antibody::design Namespace Reference

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

Function Documentation

adapt_graft()

BooleanOptionKey const antibody::design::adapt_graft

(

"antibody:design:adapt_graft"

)

References design().

add_backrub_pivots()

StringVectorOptionKey const antibody::design::add_backrub_pivots

(

"antibody:design:add_backrub_pivots"

)

References design().

add_graft_log_to_pdb()

BooleanOptionKey const antibody::design::add_graft_log_to_pdb

(

"antibody:design:add_graft_log_to_pdb"

)

References design().

antibody_database()

StringOptionKey const antibody::design::antibody_database

(

"antibody:design:antibody_database"

)

References design().

atom_pair_cst_weight()

RealOptionKey const antibody::design::atom_pair_cst_weight

(

"antibody:design:atom_pair_cst_weight"

)

References design().

base_cdr_instructions()

StringOptionKey const antibody::design::base_cdr_instructions

(

"antibody:design:base_cdr_instructions"

)

References design().

cdr_instructions()

StringOptionKey const antibody::design::cdr_instructions

(

"antibody:design:cdr_instructions"

)

References design().

cdr_set_cache_limit()

IntegerOptionKey const antibody::design::cdr_set_cache_limit

(

"antibody:design:cdr_set_cache_limit"

)

References design().

conservative_framework_design()

BooleanOptionKey const antibody::design::conservative_framework_design

(

"antibody:design:conservative_framework_design"

)

References design().

design()

BooleanOptionKey const antibody::design::design

(

"antibody:design"

)

Referenced by adapt_graft(), add_backrub_pivots(), add_graft_log_to_pdb(), antibody_database(), atom_pair_cst_weight(), base_cdr_instructions(), cdr_instructions(), cdr_set_cache_limit(), conservative_framework_design(), design_antigen(), design_framework(), design_H3_stem(), design_proline(), design_protocol(), dihedral_cst_weight(), disallow_aa(), do_dock(), dock_cycle_rounds(), dock_first_cycles(), dock_second_cycles(), enable_adapt_graft_cartesian(), epitope(), force_mutate_framework_for_cluster(), global_atom_pair_cst_scoring(), global_dihedral_cst_scoring(), graft_design_cdrs(), high_mem_mode(), idealize_graft_cdrs(), inner_cycle_rounds(), inner_kt(), interface_dis(), mintype(), mutate_framework_for_cluster(), neighbor_dis(), no_profile_probabilities(), outer_cycle_rounds(), outer_kt(), paper_ab_db(), paper_ab_db_path(), paratope(), primary_cdrs(), random_start(), relax_cycle_rounds(), remove_antigen(), run_interface_analyzer(), run_relax(), sample_zero_probs_at(), seq_design_cdrs(), seq_design_profile_samples(), seq_design_stats_cutoff(), top_designs(), use_epitope_constraints(), use_H3_graft_outliers(), use_only_H3_kinked(), use_outliers(), and view().

design_antigen()

BooleanOptionKey const antibody::design::design_antigen

(

"antibody:design:design_antigen"

)

References design().

design_framework()

BooleanOptionKey const antibody::design::design_framework

(

"antibody:design:design_framework"

)

References design().

design_H3_stem()

BooleanOptionKey const antibody::design::design_H3_stem

(

"antibody:design:design_H3_stem"

)

References design().

design_proline()

BooleanOptionKey const antibody::design::design_proline

(

"antibody:design:design_proline"

)

References design().

design_protocol()

StringOptionKey const antibody::design::design_protocol

(

"antibody:design:design_protocol"

)

References design().

dihedral_cst_weight()

RealOptionKey const antibody::design::dihedral_cst_weight

(

"antibody:design:dihedral_cst_weight"

)

References design().

disallow_aa()

StringVectorOptionKey const antibody::design::disallow_aa

(

"antibody:design:disallow_aa"

)

References design().

do_dock()

BooleanOptionKey const antibody::design::do_dock

(

"antibody:design:do_dock"

)

References design().

dock_cycle_rounds()

IntegerOptionKey const antibody::design::dock_cycle_rounds

(

"antibody:design:dock_cycle_rounds"

)

References design().

dock_first_cycles()

IntegerOptionKey const antibody::design::dock_first_cycles

(

"antibody:design:dock_first_cycles"

)

References design().

dock_second_cycles()

IntegerOptionKey const antibody::design::dock_second_cycles

(

"antibody:design:dock_second_cycles"

)

References design().

enable_adapt_graft_cartesian()

BooleanOptionKey const antibody::design::enable_adapt_graft_cartesian

(

"antibody:design:enable_adapt_graft_cartesian"

)

References design().

epitope()

StringVectorOptionKey const antibody::design::epitope

(

"antibody:design:epitope"

)

References design().

force_mutate_framework_for_cluster()

BooleanOptionKey const antibody::design::force_mutate_framework_for_cluster

(

"antibody:design:force_mutate_framework_for_cluster"

)

References design().

global_atom_pair_cst_scoring()

BooleanOptionKey const antibody::design::global_atom_pair_cst_scoring

(

"antibody:design:global_atom_pair_cst_scoring"

)

References design().

global_dihedral_cst_scoring()

BooleanOptionKey const antibody::design::global_dihedral_cst_scoring

(

"antibody:design:global_dihedral_cst_scoring"

)

References design().

graft_design_cdrs()

StringVectorOptionKey const antibody::design::graft_design_cdrs

(

"antibody:design:graft_design_cdrs"

)

References design().

high_mem_mode()

BooleanOptionKey const antibody::design::high_mem_mode

(

"antibody:design:high_mem_mode"

)

References design().

idealize_graft_cdrs()

BooleanOptionKey const antibody::design::idealize_graft_cdrs

(

"antibody:design:idealize_graft_cdrs"

)

References design().

inner_cycle_rounds()

IntegerOptionKey const antibody::design::inner_cycle_rounds

(

"antibody:design:inner_cycle_rounds"

)

References design().

inner_kt()

RealOptionKey const antibody::design::inner_kt

(

"antibody:design:inner_kt"

)

References design().

interface_dis()

RealOptionKey const antibody::design::interface_dis

(

"antibody:design:interface_dis"

)

References design().

mintype()

StringOptionKey const antibody::design::mintype

(

"antibody:design:mintype"

)

References design().

mutate_framework_for_cluster()

BooleanOptionKey const antibody::design::mutate_framework_for_cluster

(

"antibody:design:mutate_framework_for_cluster"

)

References design().

neighbor_dis()

RealOptionKey const antibody::design::neighbor_dis

(

"antibody:design:neighbor_dis"

)

References design().

no_profile_probabilities()

BooleanOptionKey const antibody::design::no_profile_probabilities

(

"antibody:design:no_profile_probabilities"

)

References design().

outer_cycle_rounds()

IntegerOptionKey const antibody::design::outer_cycle_rounds

(

"antibody:design:outer_cycle_rounds"

)

References design().

outer_kt()

RealOptionKey const antibody::design::outer_kt

(

"antibody:design:outer_kt"

)

References design().

paper_ab_db()

BooleanOptionKey const antibody::design::paper_ab_db

(

"antibody:design:paper_ab_db"

)

References design().

paper_ab_db_path()

StringOptionKey const antibody::design::paper_ab_db_path

(

"antibody:design:paper_ab_db_path"

)

References design().

paratope()

StringVectorOptionKey const antibody::design::paratope

(

"antibody:design:paratope"

)

References design().

primary_cdrs()

StringVectorOptionKey const antibody::design::primary_cdrs

(

"antibody:design:primary_cdrs"

)

References design().

random_start()

BooleanOptionKey const antibody::design::random_start

(

"antibody:design:random_start"

)

References design().

relax_cycle_rounds()

IntegerOptionKey const antibody::design::relax_cycle_rounds

(

"antibody:design:relax_cycle_rounds"

)

References design().

remove_antigen()

BooleanOptionKey const antibody::design::remove_antigen

(

"antibody:design:remove_antigen"

)

References design().

run_interface_analyzer()

BooleanOptionKey const antibody::design::run_interface_analyzer

(

"antibody:design:run_interface_analyzer"

)

References design().

run_relax()

BooleanOptionKey const antibody::design::run_relax

(

"antibody:design:run_relax"

)

References design().

sample_zero_probs_at()

RealOptionKey const antibody::design::sample_zero_probs_at

(

"antibody:design:sample_zero_probs_at"

)

References design().

seq_design_cdrs()

StringVectorOptionKey const antibody::design::seq_design_cdrs

(

"antibody:design:seq_design_cdrs"

)

References design().

seq_design_profile_samples()

IntegerOptionKey const antibody::design::seq_design_profile_samples

(

"antibody:design:seq_design_profile_samples"

)

References design().

seq_design_stats_cutoff()

IntegerOptionKey const antibody::design::seq_design_stats_cutoff

(

"antibody:design:seq_design_stats_cutoff"

)

References design().

top_designs()

IntegerOptionKey const antibody::design::top_designs

(

"antibody:design:top_designs"

)

References design().

use_epitope_constraints()

BooleanOptionKey const antibody::design::use_epitope_constraints

(

"antibody:design:use_epitope_constraints"

)

References design().

use_H3_graft_outliers()

BooleanOptionKey const antibody::design::use_H3_graft_outliers

(

"antibody:design:use_H3_graft_outliers"

)

References design().

use_only_H3_kinked()

BooleanOptionKey const antibody::design::use_only_H3_kinked

(

"antibody:design:use_only_H3_kinked"

)

References design().

use_outliers()

BooleanOptionKey const antibody::design::use_outliers

(

"antibody:design:use_outliers"

)

References design().

view()

BooleanOptionKey const antibody::design::view

(

"antibody:design:view"

)

References design().