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

add_buffer_res()

BooleanOptionKey const pepspec::add_buffer_res

(

"pepspec:add_buffer_res"

)

Referenced by RunPepSpec().

anchor_type()

StringOptionKey const pepspec::anchor_type

(

"pepspec:anchor_type"

)

Referenced by run_pep_prep().

binding_score()

BooleanOptionKey const pepspec::binding_score

(

"pepspec:binding_score"

)

Referenced by print_pep_analysis(), and RunPepSpec().

calc_sasa()

BooleanOptionKey const pepspec::calc_sasa

(

"pepspec:calc_sasa"

)

Referenced by print_pep_analysis().

cen_wts()

StringOptionKey const pepspec::cen_wts

(

"pepspec:cen_wts"

)

Referenced by RunPepSpec().

cg_res_type()

StringOptionKey const pepspec::cg_res_type

(

"pepspec:cg_res_type"

)

Referenced by gen_pep_bb_sequential(), and initialize_peptide().

clash_cutoff()

RealOptionKey const pepspec::clash_cutoff

(

"pepspec:clash_cutoff"

)

Referenced by gen_pep_bb_sequential(), and run_pep_prep().

diversify_lvl()

IntegerOptionKey const pepspec::diversify_lvl

(

"pepspec:diversify_lvl"

)

Referenced by RunPepSpec().

diversify_pep_seqs()

BooleanOptionKey const pepspec::diversify_pep_seqs

(

"pepspec:diversify_pep_seqs"

)

Referenced by RunPepSpec().

dump_cg_bb()

BooleanOptionKey const pepspec::dump_cg_bb

(

"pepspec:dump_cg_bb"

)

Referenced by RunPepSpec().

gen_pep_bb_sequential()

BooleanOptionKey const pepspec::gen_pep_bb_sequential

(

"pepspec:gen_pep_bb_sequential"

)

Referenced by gen_pep_bb_sequential().

homol_csts()

StringOptionKey const pepspec::homol_csts

(

"pepspec:homol_csts"

)

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

input_seq()

StringOptionKey const pepspec::input_seq

(

"pepspec:input_seq"

)

Referenced by gen_pep_bb_sequential(), initialize_peptide(), make_1mer_frags(), and RunPepSpec().

interface_cutoff()

RealOptionKey const pepspec::interface_cutoff

(

"pepspec:interface_cutoff"

)

Referenced by RunPepSpec().

n_anchor_dock_std_devs()

RealOptionKey const pepspec::n_anchor_dock_std_devs

(

"pepspec:n_anchor_dock_std_devs"

)

Referenced by run_pep_prep().

n_append()

IntegerOptionKey const pepspec::n_append

(

"pepspec:n_append"

)

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

n_build_loop()

IntegerOptionKey const pepspec::n_build_loop

(

"pepspec:n_build_loop"

)

Referenced by gen_pep_bb_sequential(), and RunPepSpec().

n_cgrelax_loop()

IntegerOptionKey const pepspec::n_cgrelax_loop

(

"pepspec:n_cgrelax_loop"

)

Referenced by RunPepSpec().

n_dock_loop()

IntegerOptionKey const pepspec::n_dock_loop

(

"pepspec:n_dock_loop"

)

Referenced by run_pep_prep().

n_peptides()

IntegerOptionKey const pepspec::n_peptides

(

"pepspec:n_peptides"

)

Referenced by run_pep_prep(), and RunPepSpec().

n_prepend()

IntegerOptionKey const pepspec::n_prepend

(

"pepspec:n_prepend"

)

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

native_align()

BooleanOptionKey const pepspec::native_align

(

"pepspec:native_align"

)

Referenced by pep_rmsd_analysis().

native_pep_anchor()

IntegerOptionKey const pepspec::native_pep_anchor

(

"pepspec:native_pep_anchor"

)

Referenced by pep_phipsi_analysis(), and pep_rmsd_analysis().

native_pep_chain()

StringOptionKey const pepspec::native_pep_chain

(

"pepspec:native_pep_chain"

)

Referenced by pep_phipsi_analysis(), and pep_rmsd_analysis().

no_cen()

BooleanOptionKey const pepspec::no_cen

(

"pepspec:no_cen"

)

Referenced by RunPepSpec().

no_cen_rottrials()

BooleanOptionKey const pepspec::no_cen_rottrials

(

"pepspec:no_cen_rottrials"

)

Referenced by gen_pep_bb_sequential().

no_design()

BooleanOptionKey const pepspec::no_design

(

"pepspec:no_design"

)

Referenced by initialize_peptide(), and RunPepSpec().

no_prepack_prot()

BooleanOptionKey const pepspec::no_prepack_prot

(

"pepspec:no_prepack_prot"

)

Referenced by run_pep_prep().

p_homol_csts()

RealOptionKey const pepspec::p_homol_csts

(

"pepspec:p_homol_csts"

)

Referenced by print_pep_csts(), and set_pep_csts().

pdb_list()

StringOptionKey const pepspec::pdb_list

(

"pepspec:pdb_list"

)

Referenced by run_pep_prep(), and RunPepSpec().

pep_anchor()

IntegerOptionKey const pepspec::pep_anchor

(

"pepspec:pep_anchor"

)

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

pep_chain()

StringOptionKey const pepspec::pep_chain

(

"pepspec:pep_chain"

)

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

pepspec()

BooleanOptionKey const pepspec::pepspec

(

"pepspec"

)

prep_align_prot_to()

StringOptionKey const pepspec::prep_align_prot_to

(

"pepspec:prep_align_prot_to"

)

Referenced by run_pep_prep().

prep_rot_std_dev()

RealOptionKey const pepspec::prep_rot_std_dev

(

"pepspec:prep_rot_std_dev"

)

Referenced by run_pep_prep().

prep_trans_std_dev()

RealOptionKey const pepspec::prep_trans_std_dev

(

"pepspec:prep_trans_std_dev"

)

Referenced by run_pep_prep().

prep_use_ref_rotamers()

BooleanOptionKey const pepspec::prep_use_ref_rotamers

(

"pepspec:prep_use_ref_rotamers"

)

Referenced by run_pep_prep().

ref_pdb_list()

StringOptionKey const pepspec::ref_pdb_list

(

"pepspec:ref_pdb_list"

)

Referenced by run_pep_prep().

remove_input_bb()

BooleanOptionKey const pepspec::remove_input_bb

(

"pepspec:remove_input_bb"

)

Referenced by initialize_peptide(), and run_pep_prep().

rmsd_analysis()

BooleanOptionKey const pepspec::rmsd_analysis

(

"pepspec:rmsd_analysis"

)

Referenced by run_pep_prep().

run_sequential()

BooleanOptionKey const pepspec::run_sequential

(

"pepspec:run_sequential"

)

Referenced by run_pep_prep(), and RunPepSpec().

save_all_pdbs()

BooleanOptionKey const pepspec::save_all_pdbs

(

"pepspec:save_all_pdbs"

)

Referenced by RunPepSpec().

save_low_pdbs()

BooleanOptionKey const pepspec::save_low_pdbs

(

"pepspec:save_low_pdbs"

)

Referenced by RunPepSpec().

seq_align()

BooleanOptionKey const pepspec::seq_align

(

"pepspec:seq_align"

)

Referenced by run_pep_prep().

soft_wts()

StringOptionKey const pepspec::soft_wts

(

"pepspec:soft_wts"

)

Referenced by run_pep_prep(), and RunPepSpec().

ss_type()

StringOptionKey const pepspec::ss_type

(

"pepspec:ss_type"

)

Referenced by make_1mer_frags().

upweight_interface()

BooleanOptionKey const pepspec::upweight_interface

(

"pepspec:upweight_interface"

)

Referenced by print_pep_analysis(), and RunPepSpec().

use_input_bb()

BooleanOptionKey const pepspec::use_input_bb

(

"pepspec:use_input_bb"

)

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