Namespaces
	design

Functions
BooleanOptionKey const	antibody ("antibody")

StringOptionKey const	input_ab_scheme ("antibody:input_ab_scheme")

StringOptionKey const	output_ab_scheme ("antibody:output_ab_scheme")

StringOptionKey const	cdr_definition ("antibody:cdr_definition")

StringOptionKey const	light_chain ("antibody:light_chain")

BooleanOptionKey const	check_cdr_chainbreaks ("antibody:check_cdr_chainbreaks")

BooleanOptionKey const	check_cdr_pep_bond_geom ("antibody:check_cdr_pep_bond_geom")

BooleanOptionKey const	constrain_cter ("antibody:constrain_cter")

BooleanOptionKey const	auto_generate_kink_constraint ("antibody:auto_generate_kink_constraint")

BooleanOptionKey const	all_atom_mode_kink_constraint ("antibody:all_atom_mode_kink_constraint")

StringOptionKey const	numbering_scheme ("antibody:numbering_scheme")

BooleanOptionKey const	graft_l1 ("antibody:graft_l1")

StringOptionKey const	l1_template ("antibody:l1_template")

BooleanOptionKey const	graft_l2 ("antibody:graft_l2")

StringOptionKey const	l2_template ("antibody:l2_template")

BooleanOptionKey const	graft_l3 ("antibody:graft_l3")

StringOptionKey const	l3_template ("antibody:l3_template")

BooleanOptionKey const	graft_h1 ("antibody:graft_h1")

StringOptionKey const	h1_template ("antibody:h1_template")

BooleanOptionKey const	graft_h2 ("antibody:graft_h2")

StringOptionKey const	h2_template ("antibody:h2_template")

BooleanOptionKey const	graft_h3 ("antibody:graft_h3")

StringOptionKey const	h3_template ("antibody:h3_template")

StringOptionKey const	light_heavy_template ("antibody:light_heavy_template")

StringOptionKey const	frl_template ("antibody:frl_template")

StringOptionKey const	frh_template ("antibody:frh_template")

BooleanOptionKey const	run_snugdock ("antibody:run_snugdock")

BooleanOptionKey const	h3_no_stem_graft ("antibody:h3_no_stem_graft")

BooleanOptionKey const	packonly_after_graft ("antibody:packonly_after_graft")

BooleanOptionKey const	stem_optimize ("antibody:stem_optimize")

IntegerOptionKey const	stem_optimize_size ("antibody:stem_optimize_size")

StringOptionKey const	preprocessing_script_version ("antibody:preprocessing_script_version")

BooleanOptionKey const	model_h3 ("antibody:model_h3")

BooleanOptionKey const	snugfit ("antibody:snugfit")

BooleanOptionKey const	refine_h3 ("antibody:refine_h3")

BooleanOptionKey const	h3_filter ("antibody:h3_filter")

RealOptionKey const	h3_filter_tolerance ("antibody:h3_filter_tolerance")

BooleanOptionKey const	sc_min ("antibody:sc_min")

BooleanOptionKey const	rt_min ("antibody:rt_min")

BooleanOptionKey const	extend_h3_before_modeling ("antibody:extend_h3_before_modeling")

StringOptionKey const	centroid_refine ("antibody:centroid_refine")

BooleanOptionKey const	h3_loop_csts_lr ("antibody:h3_loop_csts_lr")

BooleanOptionKey const	h3_loop_csts_hr ("antibody:h3_loop_csts_hr")

BooleanOptionKey const	auto_generate_h3_kink_constraint ("antibody:auto_generate_h3_kink_constraint")

BooleanOptionKey const	constrain_vlvh_qq ("antibody:constrain_vlvh_qq")

BooleanOptionKey const	snug_loops ("antibody:snug_loops")

FileOptionKey const	input_fv ("antibody:input_fv")

BooleanOptionKey const	camelid ("antibody:camelid")

BooleanOptionKey const	camelid_constraints ("antibody:camelid_constraints")

BooleanOptionKey const	use_mean_cluster_cst_data ("antibody:use_mean_cluster_cst_data")

BooleanOptionKey const	force_use_of_cluster_csts_with_outliers ("antibody:force_use_of_cluster_csts_with_outliers")

IntegerOptionKey const	cluster_csts_stats_cutoff ("antibody:cluster_csts_stats_cutoff")

RealOptionKey const	general_dihedral_cst_phi_sd ("antibody:general_dihedral_cst_phi_sd")

RealOptionKey const	general_dihedral_cst_psi_sd ("antibody:general_dihedral_cst_psi_sd")

BooleanOptionKey const	allow_omega_mismatches_for_north_clusters ("antibody:allow_omega_mismatches_for_north_clusters")

StringOptionKey const	prefix ("antibody:prefix")

StringOptionKey const	grafting_database ("antibody:grafting_database")

StringOptionKey const	blastp ("antibody:blastp")

StringVectorOptionKey const	exclude_pdbs ("antibody:exclude_pdbs")

BooleanOptionKey const	exclude_homologs ("antibody:exclude_homologs")

RealOptionKey const	exclude_homologs_cdr_cutoff ("antibody:exclude_homologs_cdr_cutoff")

RealOptionKey const	exclude_homologs_fr_cutoff ("antibody:exclude_homologs_fr_cutoff")

RealOptionKey const	ocd_cutoff ("antibody:ocd_cutoff")

RealOptionKey const	bfactor_cutoff ("antibody:bfactor_cutoff")

IntegerOptionKey const	n_multi_templates ("antibody:n_multi_templates")

StringOptionKey const	json_cdr ("antibody:json_cdr")

Function Documentation

◆ all_atom_mode_kink_constraint()

BooleanOptionKey const antibody::all_atom_mode_kink_constraint ( "antibody:all_atom_mode_kink_constraint" )

◆ allow_omega_mismatches_for_north_clusters()

BooleanOptionKey const antibody::allow_omega_mismatches_for_north_clusters ( "antibody:allow_omega_mismatches_for_north_clusters" )

◆ antibody()

BooleanOptionKey const antibody::antibody ( "antibody" )

◆ auto_generate_h3_kink_constraint()

BooleanOptionKey const antibody::auto_generate_h3_kink_constraint ( "antibody:auto_generate_h3_kink_constraint" )

◆ auto_generate_kink_constraint()

BooleanOptionKey const antibody::auto_generate_kink_constraint ( "antibody:auto_generate_kink_constraint" )

◆ bfactor_cutoff()

RealOptionKey const antibody::bfactor_cutoff ( "antibody:bfactor_cutoff" )

◆ blastp()

StringOptionKey const antibody::blastp ( "antibody:blastp" )

◆ camelid()

BooleanOptionKey const antibody::camelid ( "antibody:camelid" )

◆ camelid_constraints()

BooleanOptionKey const antibody::camelid_constraints ( "antibody:camelid_constraints" )

◆ cdr_definition()

StringOptionKey const antibody::cdr_definition ( "antibody:cdr_definition" )

◆ centroid_refine()

StringOptionKey const antibody::centroid_refine ( "antibody:centroid_refine" )

◆ check_cdr_chainbreaks()

BooleanOptionKey const antibody::check_cdr_chainbreaks ( "antibody:check_cdr_chainbreaks" )

◆ check_cdr_pep_bond_geom()

BooleanOptionKey const antibody::check_cdr_pep_bond_geom ( "antibody:check_cdr_pep_bond_geom" )

◆ cluster_csts_stats_cutoff()

IntegerOptionKey const antibody::cluster_csts_stats_cutoff ( "antibody:cluster_csts_stats_cutoff" )

◆ constrain_cter()

BooleanOptionKey const antibody::constrain_cter ( "antibody:constrain_cter" )

◆ constrain_vlvh_qq()

BooleanOptionKey const antibody::constrain_vlvh_qq ( "antibody:constrain_vlvh_qq" )

◆ exclude_homologs()

BooleanOptionKey const antibody::exclude_homologs ( "antibody:exclude_homologs" )

◆ exclude_homologs_cdr_cutoff()

RealOptionKey const antibody::exclude_homologs_cdr_cutoff ( "antibody:exclude_homologs_cdr_cutoff" )

◆ exclude_homologs_fr_cutoff()

RealOptionKey const antibody::exclude_homologs_fr_cutoff ( "antibody:exclude_homologs_fr_cutoff" )

◆ exclude_pdbs()

StringVectorOptionKey const antibody::exclude_pdbs ( "antibody:exclude_pdbs" )

◆ extend_h3_before_modeling()

BooleanOptionKey const antibody::extend_h3_before_modeling ( "antibody:extend_h3_before_modeling" )

◆ force_use_of_cluster_csts_with_outliers()

BooleanOptionKey const antibody::force_use_of_cluster_csts_with_outliers ( "antibody:force_use_of_cluster_csts_with_outliers" )

◆ frh_template()

StringOptionKey const antibody::frh_template ( "antibody:frh_template" )

◆ frl_template()

StringOptionKey const antibody::frl_template ( "antibody:frl_template" )

◆ general_dihedral_cst_phi_sd()

RealOptionKey const antibody::general_dihedral_cst_phi_sd ( "antibody:general_dihedral_cst_phi_sd" )

◆ general_dihedral_cst_psi_sd()

RealOptionKey const antibody::general_dihedral_cst_psi_sd ( "antibody:general_dihedral_cst_psi_sd" )

◆ graft_h1()

BooleanOptionKey const antibody::graft_h1 ( "antibody:graft_h1" )

◆ graft_h2()

BooleanOptionKey const antibody::graft_h2 ( "antibody:graft_h2" )

◆ graft_h3()

BooleanOptionKey const antibody::graft_h3 ( "antibody:graft_h3" )

◆ graft_l1()

BooleanOptionKey const antibody::graft_l1 ( "antibody:graft_l1" )

◆ graft_l2()

BooleanOptionKey const antibody::graft_l2 ( "antibody:graft_l2" )

◆ graft_l3()

BooleanOptionKey const antibody::graft_l3 ( "antibody:graft_l3" )

◆ grafting_database()

StringOptionKey const antibody::grafting_database ( "antibody:grafting_database" )

◆ h1_template()

StringOptionKey const antibody::h1_template ( "antibody:h1_template" )

◆ h2_template()

StringOptionKey const antibody::h2_template ( "antibody:h2_template" )

◆ h3_filter()

BooleanOptionKey const antibody::h3_filter ( "antibody:h3_filter" )

◆ h3_filter_tolerance()

RealOptionKey const antibody::h3_filter_tolerance ( "antibody:h3_filter_tolerance" )

◆ h3_loop_csts_hr()

BooleanOptionKey const antibody::h3_loop_csts_hr ( "antibody:h3_loop_csts_hr" )

◆ h3_loop_csts_lr()

BooleanOptionKey const antibody::h3_loop_csts_lr ( "antibody:h3_loop_csts_lr" )

◆ h3_no_stem_graft()

BooleanOptionKey const antibody::h3_no_stem_graft ( "antibody:h3_no_stem_graft" )

◆ h3_template()

StringOptionKey const antibody::h3_template ( "antibody:h3_template" )

◆ input_ab_scheme()

StringOptionKey const antibody::input_ab_scheme ( "antibody:input_ab_scheme" )

◆ input_fv()

FileOptionKey const antibody::input_fv ( "antibody:input_fv" )

◆ json_cdr()

StringOptionKey const antibody::json_cdr ( "antibody:json_cdr" )

◆ l1_template()

StringOptionKey const antibody::l1_template ( "antibody:l1_template" )

◆ l2_template()

StringOptionKey const antibody::l2_template ( "antibody:l2_template" )

◆ l3_template()

StringOptionKey const antibody::l3_template ( "antibody:l3_template" )

◆ light_chain()

StringOptionKey const antibody::light_chain ( "antibody:light_chain" )

◆ light_heavy_template()

StringOptionKey const antibody::light_heavy_template ( "antibody:light_heavy_template" )

◆ model_h3()

BooleanOptionKey const antibody::model_h3 ( "antibody:model_h3" )

◆ n_multi_templates()

IntegerOptionKey const antibody::n_multi_templates ( "antibody:n_multi_templates" )

◆ numbering_scheme()

StringOptionKey const antibody::numbering_scheme ( "antibody:numbering_scheme" )

◆ ocd_cutoff()

RealOptionKey const antibody::ocd_cutoff ( "antibody:ocd_cutoff" )

◆ output_ab_scheme()

StringOptionKey const antibody::output_ab_scheme ( "antibody:output_ab_scheme" )

◆ packonly_after_graft()

BooleanOptionKey const antibody::packonly_after_graft ( "antibody:packonly_after_graft" )

◆ prefix()

StringOptionKey const antibody::prefix ( "antibody:prefix" )

◆ preprocessing_script_version()

StringOptionKey const antibody::preprocessing_script_version ( "antibody:preprocessing_script_version" )

◆ refine_h3()

BooleanOptionKey const antibody::refine_h3 ( "antibody:refine_h3" )

◆ rt_min()

BooleanOptionKey const antibody::rt_min ( "antibody:rt_min" )

◆ run_snugdock()

BooleanOptionKey const antibody::run_snugdock ( "antibody:run_snugdock" )

◆ sc_min()

BooleanOptionKey const antibody::sc_min ( "antibody:sc_min" )

◆ snug_loops()

BooleanOptionKey const antibody::snug_loops ( "antibody:snug_loops" )

◆ snugfit()

BooleanOptionKey const antibody::snugfit ( "antibody:snugfit" )

◆ stem_optimize()

BooleanOptionKey const antibody::stem_optimize ( "antibody:stem_optimize" )

◆ stem_optimize_size()

IntegerOptionKey const antibody::stem_optimize_size ( "antibody:stem_optimize_size" )

◆ use_mean_cluster_cst_data()

BooleanOptionKey const antibody::use_mean_cluster_cst_data ( "antibody:use_mean_cluster_cst_data" )

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