Rosetta  2020.37
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Functions
antibody::design Namespace Reference

Functions

BooleanOptionKey const design ("antibody:design")
 
BooleanOptionKey const view ("antibody:design:view")
 
StringOptionKey const base_cdr_instructions ("antibody:design:base_cdr_instructions")
 
StringOptionKey const cdr_instructions ("antibody:design:cdr_instructions")
 
StringOptionKey const antibody_database ("antibody:design:antibody_database")
 
BooleanOptionKey const paper_ab_db ("antibody:design:paper_ab_db")
 
StringOptionKey const paper_ab_db_path ("antibody:design:paper_ab_db_path")
 
StringVectorOptionKey const seq_design_cdrs ("antibody:design:seq_design_cdrs")
 
StringVectorOptionKey const graft_design_cdrs ("antibody:design:graft_design_cdrs")
 
StringVectorOptionKey const primary_cdrs ("antibody:design:primary_cdrs")
 
StringOptionKey const mintype ("antibody:design:mintype")
 
StringVectorOptionKey const disallow_aa ("antibody:design:disallow_aa")
 
IntegerOptionKey const top_designs ("antibody:design:top_designs")
 
BooleanOptionKey const high_mem_mode ("antibody:design:high_mem_mode")
 
IntegerOptionKey const cdr_set_cache_limit ("antibody:design:cdr_set_cache_limit")
 
StringOptionKey const design_protocol ("antibody:design:design_protocol")
 
BooleanOptionKey const run_relax ("antibody:design:run_relax")
 
BooleanOptionKey const run_interface_analyzer ("antibody:design:run_interface_analyzer")
 
StringVectorOptionKey const paratope ("antibody:design:paratope")
 
StringVectorOptionKey const epitope ("antibody:design:epitope")
 
BooleanOptionKey const use_epitope_constraints ("antibody:design:use_epitope_constraints")
 
RealOptionKey const dihedral_cst_weight ("antibody:design:dihedral_cst_weight")
 
RealOptionKey const atom_pair_cst_weight ("antibody:design:atom_pair_cst_weight")
 
BooleanOptionKey const global_dihedral_cst_scoring ("antibody:design:global_dihedral_cst_scoring")
 
BooleanOptionKey const global_atom_pair_cst_scoring ("antibody:design:global_atom_pair_cst_scoring")
 
BooleanOptionKey const do_dock ("antibody:design:do_dock")
 
IntegerOptionKey const outer_cycle_rounds ("antibody:design:outer_cycle_rounds")
 
IntegerOptionKey const inner_cycle_rounds ("antibody:design:inner_cycle_rounds")
 
IntegerOptionKey const dock_cycle_rounds ("antibody:design:dock_cycle_rounds")
 
RealOptionKey const interface_dis ("antibody:design:interface_dis")
 
RealOptionKey const neighbor_dis ("antibody:design:neighbor_dis")
 
BooleanOptionKey const use_outliers ("antibody:design:use_outliers")
 
BooleanOptionKey const use_H3_graft_outliers ("antibody:design:use_H3_graft_outliers")
 
BooleanOptionKey const use_only_H3_kinked ("antibody:design:use_only_H3_kinked")
 
BooleanOptionKey const design_antigen ("antibody:design:design_antigen")
 
BooleanOptionKey const design_framework ("antibody:design:design_framework")
 
BooleanOptionKey const conservative_framework_design ("antibody:design:conservative_framework_design")
 
BooleanOptionKey const design_H3_stem ("antibody:design:design_H3_stem")
 
BooleanOptionKey const design_proline ("antibody:design:design_proline")
 
RealOptionKey const sample_zero_probs_at ("antibody:design:sample_zero_probs_at")
 
BooleanOptionKey const force_mutate_framework_for_cluster ("antibody:design:force_mutate_framework_for_cluster")
 
BooleanOptionKey const no_profile_probabilities ("antibody:design:no_profile_probabilities")
 
IntegerOptionKey const seq_design_stats_cutoff ("antibody:design:seq_design_stats_cutoff")
 
IntegerOptionKey const seq_design_profile_samples ("antibody:design:seq_design_profile_samples")
 
BooleanOptionKey const idealize_graft_cdrs ("antibody:design:idealize_graft_cdrs")
 
StringVectorOptionKey const add_backrub_pivots ("antibody:design:add_backrub_pivots")
 
RealOptionKey const inner_kt ("antibody:design:inner_kt")
 
RealOptionKey const outer_kt ("antibody:design:outer_kt")
 
BooleanOptionKey const random_start ("antibody:design:random_start")
 
BooleanOptionKey const adapt_graft ("antibody:design:adapt_graft")
 
BooleanOptionKey const enable_adapt_graft_cartesian ("antibody:design:enable_adapt_graft_cartesian")
 
BooleanOptionKey const remove_antigen ("antibody:design:remove_antigen")
 
BooleanOptionKey const add_graft_log_to_pdb ("antibody:design:add_graft_log_to_pdb")
 
BooleanOptionKey const mutate_framework_for_cluster ("antibody:design:mutate_framework_for_cluster")
 

Function Documentation

BooleanOptionKey const antibody::design::adapt_graft ( "antibody:design:adapt_graft"  )
StringVectorOptionKey const antibody::design::add_backrub_pivots ( "antibody:design:add_backrub_pivots"  )
BooleanOptionKey const antibody::design::add_graft_log_to_pdb ( "antibody:design:add_graft_log_to_pdb"  )
StringOptionKey const antibody::design::antibody_database ( "antibody:design:antibody_database"  )
RealOptionKey const antibody::design::atom_pair_cst_weight ( "antibody:design:atom_pair_cst_weight"  )
StringOptionKey const antibody::design::base_cdr_instructions ( "antibody:design:base_cdr_instructions"  )
StringOptionKey const antibody::design::cdr_instructions ( "antibody:design:cdr_instructions"  )
IntegerOptionKey const antibody::design::cdr_set_cache_limit ( "antibody:design:cdr_set_cache_limit"  )
BooleanOptionKey const antibody::design::conservative_framework_design ( "antibody:design:conservative_framework_design"  )
BooleanOptionKey const antibody::design::design ( "antibody:design"  )
BooleanOptionKey const antibody::design::design_antigen ( "antibody:design:design_antigen"  )
BooleanOptionKey const antibody::design::design_framework ( "antibody:design:design_framework"  )
BooleanOptionKey const antibody::design::design_H3_stem ( "antibody:design:design_H3_stem"  )
BooleanOptionKey const antibody::design::design_proline ( "antibody:design:design_proline"  )
StringOptionKey const antibody::design::design_protocol ( "antibody:design:design_protocol"  )
RealOptionKey const antibody::design::dihedral_cst_weight ( "antibody:design:dihedral_cst_weight"  )
StringVectorOptionKey const antibody::design::disallow_aa ( "antibody:design:disallow_aa"  )
BooleanOptionKey const antibody::design::do_dock ( "antibody:design:do_dock"  )
IntegerOptionKey const antibody::design::dock_cycle_rounds ( "antibody:design:dock_cycle_rounds"  )
BooleanOptionKey const antibody::design::enable_adapt_graft_cartesian ( "antibody:design:enable_adapt_graft_cartesian"  )
StringVectorOptionKey const antibody::design::epitope ( "antibody:design:epitope"  )
BooleanOptionKey const antibody::design::force_mutate_framework_for_cluster ( "antibody:design:force_mutate_framework_for_cluster"  )
BooleanOptionKey const antibody::design::global_atom_pair_cst_scoring ( "antibody:design:global_atom_pair_cst_scoring"  )
BooleanOptionKey const antibody::design::global_dihedral_cst_scoring ( "antibody:design:global_dihedral_cst_scoring"  )
StringVectorOptionKey const antibody::design::graft_design_cdrs ( "antibody:design:graft_design_cdrs"  )
BooleanOptionKey const antibody::design::high_mem_mode ( "antibody:design:high_mem_mode"  )
BooleanOptionKey const antibody::design::idealize_graft_cdrs ( "antibody:design:idealize_graft_cdrs"  )
IntegerOptionKey const antibody::design::inner_cycle_rounds ( "antibody:design:inner_cycle_rounds"  )
RealOptionKey const antibody::design::inner_kt ( "antibody:design:inner_kt"  )
RealOptionKey const antibody::design::interface_dis ( "antibody:design:interface_dis"  )
StringOptionKey const antibody::design::mintype ( "antibody:design:mintype"  )
BooleanOptionKey const antibody::design::mutate_framework_for_cluster ( "antibody:design:mutate_framework_for_cluster"  )
RealOptionKey const antibody::design::neighbor_dis ( "antibody:design:neighbor_dis"  )
BooleanOptionKey const antibody::design::no_profile_probabilities ( "antibody:design:no_profile_probabilities"  )
IntegerOptionKey const antibody::design::outer_cycle_rounds ( "antibody:design:outer_cycle_rounds"  )
RealOptionKey const antibody::design::outer_kt ( "antibody:design:outer_kt"  )
BooleanOptionKey const antibody::design::paper_ab_db ( "antibody:design:paper_ab_db"  )
StringOptionKey const antibody::design::paper_ab_db_path ( "antibody:design:paper_ab_db_path"  )
StringVectorOptionKey const antibody::design::paratope ( "antibody:design:paratope"  )
StringVectorOptionKey const antibody::design::primary_cdrs ( "antibody:design:primary_cdrs"  )
BooleanOptionKey const antibody::design::random_start ( "antibody:design:random_start"  )
BooleanOptionKey const antibody::design::remove_antigen ( "antibody:design:remove_antigen"  )
BooleanOptionKey const antibody::design::run_interface_analyzer ( "antibody:design:run_interface_analyzer"  )
BooleanOptionKey const antibody::design::run_relax ( "antibody:design:run_relax"  )
RealOptionKey const antibody::design::sample_zero_probs_at ( "antibody:design:sample_zero_probs_at"  )
StringVectorOptionKey const antibody::design::seq_design_cdrs ( "antibody:design:seq_design_cdrs"  )
IntegerOptionKey const antibody::design::seq_design_profile_samples ( "antibody:design:seq_design_profile_samples"  )
IntegerOptionKey const antibody::design::seq_design_stats_cutoff ( "antibody:design:seq_design_stats_cutoff"  )
IntegerOptionKey const antibody::design::top_designs ( "antibody:design:top_designs"  )
BooleanOptionKey const antibody::design::use_epitope_constraints ( "antibody:design:use_epitope_constraints"  )
BooleanOptionKey const antibody::design::use_H3_graft_outliers ( "antibody:design:use_H3_graft_outliers"  )
BooleanOptionKey const antibody::design::use_only_H3_kinked ( "antibody:design:use_only_H3_kinked"  )
BooleanOptionKey const antibody::design::use_outliers ( "antibody:design:use_outliers"  )
BooleanOptionKey const antibody::design::view ( "antibody:design:view"  )