basic::options::OptionKeys::pepspec Namespace Reference

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

Variable Documentation

add_buffer_res

BooleanOptionKey const basic::options::OptionKeys::pepspec::add_buffer_res

extern

Referenced by refine_fa_pep_bb(), and RunPepSpec().

anchor_type

StringOptionKey const basic::options::OptionKeys::pepspec::anchor_type

extern

Referenced by run_pep_prep().

binding_score

BooleanOptionKey const basic::options::OptionKeys::pepspec::binding_score

extern

calc_sasa

BooleanOptionKey const basic::options::OptionKeys::pepspec::calc_sasa

extern

cen_wts

StringOptionKey const basic::options::OptionKeys::pepspec::cen_wts

extern

Referenced by RunPepSpec().

cg_res_type

StringOptionKey const basic::options::OptionKeys::pepspec::cg_res_type

extern

Referenced by gen_pep_bb_sequential(), initialize_peptide(), and RunPepSpec().

clash_cutoff

RealOptionKey const basic::options::OptionKeys::pepspec::clash_cutoff

extern

Referenced by gen_pep_bb_sequential().

diversify_lvl

IntegerOptionKey const basic::options::OptionKeys::pepspec::diversify_lvl

extern

diversify_pep_seqs

BooleanOptionKey const basic::options::OptionKeys::pepspec::diversify_pep_seqs

extern

dump_cg_bb

BooleanOptionKey const basic::options::OptionKeys::pepspec::dump_cg_bb

extern

Referenced by RunPepSpec().

gen_pep_bb_sequential

BooleanOptionKey const basic::options::OptionKeys::pepspec::gen_pep_bb_sequential

extern

homol_csts

StringOptionKey const basic::options::OptionKeys::pepspec::homol_csts

extern

input_seq

StringOptionKey const basic::options::OptionKeys::pepspec::input_seq

extern

interface_cutoff

RealOptionKey const basic::options::OptionKeys::pepspec::interface_cutoff

extern

Referenced by pep_scan_analysis(), and RunPepSpec().

n_anchor_dock_std_devs

RealOptionKey const basic::options::OptionKeys::pepspec::n_anchor_dock_std_devs

extern

n_append

IntegerOptionKey const basic::options::OptionKeys::pepspec::n_append

extern

Referenced by gen_pep_bb_sequential(), initialize_peptide(), run_pep_prep(), and RunPepSpec().

n_build_loop

IntegerOptionKey const basic::options::OptionKeys::pepspec::n_build_loop

extern

Referenced by gen_pep_bb_frag(), gen_pep_bb_frag_old(), gen_pep_bb_rama(), gen_pep_bb_sequential(), and RunPepSpec().

n_cgrelax_loop

IntegerOptionKey const basic::options::OptionKeys::pepspec::n_cgrelax_loop

extern

Referenced by RunPepSpec().

n_dock_loop

IntegerOptionKey const basic::options::OptionKeys::pepspec::n_dock_loop

extern

n_peptides

IntegerOptionKey const basic::options::OptionKeys::pepspec::n_peptides

extern

Referenced by run_pep_prep(), and RunPepSpec().

n_prepend

IntegerOptionKey const basic::options::OptionKeys::pepspec::n_prepend

extern

Referenced by gen_pep_bb_sequential(), initialize_peptide(), run_pep_prep(), and RunPepSpec().

native_align

BooleanOptionKey const basic::options::OptionKeys::pepspec::native_align

extern

native_pep_anchor

IntegerOptionKey const basic::options::OptionKeys::pepspec::native_pep_anchor

extern

native_pep_chain

StringOptionKey const basic::options::OptionKeys::pepspec::native_pep_chain

extern

no_cen

BooleanOptionKey const basic::options::OptionKeys::pepspec::no_cen

extern

Referenced by gen_pep_bb_sequential(), and RunPepSpec().

no_cen_rottrials

BooleanOptionKey const basic::options::OptionKeys::pepspec::no_cen_rottrials

extern

no_design

BooleanOptionKey const basic::options::OptionKeys::pepspec::no_design

extern

no_prepack_prot

BooleanOptionKey const basic::options::OptionKeys::pepspec::no_prepack_prot

extern

p_homol_csts

RealOptionKey const basic::options::OptionKeys::pepspec::p_homol_csts

extern

pdb_list

StringOptionKey const basic::options::OptionKeys::pepspec::pdb_list

extern

pep_anchor

IntegerOptionKey const basic::options::OptionKeys::pepspec::pep_anchor

extern

Referenced by add_pep_buffer_res(), add_pep_res(), gen_pep_bb_frag(), gen_pep_bb_sequential(), get_rmsd(), initialize_peptide(), pep_phipsi_analysis(), pep_rmsd_analysis(), pep_scan_analysis(), print_pep_analysis(), refine_fa_pep_bb(), remove_pep_buffer_res(), remove_pep_res(), run_pep_prep(), RunPepSpec(), and set_pep_cst().

pep_chain

StringOptionKey const basic::options::OptionKeys::pepspec::pep_chain

extern

Referenced by derive(), get_subPose(), main(), pep_phipsi_analysis(), pep_rmsd_analysis(), print_pep_analysis(), and RunPepSpec().

pepspec

BooleanOptionKey const basic::options::OptionKeys::pepspec::pepspec

extern

prep_align_prot_to

StringOptionKey const basic::options::OptionKeys::pepspec::prep_align_prot_to

extern

prep_rot_std_dev

RealOptionKey const basic::options::OptionKeys::pepspec::prep_rot_std_dev

extern

prep_trans_std_dev

RealOptionKey const basic::options::OptionKeys::pepspec::prep_trans_std_dev

extern

prep_use_ref_rotamers

BooleanOptionKey const basic::options::OptionKeys::pepspec::prep_use_ref_rotamers

extern

ref_pdb_list

StringOptionKey const basic::options::OptionKeys::pepspec::ref_pdb_list

extern

remove_input_bb

BooleanOptionKey const basic::options::OptionKeys::pepspec::remove_input_bb

extern

rmsd_analysis

BooleanOptionKey const basic::options::OptionKeys::pepspec::rmsd_analysis

extern

Referenced by pep_rmsd_analysis(), print_pep_analysis(), and RunPepSpec().

run_sequential

BooleanOptionKey const basic::options::OptionKeys::pepspec::run_sequential

extern

Referenced by RunPepSpec().

save_all_pdbs

BooleanOptionKey const basic::options::OptionKeys::pepspec::save_all_pdbs

extern

Referenced by RunPepSpec().

save_low_pdbs

BooleanOptionKey const basic::options::OptionKeys::pepspec::save_low_pdbs

extern

Referenced by RunPepSpec().

seq_align

BooleanOptionKey const basic::options::OptionKeys::pepspec::seq_align

extern

Referenced by run_pep_prep().

soft_wts

StringOptionKey const basic::options::OptionKeys::pepspec::soft_wts

extern

Referenced by RunPepSpec().

ss_type

StringOptionKey const basic::options::OptionKeys::pepspec::ss_type

extern

Referenced by RunPepSpec(), and symmetrize_map().

upweight_interface

BooleanOptionKey const basic::options::OptionKeys::pepspec::upweight_interface

extern

Referenced by RunPepSpec().

use_input_bb

BooleanOptionKey const basic::options::OptionKeys::pepspec::use_input_bb

extern

Referenced by RunPepSpec().