remodel Namespace Reference

Namespaces
	design
	domainFusion
	RemodelLoopMover
	staged_sampling

Functions
BooleanOptionKey const	remodel ("remodel")
FileOptionKey const	blueprint ("remodel:blueprint")
FileOptionKey const	cstfile ("remodel:cstfile")
BooleanOptionKey const	cst_fa_only ("remodel:cst_fa_only")
IntegerOptionKey const	cstfilter ("remodel:cstfilter")
StringOptionKey const	cen_sfxn ("remodel:cen_sfxn")
BooleanOptionKey const	check_scored_centroid ("remodel:check_scored_centroid")
IntegerOptionKey const	num_trajectory ("remodel:num_trajectory")
IntegerOptionKey const	save_top ("remodel:save_top")
BooleanOptionKey const	swap_refine_confirm_protocols ("remodel:swap_refine_confirm_protocols")
BooleanOptionKey const	bypass_fragments ("remodel:bypass_fragments")
BooleanOptionKey const	use_same_length_fragments ("remodel:use_same_length_fragments")
BooleanOptionKey const	no_jumps ("remodel:no_jumps")
IntegerOptionKey const	reroot_tree ("remodel:reroot_tree")
BooleanOptionKey const	use_blueprint_sequence ("remodel:use_blueprint_sequence ")
BooleanOptionKey const	quick_and_dirty ("remodel:quick_and_dirty ")
BooleanOptionKey const	checkpoint ("remodel:checkpoint ")
BooleanOptionKey const	use_pose_relax ("remodel:use_pose_relax ")
BooleanOptionKey const	use_cart_relax ("remodel:use_cart_relax ")
BooleanOptionKey const	free_relax ("remodel:free_relax ")
StringOptionKey const	generic_aa ("remodel:generic_aa")
RealOptionKey const	cluster_radius ("remodel:cluster_radius")
BooleanOptionKey const	use_clusters ("remodel:use_clusters")
BooleanOptionKey const	run_confirmation ("remodel:run_confirmation")
BooleanOptionKey const	cluster_on_entire_pose ("remodel:cluster_on_entire_pose")
IntegerOptionKey const	dr_cycles ("remodel:dr_cycles")
IntegerOptionKey const	two_chain_tree ("remodel:two_chain_tree")
IntegerOptionKey const	repeat_structure ("remodel:repeat_structure")
IntegerOptionKey const	lh_ex_limit ("remodel:lh_ex_limit")
StringVectorOptionKey const	lh_filter_string ("remodel:lh_filter_string")
IntegerOptionKey const	lh_cbreak_selection ("remodel:lh_cbreak_selection")
BooleanOptionKey const	lh_closure_filter ("remodel:lh_closure_filter")
BooleanOptionKey const	cen_minimize ("remodel:cen_minimize")
IntegerOptionKey const	core_cutoff ("remodel:core_cutoff")
IntegerOptionKey const	boundary_cutoff ("remodel:boundary_cutoff")
StringOptionKey const	coreAA ("remodel:coreAA")
StringOptionKey const	boundaryAA ("remodel:boundaryAA")
StringOptionKey const	surfaceAA ("remodel:surfaceAA")
BooleanOptionKey const	design_around_ligand ("remodel:design_around_ligand")
BooleanOptionKey const	move_ligand ("remodel:move_ligand")
BooleanOptionKey const	resclass_by_sasa ("remodel:resclass_by_sasa")
RealOptionKey const	helical_rise ("remodel:helical_rise")
RealOptionKey const	helical_radius ("remodel:helical_radius")
RealOptionKey const	helical_omega ("remodel:helical_omega")
RealVectorOptionKey const	filter_rise ("remodel:filter_rise")
RealVectorOptionKey const	filter_radius ("remodel:filter_radius")
RealVectorOptionKey const	filter_omega ("remodel:filter_omega")
RealOptionKey const	COM_sd ("remodel:COM_sd")
RealOptionKey const	COM_tolerance ("remodel:COM_tolerance")
RealOptionKey const	vdw ("remodel:vdw")
RealOptionKey const	rama ("remodel:rama")
RealOptionKey const	cbeta ("remodel:cbeta")
RealOptionKey const	cenpack ("remodel:cenpack")
RealOptionKey const	rg_local ("remodel:rg_local")
RealOptionKey const	hb_lrbb ("remodel:hb_lrbb")
RealOptionKey const	hb_srbb ("remodel:hb_srbb")
RealOptionKey const	rg ("remodel:rg")
RealOptionKey const	rsigma ("remodel:rsigma")
RealOptionKey const	ss_pair ("remodel:ss_pair")
BooleanOptionKey const	build_disulf ("remodel:build_disulf")
RealOptionKey const	match_rt_limit ("remodel:match_rt_limit")
IntegerVectorOptionKey const	disulf_landing_range ("remodel:disulf_landing_range")
BooleanOptionKey const	rank_by_bsasa ("remodel:rank_by_bsasa")

Function Documentation

FileOptionKey const remodel::blueprint

(

"remodel:blueprint"

)

IntegerOptionKey const remodel::boundary_cutoff

(

"remodel:boundary_cutoff"

)

StringOptionKey const remodel::boundaryAA

(

"remodel:boundaryAA"

)

BooleanOptionKey const remodel::build_disulf

(

"remodel:build_disulf"

)

BooleanOptionKey const remodel::bypass_fragments

(

"remodel:bypass_fragments"

)

RealOptionKey const remodel::cbeta

(

"remodel:cbeta"

)

BooleanOptionKey const remodel::cen_minimize

(

"remodel:cen_minimize"

)

StringOptionKey const remodel::cen_sfxn

(

"remodel:cen_sfxn"

)

RealOptionKey const remodel::cenpack

(

"remodel:cenpack"

)

BooleanOptionKey const remodel::check_scored_centroid

(

"remodel:check_scored_centroid"

)

BooleanOptionKey const remodel::checkpoint

(

"remodel:checkpoint "

)

BooleanOptionKey const remodel::cluster_on_entire_pose

(

"remodel:cluster_on_entire_pose"

)

RealOptionKey const remodel::cluster_radius

(

"remodel:cluster_radius"

)

RealOptionKey const remodel::COM_sd

(

"remodel:COM_sd"

)

RealOptionKey const remodel::COM_tolerance

(

"remodel:COM_tolerance"

)

IntegerOptionKey const remodel::core_cutoff

(

"remodel:core_cutoff"

)

StringOptionKey const remodel::coreAA

(

"remodel:coreAA"

)

BooleanOptionKey const remodel::cst_fa_only

(

"remodel:cst_fa_only"

)

FileOptionKey const remodel::cstfile

(

"remodel:cstfile"

)

IntegerOptionKey const remodel::cstfilter

(

"remodel:cstfilter"

)

BooleanOptionKey const remodel::design_around_ligand

(

"remodel:design_around_ligand"

)

IntegerVectorOptionKey const remodel::disulf_landing_range

(

"remodel:disulf_landing_range"

)

IntegerOptionKey const remodel::dr_cycles

(

"remodel:dr_cycles"

)

RealVectorOptionKey const remodel::filter_omega

(

"remodel:filter_omega"

)

RealVectorOptionKey const remodel::filter_radius

(

"remodel:filter_radius"

)

RealVectorOptionKey const remodel::filter_rise

(

"remodel:filter_rise"

)

BooleanOptionKey const remodel::free_relax

(

"remodel:free_relax "

)

StringOptionKey const remodel::generic_aa

(

"remodel:generic_aa"

)

RealOptionKey const remodel::hb_lrbb

(

"remodel:hb_lrbb"

)

RealOptionKey const remodel::hb_srbb

(

"remodel:hb_srbb"

)

RealOptionKey const remodel::helical_omega

(

"remodel:helical_omega"

)

RealOptionKey const remodel::helical_radius

(

"remodel:helical_radius"

)

RealOptionKey const remodel::helical_rise

(

"remodel:helical_rise"

)

IntegerOptionKey const remodel::lh_cbreak_selection

(

"remodel:lh_cbreak_selection"

)

BooleanOptionKey const remodel::lh_closure_filter

(

"remodel:lh_closure_filter"

)

IntegerOptionKey const remodel::lh_ex_limit

(

"remodel:lh_ex_limit"

)

StringVectorOptionKey const remodel::lh_filter_string

(

"remodel:lh_filter_string"

)

RealOptionKey const remodel::match_rt_limit

(

"remodel:match_rt_limit"

)

BooleanOptionKey const remodel::move_ligand

(

"remodel:move_ligand"

)

BooleanOptionKey const remodel::no_jumps

(

"remodel:no_jumps"

)

IntegerOptionKey const remodel::num_trajectory

(

"remodel:num_trajectory"

)

BooleanOptionKey const remodel::quick_and_dirty

(

"remodel:quick_and_dirty "

)

RealOptionKey const remodel::rama

(

"remodel:rama"

)

BooleanOptionKey const remodel::rank_by_bsasa

(

"remodel:rank_by_bsasa"

)

BooleanOptionKey const remodel::remodel

(

"remodel"

)

IntegerOptionKey const remodel::repeat_structure

(

"remodel:repeat_structure"

)

IntegerOptionKey const remodel::reroot_tree

(

"remodel:reroot_tree"

)

BooleanOptionKey const remodel::resclass_by_sasa

(

"remodel:resclass_by_sasa"

)

RealOptionKey const remodel::rg

(

"remodel:rg"

)

RealOptionKey const remodel::rg_local

(

"remodel:rg_local"

)

RealOptionKey const remodel::rsigma

(

"remodel:rsigma"

)

BooleanOptionKey const remodel::run_confirmation

(

"remodel:run_confirmation"

)

IntegerOptionKey const remodel::save_top

(

"remodel:save_top"

)

RealOptionKey const remodel::ss_pair

(

"remodel:ss_pair"

)

StringOptionKey const remodel::surfaceAA

(

"remodel:surfaceAA"

)

BooleanOptionKey const remodel::swap_refine_confirm_protocols

(

"remodel:swap_refine_confirm_protocols"

)

IntegerOptionKey const remodel::two_chain_tree

(

"remodel:two_chain_tree"

)

BooleanOptionKey const remodel::use_blueprint_sequence

(

"remodel:use_blueprint_sequence "

)

BooleanOptionKey const remodel::use_cart_relax

(

"remodel:use_cart_relax "

)

BooleanOptionKey const remodel::use_clusters

(

"remodel:use_clusters"

)

BooleanOptionKey const remodel::use_pose_relax

(

"remodel:use_pose_relax "

)

BooleanOptionKey const remodel::use_same_length_fragments

(

"remodel:use_same_length_fragments"

)

RealOptionKey const remodel::vdw

(

"remodel:vdw"

)