract_slurm_status() (in module haddock.libs.libhpc) extract_submatrix() (in module haddock.modules.analysis.contactmap.contmap)

F

false() (in module haddock.libs.libfunc) fig_to_html() (in module haddock.libs.libplots) file_exists() (in module haddock.libs.libio) FilePathT (class in haddock.core.typing) filter_by_status() (in module haddock.clis.cli_dmn) filter_empty_vars() (in module haddock.libs.libcns) find_best_struct() (in module haddock.libs.libplots)

finish_with_error() (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method), [1] flat_yaml_cfg() (in module haddock.gear.yaml2cfg) folder_exists() (in module haddock.libs.libio) Format (class in haddock.libs.libontology) format_atom_name() (in module haddock.libs.libpdb) fuzzy_match() (in module haddock.gear.prepare_run)

G

gen_contact_dt() (in module haddock.modules.analysis.contactmap.contmap) generate_alascan_output() (in module haddock.modules.analysis.alascan.scan) generate_default_header() (in module haddock.libs.libcns) generate_output() (haddock.modules.analysis.contactmap.contmap.ContactsMap method) generate_tbl() (in module haddock.libs.librestraints) generate_topology() (in module haddock.modules.topology.topoaa) get_accessibility() (in module haddock.clis.restraints.calc_accessibility) get_adieu() (in module haddock.gear.greetings) get_align() (in module haddock.libs.libalign) get_all_ideograms_ends() (in module haddock.modules.analysis.contactmap.contmap) get_ambig_fnames() (haddock.modules.base_cns_module.BaseCNSModule method), [1] get_analysis_exec_mode() (in module haddock.modules.analysis) get_atoms() (in module haddock.libs.libalign) get_axis() (in module haddock.core.cns_paths) get_bodies() (in module haddock.libs.librestraints) get_chains_ideograms_ends() (in module haddock.modules.analysis.contactmap.contmap) get_cluster_center() (in module haddock.modules.analysis.clustrmsd.clustrmsd) get_cluster_centers() (in module haddock.modules.analysis.clustfcc.clustfcc) get_cluster_matrix_plot_clt_dt() (in module haddock.libs.libclust) get_cluster_ranking() (in module haddock.clis.cli_analyse) get_clusters() (in module haddock.modules.analysis.clustrmsd.clustrmsd) get_clusters_sets() (in module haddock.modules.analysis.contactmap.contmap) get_conda_path() (in module haddock.clis.cli_bm) get_cont_type() (in module haddock.modules.analysis.contactmap.contmap) get_current_jobs() (in module haddock.clis.cli_dmn) get_dendrogram() (in module haddock.modules.analysis.clustrmsd.clustrmsd) get_engine() (in module haddock.modules), [1] get_expandable_parameters() (in module haddock.gear.prepare_run) get_goodbye_greetings() (in module haddock.gear.greetings) get_goodbye_help() (in module haddock.gear.greetings) get_greetings() (in module haddock.gear.greetings) get_ideogram_ends() (in module haddock.modules.analysis.contactmap.contmap) get_index_list() (in module haddock.libs.libparallel)

get_initial_greeting() (in module haddock.gear.greetings) get_ion_element_from_atoms() (in module haddock.core.supported_molecules) get_matrix_path() (in module haddock.modules.analysis.clustrmsd.clustrmsd) get_md5() (haddock.modules.topology.topoaa.HaddockModule static method) get_module_name() (in module haddock.gear.config) get_module_steps_folders() (in module haddock.modules), [1] get_mol_parameters() (in module haddock.gear.expandable_parameters) get_multiple_index_groups() (in module haddock.gear.expandable_parameters) get_new_models() (in module haddock.libs.libpdb) get_number_from_path_stem() (in module haddock.libs.libutil) get_number_of_digits() (in module haddock.gear.zerofill) get_ordered_coords() (in module haddock.modules.analysis.contactmap.contmap) get_ori_names() (in module haddock.clis.cli_traceback) get_pair() (in module haddock.modules.analysis.rmsdmatrix.rmsd) get_pdb_file_suffix_variations() (in module haddock.libs.libpdb) get_perm() (in module haddock.libs.libio) get_previous_cns_step() (in module haddock.modules.analysis.caprieval.capri) get_resnames() (in module haddock.core.supported_molecules) get_result_or_same_in_list() (in module haddock.libs.libutil) get_score_string() (in module haddock.modules.analysis.alascan.scan) get_single_index_groups() (in module haddock.gear.expandable_parameters) get_status() (haddock.clis.cli_dmn.Job method) get_steps_without_pdbs() (in module haddock.clis.cli_traceback) get_supported_residues() (in module haddock.libs.libpdb) get_surface_resids() (in module haddock.libs.librestraints) get_tensors() (in module haddock.core.cns_paths) get_trail_index() (in module haddock.gear.expandable_parameters) get_translation_vectors() (in module haddock.core.cns_paths) get_water_box() (in module haddock.core.cns_paths) get_zerofill_for_modules() (in module haddock.gear.zerofill) give_same() (in module haddock.libs.libfunc) glob_folder() (in module haddock.libs.libio) gzip_files() (in module haddock.libs.libio)

H

haddock module haddock.clis module haddock.clis.cli module haddock.clis.cli_analyse module haddock.clis.cli_bm module haddock.clis.cli_cfg module haddock.clis.cli_clean module haddock.clis.cli_cp module haddock.clis.cli_dmn module haddock.clis.cli_mpi module haddock.clis.cli_pp module haddock.clis.cli_re module haddock.clis.cli_restraints module haddock.clis.cli_score module haddock.clis.cli_traceback module haddock.clis.cli_unpack module haddock.clis.re module haddock.clis.re.clustfcc module haddock.clis.re.clustrmsd module haddock.clis.re.score module haddock.clis.restraints module haddock.clis.restraints.active_passive_to_ambig module haddock.clis.restraints.calc_accessibility module haddock.clis.restraints.passive_from_active module haddock.clis.restraints.restrain_bodies module haddock.clis.restraints.validate_tbl module haddock.core module haddock.core.cns_paths module haddock.core.defaults module haddock.core.exceptions module haddock.core.supported_molecules module haddock.core.typing module haddock.gear module haddock.gear.clean_steps module haddock.gear.config module haddock.gear.expandable_parameters module haddock.gear.extend_run module haddock.gear.greetings module haddock.gear.haddockmodel module haddock.gear.parameters module haddock.gear.prepare_run module haddock.gear.preprocessing module haddock.gear.restart_run module haddock.gear.validations module haddock.gear.yaml2cfg module haddock.gear.zerofill module haddock.libs module haddock.libs.libalign module haddock.libs.libcli module haddock.libs.libclust module haddock.libs.libcns module haddock.libs.libfunc module haddock.libs.libhpc module haddock.libs.libinteractive module haddock.libs.libio module haddock.libs.liblog module haddock.libs.libmath module haddock.libs.libmpi module haddock.libs.libontology module haddock.libs.libparallel module

haddock.libs.libpdb module haddock.libs.libplots module haddock.libs.librestraints module haddock.libs.libstructure module haddock.libs.libsubprocess module haddock.libs.libtimer module haddock.libs.libutil module haddock.libs.libworkflow module haddock.modules module, [1] haddock.modules.analysis module haddock.modules.analysis.alascan module haddock.modules.analysis.alascan.scan module haddock.modules.analysis.caprieval module haddock.modules.analysis.caprieval.capri module haddock.modules.analysis.clustfcc module haddock.modules.analysis.clustfcc.clustfcc module haddock.modules.analysis.clustrmsd module haddock.modules.analysis.clustrmsd.clustrmsd module haddock.modules.analysis.contactmap module haddock.modules.analysis.contactmap.contmap module haddock.modules.analysis.ilrmsdmatrix module haddock.modules.analysis.ilrmsdmatrix.ilrmsd module haddock.modules.analysis.rmsdmatrix module haddock.modules.analysis.rmsdmatrix.rmsd module haddock.modules.analysis.seletop module haddock.modules.analysis.seletopclusts module haddock.modules.analysis.seletopclusts.seletopclusts module haddock.modules.base_cns_module module, [1] haddock.modules.extras module haddock.modules.extras.exit module haddock.modules.refinement module haddock.modules.refinement.emref module haddock.modules.refinement.flexref module haddock.modules.refinement.mdref module haddock.modules.sampling module haddock.modules.sampling.gdock module haddock.modules.sampling.lightdock module haddock.modules.sampling.rigidbody module haddock.modules.scoring module haddock.modules.scoring.emscoring module haddock.modules.scoring.mdscoring module haddock.modules.topology module haddock.modules.topology.topoaa module haddock.modules.topology.topocg module HaddockError HaddockModel (class in haddock.gear.haddockmodel) HaddockModule (class in haddock.modules.analysis.alascan) (class in haddock.modules.analysis.caprieval) (class in haddock.modules.analysis.clustfcc) (class in haddock.modules.analysis.clustrmsd) (class in haddock.modules.analysis.contactmap) (class in haddock.modules.analysis.ilrmsdmatrix) (class in haddock.modules.analysis.rmsdmatrix) (class in haddock.modules.analysis.seletop) (class in haddock.modules.analysis.seletopclusts) (class in haddock.modules.extras.exit) (class in haddock.modules.refinement.emref) (class in haddock.modules.refinement.flexref) (class in haddock.modules.refinement.mdref) (class in haddock.modules.sampling.gdock) (class in haddock.modules.sampling.lightdock) (class in haddock.modules.sampling.rigidbody) (class in haddock.modules.scoring.emscoring) (class in haddock.modules.scoring.mdscoring) (class in haddock.modules.topology.topoaa) HaddockModuleError HaddockTermination handle_clt_file() (in module haddock.libs.libinteractive) handle_ss_file() (in module haddock.libs.libinteractive) has_cluster_info() (haddock.modules.analysis.caprieval.capri.CAPRI method) heatmap_plotly() (in module haddock.libs.libplots) homogenize_chains() (in module haddock.gear.preprocessing) HPCScheduler (class in haddock.libs.libhpc) HPCWorker (class in haddock.libs.libhpc)

I

identify_chainseg() (in module haddock.libs.libpdb) identify_interface() (haddock.modules.analysis.caprieval.capri.CAPRI static method) identify_modules() (in module haddock.gear.prepare_run) ImgFormat (in module haddock.core.typing) in_capri() (in module haddock.libs.libplots) inject_in_modules() (in module haddock.gear.prepare_run)

INTERACTIVE_RE_SUFFIX (in module haddock.core.defaults) invPerm() (in module haddock.modules.analysis.contactmap.contmap) is_mol_parameter() (in module haddock.gear.expandable_parameters) is_present() (haddock.libs.libontology.Persistent method) is_step_folder() (in module haddock.modules), [1] iterate_clustering() (in module haddock.modules.analysis.clustfcc.clustfcc) iterate_min_population() (in module haddock.modules.analysis.clustrmsd.clustrmsd)

J

Job (class in haddock.clis.cli_dmn) (class in haddock.libs.libsubprocess)

JobInputFirst (class in haddock.libs.libsubprocess) JobRunningError

K

kabsch() (in module haddock.libs.libalign)

L

last_step_folder() (haddock.modules.base_cns_module.BaseCNSModule static method) (haddock.modules.BaseHaddockModule static method), [1] LineIterSource (in module haddock.core.typing) load() (haddock.libs.libontology.ModuleIO method) (in module haddock.gear.config) load_ambig() (in module haddock.libs.libcns) load_args() (in module haddock.clis.cli) (in module haddock.clis.cli_analyse) (in module haddock.clis.cli_bm) (in module haddock.clis.cli_cfg) (in module haddock.clis.cli_clean) (in module haddock.clis.cli_cp) (in module haddock.clis.cli_dmn) (in module haddock.clis.cli_mpi) (in module haddock.clis.cli_pp) (in module haddock.clis.cli_re) (in module haddock.clis.cli_restraints) (in module haddock.clis.cli_score) (in module haddock.clis.cli_traceback) (in module haddock.clis.cli_unpack)

load_axis() (in module haddock.libs.libcns) load_boxtyp20() (in module haddock.libs.libcns) load_contacts() (in module haddock.modules.analysis.caprieval.capri) load_coords() (in module haddock.libs.libalign) load_dihe() (in module haddock.libs.libcns) load_hbond() (in module haddock.libs.libcns) load_link() (in module haddock.libs.libcns) load_scatter() (in module haddock.libs.libcns) load_tensor() (in module haddock.libs.libcns) load_tensor_tbl() (in module haddock.libs.libcns) load_trans_vectors() (in module haddock.libs.libcns) load_unambig() (in module haddock.libs.libcns) load_workflow_params() (in module haddock.libs.libcns) loads() (in module haddock.gear.config) log() (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method), [1] log_error_and_exit() (in module haddock.libs.libutil) log_time() (in module haddock.libs.libtimer) look_for_capri() (in module haddock.libs.libinteractive)

M

main() (in module haddock.clis.cli) (in module haddock.clis.cli_analyse) (in module haddock.clis.cli_bm) (in module haddock.clis.cli_cfg) (in module haddock.clis.cli_clean) (in module haddock.clis.cli_cp) (in module haddock.clis.cli_dmn) (in module haddock.clis.cli_mpi) (in module haddock.clis.cli_pp) (in module haddock.clis.cli_score) (in module haddock.clis.cli_traceback) (in module haddock.clis.cli_unpack) maincli() (in module haddock.clis.cli) (in module haddock.clis.cli_analyse) (in module haddock.clis.cli_bm) (in module haddock.clis.cli_cfg) (in module haddock.clis.cli_clean) (in module haddock.clis.cli_cp) (in module haddock.clis.cli_dmn) (in module haddock.clis.cli_mpi) (in module haddock.clis.cli_pp) (in module haddock.clis.cli_re) (in module haddock.clis.cli_restraints) (in module haddock.clis.cli_score) (in module haddock.clis.cli_traceback) (in module haddock.clis.cli_unpack) make_alascan_plot() (in module haddock.libs.libplots) make_chordchart() (in module haddock.modules.analysis.contactmap.contmap) make_cmd() (haddock.libs.libsubprocess.BaseJob method) (haddock.libs.libsubprocess.Job method) (haddock.libs.libsubprocess.JobInputFirst method) (haddock.modules.analysis.rmsdmatrix.rmsd.RMSDJob method) make_contactmap_report() (in module haddock.modules.analysis.contactmap.contmap) make_daemon_job() (in module haddock.clis.cli_bm) make_ideo_shape() (in module haddock.modules.analysis.contactmap.contmap) make_ideogram_arc() (in module haddock.modules.analysis.contactmap.contmap) make_layout() (in module haddock.modules.analysis.contactmap.contmap) make_list_if_string() (in module haddock.libs.libutil) make_molecules() (in module haddock.libs.libstructure) make_output() (haddock.modules.analysis.caprieval.capri.CAPRI method) make_param_name_multiple_index() (in module haddock.gear.expandable_parameters) make_param_name_single_index() (in module haddock.gear.expandable_parameters) make_q_bezier() (in module haddock.modules.analysis.contactmap.contmap) make_range() (in module haddock.libs.libalign) make_ribbon() (in module haddock.modules.analysis.contactmap.contmap) make_ribbon_arc() (in module haddock.modules.analysis.contactmap.contmap) make_ribbon_ends() (in module haddock.modules.analysis.contactmap.contmap) make_self_contained() (haddock.modules.base_cns_module.BaseCNSModule method), [1] make_traceback_plot() (in module haddock.libs.libplots) make_writeable_recursive() (in module haddock.libs.libio) make_zero_fill() (in module haddock.gear.zerofill) MANDATORY_YAML (in module haddock.gear.parameters) map_clusters_models() (in module haddock.modules.analysis.seletopclusts.seletopclusts) match_path_criteria() (in module haddock.gear.config) MATRIX (haddock.libs.libontology.Format attribute) MAX_NUM_MODULES (in module haddock.core.defaults) merge_data() (in module haddock.modules.analysis.caprieval.capri) min_dist() (in module haddock.modules.analysis.contactmap.contmap) models_should_have_the_same_labels() (in module haddock.gear.preprocessing) ModelsDifferError module haddock haddock.clis haddock.clis.cli haddock.clis.cli_analyse haddock.clis.cli_bm haddock.clis.cli_cfg haddock.clis.cli_clean haddock.clis.cli_cp haddock.clis.cli_dmn haddock.clis.cli_mpi haddock.clis.cli_pp haddock.clis.cli_re haddock.clis.cli_restraints haddock.clis.cli_score haddock.clis.cli_traceback haddock.clis.cli_unpack haddock.clis.re haddock.clis.re.clustfcc haddock.clis.re.clustrmsd haddock.clis.re.score haddock.clis.restraints haddock.clis.restraints.active_passive_to_ambig haddock.clis.restraints.calc_accessibility haddock.clis.restraints.passive_from_active haddock.clis.restraints.restrain_bodies haddock.clis.restraints.validate_tbl haddock.core haddock.core.cns_paths haddock.core.defaults haddock.core.exceptions haddock.core.supported_molecules haddock.core.typing haddock.gear haddock.gear.clean_steps haddock.gear.config haddock.gear.expandable_parameters haddock.gear.extend_run haddock.gear.greetings haddock.gear.haddockmodel haddock.gear.parameters haddock.gear.prepare_run haddock.gear.preprocessing haddock.gear.restart_run haddock.gear.validations haddock.gear.yaml2cfg haddock.gear.zerofill haddock.libs haddock.libs.libalign haddock.libs.libcli haddock.libs.libclust haddock.libs.libcns haddock.libs.libfunc haddock.libs.libhpc haddock.libs.libinteractive haddock.libs.libio haddock.libs.liblog haddock.libs.libmath haddock.libs.libmpi haddock.libs.libontology haddock.libs.libparallel haddock.libs.libpdb haddock.libs.libplots haddock.libs.librestraints haddock.libs.libstructure haddock.libs.libsubprocess haddock.libs.libtimer haddock.libs.libutil haddock.libs.libworkflow haddock.modules, [1] haddock.modules.analysis haddock.modules.analysis.alascan haddock.modules.analysis.alascan.scan haddock.modules.analysis.caprieval haddock.modules.analysis.caprieval.capri haddock.modules.analysis.clustfcc haddock.modules.analysis.clustfcc.clustfcc haddock.modules.analysis.clustrmsd haddock.modules.analysis.clustrmsd.clustrmsd haddock.modules.analysis.contactmap haddock.modules.analysis.contactmap.contmap haddock.modules.analysis.ilrmsdmatrix haddock.modules.analysis.ilrmsdmatrix.ilrmsd haddock.modules.analysis.rmsdmatrix haddock.modules.analysis.rmsdmatrix.rmsd haddock.modules.analysis.seletop haddock.modules.analysis.seletopclusts haddock.modules.analysis.seletopclusts.seletopclusts haddock.modules.base_cns_module, [1] haddock.modules.extras haddock.modules.extras.exit haddock.modules.refinement haddock.modules.refinement.emref haddock.modules.refinement.flexref haddock.modules.refinement.mdref haddock.modules.sampling haddock.modules.sampling.gdock haddock.modules.sampling.lightdock haddock.modules.sampling.rigidbody haddock.modules.scoring haddock.modules.scoring.emscoring haddock.modules.scoring.mdscoring haddock.modules.topology haddock.modules.topology.topoaa haddock.modules.topology.topocg

MODULE_IO_FILE (in module haddock.core.defaults) MODULE_PATH_NAME (in module haddock.core.defaults) ModuleError ModuleIO (class in haddock.libs.libontology) ModuleParams (in module haddock.core.typing) modules_category (in module haddock.modules), [1] moduloAB() (in module haddock.modules.analysis.contactmap.contmap) Molecule (class in haddock.libs.libstructure) MPIScheduler (class in haddock.libs.libmpi) mutate() (in module haddock.modules.analysis.alascan.scan)

N

name (haddock.modules.analysis.alascan.HaddockModule attribute) (haddock.modules.analysis.caprieval.HaddockModule attribute) (haddock.modules.analysis.clustfcc.HaddockModule attribute) (haddock.modules.analysis.clustrmsd.HaddockModule attribute) (haddock.modules.analysis.contactmap.HaddockModule attribute) (haddock.modules.analysis.ilrmsdmatrix.HaddockModule attribute) (haddock.modules.analysis.rmsdmatrix.HaddockModule attribute) (haddock.modules.analysis.seletop.HaddockModule attribute) (haddock.modules.analysis.seletopclusts.HaddockModule attribute) (haddock.modules.base_cns_module.BaseCNSModule attribute) (haddock.modules.BaseHaddockModule attribute) (haddock.modules.extras.exit.HaddockModule attribute) (haddock.modules.refinement.emref.HaddockModule attribute) (haddock.modules.refinement.flexref.HaddockModule attribute) (haddock.modules.refinement.mdref.HaddockModule attribute) (haddock.modules.sampling.gdock.HaddockModule attribute) (haddock.modules.sampling.lightdock.HaddockModule attribute) (haddock.modules.sampling.rigidbody.HaddockModule attribute) (haddock.modules.scoring.CNSScoringModule attribute) (haddock.modules.scoring.emscoring.HaddockModule attribute) (haddock.modules.scoring.mdscoring.HaddockModule attribute) (haddock.modules.scoring.ScoringModule attribute) (haddock.modules.topology.topoaa.HaddockModule attribute)

nan() (in module haddock.libs.libfunc) non_negative_int() (in module haddock.libs.libutil) none() (in module haddock.libs.libfunc) not_none() (in module haddock.libs.libfunc) num_processes (haddock.libs.libparallel.Scheduler property)

O

open_files_to_lines() (in module haddock.libs.libio) OPTIONAL_YAML (in module haddock.gear.parameters) order_traceback_df() (in module haddock.clis.cli_traceback)

output() (haddock.modules.analysis.alascan.scan.Scan method) (haddock.modules.analysis.ilrmsdmatrix.ilrmsd.Contact method) (haddock.modules.scoring.ScoringModule method)

P

ParamDict (in module haddock.core.typing) ParamDictT (class in haddock.core.typing) ParamMap (in module haddock.core.typing) ParamMapT (class in haddock.core.typing) params (haddock.modules.base_cns_module.BaseCNSModule property) (haddock.modules.BaseHaddockModule property), [1] parse_actpass_file() (in module haddock.libs.librestraints) parse_ncores() (in module haddock.libs.libutil) passive_from_active() (in module haddock.clis.restraints.passive_from_active) PDB (haddock.libs.libontology.Format attribute) pdb2fastadic() (in module haddock.libs.libalign) PDB_ENSEMBLE (haddock.libs.libontology.Format attribute) pdb_path_exists() (in module haddock.libs.libio) PDBFile (class in haddock.libs.libontology) PDBPathT (class in haddock.libs.libontology) Persistent (class in haddock.libs.libontology) plot_cluster_matrix() (in module haddock.libs.libclust)

populate_mol_parameters() (in module haddock.gear.prepare_run) populate_mol_parameters_in_module() (in module haddock.gear.expandable_parameters) populate_topology_molecule_params() (in module haddock.gear.prepare_run) postprocess() (haddock.libs.libworkflow.WorkflowManager method) postprocess_alignment() (haddock.libs.libalign.SeqAlign method) prepare_cns_input() (in module haddock.libs.libcns) prepare_expected_pdb() (in module haddock.libs.libcns) prepare_job_file() (haddock.libs.libhpc.HPCWorker method) prepare_multiple_input() (in module haddock.libs.libcns) prepare_output() (in module haddock.libs.libcns) prepare_single_input() (in module haddock.libs.libcns) previous_path() (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method), [1] process_job_execution_status() (in module haddock.clis.cli_bm) process_pdbs() (in module haddock.gear.preprocessing) process_target() (in module haddock.clis.cli_bm) PT (class in haddock.core.typing)

R

randint() (haddock.libs.libmath.RandomNumberGenerator method) RandomNumberGenerator (class in haddock.libs.libmath) rank_clust_order() (in module haddock.modules.analysis.seletopclusts.seletopclusts) rank_clusters() (in module haddock.libs.libclust) read_capri_table() (in module haddock.libs.libplots) read_chainids() (in module haddock.libs.libpdb) read_from_yaml() (in module haddock.libs.libio) read_from_yaml_config() (in module haddock.gear.yaml2cfg) read_lines() (in module haddock.libs.libio) read_matrix() (in module haddock.modules.analysis.clustrmsd.clustrmsd) read_mol_parameters() (in module haddock.gear.expandable_parameters) read_multiple_idx_groups_user_config() (in module haddock.gear.expandable_parameters) read_num_molecules_from_folder() (in module haddock.gear.extend_run) read_RECORD_section() (in module haddock.libs.libpdb) read_residues_from_top_file() (in module haddock.core.supported_molecules) read_segids() (in module haddock.libs.libpdb) read_simplest_expandable() (in module haddock.gear.expandable_parameters) read_single_idx_groups_user_config() (in module haddock.gear.expandable_parameters) read_structure() (in module haddock.libs.librestraints) read_supported_residues() (in module haddock.core.supported_molecules) rearrange_ss_capri_output() (in module haddock.modules.analysis.caprieval.capri) rearrange_xyz_files() (in module haddock.libs.libalign) reclustfcc() (in module haddock.clis.re.clustfcc) reclustrmsd() (in module haddock.clis.re.clustrmsd) recursive_convert_paths_to_strings() (in module haddock.libs.libutil) recursive_dict_update() (in module haddock.libs.libutil) rejoin_parts_multiple_index() (in module haddock.gear.expandable_parameters) rejoin_parts_single_index() (in module haddock.gear.expandable_parameters) remove_dict_keys() (in module haddock.libs.libutil) remove_files_with_ext() (in module haddock.libs.libio) remove_folder() (in module haddock.libs.libutil) remove_folders_after_number() (in module haddock.gear.restart_run) remove_ghost_groups() (in module haddock.gear.expandable_parameters) remove_missing() (haddock.libs.libontology.ModuleIO method) remove_trail_idx() (in module haddock.gear.expandable_parameters) remove_unsupported_atom() (in module haddock.gear.preprocessing) remove_unsupported_hetatm() (in module haddock.gear.preprocessing) remove_unsupported_molecules() (in module haddock.gear.preprocessing) renum_step_folders() (in module haddock.gear.extend_run) replace_HETATM_to_ATOM() (in module haddock.gear.preprocessing) replace_HID_to_HIS() (in module haddock.gear.preprocessing) replace_HIE_to_HIS() (in module haddock.gear.preprocessing)

replace_HSD_to_HIS() (in module haddock.gear.preprocessing) replace_HSE_to_HIS() (in module haddock.gear.preprocessing) replace_MSE_to_MET() (in module haddock.gear.preprocessing) replace_residue() (in module haddock.gear.preprocessing) report_generator() (in module haddock.libs.libplots) report_plots_handler() (in module haddock.libs.libplots) ResCode (in module haddock.libs.libalign) rescore() (in module haddock.clis.re.score) reset_params() (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method), [1] resname (haddock.core.supported_molecules.CNSTopologyResidue property) restart() (haddock.clis.cli_dmn.Job method) restrain_bodies() (in module haddock.clis.restraints.restrain_bodies) retrieve_models() (haddock.libs.libontology.ModuleIO method) rewrite_capri_tables() (in module haddock.libs.libinteractive) rmsd_dispatcher() (in module haddock.modules.analysis.rmsdmatrix.rmsd) RMSDFile (class in haddock.libs.libontology) RMSDJob (class in haddock.modules.analysis.rmsdmatrix.rmsd) run() (haddock.core.typing.SupportsRun method) (haddock.gear.extend_run.WorkflowManagerExtend method) (haddock.libs.libhpc.HPCScheduler method) (haddock.libs.libhpc.HPCWorker method) (haddock.libs.libmpi.MPIScheduler method) (haddock.libs.libparallel.Scheduler method) (haddock.libs.libparallel.Worker method) (haddock.libs.libsubprocess.BaseJob method) (haddock.libs.libsubprocess.CNSJob method) (haddock.libs.libworkflow.WorkflowManager method) (haddock.modules.analysis.alascan.scan.Scan method) (haddock.modules.analysis.alascan.scan.ScanJob method) (haddock.modules.analysis.caprieval.capri.CAPRI method) (haddock.modules.analysis.contactmap.contmap.ClusteredContactMap method) (haddock.modules.analysis.contactmap.contmap.ContactsMap method) (haddock.modules.analysis.contactmap.contmap.ContactsMapJob method) (haddock.modules.analysis.ilrmsdmatrix.ilrmsd.Contact method) (haddock.modules.analysis.ilrmsdmatrix.ilrmsd.ContactJob method) (haddock.modules.analysis.rmsdmatrix.rmsd.XYZWriter method) (haddock.modules.analysis.rmsdmatrix.rmsd.XYZWriterJob method) (haddock.modules.base_cns_module.BaseCNSModule method), [1] (haddock.modules.BaseHaddockModule method), [1] run_capri_analysis() (in module haddock.clis.cli_analyse) RUNDIR (in module haddock.core.defaults)

S

sanitize() (in module haddock.libs.libpdb) save() (haddock.libs.libontology.ModuleIO method) (in module haddock.gear.config) save_config() (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method), [1] save_configuration_files() (in module haddock.gear.prepare_run) save_envvars() (haddock.modules.base_cns_module.BaseCNSModule method), [1] save_lines_to_files() (in module haddock.libs.libio) save_scoring_weights() (in module haddock.modules.analysis.caprieval.capri) Scan (class in haddock.modules.analysis.alascan.scan) ScanJob (class in haddock.modules.analysis.alascan.scan) scatter_plot_data() (in module haddock.libs.libplots) scatter_plot_handler() (in module haddock.libs.libplots) scatter_plot_plotly() (in module haddock.libs.libplots) Scheduler (class in haddock.libs.libparallel) ScoringModule (class in haddock.modules.scoring) select_top_clusts_models() (in module haddock.modules.analysis.seletopclusts.seletopclusts) SeqAlign (class in haddock.libs.libalign) sequence_alignment() (in module haddock.libs.libalign) setup_haddock3_job() (in module haddock.clis.cli_bm) setup_run() (in module haddock.gear.prepare_run) SetupError size_clust_order() (in module haddock.modules.analysis.seletopclusts.seletopclusts) solve_no_chainID_no_segID() (in module haddock.gear.preprocessing) sort_models() (in module haddock.modules.analysis.seletopclusts.seletopclusts) sort_numbered_paths() (in module haddock.libs.libutil) split_by_chain() (in module haddock.libs.libpdb) split_ensemble() (in module haddock.libs.libpdb) split_labels_by_chains() (in module haddock.modules.analysis.contactmap.contmap)

split_tasks() (in module haddock.clis.cli_mpi) (in module haddock.libs.libparallel) Step (class in haddock.libs.libworkflow) step_folder_regex (in module haddock.modules), [1] step_folder_regex_re (in module haddock.modules), [1] StepError submit() (haddock.clis.cli_dmn.Job method) subset_traceback() (in module haddock.clis.cli_traceback) supported_aminoacids_resnames (in module haddock.core.supported_molecules) supported_ATOM (in module haddock.core.supported_molecules) supported_carbo_resnames (in module haddock.core.supported_molecules) supported_fragments_resnames (in module haddock.core.supported_molecules) supported_hemes_resnames (in module haddock.core.supported_molecules) supported_HETATM (in module haddock.core.supported_molecules) supported_multiatom_ions_resnames (in module haddock.core.supported_molecules) supported_nucleic_resnames (in module haddock.core.supported_molecules) supported_residues (in module haddock.core.supported_molecules) supported_shape_resnames (in module haddock.core.supported_molecules) supported_single_ions_atoms (in module haddock.core.supported_molecules) supported_single_ions_atoms_map (in module haddock.core.supported_molecules) supported_single_ions_elements (in module haddock.core.supported_molecules) supported_single_ions_elements_map (in module haddock.core.supported_molecules) supported_single_ions_resnames (in module haddock.core.supported_molecules) supported_single_ions_resnames_map (in module haddock.core.supported_molecules) supported_solvents_resnames (in module haddock.core.supported_molecules) SupportsAdd (class in haddock.core.typing) SupportsAddT (class in haddock.core.typing) SupportsRun (class in haddock.core.typing) SupportsRunT (class in haddock.core.typing) swap_segid_chain() (in module haddock.libs.libpdb)

T

terminate() (haddock.libs.libhpc.HPCScheduler method) (haddock.libs.libparallel.Scheduler method) tidy() (in module haddock.libs.libpdb) to_color_weight() (in module haddock.modules.analysis.contactmap.contmap) to_full_matrix() (in module haddock.modules.analysis.contactmap.contmap) to_nice_label() (in module haddock.modules.analysis.contactmap.contmap) to_rgba_color_string() (in module haddock.modules.analysis.contactmap.contmap) to_torque_time() (in module haddock.libs.libhpc)

TOPOLOGY (haddock.libs.libontology.Format attribute) TopologyFile (class in haddock.libs.libontology) topX_models() (in module haddock.modules.analysis.contactmap.contmap) traceback_dataframe() (in module haddock.clis.cli_traceback) transform_to_list() (in module haddock.libs.libutil) true() (in module haddock.libs.libfunc) tsv_to_chordchart() (in module haddock.modules.analysis.contactmap.contmap) tsv_to_heatmap() (in module haddock.modules.analysis.contactmap.contmap)

U

unpack_compressed_and_archived_files() (in module haddock.gear.clean_steps) update_capri_dict() (in module haddock.clis.cli_analyse) update_contents_of_new_steps() (in module haddock.gear.extend_run) update_layout_plotly() (in module haddock.libs.libplots) update_params() (haddock.modules.analysis.rmsdmatrix.HaddockModule method) (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method), [1]

update_paths() (in module haddock.clis.cli_analyse) update_paths_in_capri_dict() (in module haddock.clis.cli_analyse) update_status() (haddock.libs.libhpc.HPCWorker method) update_step_contents_to_step_names() (in module haddock.gear.prepare_run) update_step_names_in_file() (in module haddock.gear.prepare_run) update_step_names_in_subfolders() (in module haddock.gear.prepare_run) update_unpacked_names() (in module haddock.gear.clean_steps)

V

v_rundir() (in module haddock.gear.validations) validate_module_names_are_not_misspelled() (in module haddock.gear.prepare_run) validate_module_params_values() (in module haddock.gear.prepare_run) validate_modules_names() (in module haddock.gear.prepare_run) validate_modules_params() (in module haddock.gear.prepare_run) validate_param_range() (in module haddock.gear.prepare_run)

validate_param_type() (in module haddock.gear.prepare_run) validate_parameters_are_not_misspelled() (in module haddock.gear.prepare_run) validate_params() (in module haddock.gear.prepare_run) validate_tbl() (in module haddock.clis.restraints.validate_tbl) validate_tbldata() (in module haddock.libs.librestraints) validate_value() (in module haddock.gear.prepare_run)

W

with_config_error() (in module haddock.gear.prepare_run) within_2PI() (in module haddock.modules.analysis.contactmap.contmap) Worker (class in haddock.libs.libparallel) Workflow (class in haddock.libs.libworkflow) WorkflowManager (class in haddock.libs.libworkflow) WorkflowManagerExtend (class in haddock.gear.extend_run) working_directory() (in module haddock.libs.libio) workload_manager_launch (in module haddock.clis.cli_dmn) write_alignment() (in module haddock.libs.libalign)

write_clusters() (in module haddock.modules.analysis.clustfcc.clustfcc) (in module haddock.modules.analysis.clustrmsd.clustrmsd) write_clustfcc_file() (in module haddock.modules.analysis.clustfcc.clustfcc) write_clustrmsd_file() (in module haddock.modules.analysis.clustrmsd.clustrmsd) write_dic_to_file() (in module haddock.libs.libio) write_eval_line() (in module haddock.libs.libcns) write_nested_dic_to_file() (in module haddock.libs.libio) write_res_contacts() (in module haddock.modules.analysis.contactmap.contmap) write_selected_models() (in module haddock.modules.analysis.seletopclusts.seletopclusts) write_structure_list() (in module haddock.libs.libclust)

X

XYZWriter (class in haddock.modules.analysis.rmsdmatrix.rmsd)

XYZWriterJob (class in haddock.modules.analysis.rmsdmatrix.rmsd)

Y

yaml2cfg_text() (in module haddock.gear.yaml2cfg)

Z

zip_top_ranked() (in module haddock.clis.cli_analyse)