This class designs antibodies by grafting, using cluster information and constraints to help. It represents the first step in The Rosetta Antibody Designer, but can be used outside of the application. A 2011 Antibody Database is included in the rosetta datase. Up-to-date versions can be downloaded from. More...

#include <AntibodyDesignMover.hh>

Inheritance diagram for protocols::antibody::design::AntibodyDesignMover:

[legend]

Public Member Functions
	AntibodyDesignMover ()

	AntibodyDesignMover (AntibodyDesignMover const &src)

	~AntibodyDesignMover () override

void	set_defaults ()
	Reads default CDRGraftInstruction file and creates structs. More...

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	Parse my tag for RosettaScripts. Main RS interface to full antibody design protocol. More...

void	apply (core::pose::Pose &pose) override
	Main Method. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	set_light_chain (std::string const &light_chain)
	Set the light chain - lambda or kappa. More...

void	set_random_start (bool const random_start)
	Set the protocol to start with random grafted CDRs for the CDRs set to graft design. Useful for starting a high-energy structure or doing benchmarks. More...

void	set_design_protocol (AntibodyDesignProtocolEnum design_protocol)
	Set the design protocol. Default is classic_monte_carlo. Available options are: generalized_monte_carlo, deterministc_graft. More...

void	set_seq_design_cdrs (utility::vector1< CDRNameEnum > seq_design_cdrs)
	Set the CDRs which will undergo Sequence-Design. More...

void	set_graft_design_cdrs (utility::vector1< CDRNameEnum > graft_design_cdrs)
	Set the CDRs which will undergo Graft-Design. More...

void	set_primary_cdrs (utility::vector1< CDRNameEnum > primary_cdrs)
	Manually set the CDRs which can be chosen in the outer cycle. More...

void	set_outer_cycles (core::Size outer_cycles)
	Set the number of overall rounds. Each round will choose a CDR and design it and others based on options Default = 25. More...

void	set_inner_cycles (core::Size inner_cycles)
	Set the number of inner cycles, which optimizes the structure and sequence of the antibody after any graft. Essentially min cycles. More...

void	set_relax_cycles (core::Size relax_cycles)
	Set the number of relax cycles to run after each outer cycles. Only makes sense with mintype relax. More...

void	set_paratope_cdrs (utility::vector1< bool > const &cdrs)
	Set any paratope CDRs. If not set, will use all CDRs as the paratope where needed. Used mainly for constraints. More...

void	set_epitope_residues (utility::vector1< PDBNumbering > epitope_residues)
	Set any epitope residues in PDB numbering. If not set, they will be detected automatically via the interface. More...

void	set_use_epitope_constraints (bool use_epitope_csts)
	Setting to use epitope constraints. Without this false, will not use any set epitope residues. More...

void	set_instruction_file (std::string instruction_file)
	Set the instruction file path to load options from instead of setting these via associated options functions Or loading via cmd-line option. Gotta love supporting 3 different Rosetta interfaces. More...

void	set_cdr_set_options (AntibodyCDRSetOptions cdr_set_options)
	Set the options which will be used for querying the database. More...

void	set_graft_design_options (AntibodyCDRGraftDesignOptions graft_design_options)
	Set CDR-specific GraftDesign options. More...

void	set_seq_design_options (AntibodyCDRSeqDesignOptions seq_design_options)
	Set CDR-specific SeqDesign options. More...

void	set_scorefunction (core::scoring::ScoreFunctionOP scorefxn)

void	set_scorefunction_min (core::scoring::ScoreFunctionOP min_scorefxn)

void	set_dock_post_graft (bool dock_post_graft)
	Set the algorithm to run a low-resolution docking step after each graft. Default false. More...

void	set_dock_rounds (core::Size dock_rounds)

void	set_dock_first_cycles (core::Size dock_first_cycles)
	Set the first cycles of the High-res MCM dock protocol. Default for RAbD is 2. Default for FULL docking protocol is 4. More...

void	set_dock_second_cycles (core::Size dock_second_cycles)
	Set the first cycles of the High-res MCM dock protocol. Default for RAbD is 2. (Used as A SHORT optimization step) Default for FULL docking protocol is 45. More...

void	set_keep_top_designs (core::Size top_designs)
	Sets the protocol to keep a specific number of top designs. Default is 10. More...

utility::vector1< core::pose::PoseOP >	get_top_designs ()
	Get the top designs found. You can then use them in other protocols, dump them, etc. They are in order. More...

void	set_interface_dis (core::Real interface_dis)

void	set_neighbor_dis (core::Real neighbor_dis)

void	show (std::ostream &output=std::cout) const override
	Outputs details about the Mover, including current settings. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

core::pose::PoseOP	get_additional_output () override
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Member Functions
void	read_command_line_options ()

void	setup_options_classes ()
	Setup ALL options classes. More...

void	setup_native_clusters (core::pose::Pose &pose)

void	setup_native_sequence (core::pose::Pose &pose)

void	setup_epitope_residues (core::pose::Pose const &pose)

void	setup_paratope_epitope_constraints (core::pose::Pose &pose)

void	setup_cart_minimizer ()

void	setup_modeler ()

void	finalize_setup (core::pose::Pose &pose)

void	setup_scorefxn ()

void	setup_random_start_pose (core::pose::Pose &pose, utility::vector1< CDRNameEnum > &cdrs_to_design)
	Extend the native CDRs to be designed for benchmarking. More...

void	setup_default_graft_settings ()

void	setup_cdr_pose_sampling_strategies ()
	Setup alternative cdr pose indexes and sampling strategies. More...

void	initialize_cdr_set (core::pose::Pose const &pose)
	Uses instructions to Query the AntibodyDatabase and load poses. More...

void	check_for_top_designs (core::pose::Pose &pose)

utility::vector1< utility::vector1< core::Size > >	get_cdr_set_index_list ()
	Gets a list of vectors whose indexes correspond to CDRNameEnum, and whose values correspond to the cdr_set index. If the value is 0, it means no cdr in set. More...

bool	apply_to_cdr (core::pose::Pose &pose, CDRNameEnum cdr, core::Size index, bool min_post_graft=true)

bool	graft_in_cdr (core::pose::Pose &pose, CDRNameEnum const cdr, CDRDBPose &cdr_pose)
	Grafts a single CDR into framework. Index is the vector index of CDRSet/CDRClusterMap. More...

std::pair< bool, core::Size >	run_graft (core::pose::Pose &pose, core::pose::Pose const &grafting_pose, CDRNameEnum const cdr, clusters::CDRClusterEnum const cluster, protocols::grafting::AnchoredGraftMoverOP grafter)

void	run_optimization_cycle (core::pose::Pose &pose, protocols::moves::MonteCarlo &mc, CDRNameEnum cdr)
	Run the inner structure/sequence optimization cycle. More...

void	run_final_IAM (bool run_IAM)
	Mutates framework residues needed to stay within a particular cluster. Only one (L1-11-1) is known to have framework dependencies. For now. Will be replaced by AntibodyDesignOptimizer. More...

void	run_deterministic_graft_algorithm (core::pose::Pose &pose, utility::vector1< CDRNameEnum > &cdrs_to_design)
	. If rounds >= number of possible combinations - Try them all. More...

void	run_basic_mc_algorithm (core::pose::Pose &pose, utility::vector1< CDRNameEnum > &cdrs_to_design, AntibodyDesignProtocolEnum mc_algorithm)
	Basic mc algorithm that randomly samples from the cdr set. More...

void	print_str_vec (std::string const name, utility::vector1< std::string > const &vec, std::ostream &output=std::cout) const

void	finalize_pose (AntibodyInfoCOP ab_info, core::pose::Pose &pose)
	Add cluster comments, fixes CDR numbering for certain cases, runs IAM. More...

AntibodyInfoOP	init_ab_info (core::pose::Pose const &pose)

Private Attributes
AntibodyInfoOP	ab_info_ = nullptr

AntibodyDesignEnumManagerOP	design_enum_manager_ = nullptr

AntibodyDatabaseManagerOP	db_manager_ = nullptr

AntibodyCDRSetOptions	cdr_set_options_

AntibodyCDRGraftDesignOptions	cdr_graft_design_options_

AntibodyCDRSeqDesignOptions	cdr_seq_design_options_

AntibodySeqDesignTFCreatorOP	seq_design_creator_ = nullptr

std::map< CDRNameEnum, utility::vector1< CDRDBPose > >	cdr_set_

std::map< CDRNameEnum, std::map< clusters::CDRClusterEnum, utility::vector1< core::Size > > >	cluster_based_CDRDBPose_indexes_
	Even cluster sampling (even_cluster_mc protocol) More...

std::map< CDRNameEnum, std::map< core::Size, std::map< clusters::CDRClusterEnum, utility::vector1< core::Size > > > >	length_based_CDRDBPose_indexes_
	Even Length and Cluster sampling (even_length_cluster_mc protocol) More...

protocols::grafting::CCDEndsGraftMoverOP	graft_mover_

protocols::grafting::AnchoredGraftMoverOP	anchored_graft_mover_

MutateFrameworkForClusterOP	framework_mutator_ = nullptr

core::scoring::ScoreFunctionOP	scorefxn_ = nullptr

core::scoring::ScoreFunctionOP	scorefxn_min_ = nullptr

core::scoring::ScoreFunctionOP	scorefxn_cart_graft_ = nullptr

GeneralAntibodyModelerOP	modeler_ = nullptr

protocols::minimization_packing::MinMoverOP	cart_min_graft_ = nullptr

protocols::moves::MonteCarloOP	mc_ = nullptr

protocols::moves::MonteCarloOP	inner_mc_ = nullptr

constraints::ParatopeEpitopeSiteConstraintMoverOP	paratope_epitope_cst_mover_ = nullptr

constraints::ParatopeSiteConstraintMoverOP	paratope_cst_mover_ = nullptr

constraints::CDRDihedralConstraintMoverOP	cdr_dihedral_cst_mover_ = nullptr

core::Size	overhang_

core::Size	outer_cycles_

core::Size	inner_cycles_

core::Size	relax_cycles_

core::Size	dock_cycles_

core::Size	num_top_designs_

core::Real	interface_dis_

core::Real	neighbor_dis_

utility::vector1< core::pose::PoseOP >	top_designs_

utility::vector1< core::Real >	top_scores_

core::Size	total_permutations_

bool	dock_post_graft_

bool	rb_min_post_graft_

utility::vector1< bool >	paratope_cdrs_

utility::vector1< PDBNumbering >	epitope_residues_

bool	adapt_graft_

bool	enable_adapt_graft_cartesian_

bool	benchmark_

bool	use_light_chain_type_

bool	use_epitope_constraints_

bool	print_tracer_info_

bool	idealize_graft_cdrs_

bool	add_log_to_pose_

utility::vector1< std::string >	graft_log_

utility::vector1< std::string >	accept_log_

core::Real	outer_kt_

core::Real	inner_kt_

AntibodyDesignProtocolEnum	design_protocol_

utility::vector1< CDRNameEnum >	seq_design_override_

utility::vector1< CDRNameEnum >	graft_design_override_

utility::vector1< CDRNameEnum >	cdrs_to_design_

utility::vector1< CDRNameEnum >	primary_cdrs_

std::string	instruction_file_ = "NA"

core::Size	stats_cutoff_

bool	mutate_framework_for_cluster_

std::string	mintype_ = "NA"

bool	mc_optimize_dG_ = false

core::Real	mc_interface_weight_ = 1.0

core::Real	mc_total_weight_ = 0.0

bool	run_final_AIM_ = true

bool	remove_antigen_ = false

std::string	light_chain_ = ""

core::Size	additional_outputs_returned_ = 0

core::Size	dock_first_cycles_ = 2

core::Size	dock_second_cycles_ = 2

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

This class designs antibodies by grafting, using cluster information and constraints to help. It represents the first step in The Rosetta Antibody Designer, but can be used outside of the application. A 2011 Antibody Database is included in the rosetta datase. Up-to-date versions can be downloaded from.

To use this class: 1) Use default instruction path, or set one. Loads CDRs from AntibodyDatabase *See rosetta_database/sampling/antibodies for file format. 2) Use class interface settings to control sampling. Loads CDRs from AntibodyDatabase. 3) Use set_cdr_sets to set your own CDRs to graft.

Constructor & Destructor Documentation

◆ AntibodyDesignMover() [1/2]

protocols::antibody::design::AntibodyDesignMover::AntibodyDesignMover ( )

References design_enum_manager_, read_command_line_options(), and set_defaults().

◆ AntibodyDesignMover() [2/2]

protocols::antibody::design::AntibodyDesignMover::AntibodyDesignMover ( AntibodyDesignMover const & src )

References ab_info_, anchored_graft_mover_, cart_min_graft_, cdr_dihedral_cst_mover_, db_manager_, design_enum_manager_, framework_mutator_, graft_mover_, inner_mc_, mc_, modeler_, paratope_cst_mover_, paratope_epitope_cst_mover_, scorefxn_, scorefxn_cart_graft_, scorefxn_min_, seq_design_creator_, and top_designs_.

◆ ~AntibodyDesignMover()

protocols::antibody::design::AntibodyDesignMover::~AntibodyDesignMover ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::antibody::design::AntibodyDesignMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References ab_info_, accept_log_, core::pose::add_comment(), protocols::viewer::add_conformation_viewer(), add_log_to_pose_, protocols::simple_moves::DeleteChainsMover::apply(), benchmark_, cdrs_to_design_, core::pose::Pose::conformation(), design_protocol_, protocols::antibody::design::deterministic_graft, protocols::simple_filters::dssp(), finalize_pose(), finalize_setup(), graft_log_, init_ab_info(), inner_kt_, inner_mc_, mc_, mc_optimize_dG_, modeler_, core::conformation::membrane::out, outer_kt_, remove_antigen_, run_basic_mc_algorithm(), run_deterministic_graft_algorithm(), scorefxn_, protocols::simple_moves::DeleteChainsMover::set_chains(), setup_cart_minimizer(), setup_epitope_residues(), setup_modeler(), setup_native_clusters(), setup_native_sequence(), setup_options_classes(), setup_paratope_epitope_constraints(), setup_random_start_pose(), setup_scorefxn(), show(), core::id::to_string(), top_designs_, top_scores_, and protocols::antibody::TR().

◆ apply_to_cdr()

bool protocols::antibody::design::AntibodyDesignMover::apply_to_cdr	(	core::pose::Pose &	pose,
		CDRNameEnum	cdr,
		core::Size	index,
		bool	min_post_graft = `true`
	)

private

Applies graft, modeling, etc. to a single CDR.

References ab_info_, adapt_graft_, core::pose::add_comment(), add_log_to_pose_, anchored_graft_mover_, cdr_dihedral_cst_mover_, cdr_graft_design_options_, cdr_set_, protocols::antibody::CDRDBPose::cluster, db_manager_, protocols::antibody::CDRDBPose::distance, protocols::simple_filters::dssp(), core::sequence::end, core::pose::Pose::fold_tree(), framework_mutator_, graft_log_, graft_mover_, inner_cycles_, inner_mc_, mutate_framework_for_cluster_, core::conformation::membrane::out, protocols::jd2::output_intermediate_pose(), protocols::antibody::CDRDBPose::pdb, core::pose::Pose::pdb_info(), protocols::antibody::CDRDBPose::pose, print_tracer_info_, core::pose::Pose::remove_constraints(), run_graft(), run_optimization_cycle(), protocols::antibody::design::set_native_cdr_sequence(), setup_paratope_epitope_constraints(), protocols::loops::start, core::id::to_string(), and protocols::antibody::TR().

Referenced by run_basic_mc_algorithm(), run_deterministic_graft_algorithm(), and setup_random_start_pose().

◆ check_for_top_designs()

void protocols::antibody::design::AntibodyDesignMover::check_for_top_designs ( core::pose::Pose & pose )

private

References num_top_designs_, protocols::hybridization::score, top_designs_, and top_scores_.

Referenced by finalize_setup(), run_basic_mc_algorithm(), and run_deterministic_graft_algorithm().

◆ clone()

protocols::moves::MoverOP protocols::antibody::design::AntibodyDesignMover::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ finalize_pose()

void protocols::antibody::design::AntibodyDesignMover::finalize_pose	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose &	pose
	)

private

Add cluster comments, fixes CDR numbering for certain cases, runs IAM.

References protocols::antibody::clusters::add_cluster_comments_to_pose(), protocols::analysis::InterfaceAnalyzerMover::add_score_info_to_pose(), protocols::analysis::InterfaceAnalyzerMover::apply(), protocols::antibody::check_fix_aho_cdr_numbering(), protocols::antibody::design::get_dock_chains_from_ab_dock_chains(), protocols::analysis::InterfaceAnalyzerMover::init_on_new_input(), run_final_AIM_, and scorefxn_.

Referenced by apply(), and get_additional_output().

◆ finalize_setup()

void protocols::antibody::design::AntibodyDesignMover::finalize_setup ( core::pose::Pose & pose )

private

◆ fresh_instance()

protocols::moves::MoverOP protocols::antibody::design::AntibodyDesignMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_additional_output()

core::pose::PoseOP protocols::antibody::design::AntibodyDesignMover::get_additional_output ( )

overridevirtual

Mechanism by which a mover may return multiple output poses from a single input pose.

fpd

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented from protocols::moves::Mover.

References ab_info_, additional_outputs_returned_, finalize_pose(), init_ab_info(), and top_designs_.

◆ get_cdr_set_index_list()

vector1< vector1< core::Size > > protocols::antibody::design::AntibodyDesignMover::get_cdr_set_index_list ( )

private

Gets a list of vectors whose indexes correspond to CDRNameEnum, and whose values correspond to the cdr_set index. If the value is 0, it means no cdr in set.

References cdr_set_, protocols::antibody::CDRNameEnum_start, protocols::antibody::CDRNameEnum_total, and protocols::antibody::design::get_all_graft_permutations().

◆ get_name()

std::string protocols::antibody::design::AntibodyDesignMover::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

◆ get_top_designs()

utility::vector1< core::pose::PoseOP> protocols::antibody::design::AntibodyDesignMover::get_top_designs ( )

inline

Get the top designs found. You can then use them in other protocols, dump them, etc. They are in order.

This should be refactored to get_additional_output.

References top_designs_.

◆ graft_in_cdr()

bool protocols::antibody::design::AntibodyDesignMover::graft_in_cdr	(	core::pose::Pose &	pose,
		CDRNameEnum const	cdr,
		CDRDBPose &	cdr_pose
	)

private

Grafts a single CDR into framework. Index is the vector index of CDRSet/CDRClusterMap.

Return success or failure

◆ init_ab_info()

AntibodyInfoOP protocols::antibody::design::AntibodyDesignMover::init_ab_info ( core::pose::Pose const & pose )

private

References protocols::antibody::AHO_Scheme, light_chain_, and protocols::antibody::North.

Referenced by apply(), and get_additional_output().

◆ initialize_cdr_set()

void protocols::antibody::design::AntibodyDesignMover::initialize_cdr_set ( core::pose::Pose const & pose )

private

Uses instructions to Query the AntibodyDatabase and load poses.

References ab_info_, cdr_set_, cdr_set_options_, and db_manager_.

Referenced by finalize_setup().

◆ mover_name()

std::string protocols::antibody::design::AntibodyDesignMover::mover_name ( )

static

Referenced by get_name(), protocols::antibody::design::AntibodyDesignMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::antibody::design::AntibodyDesignMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Parse my tag for RosettaScripts. Main RS interface to full antibody design protocol.

Reimplemented from protocols::moves::Mover.

References benchmark_, protocols::antibody::AntibodyEnumManager::cdr_name_string_to_enum(), design_enum_manager_, design_protocol_, dock_cycles_, dock_first_cycles_, dock_post_graft_, dock_second_cycles_, epitope_residues_, protocols::antibody::design::get_ab_design_global_scorefxn(), protocols::antibody::design::get_ab_design_min_scorefxn(), protocols::antibody::get_cdr_bool_from_tag(), protocols::antibody::design::get_pdb_numbering_from_strings(), graft_design_override_, inner_cycles_, inner_kt_, instruction_file_, interface_dis_, light_chain_, mc_interface_weight_, mc_optimize_dG_, mc_total_weight_, mintype_, mutate_framework_for_cluster_, neighbor_dis_, num_top_designs_, outer_cycles_, outer_kt_, paratope_cdrs_, primary_cdrs_, relax_cycles_, remove_antigen_, scorefxn_, scorefxn_min_, seq_design_override_, and use_epitope_constraints_.

◆ print_str_vec()

void protocols::antibody::design::AntibodyDesignMover::print_str_vec	(	std::string const	name,
		utility::vector1< std::string > const &	vec,
		std::ostream &	output = `std::cout`
	)		const

private

References protocols::moves::Mover::name(), and core::id::to_string().

Referenced by show().

◆ provide_citation_info()

void protocols::antibody::design::AntibodyDesignMover::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

◆ provide_xml_schema()

void protocols::antibody::design::AntibodyDesignMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::antibody::design::attributes_for_get_ab_design_global_scorefxn(), protocols::antibody::design::attributes_for_get_ab_design_min_scorefxn(), protocols::antibody::attributes_for_get_cdr_bool_from_tag(), protocols::antibody::design::AntibodyDesignEnumManager::get_recognized_design_protocols(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::antibody::design::AntibodyDesignMoverCreator::provide_xml_schema().

◆ read_command_line_options()

void protocols::antibody::design::AntibodyDesignMover::read_command_line_options ( )

private

◆ run_basic_mc_algorithm()

void protocols::antibody::design::AntibodyDesignMover::run_basic_mc_algorithm	(	core::pose::Pose &	pose,
		utility::vector1< CDRNameEnum > &	cdrs_to_design,
		AntibodyDesignProtocolEnum	mc_algorithm
	)

private

Basic mc algorithm that randomly samples from the cdr set.

References accept_log_, apply_to_cdr(), cdr_graft_design_options_, cdr_set_, check_for_top_designs(), cluster_based_CDRDBPose_indexes_, protocols::antibody::design::even_cluster_monte_carlo, protocols::antibody::design::even_length_cluster_monte_carlo, protocols::antibody::design::generalized_monte_carlo, length_based_CDRDBPose_indexes_, mc_, core::conformation::membrane::out, outer_cycles_, core::scoring::rg, scorefxn_, core::id::to_string(), top_designs_, top_scores_, and protocols::antibody::TR().

Referenced by apply().

◆ run_deterministic_graft_algorithm()

void protocols::antibody::design::AntibodyDesignMover::run_deterministic_graft_algorithm	(	core::pose::Pose &	pose,
		utility::vector1< CDRNameEnum > &	cdrs_to_design
	)

private

. If rounds >= number of possible combinations - Try them all.

Grafts CDRs on the input structure, in a random order.

References apply_to_cdr(), cdr_set_, check_for_top_designs(), mc_, and protocols::antibody::TR().

Referenced by apply().

◆ run_final_IAM()

void protocols::antibody::design::AntibodyDesignMover::run_final_IAM ( bool run_IAM )

private

Mutates framework residues needed to stay within a particular cluster. Only one (L1-11-1) is known to have framework dependencies. For now. Will be replaced by AntibodyDesignOptimizer.

Run a final IAM at the end of the protocol? Default True.

◆ run_graft()

std::pair< bool, core::Size > protocols::antibody::design::AntibodyDesignMover::run_graft	(	core::pose::Pose &	pose,
		core::pose::Pose const &	grafting_pose,
		CDRNameEnum const	cdr,
		clusters::CDRClusterEnum const	cluster,
		protocols::grafting::AnchoredGraftMoverOP	grafter
	)

private

References ab_info_, adapt_graft_, cart_min_graft_, cdr_dihedral_cst_mover_, protocols::antibody::design::check_cb(), enable_adapt_graft_cartesian_, protocols::loops::has_severe_pep_bond_geom_issues(), modeler_, overhang_, protocols::loops::remove_cutpoint_variants(), scorefxn_, scorefxn_cart_graft_, core::pose::Pose::size(), and protocols::antibody::TR().

Referenced by apply_to_cdr().

◆ run_optimization_cycle()

void protocols::antibody::design::AntibodyDesignMover::run_optimization_cycle	(	core::pose::Pose &	pose,
		protocols::moves::MonteCarlo &	mc,
		CDRNameEnum	cdr
	)

private

◆ set_cdr_set_options()

void protocols::antibody::design::AntibodyDesignMover::set_cdr_set_options ( AntibodyCDRSetOptions cdr_set_options )

Set the options which will be used for querying the database.

References cdr_set_options_.

◆ set_defaults()

void protocols::antibody::design::AntibodyDesignMover::set_defaults ( )

Reads default CDRGraftInstruction file and creates structs.

References cdr_graft_design_options_, cdr_seq_design_options_, cdr_set_options_, epitope_residues_, overhang_, paratope_cdrs_, and print_tracer_info_.

Referenced by AntibodyDesignMover().

◆ set_design_protocol()

void protocols::antibody::design::AntibodyDesignMover::set_design_protocol ( AntibodyDesignProtocolEnum design_protocol )

Set the design protocol. Default is classic_monte_carlo. Available options are: generalized_monte_carlo, deterministc_graft.

. Deterministic Protocol only available if GraftDesigning a single CDR.

References design_protocol_.

◆ set_dock_first_cycles()

void protocols::antibody::design::AntibodyDesignMover::set_dock_first_cycles ( core::Size dock_first_cycles )

Set the first cycles of the High-res MCM dock protocol. Default for RAbD is 2. Default for FULL docking protocol is 4.

References dock_first_cycles_.

◆ set_dock_post_graft()

void protocols::antibody::design::AntibodyDesignMover::set_dock_post_graft ( bool dock_post_graft )

Set the algorithm to run a low-resolution docking step after each graft. Default false.

Uses command-line options for docking. Lower inner or outer cycles if you are grafting many CDRs. Still quicker then relax.

References dock_post_graft_.

Referenced by read_command_line_options().

◆ set_dock_rounds()

void protocols::antibody::design::AntibodyDesignMover::set_dock_rounds ( core::Size dock_rounds )

References dock_cycles_.

Referenced by read_command_line_options().

◆ set_dock_second_cycles()

void protocols::antibody::design::AntibodyDesignMover::set_dock_second_cycles ( core::Size dock_second_cycles )

Set the first cycles of the High-res MCM dock protocol. Default for RAbD is 2. (Used as A SHORT optimization step) Default for FULL docking protocol is 45.

References dock_second_cycles_.

◆ set_epitope_residues()

void protocols::antibody::design::AntibodyDesignMover::set_epitope_residues ( utility::vector1< PDBNumbering > epitope_residues )

Set any epitope residues in PDB numbering. If not set, they will be detected automatically via the interface.

References epitope_residues_.

◆ set_graft_design_cdrs()

void protocols::antibody::design::AntibodyDesignMover::set_graft_design_cdrs ( utility::vector1< CDRNameEnum > graft_design_cdrs )

Set the CDRs which will undergo Graft-Design.

References graft_design_override_.

◆ set_graft_design_options()

void protocols::antibody::design::AntibodyDesignMover::set_graft_design_options ( AntibodyCDRGraftDesignOptions graft_design_options )

Set CDR-specific GraftDesign options.

References cdr_graft_design_options_.

◆ set_inner_cycles()

void protocols::antibody::design::AntibodyDesignMover::set_inner_cycles ( core::Size inner_cycles )

Set the number of inner cycles, which optimizes the structure and sequence of the antibody after any graft. Essentially min cycles.

References inner_cycles_.

◆ set_instruction_file()

void protocols::antibody::design::AntibodyDesignMover::set_instruction_file ( std::string instruction_file )

Set the instruction file path to load options from instead of setting these via associated options functions Or loading via cmd-line option. Gotta love supporting 3 different Rosetta interfaces.

References instruction_file_.

◆ set_interface_dis()

void protocols::antibody::design::AntibodyDesignMover::set_interface_dis ( core::Real interface_dis )

References interface_dis_.

◆ set_keep_top_designs()

void protocols::antibody::design::AntibodyDesignMover::set_keep_top_designs ( core::Size top_designs )

Sets the protocol to keep a specific number of top designs. Default is 10.

References num_top_designs_.

Referenced by read_command_line_options().

◆ set_light_chain()

void protocols::antibody::design::AntibodyDesignMover::set_light_chain ( std::string const & light_chain )

Set the light chain - lambda or kappa.

References light_chain_.

◆ set_neighbor_dis()

void protocols::antibody::design::AntibodyDesignMover::set_neighbor_dis ( core::Real neighbor_dis )

References neighbor_dis_.

◆ set_outer_cycles()

void protocols::antibody::design::AntibodyDesignMover::set_outer_cycles ( core::Size outer_cycles )

Set the number of overall rounds. Each round will choose a CDR and design it and others based on options Default = 25.

References outer_cycles_.

◆ set_paratope_cdrs()

void protocols::antibody::design::AntibodyDesignMover::set_paratope_cdrs ( utility::vector1< bool > const & cdrs )

Set any paratope CDRs. If not set, will use all CDRs as the paratope where needed. Used mainly for constraints.

References paratope_cdrs_.

◆ set_primary_cdrs()

void protocols::antibody::design::AntibodyDesignMover::set_primary_cdrs ( utility::vector1< CDRNameEnum > primary_cdrs )

Manually set the CDRs which can be chosen in the outer cycle.

These should be on for either Sequence-Design or Graft-Design. Normally, the outer cycles are whatever CDRs we are designing, including CDRs which are sequence-design only. Use this if you are primarily interested in specific CDRs (such as graft-designing H3 and allowing H1 and L3 to sequence design during the inner cycle.

References primary_cdrs_.

◆ set_random_start()

void protocols::antibody::design::AntibodyDesignMover::set_random_start ( bool const random_start )

Set the protocol to start with random grafted CDRs for the CDRs set to graft design. Useful for starting a high-energy structure or doing benchmarks.

References benchmark_.

◆ set_relax_cycles()

void protocols::antibody::design::AntibodyDesignMover::set_relax_cycles ( core::Size relax_cycles )

Set the number of relax cycles to run after each outer cycles. Only makes sense with mintype relax.

References relax_cycles_.

◆ set_scorefunction()

void protocols::antibody::design::AntibodyDesignMover::set_scorefunction ( core::scoring::ScoreFunctionOP scorefxn )

References scorefxn_.

◆ set_scorefunction_min()

void protocols::antibody::design::AntibodyDesignMover::set_scorefunction_min ( core::scoring::ScoreFunctionOP min_scorefxn )

References scorefxn_min_.

◆ set_seq_design_cdrs()

void protocols::antibody::design::AntibodyDesignMover::set_seq_design_cdrs ( utility::vector1< CDRNameEnum > seq_design_cdrs )

Set the CDRs which will undergo Sequence-Design.

References seq_design_override_.

◆ set_seq_design_options()

void protocols::antibody::design::AntibodyDesignMover::set_seq_design_options ( AntibodyCDRSeqDesignOptions seq_design_options )

Set CDR-specific SeqDesign options.

References cdr_seq_design_options_.

◆ set_use_epitope_constraints()

void protocols::antibody::design::AntibodyDesignMover::set_use_epitope_constraints ( bool use_epitope_csts )

Setting to use epitope constraints. Without this false, will not use any set epitope residues.

References use_epitope_constraints_.

◆ setup_cart_minimizer()

void protocols::antibody::design::AntibodyDesignMover::setup_cart_minimizer ( )

private

References cart_min_graft_, and scorefxn_cart_graft_.

Referenced by apply().

◆ setup_cdr_pose_sampling_strategies()

void protocols::antibody::design::AntibodyDesignMover::setup_cdr_pose_sampling_strategies ( )

private

Setup alternative cdr pose indexes and sampling strategies.

References ab_info_, cdr_set_, cluster_based_CDRDBPose_indexes_, and length_based_CDRDBPose_indexes_.

Referenced by finalize_setup().

◆ setup_default_graft_settings()

void protocols::antibody::design::AntibodyDesignMover::setup_default_graft_settings ( )

private

References anchored_graft_mover_, graft_mover_, idealize_graft_cdrs_, neighbor_dis_, and scorefxn_.

Referenced by finalize_setup().

◆ setup_epitope_residues()

void protocols::antibody::design::AntibodyDesignMover::setup_epitope_residues ( core::pose::Pose const & pose )

private

References ab_info_, protocols::antibody::design::PDBNumbering::chain, epitope_residues_, protocols::antibody::design::PDBNumbering::icode, interface_dis_, core::pose::Pose::pdb_info(), protocols::antibody::design::PDBNumbering::resnum, protocols::antibody::select_epitope_residues(), and core::pose::Pose::size().

Referenced by apply().

◆ setup_modeler()

void protocols::antibody::design::AntibodyDesignMover::setup_modeler ( )

private

References ab_info_, interface_dis_, modeler_, neighbor_dis_, scorefxn_, and scorefxn_min_.

Referenced by apply().

◆ setup_native_clusters()

void protocols::antibody::design::AntibodyDesignMover::setup_native_clusters ( core::pose::Pose & pose )

private

References ab_info_.

Referenced by apply().

◆ setup_native_sequence()

void protocols::antibody::design::AntibodyDesignMover::setup_native_sequence ( core::pose::Pose & pose )

private

References ab_info_, core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::NATIVE_ANTIBODY_SEQ.

Referenced by apply().

◆ setup_options_classes()

void protocols::antibody::design::AntibodyDesignMover::setup_options_classes ( )

private

Setup ALL options classes.

References ab_info_, cdr_graft_design_options_, cdr_seq_design_options_, cdr_set_options_, protocols::antibody::CDRNameEnum_proto_total, design_enum_manager_, protocols::antibody::design::get_cdr_set_options(), protocols::antibody::design::get_graft_design_options(), protocols::antibody::design::get_seq_design_options(), graft_design_override_, protocols::antibody::h4, instruction_file_, protocols::antibody::l4, mintype_, and seq_design_override_.

Referenced by apply().

◆ setup_paratope_epitope_constraints()

void protocols::antibody::design::AntibodyDesignMover::setup_paratope_epitope_constraints ( core::pose::Pose & pose )

private

References ab_info_, cdr_dihedral_cst_mover_, dock_post_graft_, epitope_residues_, interface_dis_, paratope_cdrs_, paratope_cst_mover_, paratope_epitope_cst_mover_, and use_epitope_constraints_.

Referenced by apply(), and apply_to_cdr().

◆ setup_random_start_pose()

void protocols::antibody::design::AntibodyDesignMover::setup_random_start_pose	(	core::pose::Pose &	pose,
		utility::vector1< CDRNameEnum > &	cdrs_to_design
	)

private

Extend the native CDRs to be designed for benchmarking.

References ab_info_, adapt_graft_, apply_to_cdr(), cdr_graft_design_options_, cdr_set_, protocols::grafting::graft_closed(), print_tracer_info_, core::scoring::rg, and protocols::antibody::TR().

Referenced by apply().

◆ setup_scorefxn()

void protocols::antibody::design::AntibodyDesignMover::setup_scorefxn ( )

private

References core::scoring::atom_pair_constraint, core::scoring::cart_bonded, core::scoring::dihedral_constraint, protocols::antibody::design::get_ab_design_global_scorefxn(), protocols::antibody::design::get_ab_design_min_scorefxn(), core::scoring::pro_close, scorefxn_, scorefxn_cart_graft_, and scorefxn_min_.

Referenced by apply().

◆ show()

void protocols::antibody::design::AntibodyDesignMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References ab_info_, cdr_graft_design_options_, cdr_seq_design_options_, cdr_set_options_, design_enum_manager_, design_protocol_, dock_post_graft_, protocols::antibody::h3, inner_cycles_, outer_cycles_, print_str_vec(), protocols::antibody::design::seq_design_basic, protocols::antibody::design::seq_design_conservative, protocols::antibody::design::seq_design_none, protocols::antibody::design::seq_design_profiles, protocols::antibody::design::SeqDesignStrategyEnum_total, and core::id::to_string().

Referenced by apply().

Member Data Documentation

◆ ab_info_

AntibodyInfoOP protocols::antibody::design::AntibodyDesignMover::ab_info_ = nullptr

private

Referenced by AntibodyDesignMover(), apply(), apply_to_cdr(), finalize_setup(), get_additional_output(), initialize_cdr_set(), run_graft(), run_optimization_cycle(), setup_cdr_pose_sampling_strategies(), setup_epitope_residues(), setup_modeler(), setup_native_clusters(), setup_native_sequence(), setup_options_classes(), setup_paratope_epitope_constraints(), setup_random_start_pose(), and show().

◆ accept_log_

utility::vector1<std::string> protocols::antibody::design::AntibodyDesignMover::accept_log_

private

Referenced by apply(), and run_basic_mc_algorithm().

◆ adapt_graft_

bool protocols::antibody::design::AntibodyDesignMover::adapt_graft_

private

Referenced by apply_to_cdr(), read_command_line_options(), run_graft(), and setup_random_start_pose().

◆ add_log_to_pose_

bool protocols::antibody::design::AntibodyDesignMover::add_log_to_pose_

private

Referenced by apply(), apply_to_cdr(), and read_command_line_options().

◆ additional_outputs_returned_

core::Size protocols::antibody::design::AntibodyDesignMover::additional_outputs_returned_ = 0

private

Referenced by get_additional_output().

◆ anchored_graft_mover_

protocols::grafting::AnchoredGraftMoverOP protocols::antibody::design::AntibodyDesignMover::anchored_graft_mover_

private

Referenced by AntibodyDesignMover(), apply_to_cdr(), finalize_setup(), and setup_default_graft_settings().

◆ benchmark_

bool protocols::antibody::design::AntibodyDesignMover::benchmark_

private

Referenced by apply(), parse_my_tag(), read_command_line_options(), and set_random_start().

◆ cart_min_graft_

protocols::minimization_packing::MinMoverOP protocols::antibody::design::AntibodyDesignMover::cart_min_graft_ = nullptr

private

Referenced by AntibodyDesignMover(), run_graft(), and setup_cart_minimizer().

◆ cdr_dihedral_cst_mover_

constraints::CDRDihedralConstraintMoverOP protocols::antibody::design::AntibodyDesignMover::cdr_dihedral_cst_mover_ = nullptr

private

Referenced by AntibodyDesignMover(), apply_to_cdr(), run_graft(), and setup_paratope_epitope_constraints().

◆ cdr_graft_design_options_

AntibodyCDRGraftDesignOptions protocols::antibody::design::AntibodyDesignMover::cdr_graft_design_options_

private

Referenced by apply_to_cdr(), finalize_setup(), run_basic_mc_algorithm(), run_optimization_cycle(), set_defaults(), set_graft_design_options(), setup_options_classes(), setup_random_start_pose(), and show().

◆ cdr_seq_design_options_

AntibodyCDRSeqDesignOptions protocols::antibody::design::AntibodyDesignMover::cdr_seq_design_options_

private

Referenced by finalize_setup(), run_optimization_cycle(), set_defaults(), set_seq_design_options(), setup_options_classes(), and show().

◆ cdr_set_

std::map< CDRNameEnum, utility::vector1< CDRDBPose > > protocols::antibody::design::AntibodyDesignMover::cdr_set_

private

Referenced by apply_to_cdr(), finalize_setup(), get_cdr_set_index_list(), initialize_cdr_set(), run_basic_mc_algorithm(), run_deterministic_graft_algorithm(), setup_cdr_pose_sampling_strategies(), and setup_random_start_pose().

◆ cdr_set_options_

AntibodyCDRSetOptions protocols::antibody::design::AntibodyDesignMover::cdr_set_options_

private

Referenced by initialize_cdr_set(), set_cdr_set_options(), set_defaults(), setup_options_classes(), and show().

◆ cdrs_to_design_

utility::vector1<CDRNameEnum> protocols::antibody::design::AntibodyDesignMover::cdrs_to_design_

private

Referenced by apply(), and finalize_setup().

◆ cluster_based_CDRDBPose_indexes_

std::map< CDRNameEnum, std::map< clusters::CDRClusterEnum, utility::vector1< core::Size > > > protocols::antibody::design::AntibodyDesignMover::cluster_based_CDRDBPose_indexes_

private

Even cluster sampling (even_cluster_mc protocol)

Referenced by run_basic_mc_algorithm(), and setup_cdr_pose_sampling_strategies().

◆ db_manager_

AntibodyDatabaseManagerOP protocols::antibody::design::AntibodyDesignMover::db_manager_ = nullptr

private

Referenced by AntibodyDesignMover(), apply_to_cdr(), and initialize_cdr_set().

◆ design_enum_manager_

AntibodyDesignEnumManagerOP protocols::antibody::design::AntibodyDesignMover::design_enum_manager_ = nullptr

private

Referenced by AntibodyDesignMover(), parse_my_tag(), read_command_line_options(), setup_options_classes(), and show().

◆ design_protocol_

AntibodyDesignProtocolEnum protocols::antibody::design::AntibodyDesignMover::design_protocol_

private

Referenced by apply(), parse_my_tag(), read_command_line_options(), set_design_protocol(), and show().

◆ dock_cycles_

core::Size protocols::antibody::design::AntibodyDesignMover::dock_cycles_

private

Referenced by parse_my_tag(), run_optimization_cycle(), and set_dock_rounds().

◆ dock_first_cycles_

core::Size protocols::antibody::design::AntibodyDesignMover::dock_first_cycles_ = 2

private

Referenced by parse_my_tag(), read_command_line_options(), run_optimization_cycle(), and set_dock_first_cycles().

◆ dock_post_graft_

bool protocols::antibody::design::AntibodyDesignMover::dock_post_graft_

private

Referenced by parse_my_tag(), run_optimization_cycle(), set_dock_post_graft(), setup_paratope_epitope_constraints(), and show().

◆ dock_second_cycles_

core::Size protocols::antibody::design::AntibodyDesignMover::dock_second_cycles_ = 2

private

Referenced by parse_my_tag(), read_command_line_options(), run_optimization_cycle(), and set_dock_second_cycles().

◆ enable_adapt_graft_cartesian_

bool protocols::antibody::design::AntibodyDesignMover::enable_adapt_graft_cartesian_

private

Referenced by read_command_line_options(), and run_graft().

◆ epitope_residues_

utility::vector1<PDBNumbering > protocols::antibody::design::AntibodyDesignMover::epitope_residues_

private

Referenced by parse_my_tag(), read_command_line_options(), set_defaults(), set_epitope_residues(), setup_epitope_residues(), and setup_paratope_epitope_constraints().

◆ framework_mutator_

MutateFrameworkForClusterOP protocols::antibody::design::AntibodyDesignMover::framework_mutator_ = nullptr

private

Referenced by AntibodyDesignMover(), apply_to_cdr(), and finalize_setup().

◆ graft_design_override_

utility::vector1<CDRNameEnum> protocols::antibody::design::AntibodyDesignMover::graft_design_override_

private

Referenced by parse_my_tag(), read_command_line_options(), set_graft_design_cdrs(), and setup_options_classes().

◆ graft_log_

utility::vector1<std::string> protocols::antibody::design::AntibodyDesignMover::graft_log_

private

Referenced by apply(), apply_to_cdr(), and finalize_setup().

◆ graft_mover_

protocols::grafting::CCDEndsGraftMoverOP protocols::antibody::design::AntibodyDesignMover::graft_mover_

private

Referenced by AntibodyDesignMover(), apply_to_cdr(), finalize_setup(), and setup_default_graft_settings().

◆ idealize_graft_cdrs_

bool protocols::antibody::design::AntibodyDesignMover::idealize_graft_cdrs_

private

Referenced by read_command_line_options(), and setup_default_graft_settings().

◆ inner_cycles_

core::Size protocols::antibody::design::AntibodyDesignMover::inner_cycles_

private

Referenced by apply_to_cdr(), parse_my_tag(), read_command_line_options(), set_inner_cycles(), and show().

◆ inner_kt_

core::Real protocols::antibody::design::AntibodyDesignMover::inner_kt_

private

Referenced by apply(), parse_my_tag(), and read_command_line_options().

◆ inner_mc_

protocols::moves::MonteCarloOP protocols::antibody::design::AntibodyDesignMover::inner_mc_ = nullptr

private

Referenced by AntibodyDesignMover(), apply(), and apply_to_cdr().

◆ instruction_file_

std::string protocols::antibody::design::AntibodyDesignMover::instruction_file_ = "NA"

private

Referenced by parse_my_tag(), read_command_line_options(), set_instruction_file(), and setup_options_classes().

◆ interface_dis_

core::Real protocols::antibody::design::AntibodyDesignMover::interface_dis_

private

Referenced by parse_my_tag(), read_command_line_options(), run_optimization_cycle(), set_interface_dis(), setup_epitope_residues(), setup_modeler(), and setup_paratope_epitope_constraints().

◆ length_based_CDRDBPose_indexes_

std::map< CDRNameEnum, std::map< core::Size, std::map< clusters::CDRClusterEnum, utility::vector1< core::Size > > > > protocols::antibody::design::AntibodyDesignMover::length_based_CDRDBPose_indexes_

private

Even Length and Cluster sampling (even_length_cluster_mc protocol)

Referenced by run_basic_mc_algorithm(), and setup_cdr_pose_sampling_strategies().

◆ light_chain_

std::string protocols::antibody::design::AntibodyDesignMover::light_chain_ = ""

private

Referenced by init_ab_info(), parse_my_tag(), and set_light_chain().

◆ mc_

protocols::moves::MonteCarloOP protocols::antibody::design::AntibodyDesignMover::mc_ = nullptr

private

Referenced by AntibodyDesignMover(), apply(), run_basic_mc_algorithm(), and run_deterministic_graft_algorithm().

◆ mc_interface_weight_

core::Real protocols::antibody::design::AntibodyDesignMover::mc_interface_weight_ = 1.0

private

Referenced by parse_my_tag().

◆ mc_optimize_dG_

bool protocols::antibody::design::AntibodyDesignMover::mc_optimize_dG_ = false

private

Referenced by apply(), parse_my_tag(), and read_command_line_options().

◆ mc_total_weight_

core::Real protocols::antibody::design::AntibodyDesignMover::mc_total_weight_ = 0.0

private

Referenced by parse_my_tag().

◆ mintype_

std::string protocols::antibody::design::AntibodyDesignMover::mintype_ = "NA"

private

Referenced by parse_my_tag(), read_command_line_options(), and setup_options_classes().

◆ modeler_

GeneralAntibodyModelerOP protocols::antibody::design::AntibodyDesignMover::modeler_ = nullptr

private

Referenced by AntibodyDesignMover(), apply(), finalize_setup(), run_graft(), run_optimization_cycle(), and setup_modeler().

◆ mutate_framework_for_cluster_

bool protocols::antibody::design::AntibodyDesignMover::mutate_framework_for_cluster_

private

Referenced by apply_to_cdr(), parse_my_tag(), and read_command_line_options().

◆ neighbor_dis_

core::Real protocols::antibody::design::AntibodyDesignMover::neighbor_dis_

private

Referenced by finalize_setup(), parse_my_tag(), read_command_line_options(), set_neighbor_dis(), setup_default_graft_settings(), and setup_modeler().

◆ num_top_designs_

core::Size protocols::antibody::design::AntibodyDesignMover::num_top_designs_

private

Referenced by check_for_top_designs(), parse_my_tag(), and set_keep_top_designs().

◆ outer_cycles_

core::Size protocols::antibody::design::AntibodyDesignMover::outer_cycles_

private

Referenced by parse_my_tag(), read_command_line_options(), run_basic_mc_algorithm(), set_outer_cycles(), and show().

◆ outer_kt_

core::Real protocols::antibody::design::AntibodyDesignMover::outer_kt_

private

Referenced by apply(), parse_my_tag(), and read_command_line_options().

◆ overhang_

core::Size protocols::antibody::design::AntibodyDesignMover::overhang_

private

Referenced by run_graft(), and set_defaults().

◆ paratope_cdrs_

utility::vector1<bool> protocols::antibody::design::AntibodyDesignMover::paratope_cdrs_

private

Referenced by parse_my_tag(), read_command_line_options(), set_defaults(), set_paratope_cdrs(), and setup_paratope_epitope_constraints().

◆ paratope_cst_mover_

constraints::ParatopeSiteConstraintMoverOP protocols::antibody::design::AntibodyDesignMover::paratope_cst_mover_ = nullptr

private

Referenced by AntibodyDesignMover(), and setup_paratope_epitope_constraints().

◆ paratope_epitope_cst_mover_

constraints::ParatopeEpitopeSiteConstraintMoverOP protocols::antibody::design::AntibodyDesignMover::paratope_epitope_cst_mover_ = nullptr

private

Referenced by AntibodyDesignMover(), and setup_paratope_epitope_constraints().

◆ primary_cdrs_

utility::vector1<CDRNameEnum> protocols::antibody::design::AntibodyDesignMover::primary_cdrs_

private

Referenced by finalize_setup(), parse_my_tag(), read_command_line_options(), and set_primary_cdrs().

◆ print_tracer_info_

bool protocols::antibody::design::AntibodyDesignMover::print_tracer_info_

private

Referenced by apply_to_cdr(), set_defaults(), and setup_random_start_pose().

◆ rb_min_post_graft_

bool protocols::antibody::design::AntibodyDesignMover::rb_min_post_graft_

private

◆ relax_cycles_

core::Size protocols::antibody::design::AntibodyDesignMover::relax_cycles_

private

Referenced by parse_my_tag(), read_command_line_options(), run_optimization_cycle(), and set_relax_cycles().

◆ remove_antigen_

bool protocols::antibody::design::AntibodyDesignMover::remove_antigen_ = false

private

Referenced by apply(), parse_my_tag(), and read_command_line_options().

◆ run_final_AIM_

bool protocols::antibody::design::AntibodyDesignMover::run_final_AIM_ = true

private

Referenced by finalize_pose(), and read_command_line_options().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::antibody::design::AntibodyDesignMover::scorefxn_ = nullptr

private

Referenced by AntibodyDesignMover(), apply(), finalize_pose(), finalize_setup(), parse_my_tag(), run_basic_mc_algorithm(), run_graft(), run_optimization_cycle(), set_scorefunction(), setup_default_graft_settings(), setup_modeler(), and setup_scorefxn().

◆ scorefxn_cart_graft_

core::scoring::ScoreFunctionOP protocols::antibody::design::AntibodyDesignMover::scorefxn_cart_graft_ = nullptr

private

Referenced by AntibodyDesignMover(), run_graft(), setup_cart_minimizer(), and setup_scorefxn().

◆ scorefxn_min_

core::scoring::ScoreFunctionOP protocols::antibody::design::AntibodyDesignMover::scorefxn_min_ = nullptr

private

Referenced by AntibodyDesignMover(), parse_my_tag(), set_scorefunction_min(), setup_modeler(), and setup_scorefxn().

◆ seq_design_creator_

AntibodySeqDesignTFCreatorOP protocols::antibody::design::AntibodyDesignMover::seq_design_creator_ = nullptr

private

Referenced by AntibodyDesignMover(), finalize_setup(), and run_optimization_cycle().

◆ seq_design_override_

utility::vector1<CDRNameEnum> protocols::antibody::design::AntibodyDesignMover::seq_design_override_

private

Referenced by parse_my_tag(), read_command_line_options(), set_seq_design_cdrs(), and setup_options_classes().

◆ stats_cutoff_

core::Size protocols::antibody::design::AntibodyDesignMover::stats_cutoff_

private

◆ top_designs_

utility::vector1< core::pose::PoseOP > protocols::antibody::design::AntibodyDesignMover::top_designs_

private

Referenced by AntibodyDesignMover(), apply(), check_for_top_designs(), finalize_setup(), get_additional_output(), get_top_designs(), and run_basic_mc_algorithm().

◆ top_scores_

utility::vector1< core::Real> protocols::antibody::design::AntibodyDesignMover::top_scores_

private

Referenced by apply(), check_for_top_designs(), finalize_setup(), and run_basic_mc_algorithm().

◆ total_permutations_

core::Size protocols::antibody::design::AntibodyDesignMover::total_permutations_

private

Referenced by finalize_setup().

◆ use_epitope_constraints_

bool protocols::antibody::design::AntibodyDesignMover::use_epitope_constraints_

private

Referenced by parse_my_tag(), read_command_line_options(), set_use_epitope_constraints(), and setup_paratope_epitope_constraints().

◆ use_light_chain_type_

bool protocols::antibody::design::AntibodyDesignMover::use_light_chain_type_

private

The documentation for this class was generated from the following files:

src/protocols/antibody/design/AntibodyDesignMover.hh
src/protocols/antibody/design/AntibodyDesignMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AntibodyDesignMover() [1/2]

◆ AntibodyDesignMover() [2/2]

◆ ~AntibodyDesignMover()

Member Function Documentation

◆ apply()

◆ apply_to_cdr()

◆ check_for_top_designs()

◆ clone()

◆ finalize_pose()

◆ finalize_setup()

◆ fresh_instance()

◆ get_additional_output()

◆ get_cdr_set_index_list()

◆ get_name()

◆ get_top_designs()

◆ graft_in_cdr()

◆ init_ab_info()

◆ initialize_cdr_set()

◆ mover_name()

◆ parse_my_tag()

◆ print_str_vec()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ read_command_line_options()

◆ run_basic_mc_algorithm()

◆ run_deterministic_graft_algorithm()

◆ run_final_IAM()

◆ run_graft()

◆ run_optimization_cycle()

◆ set_cdr_set_options()

◆ set_defaults()

◆ set_design_protocol()

◆ set_dock_first_cycles()

◆ set_dock_post_graft()

◆ set_dock_rounds()

◆ set_dock_second_cycles()

◆ set_epitope_residues()

◆ set_graft_design_cdrs()

◆ set_graft_design_options()

◆ set_inner_cycles()

◆ set_instruction_file()

◆ set_interface_dis()

◆ set_keep_top_designs()

◆ set_light_chain()

◆ set_neighbor_dis()

◆ set_outer_cycles()

◆ set_paratope_cdrs()

◆ set_primary_cdrs()

◆ set_random_start()

◆ set_relax_cycles()

◆ set_scorefunction()

◆ set_scorefunction_min()

◆ set_seq_design_cdrs()

◆ set_seq_design_options()

◆ set_use_epitope_constraints()

◆ setup_cart_minimizer()

◆ setup_cdr_pose_sampling_strategies()

◆ setup_default_graft_settings()

◆ setup_epitope_residues()

◆ setup_modeler()

◆ setup_native_clusters()

◆ setup_native_sequence()

◆ setup_options_classes()

◆ setup_paratope_epitope_constraints()

◆ setup_random_start_pose()

◆ setup_scorefxn()

◆ show()

Member Data Documentation

◆ ab_info_

◆ accept_log_

◆ adapt_graft_

◆ add_log_to_pose_

◆ additional_outputs_returned_