dna::specificity Namespace Reference

Functions
BooleanOptionKey const	specificity ("dna:specificity")
BooleanOptionKey const	exclude_dna_dna ("dna:specificity:exclude_dna_dna")
RealVectorOptionKey const	params ("dna:specificity:params")
FileVectorOptionKey const	frag_files ("dna:specificity:frag_files")
BooleanOptionKey const	only_repack ("dna:specificity:only_repack")
BooleanOptionKey const	design_DNA ("dna:specificity:design_DNA")
BooleanOptionKey const	soft_rep ("dna:specificity:soft_rep")
BooleanOptionKey const	dump_pdbs ("dna:specificity:dump_pdbs")
BooleanOptionKey const	fast ("dna:specificity:fast")
BooleanOptionKey const	randomize_motif ("dna:specificity:randomize_motif")
RealOptionKey const	Wfa_elec ("dna:specificity:Wfa_elec")
RealOptionKey const	Wdna_bs ("dna:specificity:Wdna_bs")
RealOptionKey const	Wdna_bp ("dna:specificity:Wdna_bp")
RealOptionKey const	minimize_tolerance ("dna:specificity:minimize_tolerance")
StringOptionKey const	weights_tag ("dna:specificity:weights_tag")
StringOptionKey const	weights_tag_list ("dna:specificity:weights_tag_list")
StringOptionKey const	min_type ("dna:specificity:min_type")
StringOptionKey const	mode ("dna:specificity:mode")
StringOptionKey const	score_function ("dna:specificity:score_function")
BooleanOptionKey const	pre_minimize ("dna:specificity:pre_minimize")
BooleanOptionKey const	post_minimize ("dna:specificity:post_minimize")
BooleanOptionKey const	pre_pack ("dna:specificity:pre_pack")
IntegerOptionKey const	nloop ("dna:specificity:nloop")
IntegerOptionKey const	n_inner ("dna:specificity:n_inner")
IntegerOptionKey const	n_outer ("dna:specificity:n_outer")
IntegerOptionKey const	nstep_water ("dna:specificity:nstep_water")
IntegerOptionKey const	moving_jump ("dna:specificity:moving_jump")
IntegerOptionKey const	motif_begin ("dna:specificity:motif_begin")
IntegerOptionKey const	motif_size ("dna:specificity:motif_size")
StringVectorOptionKey const	pdb_pos ("dna:specificity:pdb_pos")
StringVectorOptionKey const	methylate ("dna:specificity:methylate")
RealVectorOptionKey const	dna_backbone_torsion_sdevs ("dna:specificity:dna_backbone_torsion_sdevs")
RealOptionKey const	dna_sugar_torsion_sdev ("dna:specificity:dna_sugar_torsion_sdev")
RealOptionKey const	dna_chi_torsion_sdev ("dna:specificity:dna_chi_torsion_sdev")
StringOptionKey const	lk_ball_wtd_tag ("dna:specificity:lk_ball_wtd_tag")
BooleanOptionKey const	lk_ball_for_bb ("dna:specificity:lk_ball_for_bb")
RealOptionKey const	lk_ball_ramp_width_A2 ("dna:specificity:lk_ball_ramp_width_A2")
RealOptionKey const	lk_ball_overlap_gap ("dna:specificity:lk_ball_overlap_gap")
RealOptionKey const	lk_ball_overlap_width_A2 ("dna:specificity:lk_ball_overlap_width_A2")
RealOptionKey const	lk_ball_water_fade ("dna:specificity:lk_ball_water_fade")
RealVectorOptionKey const	lk_ball_wtd_prefactors ("dna:specificity:lk_ball_wtd_prefactors")
RealVectorOptionKey const	lk_ball_waters_sp2 ("dna:specificity:lk_ball_waters_sp2")
RealVectorOptionKey const	lk_ball_waters_sp3 ("dna:specificity:lk_ball_waters_sp3")
RealVectorOptionKey const	lk_ball_waters_ring ("dna:specificity:lk_ball_waters_ring")
RealOptionKey const	lk_ball_waters_donor ("dna:specificity:lk_ball_waters_donor")
RealOptionKey const	lk_ball_bridge_angle_widthscale ("dna:specificity:lk_ball_bridge_angle_widthscale")
RealOptionKey const	lk_dome_max_angle ("dna:specificity:lk_dome_max_angle")
RealOptionKey const	lk_dome_min_angle ("dna:specificity:lk_dome_min_angle")
RealOptionKey const	lk_dome_occlusion_min ("dna:specificity:lk_dome_occlusion_min")
RealOptionKey const	lk_dome_occlusion_max ("dna:specificity:lk_dome_occlusion_max")
RealOptionKey const	lk_dome_h2o_radius ("dna:specificity:lk_dome_h2o_radius")
RealOptionKey const	lk_dome_ramp_width_A2 ("dna:specificity:lk_dome_ramp_width_A2")
RealOptionKey const	lk_dome_overlap_width_A2 ("dna:specificity:lk_dome_overlap_width_A2")
RealOptionKey const	lk_dome_ball_overlap_width_A2 ("dna:specificity:lk_dome_ball_overlap_width_A2")
RealOptionKey const	lk_dome_water_dist ("dna:specificity:lk_dome_water_dist")
RealOptionKey const	lk_dome_water_adjust ("dna:specificity:lk_dome_water_adjust")

Function Documentation

design_DNA()

BooleanOptionKey const dna::specificity::design_DNA

(

"dna:specificity:design_DNA"

)

References dna::design::specificity::specificity().

dna_backbone_torsion_sdevs()

RealVectorOptionKey const dna::specificity::dna_backbone_torsion_sdevs

(

"dna:specificity:dna_backbone_torsion_sdevs"

)

References dna::design::specificity::specificity().

dna_chi_torsion_sdev()

RealOptionKey const dna::specificity::dna_chi_torsion_sdev

(

"dna:specificity:dna_chi_torsion_sdev"

)

References dna::design::specificity::specificity().

dna_sugar_torsion_sdev()

RealOptionKey const dna::specificity::dna_sugar_torsion_sdev

(

"dna:specificity:dna_sugar_torsion_sdev"

)

References dna::design::specificity::specificity().

dump_pdbs()

BooleanOptionKey const dna::specificity::dump_pdbs

(

"dna:specificity:dump_pdbs"

)

References dna::design::specificity::specificity().

exclude_dna_dna()

BooleanOptionKey const dna::specificity::exclude_dna_dna

(

"dna:specificity:exclude_dna_dna"

)

References dna::design::specificity::specificity().

fast()

BooleanOptionKey const dna::specificity::fast

(

"dna:specificity:fast"

)

References dna::design::specificity::specificity().

frag_files()

FileVectorOptionKey const dna::specificity::frag_files

(

"dna:specificity:frag_files"

)

References dna::design::specificity::specificity().

lk_ball_bridge_angle_widthscale()

RealOptionKey const dna::specificity::lk_ball_bridge_angle_widthscale

(

"dna:specificity:lk_ball_bridge_angle_widthscale"

)

References dna::design::specificity::specificity().

lk_ball_for_bb()

BooleanOptionKey const dna::specificity::lk_ball_for_bb

(

"dna:specificity:lk_ball_for_bb"

)

References dna::design::specificity::specificity().

lk_ball_overlap_gap()

RealOptionKey const dna::specificity::lk_ball_overlap_gap

(

"dna:specificity:lk_ball_overlap_gap"

)

References dna::design::specificity::specificity().

lk_ball_overlap_width_A2()

RealOptionKey const dna::specificity::lk_ball_overlap_width_A2

(

"dna:specificity:lk_ball_overlap_width_A2"

)

References dna::design::specificity::specificity().

lk_ball_ramp_width_A2()

RealOptionKey const dna::specificity::lk_ball_ramp_width_A2

(

"dna:specificity:lk_ball_ramp_width_A2"

)

References dna::design::specificity::specificity().

lk_ball_water_fade()

RealOptionKey const dna::specificity::lk_ball_water_fade

(

"dna:specificity:lk_ball_water_fade"

)

References dna::design::specificity::specificity().

lk_ball_waters_donor()

RealOptionKey const dna::specificity::lk_ball_waters_donor

(

"dna:specificity:lk_ball_waters_donor"

)

References dna::design::specificity::specificity().

lk_ball_waters_ring()

RealVectorOptionKey const dna::specificity::lk_ball_waters_ring

(

"dna:specificity:lk_ball_waters_ring"

)

References dna::design::specificity::specificity().

lk_ball_waters_sp2()

RealVectorOptionKey const dna::specificity::lk_ball_waters_sp2

(

"dna:specificity:lk_ball_waters_sp2"

)

References dna::design::specificity::specificity().

lk_ball_waters_sp3()

RealVectorOptionKey const dna::specificity::lk_ball_waters_sp3

(

"dna:specificity:lk_ball_waters_sp3"

)

References dna::design::specificity::specificity().

lk_ball_wtd_prefactors()

RealVectorOptionKey const dna::specificity::lk_ball_wtd_prefactors

(

"dna:specificity:lk_ball_wtd_prefactors"

)

References dna::design::specificity::specificity().

lk_ball_wtd_tag()

StringOptionKey const dna::specificity::lk_ball_wtd_tag

(

"dna:specificity:lk_ball_wtd_tag"

)

References dna::design::specificity::specificity().

lk_dome_ball_overlap_width_A2()

RealOptionKey const dna::specificity::lk_dome_ball_overlap_width_A2

(

"dna:specificity:lk_dome_ball_overlap_width_A2"

)

References dna::design::specificity::specificity().

lk_dome_h2o_radius()

RealOptionKey const dna::specificity::lk_dome_h2o_radius

(

"dna:specificity:lk_dome_h2o_radius"

)

References dna::design::specificity::specificity().

lk_dome_max_angle()

RealOptionKey const dna::specificity::lk_dome_max_angle

(

"dna:specificity:lk_dome_max_angle"

)

References dna::design::specificity::specificity().

lk_dome_min_angle()

RealOptionKey const dna::specificity::lk_dome_min_angle

(

"dna:specificity:lk_dome_min_angle"

)

References dna::design::specificity::specificity().

lk_dome_occlusion_max()

RealOptionKey const dna::specificity::lk_dome_occlusion_max

(

"dna:specificity:lk_dome_occlusion_max"

)

References dna::design::specificity::specificity().

lk_dome_occlusion_min()

RealOptionKey const dna::specificity::lk_dome_occlusion_min

(

"dna:specificity:lk_dome_occlusion_min"

)

References dna::design::specificity::specificity().

lk_dome_overlap_width_A2()

RealOptionKey const dna::specificity::lk_dome_overlap_width_A2

(

"dna:specificity:lk_dome_overlap_width_A2"

)

References dna::design::specificity::specificity().

lk_dome_ramp_width_A2()

RealOptionKey const dna::specificity::lk_dome_ramp_width_A2

(

"dna:specificity:lk_dome_ramp_width_A2"

)

References dna::design::specificity::specificity().

lk_dome_water_adjust()

RealOptionKey const dna::specificity::lk_dome_water_adjust

(

"dna:specificity:lk_dome_water_adjust"

)

References dna::design::specificity::specificity().

lk_dome_water_dist()

RealOptionKey const dna::specificity::lk_dome_water_dist

(

"dna:specificity:lk_dome_water_dist"

)

References dna::design::specificity::specificity().

methylate()

StringVectorOptionKey const dna::specificity::methylate

(

"dna:specificity:methylate"

)

References dna::design::specificity::specificity().

min_type()

StringOptionKey const dna::specificity::min_type

(

"dna:specificity:min_type"

)

References dna::design::specificity::specificity().

minimize_tolerance()

RealOptionKey const dna::specificity::minimize_tolerance

(

"dna:specificity:minimize_tolerance"

)

References dna::design::specificity::specificity().

mode()

StringOptionKey const dna::specificity::mode

(

"dna:specificity:mode"

)

References dna::design::specificity::specificity().

Referenced by my_main().

motif_begin()

IntegerOptionKey const dna::specificity::motif_begin

(

"dna:specificity:motif_begin"

)

References dna::design::specificity::specificity().

motif_size()

IntegerOptionKey const dna::specificity::motif_size

(

"dna:specificity:motif_size"

)

References dna::design::specificity::specificity().

moving_jump()

IntegerOptionKey const dna::specificity::moving_jump

(

"dna:specificity:moving_jump"

)

References dna::design::specificity::specificity().

n_inner()

IntegerOptionKey const dna::specificity::n_inner

(

"dna:specificity:n_inner"

)

References dna::design::specificity::specificity().

n_outer()

IntegerOptionKey const dna::specificity::n_outer

(

"dna:specificity:n_outer"

)

References dna::design::specificity::specificity().

nloop()

IntegerOptionKey const dna::specificity::nloop

(

"dna:specificity:nloop"

)

References dna::design::specificity::specificity().

nstep_water()

IntegerOptionKey const dna::specificity::nstep_water

(

"dna:specificity:nstep_water"

)

References dna::design::specificity::specificity().

only_repack()

BooleanOptionKey const dna::specificity::only_repack

(

"dna:specificity:only_repack"

)

References dna::design::specificity::specificity().

params()

RealVectorOptionKey const dna::specificity::params

(

"dna:specificity:params"

)

References dna::design::specificity::specificity().

pdb_pos()

StringVectorOptionKey const dna::specificity::pdb_pos

(

"dna:specificity:pdb_pos"

)

References dna::design::specificity::specificity().

post_minimize()

BooleanOptionKey const dna::specificity::post_minimize

(

"dna:specificity:post_minimize"

)

References dna::design::specificity::specificity().

pre_minimize()

BooleanOptionKey const dna::specificity::pre_minimize

(

"dna:specificity:pre_minimize"

)

References dna::design::specificity::specificity().

pre_pack()

BooleanOptionKey const dna::specificity::pre_pack

(

"dna:specificity:pre_pack"

)

References dna::design::specificity::specificity().

randomize_motif()

BooleanOptionKey const dna::specificity::randomize_motif

(

"dna:specificity:randomize_motif"

)

References dna::design::specificity::specificity().

score_function()

StringOptionKey const dna::specificity::score_function

(

"dna:specificity:score_function"

)

References dna::design::specificity::specificity().

soft_rep()

BooleanOptionKey const dna::specificity::soft_rep

(

"dna:specificity:soft_rep"

)

References dna::design::specificity::specificity().

specificity()

BooleanOptionKey const dna::specificity::specificity

(

"dna:specificity"

)

References dna::design::specificity::specificity().

Wdna_bp()

RealOptionKey const dna::specificity::Wdna_bp

(

"dna:specificity:Wdna_bp"

)

References dna::design::specificity::specificity().

Wdna_bs()

RealOptionKey const dna::specificity::Wdna_bs

(

"dna:specificity:Wdna_bs"

)

References dna::design::specificity::specificity().

weights_tag()

StringOptionKey const dna::specificity::weights_tag

(

"dna:specificity:weights_tag"

)

References dna::design::specificity::specificity().

weights_tag_list()

StringOptionKey const dna::specificity::weights_tag_list

(

"dna:specificity:weights_tag_list"

)

References dna::design::specificity::specificity().

Wfa_elec()

RealOptionKey const dna::specificity::Wfa_elec

(

"dna:specificity:Wfa_elec"

)

References dna::design::specificity::specificity().