flexPepDocking Namespace Reference

Functions
BooleanOptionKey const	flexPepDocking ("flexPepDocking")
StringOptionKey const	params_file ("flexPepDocking:params_file")
IntegerOptionKey const	peptide_anchor ("flexPepDocking:peptide_anchor")
StringOptionKey const	receptor_chain ("flexPepDocking:receptor_chain")
StringOptionKey const	peptide_chain ("flexPepDocking:peptide_chain")
BooleanOptionKey const	pep_fold_only ("flexPepDocking:pep_fold_only")
BooleanOptionKey const	lowres_abinitio ("flexPepDocking:lowres_abinitio")
BooleanOptionKey const	lowres_preoptimize ("flexPepDocking:lowres_preoptimize")
BooleanOptionKey const	flexPepDockingMinimizeOnly ("flexPepDocking:flexPepDockingMinimizeOnly")
BooleanOptionKey const	extend_peptide ("flexPepDocking:extend_peptide")
BooleanOptionKey const	place_peptide_on_binding_site ("flexPepDocking:place_peptide_on_binding_site")
IntegerOptionKey const	sample_pcs ("flexPepDocking:sample_pcs")
BooleanOptionKey const	SlideIntoContact ("flexPepDocking:SlideIntoContact")
BooleanOptionKey const	recalculate_foldtree ("flexPepDocking:recalculate_foldtree")
BooleanOptionKey const	pep_refine ("flexPepDocking:pep_refine")
BooleanOptionKey const	rbMCM ("flexPepDocking:rbMCM")
BooleanOptionKey const	torsionsMCM ("flexPepDocking:torsionsMCM")
BooleanOptionKey const	peptide_loop_model ("flexPepDocking:peptide_loop_model")
BooleanOptionKey const	backrub_peptide ("flexPepDocking:backrub_peptide")
BooleanOptionKey const	boost_fa_atr ("flexPepDocking:boost_fa_atr")
BooleanOptionKey const	ramp_fa_rep ("flexPepDocking:ramp_fa_rep")
BooleanOptionKey const	ramp_rama ("flexPepDocking:ramp_rama")
BooleanOptionKey const	flexpep_score_only ("flexPepDocking:flexpep_score_only")
FileOptionKey const	ref_startstruct ("flexPepDocking:ref_startstruct")
BooleanOptionKey const	use_cen_score ("flexPepDocking:use_cen_score")
BooleanOptionKey const	design_peptide ("flexPepDocking:design_peptide")
IntegerOptionKey const	rep_ramp_cycles ("flexPepDocking:rep_ramp_cycles")
IntegerOptionKey const	mcm_cycles ("flexPepDocking:mcm_cycles")
RealOptionKey const	random_phi_psi_preturbation ("flexPepDocking:random_phi_psi_preturbation")
RealOptionKey const	smove_angle_range ("flexPepDocking:smove_angle_range")
BooleanOptionKey const	min_receptor_bb ("flexPepDocking:min_receptor_bb")
RealOptionKey const	random_trans_start ("flexPepDocking:random_trans_start")
RealOptionKey const	random_rot_start ("flexPepDocking:random_rot_start")
BooleanOptionKey const	flexpep_prepack ("flexPepDocking:flexpep_prepack")
BooleanOptionKey const	flexpep_noprepack1 ("flexPepDocking:flexpep_noprepack1")
BooleanOptionKey const	flexpep_noprepack2 ("flexPepDocking:flexpep_noprepack2")
RealOptionKey const	score_filter ("flexPepDocking:score_filter")
IntegerOptionKey const	hb_filter ("flexPepDocking:hb_filter")
IntegerOptionKey const	hotspot_filter ("flexPepDocking:hotspot_filter")
StringOptionKey const	frag5 ("flexPepDocking:frag5")
RealOptionKey const	frag9_weight ("flexPepDocking:frag9_weight")
RealOptionKey const	frag5_weight ("flexPepDocking:frag5_weight")
RealOptionKey const	frag3_weight ("flexPepDocking:frag3_weight")
BooleanOptionKey const	pSer2Asp_centroid ("flexPepDocking:pSer2Asp_centroid")
BooleanOptionKey const	pSer2Glu_centroid ("flexPepDocking:pSer2Glu_centroid")
BooleanOptionKey const	dumpPDB_abinitio ("flexPepDocking:dumpPDB_abinitio")
BooleanOptionKey const	dumpPDB_lowres ("flexPepDocking:dumpPDB_lowres")
BooleanOptionKey const	dumpPDB_hires ("flexPepDocking:dumpPDB_hires")

Function Documentation

backrub_peptide()

BooleanOptionKey const flexPepDocking::backrub_peptide

(

"flexPepDocking:backrub_peptide"

)

boost_fa_atr()

BooleanOptionKey const flexPepDocking::boost_fa_atr

(

"flexPepDocking:boost_fa_atr"

)

design_peptide()

BooleanOptionKey const flexPepDocking::design_peptide

(

"flexPepDocking:design_peptide"

)

dumpPDB_abinitio()

BooleanOptionKey const flexPepDocking::dumpPDB_abinitio

(

"flexPepDocking:dumpPDB_abinitio"

)

dumpPDB_hires()

BooleanOptionKey const flexPepDocking::dumpPDB_hires

(

"flexPepDocking:dumpPDB_hires"

)

dumpPDB_lowres()

BooleanOptionKey const flexPepDocking::dumpPDB_lowres

(

"flexPepDocking:dumpPDB_lowres"

)

extend_peptide()

BooleanOptionKey const flexPepDocking::extend_peptide

(

"flexPepDocking:extend_peptide"

)

flexpep_noprepack1()

BooleanOptionKey const flexPepDocking::flexpep_noprepack1

(

"flexPepDocking:flexpep_noprepack1"

)

flexpep_noprepack2()

BooleanOptionKey const flexPepDocking::flexpep_noprepack2

(

"flexPepDocking:flexpep_noprepack2"

)

flexpep_prepack()

BooleanOptionKey const flexPepDocking::flexpep_prepack

(

"flexPepDocking:flexpep_prepack"

)

flexpep_score_only()

BooleanOptionKey const flexPepDocking::flexpep_score_only

(

"flexPepDocking:flexpep_score_only"

)

flexPepDocking()

BooleanOptionKey const flexPepDocking::flexPepDocking

(

"flexPepDocking"

)

flexPepDockingMinimizeOnly()

BooleanOptionKey const flexPepDocking::flexPepDockingMinimizeOnly

(

"flexPepDocking:flexPepDockingMinimizeOnly"

)

frag3_weight()

RealOptionKey const flexPepDocking::frag3_weight

(

"flexPepDocking:frag3_weight"

)

frag5()

StringOptionKey const flexPepDocking::frag5

(

"flexPepDocking:frag5"

)

frag5_weight()

RealOptionKey const flexPepDocking::frag5_weight

(

"flexPepDocking:frag5_weight"

)

frag9_weight()

RealOptionKey const flexPepDocking::frag9_weight

(

"flexPepDocking:frag9_weight"

)

hb_filter()

IntegerOptionKey const flexPepDocking::hb_filter

(

"flexPepDocking:hb_filter"

)

hotspot_filter()

IntegerOptionKey const flexPepDocking::hotspot_filter

(

"flexPepDocking:hotspot_filter"

)

lowres_abinitio()

BooleanOptionKey const flexPepDocking::lowres_abinitio

(

"flexPepDocking:lowres_abinitio"

)

lowres_preoptimize()

BooleanOptionKey const flexPepDocking::lowres_preoptimize

(

"flexPepDocking:lowres_preoptimize"

)

mcm_cycles()

IntegerOptionKey const flexPepDocking::mcm_cycles

(

"flexPepDocking:mcm_cycles"

)

min_receptor_bb()

BooleanOptionKey const flexPepDocking::min_receptor_bb

(

"flexPepDocking:min_receptor_bb"

)

params_file()

StringOptionKey const flexPepDocking::params_file

(

"flexPepDocking:params_file"

)

pep_fold_only()

BooleanOptionKey const flexPepDocking::pep_fold_only

(

"flexPepDocking:pep_fold_only"

)

pep_refine()

BooleanOptionKey const flexPepDocking::pep_refine

(

"flexPepDocking:pep_refine"

)

peptide_anchor()

IntegerOptionKey const flexPepDocking::peptide_anchor

(

"flexPepDocking:peptide_anchor"

)

peptide_chain()

StringOptionKey const flexPepDocking::peptide_chain

(

"flexPepDocking:peptide_chain"

)

peptide_loop_model()

BooleanOptionKey const flexPepDocking::peptide_loop_model

(

"flexPepDocking:peptide_loop_model"

)

place_peptide_on_binding_site()

BooleanOptionKey const flexPepDocking::place_peptide_on_binding_site

(

"flexPepDocking:place_peptide_on_binding_site"

)

pSer2Asp_centroid()

BooleanOptionKey const flexPepDocking::pSer2Asp_centroid

(

"flexPepDocking:pSer2Asp_centroid"

)

pSer2Glu_centroid()

BooleanOptionKey const flexPepDocking::pSer2Glu_centroid

(

"flexPepDocking:pSer2Glu_centroid"

)

ramp_fa_rep()

BooleanOptionKey const flexPepDocking::ramp_fa_rep

(

"flexPepDocking:ramp_fa_rep"

)

ramp_rama()

BooleanOptionKey const flexPepDocking::ramp_rama

(

"flexPepDocking:ramp_rama"

)

random_phi_psi_preturbation()

RealOptionKey const flexPepDocking::random_phi_psi_preturbation

(

"flexPepDocking:random_phi_psi_preturbation"

)

random_rot_start()

RealOptionKey const flexPepDocking::random_rot_start

(

"flexPepDocking:random_rot_start"

)

random_trans_start()

RealOptionKey const flexPepDocking::random_trans_start

(

"flexPepDocking:random_trans_start"

)

rbMCM()

BooleanOptionKey const flexPepDocking::rbMCM

(

"flexPepDocking:rbMCM"

)

recalculate_foldtree()

BooleanOptionKey const flexPepDocking::recalculate_foldtree

(

"flexPepDocking:recalculate_foldtree"

)

receptor_chain()

StringOptionKey const flexPepDocking::receptor_chain

(

"flexPepDocking:receptor_chain"

)

ref_startstruct()

FileOptionKey const flexPepDocking::ref_startstruct

(

"flexPepDocking:ref_startstruct"

)

rep_ramp_cycles()

IntegerOptionKey const flexPepDocking::rep_ramp_cycles

(

"flexPepDocking:rep_ramp_cycles"

)

sample_pcs()

IntegerOptionKey const flexPepDocking::sample_pcs

(

"flexPepDocking:sample_pcs"

)

score_filter()

RealOptionKey const flexPepDocking::score_filter

(

"flexPepDocking:score_filter"

)

SlideIntoContact()

BooleanOptionKey const flexPepDocking::SlideIntoContact

(

"flexPepDocking:SlideIntoContact"

)

smove_angle_range()

RealOptionKey const flexPepDocking::smove_angle_range

(

"flexPepDocking:smove_angle_range"

)

torsionsMCM()

BooleanOptionKey const flexPepDocking::torsionsMCM

(

"flexPepDocking:torsionsMCM"

)

use_cen_score()

BooleanOptionKey const flexPepDocking::use_cen_score

(

"flexPepDocking:use_cen_score"

)