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

Variables
BooleanOptionKey const	design
BooleanOptionKey const	view
StringOptionKey const	base_cdr_instructions
StringOptionKey const	cdr_instructions
StringOptionKey const	antibody_database
BooleanOptionKey const	paper_ab_db
StringOptionKey const	paper_ab_db_path
StringVectorOptionKey const	seq_design_cdrs
StringVectorOptionKey const	graft_design_cdrs
StringVectorOptionKey const	primary_cdrs
StringOptionKey const	mintype
StringVectorOptionKey const	disallow_aa
IntegerOptionKey const	top_designs
BooleanOptionKey const	high_mem_mode
IntegerOptionKey const	cdr_set_cache_limit
StringOptionKey const	design_protocol
BooleanOptionKey const	run_relax
BooleanOptionKey const	run_interface_analyzer
StringVectorOptionKey const	paratope
StringVectorOptionKey const	epitope
BooleanOptionKey const	use_epitope_constraints
RealOptionKey const	dihedral_cst_weight
RealOptionKey const	atom_pair_cst_weight
BooleanOptionKey const	global_dihedral_cst_scoring
BooleanOptionKey const	global_atom_pair_cst_scoring
BooleanOptionKey const	do_dock
IntegerOptionKey const	dock_first_cycles
IntegerOptionKey const	dock_second_cycles
IntegerOptionKey const	outer_cycle_rounds
IntegerOptionKey const	inner_cycle_rounds
IntegerOptionKey const	dock_cycle_rounds
IntegerOptionKey const	relax_cycle_rounds
RealOptionKey const	interface_dis
RealOptionKey const	neighbor_dis
BooleanOptionKey const	use_outliers
BooleanOptionKey const	use_H3_graft_outliers
BooleanOptionKey const	use_only_H3_kinked
BooleanOptionKey const	design_antigen
BooleanOptionKey const	design_framework
BooleanOptionKey const	conservative_framework_design
BooleanOptionKey const	design_H3_stem
BooleanOptionKey const	design_proline
RealOptionKey const	sample_zero_probs_at
BooleanOptionKey const	force_mutate_framework_for_cluster
BooleanOptionKey const	no_profile_probabilities
IntegerOptionKey const	seq_design_stats_cutoff
IntegerOptionKey const	seq_design_profile_samples
BooleanOptionKey const	idealize_graft_cdrs
StringVectorOptionKey const	add_backrub_pivots
RealOptionKey const	inner_kt
RealOptionKey const	outer_kt
BooleanOptionKey const	random_start
BooleanOptionKey const	adapt_graft
BooleanOptionKey const	enable_adapt_graft_cartesian
BooleanOptionKey const	remove_antigen
BooleanOptionKey const	add_graft_log_to_pdb
BooleanOptionKey const	mutate_framework_for_cluster

Variable Documentation

adapt_graft

BooleanOptionKey const basic::options::OptionKeys::antibody::design::adapt_graft

extern

add_backrub_pivots

StringVectorOptionKey const basic::options::OptionKeys::antibody::design::add_backrub_pivots

extern

add_graft_log_to_pdb

BooleanOptionKey const basic::options::OptionKeys::antibody::design::add_graft_log_to_pdb

extern

antibody_database

StringOptionKey const basic::options::OptionKeys::antibody::design::antibody_database

extern

atom_pair_cst_weight

RealOptionKey const basic::options::OptionKeys::antibody::design::atom_pair_cst_weight

extern

base_cdr_instructions

StringOptionKey const basic::options::OptionKeys::antibody::design::base_cdr_instructions

extern

cdr_instructions

StringOptionKey const basic::options::OptionKeys::antibody::design::cdr_instructions

extern

cdr_set_cache_limit

IntegerOptionKey const basic::options::OptionKeys::antibody::design::cdr_set_cache_limit

extern

conservative_framework_design

BooleanOptionKey const basic::options::OptionKeys::antibody::design::conservative_framework_design

extern

design

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

extern

design_antigen

BooleanOptionKey const basic::options::OptionKeys::antibody::design::design_antigen

extern

design_framework

BooleanOptionKey const basic::options::OptionKeys::antibody::design::design_framework

extern

design_H3_stem

BooleanOptionKey const basic::options::OptionKeys::antibody::design::design_H3_stem

extern

design_proline

BooleanOptionKey const basic::options::OptionKeys::antibody::design::design_proline

extern

design_protocol

StringOptionKey const basic::options::OptionKeys::antibody::design::design_protocol

extern

Referenced by main().

dihedral_cst_weight

RealOptionKey const basic::options::OptionKeys::antibody::design::dihedral_cst_weight

extern

disallow_aa

StringVectorOptionKey const basic::options::OptionKeys::antibody::design::disallow_aa

extern

do_dock

BooleanOptionKey const basic::options::OptionKeys::antibody::design::do_dock

extern

dock_cycle_rounds

IntegerOptionKey const basic::options::OptionKeys::antibody::design::dock_cycle_rounds

extern

dock_first_cycles

IntegerOptionKey const basic::options::OptionKeys::antibody::design::dock_first_cycles

extern

dock_second_cycles

IntegerOptionKey const basic::options::OptionKeys::antibody::design::dock_second_cycles

extern

enable_adapt_graft_cartesian

BooleanOptionKey const basic::options::OptionKeys::antibody::design::enable_adapt_graft_cartesian

extern

epitope

StringVectorOptionKey const basic::options::OptionKeys::antibody::design::epitope

extern

force_mutate_framework_for_cluster

BooleanOptionKey const basic::options::OptionKeys::antibody::design::force_mutate_framework_for_cluster

extern

global_atom_pair_cst_scoring

BooleanOptionKey const basic::options::OptionKeys::antibody::design::global_atom_pair_cst_scoring

extern

global_dihedral_cst_scoring

BooleanOptionKey const basic::options::OptionKeys::antibody::design::global_dihedral_cst_scoring

extern

graft_design_cdrs

StringVectorOptionKey const basic::options::OptionKeys::antibody::design::graft_design_cdrs

extern

high_mem_mode

BooleanOptionKey const basic::options::OptionKeys::antibody::design::high_mem_mode

extern

idealize_graft_cdrs

BooleanOptionKey const basic::options::OptionKeys::antibody::design::idealize_graft_cdrs

extern

inner_cycle_rounds

IntegerOptionKey const basic::options::OptionKeys::antibody::design::inner_cycle_rounds

extern

inner_kt

RealOptionKey const basic::options::OptionKeys::antibody::design::inner_kt

extern

interface_dis

RealOptionKey const basic::options::OptionKeys::antibody::design::interface_dis

extern

Referenced by protocols::antibody::design::AntibodyDesignMoverGenerator::read_command_line_options().

mintype

StringOptionKey const basic::options::OptionKeys::antibody::design::mintype

extern

mutate_framework_for_cluster

BooleanOptionKey const basic::options::OptionKeys::antibody::design::mutate_framework_for_cluster

extern

neighbor_dis

RealOptionKey const basic::options::OptionKeys::antibody::design::neighbor_dis

extern

Referenced by protocols::antibody::design::AntibodyDesignMoverGenerator::read_command_line_options().

no_profile_probabilities

BooleanOptionKey const basic::options::OptionKeys::antibody::design::no_profile_probabilities

extern

outer_cycle_rounds

IntegerOptionKey const basic::options::OptionKeys::antibody::design::outer_cycle_rounds

extern

outer_kt

RealOptionKey const basic::options::OptionKeys::antibody::design::outer_kt

extern

paper_ab_db

BooleanOptionKey const basic::options::OptionKeys::antibody::design::paper_ab_db

extern

paper_ab_db_path

StringOptionKey const basic::options::OptionKeys::antibody::design::paper_ab_db_path

extern

paratope

StringVectorOptionKey const basic::options::OptionKeys::antibody::design::paratope

extern

primary_cdrs

StringVectorOptionKey const basic::options::OptionKeys::antibody::design::primary_cdrs

extern

random_start

BooleanOptionKey const basic::options::OptionKeys::antibody::design::random_start

extern

Referenced by run_parallel_docking().

relax_cycle_rounds

IntegerOptionKey const basic::options::OptionKeys::antibody::design::relax_cycle_rounds

extern

remove_antigen

BooleanOptionKey const basic::options::OptionKeys::antibody::design::remove_antigen

extern

run_interface_analyzer

BooleanOptionKey const basic::options::OptionKeys::antibody::design::run_interface_analyzer

extern

run_relax

BooleanOptionKey const basic::options::OptionKeys::antibody::design::run_relax

extern

sample_zero_probs_at

RealOptionKey const basic::options::OptionKeys::antibody::design::sample_zero_probs_at

extern

seq_design_cdrs

StringVectorOptionKey const basic::options::OptionKeys::antibody::design::seq_design_cdrs

extern

seq_design_profile_samples

IntegerOptionKey const basic::options::OptionKeys::antibody::design::seq_design_profile_samples

extern

seq_design_stats_cutoff

IntegerOptionKey const basic::options::OptionKeys::antibody::design::seq_design_stats_cutoff

extern

top_designs

IntegerOptionKey const basic::options::OptionKeys::antibody::design::top_designs

extern

use_epitope_constraints

BooleanOptionKey const basic::options::OptionKeys::antibody::design::use_epitope_constraints

extern

use_H3_graft_outliers

BooleanOptionKey const basic::options::OptionKeys::antibody::design::use_H3_graft_outliers

extern

use_only_H3_kinked

BooleanOptionKey const basic::options::OptionKeys::antibody::design::use_only_H3_kinked

extern

use_outliers

BooleanOptionKey const basic::options::OptionKeys::antibody::design::use_outliers

extern

view

BooleanOptionKey const basic::options::OptionKeys::antibody::design::view

extern

Referenced by main(), and pyrosetta.distributed.viewer.core.Viewer::show().