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antibody.OptionKeys.gen.hh File Reference

basic::options::OptionKeys collection More...

#include <basic/options/keys/OptionKeys.hh>

Namespaces

 basic
 Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.
 
 basic::options
 
 basic::options::OptionKeys
 
 basic::options::OptionKeys::antibody
 
 basic::options::OptionKeys::antibody::design
 

Variables

BooleanOptionKey const basic::options::OptionKeys::antibody::antibody
 
StringOptionKey const basic::options::OptionKeys::antibody::input_ab_scheme
 
StringOptionKey const basic::options::OptionKeys::antibody::output_ab_scheme
 
StringOptionKey const basic::options::OptionKeys::antibody::cdr_definition
 
StringOptionKey const basic::options::OptionKeys::antibody::light_chain
 
BooleanOptionKey const basic::options::OptionKeys::antibody::check_cdr_chainbreaks
 
BooleanOptionKey const basic::options::OptionKeys::antibody::check_cdr_pep_bond_geom
 
BooleanOptionKey const basic::options::OptionKeys::antibody::constrain_cter
 
BooleanOptionKey const basic::options::OptionKeys::antibody::auto_generate_kink_constraint
 
BooleanOptionKey const basic::options::OptionKeys::antibody::all_atom_mode_kink_constraint
 
StringOptionKey const basic::options::OptionKeys::antibody::numbering_scheme
 
BooleanOptionKey const basic::options::OptionKeys::antibody::graft_l1
 
StringOptionKey const basic::options::OptionKeys::antibody::l1_template
 
BooleanOptionKey const basic::options::OptionKeys::antibody::graft_l2
 
StringOptionKey const basic::options::OptionKeys::antibody::l2_template
 
BooleanOptionKey const basic::options::OptionKeys::antibody::graft_l3
 
StringOptionKey const basic::options::OptionKeys::antibody::l3_template
 
BooleanOptionKey const basic::options::OptionKeys::antibody::graft_h1
 
StringOptionKey const basic::options::OptionKeys::antibody::h1_template
 
BooleanOptionKey const basic::options::OptionKeys::antibody::graft_h2
 
StringOptionKey const basic::options::OptionKeys::antibody::h2_template
 
BooleanOptionKey const basic::options::OptionKeys::antibody::graft_h3
 
StringOptionKey const basic::options::OptionKeys::antibody::h3_template
 
StringOptionKey const basic::options::OptionKeys::antibody::light_heavy_template
 
StringOptionKey const basic::options::OptionKeys::antibody::frl_template
 
StringOptionKey const basic::options::OptionKeys::antibody::frh_template
 
BooleanOptionKey const basic::options::OptionKeys::antibody::run_snugdock
 
BooleanOptionKey const basic::options::OptionKeys::antibody::h3_no_stem_graft
 
BooleanOptionKey const basic::options::OptionKeys::antibody::packonly_after_graft
 
BooleanOptionKey const basic::options::OptionKeys::antibody::stem_optimize
 
IntegerOptionKey const basic::options::OptionKeys::antibody::stem_optimize_size
 
StringOptionKey const basic::options::OptionKeys::antibody::preprocessing_script_version
 
BooleanOptionKey const basic::options::OptionKeys::antibody::model_h3
 
BooleanOptionKey const basic::options::OptionKeys::antibody::snugfit
 
BooleanOptionKey const basic::options::OptionKeys::antibody::refine_h3
 
BooleanOptionKey const basic::options::OptionKeys::antibody::h3_filter
 
RealOptionKey const basic::options::OptionKeys::antibody::h3_filter_tolerance
 
BooleanOptionKey const basic::options::OptionKeys::antibody::sc_min
 
BooleanOptionKey const basic::options::OptionKeys::antibody::rt_min
 
BooleanOptionKey const basic::options::OptionKeys::antibody::extend_h3_before_modeling
 
StringOptionKey const basic::options::OptionKeys::antibody::centroid_refine
 
BooleanOptionKey const basic::options::OptionKeys::antibody::h3_loop_csts_lr
 
BooleanOptionKey const basic::options::OptionKeys::antibody::h3_loop_csts_hr
 
BooleanOptionKey const basic::options::OptionKeys::antibody::auto_generate_h3_kink_constraint
 
BooleanOptionKey const basic::options::OptionKeys::antibody::constrain_vlvh_qq
 
BooleanOptionKey const basic::options::OptionKeys::antibody::snug_loops
 
FileOptionKey const basic::options::OptionKeys::antibody::input_fv
 
BooleanOptionKey const basic::options::OptionKeys::antibody::camelid
 
BooleanOptionKey const basic::options::OptionKeys::antibody::camelid_constraints
 
BooleanOptionKey const basic::options::OptionKeys::antibody::use_mean_cluster_cst_data
 
BooleanOptionKey const basic::options::OptionKeys::antibody::force_use_of_cluster_csts_with_outliers
 
IntegerOptionKey const basic::options::OptionKeys::antibody::cluster_csts_stats_cutoff
 
RealOptionKey const basic::options::OptionKeys::antibody::general_dihedral_cst_phi_sd
 
RealOptionKey const basic::options::OptionKeys::antibody::general_dihedral_cst_psi_sd
 
BooleanOptionKey const basic::options::OptionKeys::antibody::allow_omega_mismatches_for_north_clusters
 
StringOptionKey const basic::options::OptionKeys::antibody::prefix
 
StringOptionKey const basic::options::OptionKeys::antibody::grafting_database
 
StringOptionKey const basic::options::OptionKeys::antibody::blastp
 
StringVectorOptionKey const basic::options::OptionKeys::antibody::exclude_pdbs
 
BooleanOptionKey const basic::options::OptionKeys::antibody::exclude_homologs
 
RealOptionKey const basic::options::OptionKeys::antibody::exclude_homologs_cdr_cutoff
 
RealOptionKey const basic::options::OptionKeys::antibody::exclude_homologs_fr_cutoff
 
RealOptionKey const basic::options::OptionKeys::antibody::ocd_cutoff
 
RealOptionKey const basic::options::OptionKeys::antibody::bfactor_cutoff
 
IntegerOptionKey const basic::options::OptionKeys::antibody::n_multi_templates
 
StringOptionKey const basic::options::OptionKeys::antibody::json_cdr
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::design
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::view
 
StringOptionKey const basic::options::OptionKeys::antibody::design::base_cdr_instructions
 
StringOptionKey const basic::options::OptionKeys::antibody::design::cdr_instructions
 
StringOptionKey const basic::options::OptionKeys::antibody::design::antibody_database
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::paper_ab_db
 
StringOptionKey const basic::options::OptionKeys::antibody::design::paper_ab_db_path
 
StringVectorOptionKey const basic::options::OptionKeys::antibody::design::seq_design_cdrs
 
StringVectorOptionKey const basic::options::OptionKeys::antibody::design::graft_design_cdrs
 
StringVectorOptionKey const basic::options::OptionKeys::antibody::design::primary_cdrs
 
StringOptionKey const basic::options::OptionKeys::antibody::design::mintype
 
StringVectorOptionKey const basic::options::OptionKeys::antibody::design::disallow_aa
 
IntegerOptionKey const basic::options::OptionKeys::antibody::design::top_designs
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::high_mem_mode
 
IntegerOptionKey const basic::options::OptionKeys::antibody::design::cdr_set_cache_limit
 
StringOptionKey const basic::options::OptionKeys::antibody::design::design_protocol
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::run_relax
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::run_interface_analyzer
 
StringVectorOptionKey const basic::options::OptionKeys::antibody::design::paratope
 
StringVectorOptionKey const basic::options::OptionKeys::antibody::design::epitope
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::use_epitope_constraints
 
RealOptionKey const basic::options::OptionKeys::antibody::design::dihedral_cst_weight
 
RealOptionKey const basic::options::OptionKeys::antibody::design::atom_pair_cst_weight
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::global_dihedral_cst_scoring
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::global_atom_pair_cst_scoring
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::do_dock
 
IntegerOptionKey const basic::options::OptionKeys::antibody::design::dock_first_cycles
 
IntegerOptionKey const basic::options::OptionKeys::antibody::design::dock_second_cycles
 
IntegerOptionKey const basic::options::OptionKeys::antibody::design::outer_cycle_rounds
 
IntegerOptionKey const basic::options::OptionKeys::antibody::design::inner_cycle_rounds
 
IntegerOptionKey const basic::options::OptionKeys::antibody::design::dock_cycle_rounds
 
IntegerOptionKey const basic::options::OptionKeys::antibody::design::relax_cycle_rounds
 
RealOptionKey const basic::options::OptionKeys::antibody::design::interface_dis
 
RealOptionKey const basic::options::OptionKeys::antibody::design::neighbor_dis
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::use_outliers
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::use_H3_graft_outliers
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::use_only_H3_kinked
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::design_antigen
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::design_framework
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::conservative_framework_design
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::design_H3_stem
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::design_proline
 
RealOptionKey const basic::options::OptionKeys::antibody::design::sample_zero_probs_at
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::force_mutate_framework_for_cluster
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::no_profile_probabilities
 
IntegerOptionKey const basic::options::OptionKeys::antibody::design::seq_design_stats_cutoff
 
IntegerOptionKey const basic::options::OptionKeys::antibody::design::seq_design_profile_samples
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::idealize_graft_cdrs
 
StringVectorOptionKey const basic::options::OptionKeys::antibody::design::add_backrub_pivots
 
RealOptionKey const basic::options::OptionKeys::antibody::design::inner_kt
 
RealOptionKey const basic::options::OptionKeys::antibody::design::outer_kt
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::random_start
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::adapt_graft
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::enable_adapt_graft_cartesian
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::remove_antigen
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::add_graft_log_to_pdb
 
BooleanOptionKey const basic::options::OptionKeys::antibody::design::mutate_framework_for_cluster
 

Detailed Description

basic::options::OptionKeys collection

Author
Stuart G. Mentzer (Stuar.nosp@m.t_Me.nosp@m.ntzer.nosp@m.@obj.nosp@m.exx.c.nosp@m.om)
James M. Thompson (tex@u.nosp@m..was.nosp@m.hingt.nosp@m.on.e.nosp@m.du)