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Namespaces | Functions
packing Namespace Reference

Namespaces

 ex1
 
 ex1aro
 
 ex1aro_exposed
 
 ex2
 
 ex2aro
 
 ex2aro_exposed
 
 ex3
 
 ex4
 
 exdna
 
 packer_palette
 

Functions

BooleanOptionKey const packing ("packing")
 
BooleanOptionKey const repack_only ("packing:repack_only")
 
BooleanOptionKey const prevent_repacking ("packing:prevent_repacking")
 
RealOptionKey const cenrot_cutoff ("packing:cenrot_cutoff")
 
BooleanOptionKey const ignore_ligand_chi ("packing:ignore_ligand_chi")
 
BooleanOptionKey const quasisymmetry ("packing:quasisymmetry")
 
IntegerOptionKey const ndruns ("packing:ndruns")
 
BooleanOptionKey const soft_rep_design ("packing:soft_rep_design")
 
RealOptionKey const mainchain_h_rebuild_threshold ("packing:mainchain_h_rebuild_threshold")
 
BooleanOptionKey const use_electrostatic_repulsion ("packing:use_electrostatic_repulsion")
 
BooleanOptionKey const dump_rotamer_sets ("packing:dump_rotamer_sets")
 
RealOptionKey const dunbrack_prob_buried ("packing:dunbrack_prob_buried")
 
RealOptionKey const dunbrack_prob_nonburied ("packing:dunbrack_prob_nonburied")
 
RealOptionKey const dunbrack_prob_buried_semi ("packing:dunbrack_prob_buried_semi")
 
RealOptionKey const dunbrack_prob_nonburied_semi ("packing:dunbrack_prob_nonburied_semi")
 
BooleanOptionKey const no_optH ("packing:no_optH")
 
BooleanOptionKey const optH_MCA ("packing:optH_MCA")
 
BooleanOptionKey const pack_missing_sidechains ("packing:pack_missing_sidechains")
 
BooleanOptionKey const preserve_c_beta ("packing:preserve_c_beta")
 
BooleanOptionKey const flip_HNQ ("packing:flip_HNQ")
 
IntegerVectorOptionKey const fix_his_tautomer ("packing:fix_his_tautomer")
 
BooleanOptionKey const print_pymol_selection ("packing:print_pymol_selection")
 
IntegerOptionKey const extrachi_cutoff ("packing:extrachi_cutoff")
 
FileVectorOptionKey const resfile ("packing:resfile")
 
BooleanOptionKey const sc_branch_rotamers ("packing:sc_branch_rotamers")
 
RealOptionKey const outeriterations_scaling ("packing:outeriterations_scaling")
 
RealOptionKey const inneriterations_scaling ("packing:inneriterations_scaling")
 
StringVectorOptionKey const adducts ("packing:adducts")
 
BooleanOptionKey const use_input_sc ("packing:use_input_sc")
 
FileVectorOptionKey const unboundrot ("packing:unboundrot")
 
RealOptionKey const max_rotbump_energy ("packing:max_rotbump_energy")
 
BooleanOptionKey const lazy_ig ("packing:lazy_ig")
 
BooleanOptionKey const double_lazy_ig ("packing:double_lazy_ig")
 
IntegerOptionKey const linmem_ig ("packing:linmem_ig")
 
BooleanOptionKey const precompute_ig ("packing:precompute_ig")
 
IntegerOptionKey const multi_cool_annealer ("packing:multi_cool_annealer")
 
BooleanOptionKey const sequence_symmetric_annealer ("packing:sequence_symmetric_annealer")
 
BooleanOptionKey const smart_annealer ("packing:smart_annealer")
 
StringOptionKey const smart_annealer_model ("packing:smart_annealer_model")
 
RealOptionKey const smart_annealer_cutoff ("packing:smart_annealer_cutoff")
 
BooleanOptionKey const smart_annealer_pick_again ("packing:smart_annealer_pick_again")
 
BooleanOptionKey const smart_annealer_disable_during_quench ("packing:smart_annealer_disable_during_quench")
 
RealVectorOptionKey const minpack_temp_schedule ("packing:minpack_temp_schedule")
 
IntegerOptionKey const minpack_inner_iteration_scale ("packing:minpack_inner_iteration_scale")
 
BooleanOptionKey const minpack_disable_bumpcheck ("packing:minpack_disable_bumpcheck")
 

Function Documentation

StringVectorOptionKey const packing::adducts ( "packing:adducts"  )
RealOptionKey const packing::cenrot_cutoff ( "packing:cenrot_cutoff"  )
BooleanOptionKey const packing::double_lazy_ig ( "packing:double_lazy_ig"  )
BooleanOptionKey const packing::dump_rotamer_sets ( "packing:dump_rotamer_sets"  )
RealOptionKey const packing::dunbrack_prob_buried ( "packing:dunbrack_prob_buried"  )
RealOptionKey const packing::dunbrack_prob_buried_semi ( "packing:dunbrack_prob_buried_semi"  )
RealOptionKey const packing::dunbrack_prob_nonburied ( "packing:dunbrack_prob_nonburied"  )
RealOptionKey const packing::dunbrack_prob_nonburied_semi ( "packing:dunbrack_prob_nonburied_semi"  )
IntegerOptionKey const packing::extrachi_cutoff ( "packing:extrachi_cutoff"  )

Referenced by main().

IntegerVectorOptionKey const packing::fix_his_tautomer ( "packing:fix_his_tautomer"  )
BooleanOptionKey const packing::flip_HNQ ( "packing:flip_HNQ"  )

Referenced by main().

BooleanOptionKey const packing::ignore_ligand_chi ( "packing:ignore_ligand_chi"  )
RealOptionKey const packing::inneriterations_scaling ( "packing:inneriterations_scaling"  )
BooleanOptionKey const packing::lazy_ig ( "packing:lazy_ig"  )
IntegerOptionKey const packing::linmem_ig ( "packing:linmem_ig"  )
RealOptionKey const packing::mainchain_h_rebuild_threshold ( "packing:mainchain_h_rebuild_threshold"  )
RealOptionKey const packing::max_rotbump_energy ( "packing:max_rotbump_energy"  )
BooleanOptionKey const packing::minpack_disable_bumpcheck ( "packing:minpack_disable_bumpcheck"  )
IntegerOptionKey const packing::minpack_inner_iteration_scale ( "packing:minpack_inner_iteration_scale"  )
RealVectorOptionKey const packing::minpack_temp_schedule ( "packing:minpack_temp_schedule"  )
IntegerOptionKey const packing::multi_cool_annealer ( "packing:multi_cool_annealer"  )
IntegerOptionKey const packing::ndruns ( "packing:ndruns"  )
BooleanOptionKey const packing::no_optH ( "packing:no_optH"  )

Referenced by main().

BooleanOptionKey const packing::optH_MCA ( "packing:optH_MCA"  )
RealOptionKey const packing::outeriterations_scaling ( "packing:outeriterations_scaling"  )
BooleanOptionKey const packing::pack_missing_sidechains ( "packing:pack_missing_sidechains"  )
BooleanOptionKey const packing::packing ( "packing"  )
BooleanOptionKey const packing::precompute_ig ( "packing:precompute_ig"  )
BooleanOptionKey const packing::preserve_c_beta ( "packing:preserve_c_beta"  )
BooleanOptionKey const packing::prevent_repacking ( "packing:prevent_repacking"  )
BooleanOptionKey const packing::print_pymol_selection ( "packing:print_pymol_selection"  )
BooleanOptionKey const packing::quasisymmetry ( "packing:quasisymmetry"  )
BooleanOptionKey const packing::repack_only ( "packing:repack_only"  )
FileVectorOptionKey const packing::resfile ( "packing:resfile"  )

Referenced by main(), and sequence_tolerance_main().

BooleanOptionKey const packing::sc_branch_rotamers ( "packing:sc_branch_rotamers"  )
BooleanOptionKey const packing::sequence_symmetric_annealer ( "packing:sequence_symmetric_annealer"  )
BooleanOptionKey const packing::smart_annealer ( "packing:smart_annealer"  )
RealOptionKey const packing::smart_annealer_cutoff ( "packing:smart_annealer_cutoff"  )
BooleanOptionKey const packing::smart_annealer_disable_during_quench ( "packing:smart_annealer_disable_during_quench"  )
StringOptionKey const packing::smart_annealer_model ( "packing:smart_annealer_model"  )
BooleanOptionKey const packing::smart_annealer_pick_again ( "packing:smart_annealer_pick_again"  )
BooleanOptionKey const packing::soft_rep_design ( "packing:soft_rep_design"  )
FileVectorOptionKey const packing::unboundrot ( "packing:unboundrot"  )

Referenced by main().

BooleanOptionKey const packing::use_electrostatic_repulsion ( "packing:use_electrostatic_repulsion"  )
BooleanOptionKey const packing::use_input_sc ( "packing:use_input_sc"  )