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abinitio Namespace Reference

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BooleanOptionKey const abinitio ("abinitio")
 
BooleanOptionKey const membrane ("abinitio:membrane")
 
BooleanOptionKey const use_loophash_filter ("abinitio:use_loophash_filter")
 
RealOptionKey const loophash_filter_acceptance_rate ("abinitio:loophash_filter_acceptance_rate")
 
FileOptionKey const kill_hairpins ("abinitio:kill_hairpins")
 
RealOptionKey const kill_hairpins_frequency ("abinitio:kill_hairpins_frequency")
 
BooleanOptionKey const smooth_cycles_only ("abinitio:smooth_cycles_only")
 
BooleanOptionKey const relax ("abinitio:relax")
 
BooleanOptionKey const final_clean_relax ("abinitio:final_clean_relax")
 
BooleanOptionKey const fastrelax ("abinitio:fastrelax")
 
BooleanOptionKey const multifastrelax ("abinitio:multifastrelax")
 
BooleanOptionKey const debug ("abinitio:debug")
 
BooleanOptionKey const clear_pose_cache ("abinitio:clear_pose_cache")
 
BooleanOptionKey const explicit_pdb_debug ("abinitio:explicit_pdb_debug")
 
BooleanOptionKey const use_filters ("abinitio:use_filters")
 
RealOptionKey const increase_cycles ("abinitio:increase_cycles")
 
IntegerOptionKey const number_3mer_frags ("abinitio:number_3mer_frags")
 
IntegerOptionKey const number_9mer_frags ("abinitio:number_9mer_frags")
 
RealOptionKey const temperature ("abinitio:temperature")
 
RealOptionKey const rg_reweight ("abinitio:rg_reweight")
 
RealOptionKey const rsd_wt_helix ("abinitio:rsd_wt_helix")
 
RealOptionKey const rsd_wt_strand ("abinitio:rsd_wt_strand")
 
RealOptionKey const rsd_wt_loop ("abinitio:rsd_wt_loop")
 
BooleanOptionKey const skip_convergence_check ("abinitio:skip_convergence_check")
 
FileVectorOptionKey const stage1_patch ("abinitio:stage1_patch")
 
FileVectorOptionKey const stage2_patch ("abinitio:stage2_patch")
 
FileVectorOptionKey const stage3a_patch ("abinitio:stage3a_patch")
 
FileVectorOptionKey const stage3b_patch ("abinitio:stage3b_patch")
 
FileVectorOptionKey const stage4_patch ("abinitio:stage4_patch")
 
FileVectorOptionKey const stage5_patch ("abinitio:stage5_patch")
 
BooleanOptionKey const steal_3mers ("abinitio:steal_3mers")
 
BooleanOptionKey const steal_9mers ("abinitio:steal_9mers")
 
BooleanOptionKey const no_write_failures ("abinitio:no_write_failures")
 
BooleanOptionKey const relax_failures ("abinitio:relax_failures")
 
BooleanOptionKey const relax_with_jumps ("abinitio:relax_with_jumps")
 
BooleanOptionKey const process_store ("abinitio:process_store")
 
IntegerVectorOptionKey const fix_residues_to_native ("abinitio:fix_residues_to_native")
 
BooleanOptionKey const return_full_atom ("abinitio:return_full_atom")
 
BooleanOptionKey const detect_disulfide_before_relax ("abinitio:detect_disulfide_before_relax")
 
BooleanOptionKey const close_loops ("abinitio:close_loops")
 
BooleanOptionKey const bGDT ("abinitio:bGDT")
 
BooleanOptionKey const dump_frags ("abinitio:dump_frags")
 
BooleanOptionKey const jdist_rerun ("abinitio:jdist_rerun")
 
RealOptionKey const perturb ("abinitio:perturb")
 
BooleanOptionKey const rerun ("abinitio:rerun")
 
IntegerVectorOptionKey const rmsd_residues ("abinitio:rmsd_residues")
 
BooleanOptionKey const start_native ("abinitio:start_native")
 
BooleanOptionKey const cyclic_peptide ("abinitio:cyclic_peptide")
 
BooleanOptionKey const debug_structures ("abinitio:debug_structures")
 
FileOptionKey const log_frags ("abinitio:log_frags")
 
BooleanOptionKey const only_stage1 ("abinitio:only_stage1")
 
RealOptionKey const end_bias ("abinitio:end_bias")
 
BooleanOptionKey const apply_end_bias ("abinitio:apply_end_bias")
 
IntegerOptionKey const symmetry_residue ("abinitio:symmetry_residue")
 
RealOptionKey const vdw_weight_stage1 ("abinitio:vdw_weight_stage1")
 
BooleanOptionKey const override_vdw_all_stages ("abinitio:override_vdw_all_stages")
 
IntegerVectorOptionKey const recover_low_in_stages ("abinitio:recover_low_in_stages")
 
IntegerVectorOptionKey const skip_stages ("abinitio:skip_stages")
 
BooleanOptionKey const close_chbrk ("abinitio:close_chbrk")
 
BooleanOptionKey const include_stage5 ("abinitio:include_stage5")
 
BooleanOptionKey const close_loops_by_idealizing ("abinitio:close_loops_by_idealizing")
 
BooleanOptionKey const optimize_cutpoints_using_kic ("abinitio:optimize_cutpoints_using_kic")
 
IntegerOptionKey const optimize_cutpoints_margin ("abinitio:optimize_cutpoints_margin")
 

Function Documentation

BooleanOptionKey const abinitio::abinitio ( "abinitio"  )
BooleanOptionKey const abinitio::apply_end_bias ( "abinitio:apply_end_bias"  )
BooleanOptionKey const abinitio::bGDT ( "abinitio:bGDT"  )
BooleanOptionKey const abinitio::clear_pose_cache ( "abinitio:clear_pose_cache"  )
BooleanOptionKey const abinitio::close_chbrk ( "abinitio:close_chbrk"  )
BooleanOptionKey const abinitio::close_loops ( "abinitio:close_loops"  )
BooleanOptionKey const abinitio::close_loops_by_idealizing ( "abinitio:close_loops_by_idealizing"  )
BooleanOptionKey const abinitio::cyclic_peptide ( "abinitio:cyclic_peptide"  )
BooleanOptionKey const abinitio::debug ( "abinitio:debug"  )
BooleanOptionKey const abinitio::debug_structures ( "abinitio:debug_structures"  )
BooleanOptionKey const abinitio::detect_disulfide_before_relax ( "abinitio:detect_disulfide_before_relax"  )
BooleanOptionKey const abinitio::dump_frags ( "abinitio:dump_frags"  )
RealOptionKey const abinitio::end_bias ( "abinitio:end_bias"  )
BooleanOptionKey const abinitio::explicit_pdb_debug ( "abinitio:explicit_pdb_debug"  )
BooleanOptionKey const abinitio::fastrelax ( "abinitio:fastrelax"  )
BooleanOptionKey const abinitio::final_clean_relax ( "abinitio:final_clean_relax"  )
IntegerVectorOptionKey const abinitio::fix_residues_to_native ( "abinitio:fix_residues_to_native"  )
BooleanOptionKey const abinitio::include_stage5 ( "abinitio:include_stage5"  )
RealOptionKey const abinitio::increase_cycles ( "abinitio:increase_cycles"  )
BooleanOptionKey const abinitio::jdist_rerun ( "abinitio:jdist_rerun"  )
FileOptionKey const abinitio::kill_hairpins ( "abinitio:kill_hairpins"  )
RealOptionKey const abinitio::kill_hairpins_frequency ( "abinitio:kill_hairpins_frequency"  )
FileOptionKey const abinitio::log_frags ( "abinitio:log_frags"  )
RealOptionKey const abinitio::loophash_filter_acceptance_rate ( "abinitio:loophash_filter_acceptance_rate"  )
BooleanOptionKey const abinitio::membrane ( "abinitio:membrane"  )
BooleanOptionKey const abinitio::multifastrelax ( "abinitio:multifastrelax"  )
BooleanOptionKey const abinitio::no_write_failures ( "abinitio:no_write_failures"  )
IntegerOptionKey const abinitio::number_3mer_frags ( "abinitio:number_3mer_frags"  )
IntegerOptionKey const abinitio::number_9mer_frags ( "abinitio:number_9mer_frags"  )
BooleanOptionKey const abinitio::only_stage1 ( "abinitio:only_stage1"  )
IntegerOptionKey const abinitio::optimize_cutpoints_margin ( "abinitio:optimize_cutpoints_margin"  )
BooleanOptionKey const abinitio::optimize_cutpoints_using_kic ( "abinitio:optimize_cutpoints_using_kic"  )
BooleanOptionKey const abinitio::override_vdw_all_stages ( "abinitio:override_vdw_all_stages"  )
RealOptionKey const abinitio::perturb ( "abinitio:perturb"  )
BooleanOptionKey const abinitio::process_store ( "abinitio:process_store"  )
IntegerVectorOptionKey const abinitio::recover_low_in_stages ( "abinitio:recover_low_in_stages"  )
BooleanOptionKey const abinitio::relax ( "abinitio:relax"  )
BooleanOptionKey const abinitio::relax_failures ( "abinitio:relax_failures"  )
BooleanOptionKey const abinitio::relax_with_jumps ( "abinitio:relax_with_jumps"  )
BooleanOptionKey const abinitio::rerun ( "abinitio:rerun"  )
BooleanOptionKey const abinitio::return_full_atom ( "abinitio:return_full_atom"  )
RealOptionKey const abinitio::rg_reweight ( "abinitio:rg_reweight"  )
IntegerVectorOptionKey const abinitio::rmsd_residues ( "abinitio:rmsd_residues"  )
RealOptionKey const abinitio::rsd_wt_helix ( "abinitio:rsd_wt_helix"  )
RealOptionKey const abinitio::rsd_wt_loop ( "abinitio:rsd_wt_loop"  )
RealOptionKey const abinitio::rsd_wt_strand ( "abinitio:rsd_wt_strand"  )
BooleanOptionKey const abinitio::skip_convergence_check ( "abinitio:skip_convergence_check"  )
IntegerVectorOptionKey const abinitio::skip_stages ( "abinitio:skip_stages"  )
BooleanOptionKey const abinitio::smooth_cycles_only ( "abinitio:smooth_cycles_only"  )
FileVectorOptionKey const abinitio::stage1_patch ( "abinitio:stage1_patch"  )
FileVectorOptionKey const abinitio::stage2_patch ( "abinitio:stage2_patch"  )
FileVectorOptionKey const abinitio::stage3a_patch ( "abinitio:stage3a_patch"  )
FileVectorOptionKey const abinitio::stage3b_patch ( "abinitio:stage3b_patch"  )
FileVectorOptionKey const abinitio::stage4_patch ( "abinitio:stage4_patch"  )
FileVectorOptionKey const abinitio::stage5_patch ( "abinitio:stage5_patch"  )
BooleanOptionKey const abinitio::start_native ( "abinitio:start_native"  )
BooleanOptionKey const abinitio::steal_3mers ( "abinitio:steal_3mers"  )
BooleanOptionKey const abinitio::steal_9mers ( "abinitio:steal_9mers"  )
IntegerOptionKey const abinitio::symmetry_residue ( "abinitio:symmetry_residue"  )
RealOptionKey const abinitio::temperature ( "abinitio:temperature"  )
BooleanOptionKey const abinitio::use_filters ( "abinitio:use_filters"  )
BooleanOptionKey const abinitio::use_loophash_filter ( "abinitio:use_loophash_filter"  )
RealOptionKey const abinitio::vdw_weight_stage1 ( "abinitio:vdw_weight_stage1"  )