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Functions
pepspec Namespace Reference

Functions

BooleanOptionKey const pepspec ("pepspec")
 
StringOptionKey const soft_wts ("pepspec:soft_wts")
 
StringOptionKey const cen_wts ("pepspec:cen_wts")
 
BooleanOptionKey const binding_score ("pepspec:binding_score")
 
BooleanOptionKey const no_cen ("pepspec:no_cen")
 
BooleanOptionKey const no_cen_rottrials ("pepspec:no_cen_rottrials")
 
BooleanOptionKey const run_sequential ("pepspec:run_sequential")
 
IntegerOptionKey const pep_anchor ("pepspec:pep_anchor")
 
StringOptionKey const pep_chain ("pepspec:pep_chain")
 
IntegerOptionKey const n_peptides ("pepspec:n_peptides")
 
IntegerOptionKey const n_build_loop ("pepspec:n_build_loop")
 
IntegerOptionKey const n_cgrelax_loop ("pepspec:n_cgrelax_loop")
 
IntegerOptionKey const n_dock_loop ("pepspec:n_dock_loop")
 
RealOptionKey const interface_cutoff ("pepspec:interface_cutoff")
 
BooleanOptionKey const use_input_bb ("pepspec:use_input_bb")
 
BooleanOptionKey const remove_input_bb ("pepspec:remove_input_bb")
 
StringOptionKey const homol_csts ("pepspec:homol_csts")
 
RealOptionKey const p_homol_csts ("pepspec:p_homol_csts")
 
BooleanOptionKey const gen_pep_bb_sequential ("pepspec:gen_pep_bb_sequential")
 
StringOptionKey const input_seq ("pepspec:input_seq")
 
StringOptionKey const ss_type ("pepspec:ss_type")
 
BooleanOptionKey const upweight_interface ("pepspec:upweight_interface")
 
BooleanOptionKey const calc_sasa ("pepspec:calc_sasa")
 
BooleanOptionKey const diversify_pep_seqs ("pepspec:diversify_pep_seqs")
 
IntegerOptionKey const diversify_lvl ("pepspec:diversify_lvl")
 
BooleanOptionKey const dump_cg_bb ("pepspec:dump_cg_bb")
 
BooleanOptionKey const save_low_pdbs ("pepspec:save_low_pdbs")
 
BooleanOptionKey const save_all_pdbs ("pepspec:save_all_pdbs")
 
BooleanOptionKey const no_design ("pepspec:no_design")
 
StringOptionKey const pdb_list ("pepspec:pdb_list")
 
StringOptionKey const ref_pdb_list ("pepspec:ref_pdb_list")
 
BooleanOptionKey const add_buffer_res ("pepspec:add_buffer_res")
 
StringOptionKey const cg_res_type ("pepspec:cg_res_type")
 
IntegerOptionKey const native_pep_anchor ("pepspec:native_pep_anchor")
 
StringOptionKey const native_pep_chain ("pepspec:native_pep_chain")
 
BooleanOptionKey const native_align ("pepspec:native_align")
 
BooleanOptionKey const rmsd_analysis ("pepspec:rmsd_analysis")
 
StringOptionKey const anchor_type ("pepspec:anchor_type")
 
BooleanOptionKey const no_prepack_prot ("pepspec:no_prepack_prot")
 
BooleanOptionKey const prep_use_ref_rotamers ("pepspec:prep_use_ref_rotamers")
 
IntegerOptionKey const n_prepend ("pepspec:n_prepend")
 
IntegerOptionKey const n_append ("pepspec:n_append")
 
RealOptionKey const clash_cutoff ("pepspec:clash_cutoff")
 
RealOptionKey const n_anchor_dock_std_devs ("pepspec:n_anchor_dock_std_devs")
 
RealOptionKey const prep_trans_std_dev ("pepspec:prep_trans_std_dev")
 
RealOptionKey const prep_rot_std_dev ("pepspec:prep_rot_std_dev")
 
BooleanOptionKey const seq_align ("pepspec:seq_align")
 
StringOptionKey const prep_align_prot_to ("pepspec:prep_align_prot_to")
 

Function Documentation

BooleanOptionKey const pepspec::add_buffer_res ( "pepspec:add_buffer_res"  )

Referenced by RunPepSpec().

StringOptionKey const pepspec::anchor_type ( "pepspec:anchor_type"  )

Referenced by run_pep_prep().

BooleanOptionKey const pepspec::binding_score ( "pepspec:binding_score"  )

Referenced by print_pep_analysis(), and RunPepSpec().

BooleanOptionKey const pepspec::calc_sasa ( "pepspec:calc_sasa"  )

Referenced by print_pep_analysis().

StringOptionKey const pepspec::cen_wts ( "pepspec:cen_wts"  )

Referenced by RunPepSpec().

StringOptionKey const pepspec::cg_res_type ( "pepspec:cg_res_type"  )
RealOptionKey const pepspec::clash_cutoff ( "pepspec:clash_cutoff"  )
IntegerOptionKey const pepspec::diversify_lvl ( "pepspec:diversify_lvl"  )

Referenced by RunPepSpec().

BooleanOptionKey const pepspec::diversify_pep_seqs ( "pepspec:diversify_pep_seqs"  )

Referenced by RunPepSpec().

BooleanOptionKey const pepspec::dump_cg_bb ( "pepspec:dump_cg_bb"  )

Referenced by RunPepSpec().

BooleanOptionKey const pepspec::gen_pep_bb_sequential ( "pepspec:gen_pep_bb_sequential"  )

Referenced by gen_pep_bb_sequential().

StringOptionKey const pepspec::homol_csts ( "pepspec:homol_csts"  )
StringOptionKey const pepspec::input_seq ( "pepspec:input_seq"  )
RealOptionKey const pepspec::interface_cutoff ( "pepspec:interface_cutoff"  )

Referenced by RunPepSpec().

RealOptionKey const pepspec::n_anchor_dock_std_devs ( "pepspec:n_anchor_dock_std_devs"  )

Referenced by run_pep_prep().

IntegerOptionKey const pepspec::n_append ( "pepspec:n_append"  )
IntegerOptionKey const pepspec::n_build_loop ( "pepspec:n_build_loop"  )
IntegerOptionKey const pepspec::n_cgrelax_loop ( "pepspec:n_cgrelax_loop"  )

Referenced by RunPepSpec().

IntegerOptionKey const pepspec::n_dock_loop ( "pepspec:n_dock_loop"  )

Referenced by run_pep_prep().

IntegerOptionKey const pepspec::n_peptides ( "pepspec:n_peptides"  )

Referenced by run_pep_prep(), and RunPepSpec().

IntegerOptionKey const pepspec::n_prepend ( "pepspec:n_prepend"  )
BooleanOptionKey const pepspec::native_align ( "pepspec:native_align"  )

Referenced by pep_rmsd_analysis().

IntegerOptionKey const pepspec::native_pep_anchor ( "pepspec:native_pep_anchor"  )
StringOptionKey const pepspec::native_pep_chain ( "pepspec:native_pep_chain"  )
BooleanOptionKey const pepspec::no_cen ( "pepspec:no_cen"  )

Referenced by RunPepSpec().

BooleanOptionKey const pepspec::no_cen_rottrials ( "pepspec:no_cen_rottrials"  )

Referenced by gen_pep_bb_sequential().

BooleanOptionKey const pepspec::no_design ( "pepspec:no_design"  )

Referenced by initialize_peptide(), and RunPepSpec().

BooleanOptionKey const pepspec::no_prepack_prot ( "pepspec:no_prepack_prot"  )

Referenced by run_pep_prep().

RealOptionKey const pepspec::p_homol_csts ( "pepspec:p_homol_csts"  )

Referenced by print_pep_csts(), and set_pep_csts().

StringOptionKey const pepspec::pdb_list ( "pepspec:pdb_list"  )

Referenced by run_pep_prep(), and RunPepSpec().

IntegerOptionKey const pepspec::pep_anchor ( "pepspec:pep_anchor"  )
StringOptionKey const pepspec::pep_chain ( "pepspec:pep_chain"  )
BooleanOptionKey const pepspec::pepspec ( "pepspec"  )
StringOptionKey const pepspec::prep_align_prot_to ( "pepspec:prep_align_prot_to"  )

Referenced by run_pep_prep().

RealOptionKey const pepspec::prep_rot_std_dev ( "pepspec:prep_rot_std_dev"  )

Referenced by run_pep_prep().

RealOptionKey const pepspec::prep_trans_std_dev ( "pepspec:prep_trans_std_dev"  )

Referenced by run_pep_prep().

BooleanOptionKey const pepspec::prep_use_ref_rotamers ( "pepspec:prep_use_ref_rotamers"  )

Referenced by run_pep_prep().

StringOptionKey const pepspec::ref_pdb_list ( "pepspec:ref_pdb_list"  )

Referenced by run_pep_prep().

BooleanOptionKey const pepspec::remove_input_bb ( "pepspec:remove_input_bb"  )

Referenced by initialize_peptide(), and run_pep_prep().

BooleanOptionKey const pepspec::rmsd_analysis ( "pepspec:rmsd_analysis"  )

Referenced by run_pep_prep().

BooleanOptionKey const pepspec::run_sequential ( "pepspec:run_sequential"  )

Referenced by run_pep_prep(), and RunPepSpec().

BooleanOptionKey const pepspec::save_all_pdbs ( "pepspec:save_all_pdbs"  )

Referenced by RunPepSpec().

BooleanOptionKey const pepspec::save_low_pdbs ( "pepspec:save_low_pdbs"  )

Referenced by RunPepSpec().

BooleanOptionKey const pepspec::seq_align ( "pepspec:seq_align"  )

Referenced by run_pep_prep().

StringOptionKey const pepspec::soft_wts ( "pepspec:soft_wts"  )

Referenced by run_pep_prep(), and RunPepSpec().

StringOptionKey const pepspec::ss_type ( "pepspec:ss_type"  )

Referenced by make_1mer_frags().

BooleanOptionKey const pepspec::upweight_interface ( "pepspec:upweight_interface"  )

Referenced by print_pep_analysis(), and RunPepSpec().

BooleanOptionKey const pepspec::use_input_bb ( "pepspec:use_input_bb"  )