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Namespaces | Functions
antibody Namespace Reference

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

BooleanOptionKey const antibody::all_atom_mode_kink_constraint ( "antibody:all_atom_mode_kink_constraint"  )
BooleanOptionKey const antibody::allow_omega_mismatches_for_north_clusters ( "antibody:allow_omega_mismatches_for_north_clusters"  )
BooleanOptionKey const antibody::antibody ( "antibody"  )
BooleanOptionKey const antibody::auto_generate_h3_kink_constraint ( "antibody:auto_generate_h3_kink_constraint"  )
BooleanOptionKey const antibody::auto_generate_kink_constraint ( "antibody:auto_generate_kink_constraint"  )
RealOptionKey const antibody::bfactor_cutoff ( "antibody:bfactor_cutoff"  )
StringOptionKey const antibody::blastp ( "antibody:blastp"  )
BooleanOptionKey const antibody::camelid ( "antibody:camelid"  )
BooleanOptionKey const antibody::camelid_constraints ( "antibody:camelid_constraints"  )
StringOptionKey const antibody::cdr_definition ( "antibody:cdr_definition"  )
StringOptionKey const antibody::centroid_refine ( "antibody:centroid_refine"  )
BooleanOptionKey const antibody::check_cdr_chainbreaks ( "antibody:check_cdr_chainbreaks"  )
BooleanOptionKey const antibody::check_cdr_pep_bond_geom ( "antibody:check_cdr_pep_bond_geom"  )
IntegerOptionKey const antibody::cluster_csts_stats_cutoff ( "antibody:cluster_csts_stats_cutoff"  )
BooleanOptionKey const antibody::constrain_cter ( "antibody:constrain_cter"  )
BooleanOptionKey const antibody::constrain_vlvh_qq ( "antibody:constrain_vlvh_qq"  )
BooleanOptionKey const antibody::exclude_homologs ( "antibody:exclude_homologs"  )
RealOptionKey const antibody::exclude_homologs_cdr_cutoff ( "antibody:exclude_homologs_cdr_cutoff"  )
RealOptionKey const antibody::exclude_homologs_fr_cutoff ( "antibody:exclude_homologs_fr_cutoff"  )
StringVectorOptionKey const antibody::exclude_pdbs ( "antibody:exclude_pdbs"  )
BooleanOptionKey const antibody::extend_h3_before_modeling ( "antibody:extend_h3_before_modeling"  )
BooleanOptionKey const antibody::force_use_of_cluster_csts_with_outliers ( "antibody:force_use_of_cluster_csts_with_outliers"  )
StringOptionKey const antibody::frh_template ( "antibody:frh_template"  )
StringOptionKey const antibody::frl_template ( "antibody:frl_template"  )
RealOptionKey const antibody::general_dihedral_cst_phi_sd ( "antibody:general_dihedral_cst_phi_sd"  )
RealOptionKey const antibody::general_dihedral_cst_psi_sd ( "antibody:general_dihedral_cst_psi_sd"  )
BooleanOptionKey const antibody::graft_h1 ( "antibody:graft_h1"  )
BooleanOptionKey const antibody::graft_h2 ( "antibody:graft_h2"  )
BooleanOptionKey const antibody::graft_h3 ( "antibody:graft_h3"  )
BooleanOptionKey const antibody::graft_l1 ( "antibody:graft_l1"  )
BooleanOptionKey const antibody::graft_l2 ( "antibody:graft_l2"  )
BooleanOptionKey const antibody::graft_l3 ( "antibody:graft_l3"  )
StringOptionKey const antibody::grafting_database ( "antibody:grafting_database"  )
StringOptionKey const antibody::h1_template ( "antibody:h1_template"  )
StringOptionKey const antibody::h2_template ( "antibody:h2_template"  )
BooleanOptionKey const antibody::h3_filter ( "antibody:h3_filter"  )
RealOptionKey const antibody::h3_filter_tolerance ( "antibody:h3_filter_tolerance"  )
BooleanOptionKey const antibody::h3_loop_csts_hr ( "antibody:h3_loop_csts_hr"  )
BooleanOptionKey const antibody::h3_loop_csts_lr ( "antibody:h3_loop_csts_lr"  )
BooleanOptionKey const antibody::h3_no_stem_graft ( "antibody:h3_no_stem_graft"  )
StringOptionKey const antibody::h3_template ( "antibody:h3_template"  )
StringOptionKey const antibody::input_ab_scheme ( "antibody:input_ab_scheme"  )
FileOptionKey const antibody::input_fv ( "antibody:input_fv"  )
StringOptionKey const antibody::json_cdr ( "antibody:json_cdr"  )
StringOptionKey const antibody::l1_template ( "antibody:l1_template"  )
StringOptionKey const antibody::l2_template ( "antibody:l2_template"  )
StringOptionKey const antibody::l3_template ( "antibody:l3_template"  )
StringOptionKey const antibody::light_chain ( "antibody:light_chain"  )
StringOptionKey const antibody::light_heavy_template ( "antibody:light_heavy_template"  )
BooleanOptionKey const antibody::model_h3 ( "antibody:model_h3"  )
IntegerOptionKey const antibody::n_multi_templates ( "antibody:n_multi_templates"  )
StringOptionKey const antibody::numbering_scheme ( "antibody:numbering_scheme"  )
RealOptionKey const antibody::ocd_cutoff ( "antibody:ocd_cutoff"  )
StringOptionKey const antibody::output_ab_scheme ( "antibody:output_ab_scheme"  )
BooleanOptionKey const antibody::packonly_after_graft ( "antibody:packonly_after_graft"  )
StringOptionKey const antibody::prefix ( "antibody:prefix"  )
StringOptionKey const antibody::preprocessing_script_version ( "antibody:preprocessing_script_version"  )
BooleanOptionKey const antibody::refine_h3 ( "antibody:refine_h3"  )
BooleanOptionKey const antibody::rt_min ( "antibody:rt_min"  )
BooleanOptionKey const antibody::run_snugdock ( "antibody:run_snugdock"  )
BooleanOptionKey const antibody::sc_min ( "antibody:sc_min"  )
BooleanOptionKey const antibody::snug_loops ( "antibody:snug_loops"  )
BooleanOptionKey const antibody::snugfit ( "antibody:snugfit"  )
BooleanOptionKey const antibody::stem_optimize ( "antibody:stem_optimize"  )
IntegerOptionKey const antibody::stem_optimize_size ( "antibody:stem_optimize_size"  )
BooleanOptionKey const antibody::use_mean_cluster_cst_data ( "antibody:use_mean_cluster_cst_data"  )