Index

A

AccScore (class in haddock.modules.scoring.sasascore.sasascore) active (haddock.clis.restraints.webservice.PassiveFromActiveRequest attribute) active1 (haddock.clis.restraints.webservice.ActPassToAmbigRequest attribute) active2 (haddock.clis.restraints.webservice.ActPassToAmbigRequest attribute) active_passive_to_ambig() (in module haddock.libs.librestraints) actpass_to_ambig() (in module haddock.clis.restraints.active_passive_to_ambig) ActPassToAmbigRequest (class in haddock.clis.restraints.webservice) 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.libs.libcapri.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_dummy() (in module haddock.libs.libaa2cg) 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_member() (haddock.fcc.cluster_fcc.Cluster method) (haddock.libs.libfcc.Cluster method) add_ncores_arg() (in module haddock.libs.libcli) add_neighbor() (haddock.fcc.cluster_fcc.Element method) (haddock.libs.libfcc.Element method) add_output_dir_arg() (in module haddock.libs.libcli) add_parent_to_paths() (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method) add_pass_from_act_arguments() (in module haddock.clis.restraints.passive_from_active) add_rand_removal_arguments() (in module haddock.clis.restraints.random_removal)

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_restrain_ligand_arguments() (in module haddock.clis.restraints.restrain_ligand) 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_TER_on_chain_breaks() (in module haddock.libs.libpdb) add_validate_tbl_arguments() (in module haddock.clis.restraints.validate_tbl) add_version_arg() (in module haddock.libs.libcli) add_z_surf_restraints_arguments() (in module haddock.clis.restraints.z_surface_restraints) add_zscores() (in module haddock.libs.libscan) AddDeltaBFactor (class in haddock.libs.libscan) (class in haddock.modules.analysis.alascan.scan) (class in haddock.modules.analysis.rnascan.scan) aggregate_contacts() (haddock.modules.analysis.contactmap.contmap.ClusteredContactMap static method) align_full() (in module haddock.libs.libnotebooks) align_seq() (in module haddock.libs.libalign) align_strct() (in module haddock.libs.libalign) ALIGNError ANA_FOLDER (in module haddock.core.defaults) 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) archive_run() (in module haddock.gear.postprocessing) assign_cluster() (haddock.fcc.cluster_fcc.Element method) (haddock.libs.libfcc.Element method) atoms (haddock.core.supported_molecules.CNSTopologyResidue property) AtomsDict (in module haddock.core.typing)

B

BaseCNSModule (class in haddock.modules.base_cns_module) BaseHaddockModule (class in haddock.modules) BaseJob (class in haddock.libs.libsubprocess) bead_plan() (in module haddock.clis.restraints.z_surface_restraints) 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_interface_sets_combinations() (haddock.modules.scoring.CNSScoringModule static method) build_restraints() (in module haddock.libs.librestraints)

C

calc_acc_score() (in module haddock.modules.scoring.sasascore.sasascore) calc_accessibility() (in module haddock.clis.restraints.calc_accessibility) calc_dockq() (haddock.libs.libcapri.CAPRI method) calc_euclidean() (in module haddock.libs.librestraints) calc_fnat() (haddock.libs.libcapri.CAPRI method) calc_global_rmsd() (haddock.libs.libcapri.CAPRI method) calc_haddock_score() (haddock.gear.haddockmodel.HaddockModel method) calc_ilrmsd() (haddock.libs.libcapri.CAPRI method) calc_irmsd() (haddock.libs.libcapri.CAPRI method) calc_lrmsd() (haddock.libs.libcapri.CAPRI method) calc_rmsd() (in module haddock.libs.libalign) calc_score() (haddock.gear.haddockmodel.HaddockModel static method) (in module haddock.libs.libscan) calc_size() (in module haddock.clis.cli_dmn) calc_stats() (in module haddock.libs.libcapri) CalcAccessibilityRequest (class in haddock.clis.restraints.webservice) calculate_accessibility() (in module haddock.clis.restraints.webservice) calculate_actpass_to_ambig() (in module haddock.clis.restraints.webservice) calculate_fcc() (in module haddock.fcc.calc_fcc_matrix) (in module haddock.libs.libfcc) calculate_fcc_nc() (in module haddock.fcc.calc_fcc_matrix) (in module haddock.libs.libfcc) calculate_optimal_batch_size() (haddock.libs.libgrid.GRIDScheduler static method) calculate_pairwise_matrix() (in module haddock.fcc.calc_fcc_matrix) (in module haddock.libs.libfcc) calculate_passive_from_active() (in module haddock.clis.restraints.webservice) cancel() (haddock.libs.libhpc.HPCWorker method) CAPRI (class in haddock.libs.libcapri) capri_cluster_analysis() (in module haddock.libs.libcapri) CAPRIError center (haddock.fcc.cluster_fcc.Cluster attribute) (haddock.libs.libfcc.Cluster attribute) center_of_mass() (in module haddock.libs.libaa2cg) centroid() (in module haddock.libs.libalign) chain (haddock.clis.restraints.webservice.PassiveFromActiveRequest attribute) (haddock.libs.libscan.MutationResult attribute) chainf() (in module haddock.libs.libfunc) chainfs() (in module haddock.libs.libfunc) charge (haddock.core.supported_molecules.CNSTopologyResidue property) check_chains() (in module haddock.libs.libalign) check_combination_chains() (in module haddock.libs.libpdb) 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_mol_shape() (in module haddock.libs.libpdb) 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) check_yaml_duplicated_parameters() (in module haddock.libs.libio) CheckInstall (class in haddock.libs.libprodigy) clean() (haddock.gear.extend_run.WorkflowManagerExtend method) (haddock.libs.libgrid.GridInterface 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) (in module haddock.gear.clean_steps) clean_suffix() (in module haddock.libs.libio) clean_timings() (haddock.libs.libgrid.GridInterface method) cli() (in module haddock.clis.cli) (in module haddock.clis.cli_analyse) (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) close_logfile_handlers() (in module haddock.libs.liblog) ClRank (in module haddock.libs.libplots) clt_table_handler() (in module haddock.libs.libplots) Cluster (class in haddock.fcc.cluster_fcc) (class in haddock.libs.libfcc) cluster (haddock.fcc.cluster_fcc.Element attribute) (haddock.libs.libfcc.Element attribute) cluster_elements() (in module haddock.fcc.cluster_fcc) (in module haddock.libs.libfcc) CLUSTER_STAT_COLUMNS (in module haddock.libs.libscan) ClusteredContactMap (class in haddock.modules.analysis.contactmap.contmap) ClusterOutputer (class in haddock.libs.libscan) (class in haddock.modules.analysis.alascan.scan) (class in haddock.modules.analysis.rnascan.scan) clustrmsd_tolerance_params() (in module haddock.libs.libclust)

CNS_ERROR_OUTPUT (haddock.libs.libontology.Format attribute) 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) collect_metrics() (in module haddock.modules.analysis.caprifilter.caprifilter) COMPLETING (haddock.libs.libgrid.JobStatus attribute) CompositeGridJob (class in haddock.libs.libgrid) compress_files_ext() (in module haddock.libs.libio) compute_barycenter() (in module haddock.clis.restraints.z_surface_restraints) compute_distance_matrix() (in module haddock.modules.analysis.contactmap.contmap) compute_interfaces_score() (haddock.modules.scoring.CNSScoringModule static method) 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.caprifilter.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.filter.HaddockModule class method) (haddock.modules.analysis.ilrmsdmatrix.HaddockModule class method) (haddock.modules.analysis.rmsdmatrix.HaddockModule class method) (haddock.modules.analysis.rnascan.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) (haddock.modules.extras.exit.HaddockModule class method) (haddock.modules.refinement.cgtoaa.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.refinement.openmm.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.deeprank.HaddockModule class method) (haddock.modules.scoring.emscoring.HaddockModule class method) (haddock.modules.scoring.mdscoring.HaddockModule class method) (haddock.modules.scoring.prodigyligand.HaddockModule class method) (haddock.modules.scoring.prodigyprotein.HaddockModule class method) (haddock.modules.scoring.sasascore.HaddockModule class method) (haddock.modules.topology.topoaa.HaddockModule class method) (haddock.modules.topology.topocg.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) contains_cns_stdout_error() (haddock.libs.libsubprocess.CNSJob static method) control_pts() (in module haddock.modules.analysis.contactmap.contmap) convert_ATOM_to_HETATM() (in module haddock.gear.preprocessing) convert_chains() (haddock.modules.scoring.prodigyprotein.prodigy.ProdigyProtein static method) 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) cpu_count() (in module haddock.libs.libutil) create_batches() (haddock.libs.libgrid.GRIDScheduler method) create_CNS_export_envvars() (in module haddock.libs.libhpc) create_data_dir() (in module haddock.gear.prepare_run) create_directories() (haddock.modules.refinement.openmm.HaddockModule method) create_elements() (in module haddock.libs.libfcc) create_file_with_cryst() (in module haddock.libs.libaa2cg) create_html() (in module haddock.libs.libplots) create_jdl() (haddock.libs.libgrid.GridInterface method) create_job_script() (haddock.libs.libgrid.CompositeGridJob method) (haddock.libs.libgrid.GridInterface method) (haddock.libs.libgrid.GridJob method) create_other_cluster() (in module haddock.libs.libplots) create_slurm_header() (in module haddock.libs.libhpc) create_solvation_box() (haddock.modules.refinement.openmm.openmm.OPENMM method) create_torque_header() (in module haddock.libs.libhpc) ctrl_rib_chords() (in module haddock.modules.analysis.contactmap.contmap) cutoff (haddock.clis.restraints.webservice.CalcAccessibilityRequest attribute)

D

datakey_to_colorscale() (in module haddock.modules.analysis.contactmap.contmap) deeprank_is_available() (in module haddock.modules.scoring.deeprank.deeprank) DeeprankWrapper (class in haddock.modules.scoring.deeprank.deeprank) DEFAULT (haddock.libs.libgrid.Tag attribute) default_envvars() (haddock.modules.base_cns_module.BaseCNSModule method) default_scan_residue (haddock.libs.libscan.ClusterOutputer attribute) (haddock.modules.analysis.alascan.scan.ClusterOutputer attribute) (haddock.modules.analysis.rnascan.scan.ClusterOutputer attribute)

delhetatm (haddock.clis.restraints.webservice.PDBPreprocessRequest attribute) delta_scores (haddock.libs.libscan.MutationResult attribute) deltaG_to_pKd() (haddock.libs.libprodigy.ProdigyWorker static method) determine_hbonds() (in module haddock.libs.libaa2cg) determine_ss() (in module haddock.libs.libaa2cg) DONE (haddock.libs.libgrid.JobStatus attribute) dot_suffix() (in module haddock.libs.libio) dump_as_izone() (in module haddock.libs.libalign) dump_weights() (in module haddock.modules.analysis.caprieval.capri)

E

Element (class in haddock.fcc.cluster_fcc) (class in haddock.libs.libfcc) elements (haddock.core.supported_molecules.CNSTopologyResidue property) ENSEMBLE_NAME (haddock.modules.scoring.deeprank.deeprank.DeeprankWrapper attribute) envvars (haddock.libs.libsubprocess.CNSJob property) equilibrate_solvation_box() (haddock.modules.refinement.openmm.openmm.OPENMM method) error_msg (haddock.libs.libscan.MutationResult attribute) evaluate_complex() (haddock.libs.libprodigy.ProdigyWorker method) (haddock.modules.scoring.prodigyligand.prodigylig.ProdigyLigand method) (haddock.modules.scoring.prodigyprotein.prodigy.ProdigyProtein method) exclude (haddock.clis.restraints.webservice.RestrainBodiesRequest attribute) exec_time() (in module haddock.libs.libfunc) 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) export_passive() (in module haddock.clis.restraints.calc_accessibility)

export_plotly_figure() (in module haddock.libs.libplots) extract_data_from_accscore_class() (in module haddock.modules.scoring.sasascore.sasascore) extract_data_from_capri_class() (in module haddock.libs.libcapri) extract_files_flat() (in module haddock.libs.libio) extract_groups() (in module haddock.libs.libaa2cg) extract_heavyatom_contacts() (in module haddock.modules.analysis.contactmap.contmap) extract_interface_combinations() (haddock.modules.scoring.CNSScoringModule method) extract_keys_recursive() (in module haddock.libs.libutil) extract_models_best_references() (in module haddock.libs.libcapri) extract_multiple_index_params() (in module haddock.gear.expandable_parameters) extract_pairs_from_tbl() (in module haddock.modules.sampling.gdock.gdock) extract_pdb_coords() (in module haddock.modules.analysis.contactmap.contmap) extract_pdb_dt() (in module haddock.modules.analysis.contactmap.contmap) extract_restraint_entries() (in module haddock.libs.librestraints) 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

FAILED (haddock.libs.libgrid.JobStatus attribute) 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) filter_models() (in module haddock.modules.analysis.caprifilter.caprifilter) find_all_cns_errors() (in module haddock.gear.known_cns_errors) find_best_struct() (in module haddock.libs.libplots) find_cns_errors() (in module haddock.gear.known_cns_errors)

find_desired_linkfiles() (in module haddock.libs.libcns) find_ff() (in module haddock.libs.libstructure) find_incompatible_parameters() (in module haddock.gear.yaml2cfg) finish_with_error() (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method) 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) from_chain (haddock.clis.restraints.webservice.PDBPreprocessRequest attribute) from_string() (haddock.libs.libgrid.JobStatus class method) fuzzy_match() (in module haddock.gear.prepare_run)

G

gdock_is_available() (in module haddock.modules.sampling.gdock.gdock) GdockWrapper (class in haddock.modules.sampling.gdock.gdock) gen_bead_plans() (in module haddock.clis.restraints.z_surface_restraints) gen_cg_filename() (in module haddock.libs.libaa2cg) gen_cg_tbl_backmapping_fname() (in module haddock.libs.libaa2cg) gen_contact_dt() (in module haddock.modules.analysis.contactmap.contmap) gen_defaults_module_param_path() (in module haddock.gear.prepare_run) gen_feedback_messages() (in module haddock.gear.greetings) gen_plot() (haddock.libs.libscan.ClusterOutputer method) gen_z_restraints() (in module haddock.clis.restraints.z_surface_restraints) gen_z_surface_restraints() (in module haddock.clis.restraints.z_surface_restraints) generate_default_header() (in module haddock.libs.libcns) generate_output() (haddock.modules.analysis.contactmap.contmap.ContactsMap method) generate_output_ensemble() (haddock.modules.refinement.openmm.openmm.OPENMM method) generate_tbl() (in module haddock.libs.librestraints) generate_topology() (in module haddock.modules.topology.topoaa) (in module haddock.modules.topology.topocg) GenericTask (class in haddock.libs.libparallel) 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) get_analysis_exec_mode() (in module haddock.modules.analysis) get_arch() (in module haddock.libs.libutil) get_atoms() (in module haddock.libs.libalign) get_atoms_to_keep() (in module haddock.modules.analysis.rnascan.scan) get_available_memory() (in module haddock.libs.libutil) get_axis() (in module haddock.core.cns_paths) get_bodies() (in module haddock.libs.librestraints) get_capri_params() (in module haddock.modules.analysis.caprifilter.caprifilter) 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_cns_executable() (in module haddock.libs.libutil) 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) get_ensemble_origin() (haddock.modules.topology.topoaa.HaddockModule static method) (haddock.modules.topology.topocg.HaddockModule static method) 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) (haddock.modules.topology.topocg.HaddockModule static method) get_module_name() (in module haddock.gear.config) get_module_steps_folders() (in module haddock.modules) get_mol_parameters() (in module haddock.gear.expandable_parameters) get_mpi() (in module haddock.clis.cli_mpi) get_multiple_index_groups() (in module haddock.gear.expandable_parameters) get_necessary_memory() (in module haddock.libs.libutil) 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_pdb_filepath() (haddock.modules.refinement.openmm.openmm.OPENMM method) get_perm() (in module haddock.libs.libio) get_previous_cns_step() (in module haddock.modules.analysis.caprieval.capri) get_prodrg_exec() (in module haddock.libs.libutil) get_reference() (haddock.modules.analysis.caprieval.HaddockModule method) get_resnames() (in module haddock.core.supported_molecules) get_restraint_subset() (in module haddock.libs.librestraints) get_result_or_same_in_list() (in module haddock.libs.libutil) get_score_string() (in module haddock.libs.libscan) 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_top_ranked_mapping() (in module haddock.clis.cli_analyse) 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_worker() (haddock.libs.libprodigy.ProdigyBaseJob static method) (haddock.modules.scoring.prodigyligand.prodigylig.ProdigyJob static method) (haddock.modules.scoring.prodigyprotein.prodigy.ProdigyJob static method) get_z_coords() (in module haddock.clis.restraints.z_surface_restraints) get_zerofill_for_modules() (in module haddock.gear.zerofill) give_same() (in module haddock.libs.libfunc) glob_folder() (in module haddock.libs.libio) GridInterface (class in haddock.libs.libgrid) GridJob (class in haddock.libs.libgrid) GRIDScheduler (class in haddock.libs.libgrid) group_scan_by_cluster() (in module haddock.libs.libscan) (in module haddock.modules.analysis.alascan.scan) (in module haddock.modules.analysis.rnascan.scan) gzip_files() (in module haddock.libs.libio)

H

haddock.clis module haddock.clis.cli module haddock.clis.cli_analyse 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.random_removal module haddock.clis.restraints.restrain_bodies module haddock.clis.restraints.restrain_ligand module haddock.clis.restraints.validate_tbl module haddock.clis.restraints.webservice module haddock.clis.restraints.z_surface_restraints module haddock.clis.wrapper_haddock_restraints 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.fcc module haddock.fcc.calc_fcc_matrix module haddock.fcc.cluster_fcc 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.known_cns_errors module haddock.gear.parameters module haddock.gear.postprocessing 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.assets module haddock.libs.libaa2cg module haddock.libs.libalign module haddock.libs.libcapri module haddock.libs.libcli module haddock.libs.libclust module haddock.libs.libcns module haddock.libs.libfcc module haddock.libs.libfunc module haddock.libs.libgrid module haddock.libs.libhpc module haddock.libs.libinteractive module haddock.libs.libio module haddock.libs.libligand module haddock.libs.liblog module haddock.libs.libmath module haddock.libs.libmpi module haddock.libs.libnotebooks module haddock.libs.libontology module haddock.libs.libparallel module haddock.libs.libpdb module haddock.libs.libplots module haddock.libs.libprodigy module haddock.libs.librestraints module haddock.libs.libscan module

haddock.libs.libstructure module haddock.libs.libsubprocess module haddock.libs.libtimer module haddock.libs.libutil module haddock.libs.libworkflow module haddock.modules module 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.caprifilter module haddock.modules.analysis.caprifilter.caprifilter 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.filter 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.rnascan module haddock.modules.analysis.rnascan.scan module haddock.modules.analysis.seletop module haddock.modules.analysis.seletopclusts module haddock.modules.analysis.seletopclusts.seletopclusts module haddock.modules.base_cns_module module haddock.modules.extras module haddock.modules.extras.exit module haddock.modules.refinement module haddock.modules.refinement.cgtoaa module haddock.modules.refinement.emref module haddock.modules.refinement.flexref module haddock.modules.refinement.mdref module haddock.modules.refinement.openmm module haddock.modules.refinement.openmm.openmm module haddock.modules.sampling module haddock.modules.sampling.gdock module haddock.modules.sampling.gdock.gdock module haddock.modules.sampling.lightdock module haddock.modules.sampling.rigidbody module haddock.modules.scoring module haddock.modules.scoring.deeprank module haddock.modules.scoring.deeprank.deeprank module haddock.modules.scoring.emscoring module haddock.modules.scoring.mdscoring module haddock.modules.scoring.prodigyligand module haddock.modules.scoring.prodigyligand.prodigylig module haddock.modules.scoring.prodigyprotein module haddock.modules.scoring.prodigyprotein.prodigy module haddock.modules.scoring.sasascore module haddock.modules.scoring.sasascore.sasascore 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.caprifilter) (class in haddock.modules.analysis.clustfcc) (class in haddock.modules.analysis.clustrmsd) (class in haddock.modules.analysis.contactmap) (class in haddock.modules.analysis.filter) (class in haddock.modules.analysis.ilrmsdmatrix) (class in haddock.modules.analysis.rmsdmatrix) (class in haddock.modules.analysis.rnascan) (class in haddock.modules.analysis.seletop) (class in haddock.modules.analysis.seletopclusts) (class in haddock.modules.extras.exit) (class in haddock.modules.refinement.cgtoaa) (class in haddock.modules.refinement.emref) (class in haddock.modules.refinement.flexref) (class in haddock.modules.refinement.mdref) (class in haddock.modules.refinement.openmm) (class in haddock.modules.sampling.gdock) (class in haddock.modules.sampling.lightdock) (class in haddock.modules.sampling.rigidbody) (class in haddock.modules.scoring.deeprank) (class in haddock.modules.scoring.emscoring) (class in haddock.modules.scoring.mdscoring) (class in haddock.modules.scoring.prodigyligand) (class in haddock.modules.scoring.prodigyprotein) (class in haddock.modules.scoring.sasascore) (class in haddock.modules.topology.topoaa) (class in haddock.modules.topology.topocg) HaddockModuleError HaddockTermination handle_chainbreaks() (haddock.modules.refinement.openmm.openmm.OPENMM method) handle_clt_file() (in module haddock.libs.libinteractive) handle_input_reference() (in module haddock.libs.libpdb) handle_ss_file() (in module haddock.libs.libinteractive) has_cluster_info() (haddock.libs.libcapri.CAPRI method) hash() (in module haddock.libs.libaa2cg) 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.libs.libcapri.CAPRI static method) identify_modules() (in module haddock.gear.prepare_run) identify_pairing() (in module haddock.libs.libaa2cg) identify_unknown_hetatms() (in module haddock.libs.libligand) ImgFormat (in module haddock.core.typing) import_constraints() (haddock.modules.refinement.openmm.openmm.OPENMM method) import_prodigy_libs() (haddock.libs.libprodigy.CheckInstall static method) in_capri() (in module haddock.libs.libplots) inject_in_modules() (in module haddock.gear.prepare_run)

INTERACTIVE_RE_SUFFIX (in module haddock.core.defaults) InterfaceScanner (class in haddock.modules.analysis.alascan.scan) (class in haddock.modules.analysis.rnascan.scan) invPerm() (in module haddock.modules.analysis.contactmap.contmap) is_mol_parameter() (in module haddock.gear.expandable_parameters) is_nested() (haddock.modules.analysis.caprieval.HaddockModule static method) (haddock.modules.analysis.caprifilter.HaddockModule static method) is_present() (haddock.libs.libontology.Persistent method) is_step_folder() (in module haddock.modules) 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 JobStatus (class in haddock.libs.libgrid)

K

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

keepcoord (haddock.clis.restraints.webservice.PDBPreprocessRequest attribute) KnownCNSError

L

last_step_folder() (haddock.modules.base_cns_module.BaseCNSModule static method) (haddock.modules.BaseHaddockModule static method) 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_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.libs.libcapri) 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_matrix() (in module haddock.libs.libfcc) load_pdb_file() (in module haddock.libs.libnotebooks) load_scatter() (in module haddock.libs.libcns) load_selected_resiudes_coords() (in module haddock.clis.restraints.z_surface_restraints) load_selections() (in module haddock.clis.restraints.z_surface_restraints) 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) 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_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) (in module haddock.clis.restraints.random_removal) (in module haddock.clis.restraints.restrain_ligand) (in module haddock.clis.restraints.z_surface_restraints) (in module haddock.clis.wrapper_haddock_restraints) maincli() (in module haddock.clis.cli) (in module haddock.clis.cli_analyse) (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_cns_jobs() (haddock.modules.sampling.rigidbody.HaddockModule method) make_contactmap_report() (in module haddock.modules.analysis.contactmap.contmap) 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_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_rnascan_plot() (in module haddock.libs.libplots) make_scan_plot() (in module haddock.libs.libscan) make_self_contained() (haddock.modules.base_cns_module.BaseCNSModule method) 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_cg() (in module haddock.libs.libaa2cg) map_clusters_models() (in module haddock.modules.analysis.seletopclusts.seletopclusts) martinize() (in module haddock.libs.libaa2cg) match_path_criteria() (in module haddock.gear.config) MATCHED (haddock.libs.libgrid.JobStatus attribute) MATRIX (haddock.libs.libontology.Format attribute) MAX_NUM_MODULES (in module haddock.core.defaults) members (haddock.fcc.cluster_fcc.Cluster attribute) (haddock.libs.libfcc.Cluster attribute) min_dist() (in module haddock.modules.analysis.contactmap.contmap) model_config (haddock.clis.restraints.webservice.ActPassToAmbigRequest attribute) (haddock.clis.restraints.webservice.CalcAccessibilityRequest attribute) (haddock.clis.restraints.webservice.PassiveFromActiveRequest attribute) (haddock.clis.restraints.webservice.PDBPreprocessRequest attribute) (haddock.clis.restraints.webservice.RestrainBodiesRequest attribute) (haddock.clis.restraints.webservice.ValidateTblRequest attribute) model_id (haddock.libs.libscan.MutationResult attribute) ModelPointMutation (class in haddock.modules.analysis.alascan.scan) (class in haddock.modules.analysis.rnascan.scan) models_should_have_the_same_labels() (in module haddock.gear.preprocessing) ModelScore (class in haddock.libs.libprodigy) ModelsDifferError module haddock.clis haddock.clis.cli haddock.clis.cli_analyse 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.random_removal haddock.clis.restraints.restrain_bodies haddock.clis.restraints.restrain_ligand haddock.clis.restraints.validate_tbl haddock.clis.restraints.webservice haddock.clis.restraints.z_surface_restraints haddock.clis.wrapper_haddock_restraints haddock.core haddock.core.cns_paths haddock.core.defaults haddock.core.exceptions haddock.core.supported_molecules haddock.core.typing haddock.fcc haddock.fcc.calc_fcc_matrix haddock.fcc.cluster_fcc 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.known_cns_errors haddock.gear.parameters haddock.gear.postprocessing haddock.gear.prepare_run haddock.gear.preprocessing haddock.gear.restart_run haddock.gear.validations haddock.gear.yaml2cfg haddock.gear.zerofill haddock.libs haddock.libs.assets haddock.libs.libaa2cg haddock.libs.libalign haddock.libs.libcapri haddock.libs.libcli haddock.libs.libclust haddock.libs.libcns haddock.libs.libfcc haddock.libs.libfunc haddock.libs.libgrid haddock.libs.libhpc haddock.libs.libinteractive haddock.libs.libio haddock.libs.libligand haddock.libs.liblog haddock.libs.libmath haddock.libs.libmpi haddock.libs.libnotebooks haddock.libs.libontology haddock.libs.libparallel haddock.libs.libpdb haddock.libs.libplots haddock.libs.libprodigy haddock.libs.librestraints haddock.libs.libscan haddock.libs.libstructure haddock.libs.libsubprocess haddock.libs.libtimer haddock.libs.libutil haddock.libs.libworkflow haddock.modules haddock.modules.analysis haddock.modules.analysis.alascan haddock.modules.analysis.alascan.scan haddock.modules.analysis.caprieval haddock.modules.analysis.caprieval.capri haddock.modules.analysis.caprifilter haddock.modules.analysis.caprifilter.caprifilter 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.filter haddock.modules.analysis.ilrmsdmatrix haddock.modules.analysis.ilrmsdmatrix.ilrmsd haddock.modules.analysis.rmsdmatrix haddock.modules.analysis.rmsdmatrix.rmsd haddock.modules.analysis.rnascan haddock.modules.analysis.rnascan.scan haddock.modules.analysis.seletop haddock.modules.analysis.seletopclusts haddock.modules.analysis.seletopclusts.seletopclusts haddock.modules.base_cns_module haddock.modules.extras haddock.modules.extras.exit haddock.modules.refinement haddock.modules.refinement.cgtoaa haddock.modules.refinement.emref haddock.modules.refinement.flexref haddock.modules.refinement.mdref haddock.modules.refinement.openmm haddock.modules.refinement.openmm.openmm haddock.modules.sampling haddock.modules.sampling.gdock haddock.modules.sampling.gdock.gdock haddock.modules.sampling.lightdock haddock.modules.sampling.rigidbody haddock.modules.scoring haddock.modules.scoring.deeprank haddock.modules.scoring.deeprank.deeprank haddock.modules.scoring.emscoring haddock.modules.scoring.mdscoring haddock.modules.scoring.prodigyligand haddock.modules.scoring.prodigyligand.prodigylig haddock.modules.scoring.prodigyprotein haddock.modules.scoring.prodigyprotein.prodigy haddock.modules.scoring.sasascore haddock.modules.scoring.sasascore.sasascore haddock.modules.topology haddock.modules.topology.topoaa haddock.modules.topology.topocg

MODULE_DEFAULT_YAML (in module haddock.core.defaults) MODULE_IO_FILE (in module haddock.core.defaults) module_name (haddock.libs.libscan.AddDeltaBFactor attribute) (haddock.libs.libscan.ClusterOutputer attribute) (haddock.modules.analysis.alascan.scan.AddDeltaBFactor attribute) (haddock.modules.analysis.alascan.scan.ClusterOutputer attribute) (haddock.modules.analysis.rnascan.scan.AddDeltaBFactor attribute) (haddock.modules.analysis.rnascan.scan.ClusterOutputer attribute) 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) moduloAB() (in module haddock.modules.analysis.contactmap.contmap) Molecule (class in haddock.libs.libstructure) MPIScheduler (class in haddock.libs.libmpi) mutant_scores (haddock.libs.libscan.MutationResult attribute) mutate() (in module haddock.modules.analysis.alascan.scan) (in module haddock.modules.analysis.rnascan.scan) MutationResult (class in haddock.libs.libscan)

N

name (haddock.fcc.cluster_fcc.Cluster attribute) (haddock.fcc.cluster_fcc.Element attribute) (haddock.libs.libfcc.Cluster attribute) (haddock.libs.libfcc.Element attribute) (haddock.modules.analysis.alascan.HaddockModule attribute) (haddock.modules.analysis.caprieval.HaddockModule attribute) (haddock.modules.analysis.caprifilter.HaddockModule attribute) (haddock.modules.analysis.clustfcc.HaddockModule attribute) (haddock.modules.analysis.clustrmsd.HaddockModule attribute) (haddock.modules.analysis.contactmap.HaddockModule attribute) (haddock.modules.analysis.filter.HaddockModule attribute) (haddock.modules.analysis.ilrmsdmatrix.HaddockModule attribute) (haddock.modules.analysis.rmsdmatrix.HaddockModule attribute) (haddock.modules.analysis.rnascan.HaddockModule attribute) (haddock.modules.analysis.seletop.HaddockModule attribute) (haddock.modules.analysis.seletopclusts.HaddockModule attribute) (haddock.modules.extras.exit.HaddockModule attribute) (haddock.modules.refinement.cgtoaa.HaddockModule attribute) (haddock.modules.refinement.emref.HaddockModule attribute) (haddock.modules.refinement.flexref.HaddockModule attribute) (haddock.modules.refinement.mdref.HaddockModule attribute) (haddock.modules.refinement.openmm.HaddockModule attribute) (haddock.modules.sampling.gdock.HaddockModule attribute) (haddock.modules.sampling.lightdock.HaddockModule attribute) (haddock.modules.sampling.rigidbody.HaddockModule attribute) (haddock.modules.scoring.deeprank.HaddockModule attribute) (haddock.modules.scoring.emscoring.HaddockModule attribute) (haddock.modules.scoring.mdscoring.HaddockModule attribute) (haddock.modules.scoring.prodigyligand.HaddockModule attribute) (haddock.modules.scoring.prodigyprotein.HaddockModule attribute) (haddock.modules.scoring.sasascore.HaddockModule attribute) (haddock.modules.topology.topoaa.HaddockModule attribute) (haddock.modules.topology.topocg.HaddockModule attribute)

nan() (in module haddock.libs.libfunc) neighbors (haddock.fcc.cluster_fcc.Element attribute) (haddock.libs.libfcc.Element attribute) non_negative_int() (in module haddock.libs.libutil) none() (in module haddock.libs.libfunc) norm() (in module haddock.libs.libaa2cg) norm2() (in module haddock.libs.libaa2cg) normalize_score() (haddock.libs.libscan.AddDeltaBFactor method) not_none() (in module haddock.libs.libfunc) num_processes (haddock.libs.libparallel.Scheduler property)

O

offline_js_manager() (in module haddock.libs.libplots) open_files_to_lines() (in module haddock.libs.libio) OPENMM (class in haddock.modules.refinement.openmm.openmm) openmm_pdbfixer() (haddock.modules.refinement.openmm.openmm.OPENMM method) OPTIONAL_YAML (in module haddock.gear.parameters) order_clusters() (in module haddock.modules.analysis.clustrmsd.clustrmsd) order_traceback_df() (in module haddock.clis.cli_traceback)

ori_resname (haddock.libs.libscan.MutationResult attribute) output() (haddock.modules.analysis.ilrmsdmatrix.ilrmsd.Contact method) (haddock.modules.scoring.ScoringModule method) output_cg_restraints() (in module haddock.libs.libaa2cg) output_clusters() (in module haddock.fcc.cluster_fcc) (in module haddock.libs.libfcc) output_data() (in module haddock.clis.restraints.z_surface_restraints)

P

package() (haddock.libs.libgrid.GridInterface method) 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) parse_actpass_file() (in module haddock.libs.librestraints) parse_contact_file() (in module haddock.fcc.calc_fcc_matrix) (in module haddock.libs.libfcc) parse_input() (haddock.libs.libgrid.CompositeGridJob method) (haddock.libs.libgrid.GridInterface method) (haddock.libs.libgrid.GridJob method) parse_ncores() (in module haddock.libs.libutil) parse_output() (haddock.libs.libgrid.GridInterface static method) parse_restraints() (in module haddock.modules.sampling.gdock.gdock) partner_chain (haddock.libs.libscan.MutationResult attribute) partner_ori_resname (haddock.libs.libscan.MutationResult attribute) partner_resid (haddock.libs.libscan.MutationResult attribute) partner_target_resname (haddock.libs.libscan.MutationResult attribute) passive1 (haddock.clis.restraints.webservice.ActPassToAmbigRequest attribute) passive2 (haddock.clis.restraints.webservice.ActPassToAmbigRequest attribute) passive_from_active() (in module haddock.clis.restraints.passive_from_active) passive_from_active_raw() (in module haddock.libs.librestraints) PassiveFromActiveRequest (class in haddock.clis.restraints.webservice) pat() (in module haddock.libs.libaa2cg) pcs (haddock.clis.restraints.webservice.ValidateTblRequest attribute) 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) pdb_string_to_structure() (in module haddock.libs.libnotebooks) PDBFile (class in haddock.libs.libontology) PDBPathT (class in haddock.libs.libontology) PDBPreprocessRequest (class in haddock.clis.restraints.webservice) per_interface_output() (haddock.modules.scoring.CNSScoringModule method) Persistent (class in haddock.libs.libontology)

ping_dirac() (in module haddock.libs.libgrid) pkd_converter() (haddock.libs.libprodigy.ProdigyWorker method) plot_cluster_matrix() (in module haddock.libs.libclust) populate() (haddock.fcc.cluster_fcc.Cluster method) (haddock.libs.libfcc.Cluster method) 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_cns_input_parallel() (haddock.modules.sampling.rigidbody.HaddockModule method) prepare_cns_input_sequential() (haddock.modules.sampling.rigidbody.HaddockModule method) 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_payload() (haddock.libs.libgrid.GridInterface method) prepare_single_input() (in module haddock.libs.libcns) preprocess_pdb() (in module haddock.clis.restraints.webservice) preprocess_restart_from() (in module haddock.gear.restart_run) previous_path() (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method) probe_grid_efficiency() (haddock.libs.libgrid.GRIDScheduler method) PROBING (haddock.libs.libgrid.Tag attribute) process_input_f() (haddock.libs.libgrid.CompositeGridJob method) (haddock.libs.libgrid.GridInterface method) (haddock.libs.libgrid.GridJob method) process_job() (haddock.libs.libgrid.GRIDScheduler static method) process_pdbs() (in module haddock.gear.preprocessing) ProdigyBaseJob (class in haddock.libs.libprodigy) ProdigyJob (class in haddock.modules.scoring.prodigyligand.prodigylig) (class in haddock.modules.scoring.prodigyprotein.prodigy) ProdigyLigand (class in haddock.modules.scoring.prodigyligand.prodigylig) ProdigyProtein (class in haddock.modules.scoring.prodigyprotein.prodigy) ProdigyWorker (class in haddock.libs.libprodigy) PT (class in haddock.core.typing)

Q

quick (haddock.clis.restraints.webservice.ValidateTblRequest attribute)

R

radius (haddock.clis.restraints.webservice.PassiveFromActiveRequest attribute) randint() (haddock.libs.libmath.RandomNumberGenerator method) random_removal() (in module haddock.clis.restraints.random_removal) RandomNumberGenerator (class in haddock.libs.libmath) rank_according_to_score() (in module haddock.libs.libcapri) 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.fcc.cluster_fcc) (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_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_directories() (haddock.modules.refinement.openmm.HaddockModule method) 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_true_singletons() (in module haddock.fcc.cluster_fcc) remove_unsupported_atom() (in module haddock.gear.preprocessing) remove_unsupported_hetatm() (in module haddock.gear.preprocessing) remove_unsupported_molecules() (in module haddock.gear.preprocessing) remove_water_and_ions() (haddock.modules.refinement.openmm.openmm.OPENMM static method) rename_nucbases() (in module haddock.libs.libaa2cg) renum_step_folders() (in module haddock.gear.extend_run) reorder_results() (haddock.libs.libscan.AddDeltaBFactor method) 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) resid (haddock.libs.libscan.MutationResult attribute) resname (haddock.core.supported_molecules.CNSTopologyResidue property) restart() (haddock.clis.cli_dmn.Job method) restrain_bodies() (in module haddock.clis.restraints.restrain_bodies) (in module haddock.clis.restraints.webservice) restrain_ligand() (in module haddock.clis.restraints.restrain_ligand) RestrainBodiesRequest (class in haddock.clis.restraints.webservice) restraints_guardrail() (haddock.modules.sampling.rigidbody.HaddockModule method) retrieve_models() (haddock.libs.libontology.ModuleIO method) retrieve_output() (haddock.libs.libgrid.GridInterface 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.libcapri.CAPRI method) (haddock.libs.libgrid.GRIDScheduler method) (haddock.libs.libhpc.HPCScheduler method) (haddock.libs.libhpc.HPCWorker method) (haddock.libs.libmpi.MPIScheduler method) (haddock.libs.libparallel.GenericTask method) (haddock.libs.libparallel.Scheduler method) (haddock.libs.libparallel.Worker method) (haddock.libs.libprodigy.ProdigyBaseJob method) (haddock.libs.libprodigy.ProdigyWorker method) (haddock.libs.libscan.AddDeltaBFactor method) (haddock.libs.libscan.ClusterOutputer method) (haddock.libs.libsubprocess.BaseJob method) (haddock.libs.libsubprocess.CNSJob method) (haddock.libs.libworkflow.WorkflowManager method) (haddock.modules.analysis.alascan.scan.InterfaceScanner method) (haddock.modules.analysis.alascan.scan.ModelPointMutation method) (haddock.modules.analysis.contactmap.contmap.ClusteredContactMap method) (haddock.modules.analysis.contactmap.contmap.ContactsMap 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.analysis.rnascan.scan.InterfaceScanner method) (haddock.modules.analysis.rnascan.scan.ModelPointMutation method) (haddock.modules.base_cns_module.BaseCNSModule method) (haddock.modules.BaseHaddockModule method) (haddock.modules.refinement.openmm.openmm.OPENMM method) (haddock.modules.sampling.gdock.gdock.GdockWrapper method) (haddock.modules.scoring.deeprank.deeprank.DeeprankWrapper method) (haddock.modules.scoring.sasascore.sasascore.AccScore method) run_capri_analysis() (in module haddock.clis.cli_analyse) run_openmm() (haddock.modules.refinement.openmm.openmm.OPENMM method) run_prodrg() (in module haddock.libs.libligand) RUNDIR (in module haddock.core.defaults) RUNNING (haddock.libs.libgrid.JobStatus attribute)

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) save_configuration_files() (in module haddock.gear.prepare_run) save_envvars() (haddock.modules.base_cns_module.BaseCNSModule method) save_lines_to_files() (in module haddock.libs.libio) save_models() (haddock.modules.sampling.gdock.gdock.GdockWrapper method) save_scoring_weights() (in module haddock.modules.analysis.caprieval.capri) 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) search_previousstep_matrix() (in module haddock.clis.re.clustrmsd) segid1 (haddock.clis.restraints.webservice.ActPassToAmbigRequest attribute) segid2 (haddock.clis.restraints.webservice.ActPassToAmbigRequest attribute) select_top_clusts_models() (in module haddock.modules.analysis.seletopclusts.seletopclusts) SeqAlign (class in haddock.libs.libalign) sequence_alignment() (in module haddock.libs.libalign) set_max_cpu() (haddock.modules.refinement.openmm.HaddockModule static method) setup_logging() (in module haddock.clis.restraints.z_surface_restraints) setup_run() (in module haddock.gear.prepare_run) SetupError shape_bead() (in module haddock.clis.restraints.z_surface_restraints) size_clust_order() (in module haddock.modules.analysis.seletopclusts.seletopclusts) solve_no_chainID_no_segID() (in module haddock.gear.preprocessing) sort_columns (haddock.libs.libscan.ClusterOutputer attribute) (haddock.modules.analysis.alascan.scan.ClusterOutputer attribute) (haddock.modules.analysis.rnascan.scan.ClusterOutputer attribute) sort_models() (in module haddock.modules.analysis.seletopclusts.seletopclusts) sort_numbered_paths() (in module haddock.libs.libutil) spl() (in module haddock.libs.libaa2cg) 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) ss_classification() (in module haddock.libs.libaa2cg) STAGED (haddock.libs.libgrid.JobStatus attribute)

STANDARD_SCAN_COLUMNS (in module haddock.libs.libscan) standard_scan_row() (in module haddock.libs.libscan) Step (class in haddock.libs.libworkflow) step_coords() (in module haddock.clis.restraints.z_surface_restraints) step_folder_regex (in module haddock.modules) step_folder_regex_re (in module haddock.modules) StepError structure (haddock.clis.restraints.webservice.CalcAccessibilityRequest attribute) (haddock.clis.restraints.webservice.PassiveFromActiveRequest attribute) (haddock.clis.restraints.webservice.PDBPreprocessRequest attribute) (haddock.clis.restraints.webservice.RestrainBodiesRequest attribute) structure_to_pdb_string() (in module haddock.libs.libnotebooks) submit() (haddock.clis.cli_dmn.Job method) (haddock.libs.libgrid.GridInterface method) submit_jobs() (haddock.libs.libgrid.GRIDScheduler method) subset_traceback() (in module haddock.clis.cli_traceback) success (haddock.libs.libscan.MutationResult attribute) 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_cofactors_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) surface (haddock.clis.restraints.webservice.PassiveFromActiveRequest attribute) swap_segid_chain() (in module haddock.libs.libpdb)

T

Tag (class in haddock.libs.libgrid) target_resname (haddock.libs.libscan.MutationResult attribute) tbl (haddock.clis.restraints.webservice.ValidateTblRequest attribute) terminate() (haddock.libs.libhpc.HPCScheduler method) (haddock.libs.libparallel.Scheduler method) ThirdPartyIntallationError tidy() (in module haddock.libs.libpdb) to_chain (haddock.clis.restraints.webservice.PDBPreprocessRequest attribute) 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) TRACEBACK_FOLDER (in module haddock.core.defaults) 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) tt() (in module haddock.libs.libaa2cg) typesub() (in module haddock.libs.libaa2cg)

U

UNKNOWN (haddock.libs.libgrid.JobStatus attribute) unpack_compressed_and_archived_files() (in module haddock.gear.clean_steps) unpacked_structure() (in module haddock.clis.restraints.webservice) unpacked_tbl() (in module haddock.clis.restraints.webservice) 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)

update_paths() (in module haddock.clis.cli_analyse) update_paths_in_capri_dict() (in module haddock.clis.cli_analyse) update_pdb_scores() (haddock.modules.scoring.CNSScoringModule method) update_status() (haddock.libs.libgrid.GridInterface method) (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_defaults_yaml() (in module haddock.gear.validations) validate_dirac() (in module haddock.libs.libgrid) validate_format() (in module haddock.clis.cli_analyse) 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_ncs_params() (in module haddock.gear.prepare_run) validate_ouput_mutant_parameter() (haddock.modules.analysis.alascan.HaddockModule method) (haddock.modules.analysis.rnascan.HaddockModule method) validate_param_range() (in module haddock.gear.prepare_run)

validate_param_type() (in module haddock.gear.prepare_run) validate_parameter_scheme() (in module haddock.gear.validations) validate_parameters_are_not_incompatible() (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_scan_bases() (in module haddock.modules.analysis.rnascan.scan) validate_tbl() (in module haddock.clis.restraints.validate_tbl) (in module haddock.clis.restraints.webservice) validate_tbldata() (in module haddock.libs.librestraints) validate_value() (in module haddock.gear.prepare_run) validate_yaml_params_scheme() (in module haddock.gear.validations) ValidateTblRequest (class in haddock.clis.restraints.webservice)

W

wait_for_completion() (haddock.libs.libgrid.GRIDScheduler method) WAITING (haddock.libs.libgrid.JobStatus attribute) 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_caprifilter() (in module haddock.modules.analysis.caprifilter.caprifilter) write_caprifilter_full() (in module haddock.modules.analysis.caprifilter.caprifilter)

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_delta_score_to_pdb() (haddock.libs.libscan.AddDeltaBFactor method) 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_scan_out() (in module haddock.libs.libscan) (in module haddock.modules.analysis.alascan.scan) (in module haddock.modules.analysis.rnascan.scan) 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) zscore_reference (haddock.libs.libscan.ClusterOutputer attribute) (haddock.modules.analysis.alascan.scan.ClusterOutputer attribute) (haddock.modules.analysis.rnascan.scan.ClusterOutputer attribute)