basic::options::OptionKeys::antibody Namespace Reference

Namespaces
	design

Variables
BooleanOptionKey const	antibody
StringOptionKey const	input_ab_scheme
StringOptionKey const	output_ab_scheme
StringOptionKey const	cdr_definition
StringOptionKey const	light_chain
BooleanOptionKey const	check_cdr_chainbreaks
BooleanOptionKey const	check_cdr_pep_bond_geom
BooleanOptionKey const	constrain_cter
BooleanOptionKey const	auto_generate_kink_constraint
BooleanOptionKey const	all_atom_mode_kink_constraint
StringOptionKey const	numbering_scheme
BooleanOptionKey const	graft_l1
StringOptionKey const	l1_template
BooleanOptionKey const	graft_l2
StringOptionKey const	l2_template
BooleanOptionKey const	graft_l3
StringOptionKey const	l3_template
BooleanOptionKey const	graft_h1
StringOptionKey const	h1_template
BooleanOptionKey const	graft_h2
StringOptionKey const	h2_template
BooleanOptionKey const	graft_h3
StringOptionKey const	h3_template
StringOptionKey const	light_heavy_template
StringOptionKey const	frl_template
StringOptionKey const	frh_template
BooleanOptionKey const	run_snugdock
BooleanOptionKey const	h3_no_stem_graft
BooleanOptionKey const	packonly_after_graft
BooleanOptionKey const	stem_optimize
IntegerOptionKey const	stem_optimize_size
StringOptionKey const	preprocessing_script_version
BooleanOptionKey const	model_h3
BooleanOptionKey const	snugfit
BooleanOptionKey const	refine_h3
BooleanOptionKey const	h3_filter
RealOptionKey const	h3_filter_tolerance
BooleanOptionKey const	sc_min
BooleanOptionKey const	rt_min
BooleanOptionKey const	extend_h3_before_modeling
StringOptionKey const	centroid_refine
BooleanOptionKey const	h3_loop_csts_lr
BooleanOptionKey const	h3_loop_csts_hr
BooleanOptionKey const	auto_generate_h3_kink_constraint
BooleanOptionKey const	constrain_vlvh_qq
BooleanOptionKey const	snug_loops
FileOptionKey const	input_fv
BooleanOptionKey const	camelid
BooleanOptionKey const	camelid_constraints
BooleanOptionKey const	use_mean_cluster_cst_data
BooleanOptionKey const	force_use_of_cluster_csts_with_outliers
IntegerOptionKey const	cluster_csts_stats_cutoff
RealOptionKey const	general_dihedral_cst_phi_sd
RealOptionKey const	general_dihedral_cst_psi_sd
BooleanOptionKey const	allow_omega_mismatches_for_north_clusters
StringOptionKey const	prefix
StringOptionKey const	grafting_database
StringOptionKey const	blastp
StringVectorOptionKey const	exclude_pdbs
BooleanOptionKey const	exclude_homologs
RealOptionKey const	exclude_homologs_cdr_cutoff
RealOptionKey const	exclude_homologs_fr_cutoff
RealOptionKey const	ocd_cutoff
RealOptionKey const	bfactor_cutoff
IntegerOptionKey const	n_multi_templates
StringOptionKey const	json_cdr

Variable Documentation

all_atom_mode_kink_constraint

BooleanOptionKey const basic::options::OptionKeys::antibody::all_atom_mode_kink_constraint

extern

allow_omega_mismatches_for_north_clusters

BooleanOptionKey const basic::options::OptionKeys::antibody::allow_omega_mismatches_for_north_clusters

extern

antibody

BooleanOptionKey const basic::options::OptionKeys::antibody::antibody

extern

auto_generate_h3_kink_constraint

BooleanOptionKey const basic::options::OptionKeys::antibody::auto_generate_h3_kink_constraint

extern

auto_generate_kink_constraint

BooleanOptionKey const basic::options::OptionKeys::antibody::auto_generate_kink_constraint

extern

bfactor_cutoff

RealOptionKey const basic::options::OptionKeys::antibody::bfactor_cutoff

extern

blastp

StringOptionKey const basic::options::OptionKeys::antibody::blastp

extern

camelid

BooleanOptionKey const basic::options::OptionKeys::antibody::camelid

extern

camelid_constraints

BooleanOptionKey const basic::options::OptionKeys::antibody::camelid_constraints

extern

cdr_definition

StringOptionKey const basic::options::OptionKeys::antibody::cdr_definition

extern

centroid_refine

StringOptionKey const basic::options::OptionKeys::antibody::centroid_refine

extern

check_cdr_chainbreaks

BooleanOptionKey const basic::options::OptionKeys::antibody::check_cdr_chainbreaks

extern

check_cdr_pep_bond_geom

BooleanOptionKey const basic::options::OptionKeys::antibody::check_cdr_pep_bond_geom

extern

cluster_csts_stats_cutoff

IntegerOptionKey const basic::options::OptionKeys::antibody::cluster_csts_stats_cutoff

extern

constrain_cter

BooleanOptionKey const basic::options::OptionKeys::antibody::constrain_cter

extern

constrain_vlvh_qq

BooleanOptionKey const basic::options::OptionKeys::antibody::constrain_vlvh_qq

extern

exclude_homologs

BooleanOptionKey const basic::options::OptionKeys::antibody::exclude_homologs

extern

exclude_homologs_cdr_cutoff

RealOptionKey const basic::options::OptionKeys::antibody::exclude_homologs_cdr_cutoff

extern

exclude_homologs_fr_cutoff

RealOptionKey const basic::options::OptionKeys::antibody::exclude_homologs_fr_cutoff

extern

exclude_pdbs

StringVectorOptionKey const basic::options::OptionKeys::antibody::exclude_pdbs

extern

extend_h3_before_modeling

BooleanOptionKey const basic::options::OptionKeys::antibody::extend_h3_before_modeling

extern

force_use_of_cluster_csts_with_outliers

BooleanOptionKey const basic::options::OptionKeys::antibody::force_use_of_cluster_csts_with_outliers

extern

frh_template

StringOptionKey const basic::options::OptionKeys::antibody::frh_template

extern

frl_template

StringOptionKey const basic::options::OptionKeys::antibody::frl_template

extern

general_dihedral_cst_phi_sd

RealOptionKey const basic::options::OptionKeys::antibody::general_dihedral_cst_phi_sd

extern

general_dihedral_cst_psi_sd

RealOptionKey const basic::options::OptionKeys::antibody::general_dihedral_cst_psi_sd

extern

graft_h1

BooleanOptionKey const basic::options::OptionKeys::antibody::graft_h1

extern

graft_h2

BooleanOptionKey const basic::options::OptionKeys::antibody::graft_h2

extern

graft_h3

BooleanOptionKey const basic::options::OptionKeys::antibody::graft_h3

extern

graft_l1

BooleanOptionKey const basic::options::OptionKeys::antibody::graft_l1

extern

graft_l2

BooleanOptionKey const basic::options::OptionKeys::antibody::graft_l2

extern

graft_l3

BooleanOptionKey const basic::options::OptionKeys::antibody::graft_l3

extern

grafting_database

StringOptionKey const basic::options::OptionKeys::antibody::grafting_database

extern

h1_template

StringOptionKey const basic::options::OptionKeys::antibody::h1_template

extern

h2_template

StringOptionKey const basic::options::OptionKeys::antibody::h2_template

extern

h3_filter

BooleanOptionKey const basic::options::OptionKeys::antibody::h3_filter

extern

h3_filter_tolerance

RealOptionKey const basic::options::OptionKeys::antibody::h3_filter_tolerance

extern

h3_loop_csts_hr

BooleanOptionKey const basic::options::OptionKeys::antibody::h3_loop_csts_hr

extern

h3_loop_csts_lr

BooleanOptionKey const basic::options::OptionKeys::antibody::h3_loop_csts_lr

extern

h3_no_stem_graft

BooleanOptionKey const basic::options::OptionKeys::antibody::h3_no_stem_graft

extern

h3_template

StringOptionKey const basic::options::OptionKeys::antibody::h3_template

extern

input_ab_scheme

StringOptionKey const basic::options::OptionKeys::antibody::input_ab_scheme

extern

input_fv

FileOptionKey const basic::options::OptionKeys::antibody::input_fv

extern

json_cdr

StringOptionKey const basic::options::OptionKeys::antibody::json_cdr

extern

l1_template

StringOptionKey const basic::options::OptionKeys::antibody::l1_template

extern

l2_template

StringOptionKey const basic::options::OptionKeys::antibody::l2_template

extern

l3_template

StringOptionKey const basic::options::OptionKeys::antibody::l3_template

extern

light_chain

StringOptionKey const basic::options::OptionKeys::antibody::light_chain

extern

light_heavy_template

StringOptionKey const basic::options::OptionKeys::antibody::light_heavy_template

extern

model_h3

BooleanOptionKey const basic::options::OptionKeys::antibody::model_h3

extern

n_multi_templates

IntegerOptionKey const basic::options::OptionKeys::antibody::n_multi_templates

extern

numbering_scheme

StringOptionKey const basic::options::OptionKeys::antibody::numbering_scheme

extern

ocd_cutoff

RealOptionKey const basic::options::OptionKeys::antibody::ocd_cutoff

extern

output_ab_scheme

StringOptionKey const basic::options::OptionKeys::antibody::output_ab_scheme

extern

Referenced by IdentifyCDRClusters::apply().

packonly_after_graft

BooleanOptionKey const basic::options::OptionKeys::antibody::packonly_after_graft

extern

prefix

StringOptionKey const basic::options::OptionKeys::antibody::prefix

extern

preprocessing_script_version

StringOptionKey const basic::options::OptionKeys::antibody::preprocessing_script_version

extern

refine_h3

BooleanOptionKey const basic::options::OptionKeys::antibody::refine_h3

extern

rt_min

BooleanOptionKey const basic::options::OptionKeys::antibody::rt_min

extern

run_snugdock

BooleanOptionKey const basic::options::OptionKeys::antibody::run_snugdock

extern

sc_min

BooleanOptionKey const basic::options::OptionKeys::antibody::sc_min

extern

snug_loops

BooleanOptionKey const basic::options::OptionKeys::antibody::snug_loops

extern

snugfit

BooleanOptionKey const basic::options::OptionKeys::antibody::snugfit

extern

stem_optimize

BooleanOptionKey const basic::options::OptionKeys::antibody::stem_optimize

extern

stem_optimize_size

IntegerOptionKey const basic::options::OptionKeys::antibody::stem_optimize_size

extern

use_mean_cluster_cst_data

BooleanOptionKey const basic::options::OptionKeys::antibody::use_mean_cluster_cst_data

extern