Generates pre-configured general MoverOPs for use in AntibodyDesign and modeling Helper functions for setting up FoldTrees. Can set the generated mover to apply, which will include the needed FoldTree and any changing of typeset. FoldTree stuff will eventually be refactored in favor of the TopologyBroker/Environment system. More...

#include <AntibodyDesignMoverGenerator.hh>

Inheritance diagram for protocols::antibody::design::AntibodyDesignMoverGenerator:

[legend]

Public Member Functions
	AntibodyDesignMoverGenerator ()
	Default constructor for RosettaScripts. Do not use. More...

	AntibodyDesignMoverGenerator (AntibodyInfoCOP ab_info)

virtual	~AntibodyDesignMoverGenerator ()

void	set_as_mover (bool setting)
	Set the last setup mover as the current mover to call during apply. Default is True. See apply for more details. More...

virtual void	apply (core::pose::Pose &pose)
	Apply the last mover generated or run the set mover. Will do the following: 1) Run any set ChangeFoldTreeMover. This is set by any generated class if needed. 2) Will call set_cutpoint_variants. If there are none, no harm done. 3) Call the set mover's apply function. 4) Remove cutpoint variants and any coord csts left over from [ relax ]. Foldtree calls will eventually be replaced with the Environment/Topology Broker system. More...

simple_moves::ChangeAndResetFoldTreeMoverOP	generate_protocol_mover () const
	Generate a ChangeAndResetFoldTreeMover from any set mover, FoldTree mover, and ScoreFunction. Be careful of needed cutpoint variants. If needed, generate everything manually!! More...

void	set_defaults ()

void	set_cdr (CDRNameEnum const cdr, bool setting)
	Set to model CDRs. Default is all of them false. More...

void	set_cdr_only (CDRNameEnum const cdr, bool setting)
	Set to model only one cdr, or all others but one. More...

void	set_cdrs (utility::vector1< bool > cdrs)

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

virtual void	set_mover (protocols::moves::MoverOP mover)
	Set the mover for apply Generator functions will set this themselves, but can be changed before apply. More...

virtual protocols::moves::MoverOP	mover () const
	Get the currently set mover. More...

void	set_ft_mover (protocols::moves::ChangeFoldTreeMoverOP ft_mover)
	Set the particular ChangeFoldTreeMover to use. Generator functions will set this themselves or to NULL, but can be changed before apply. More...

protocols::moves::ChangeFoldTreeMoverCOP	ft_mover () const

void	set_task_factory (core::pack::task::TaskFactoryOP tf)
	Override the TaskFactory that will be created and use this instead (for everything that uses a task!) More...

void	interface_detection_dis (core::Real interface_distance)
	Set a value for interface detection across the class. More...

core::Real	interface_detection_dis () const

void	neighbor_detection_dis (core::Real neighbor_distance)
	Set a value for neighbor detection across the class. More...

core::Real	neighbor_detection_dis () const

void	stem_size (core::Size overhang)
	How many residues on either side of the CDR to include in CDR - modeling? (2 is a good number - more if not North) More...

void	ab_dock_chains (std::string ab_dock_chains)
	Set the ab_dock chains, which will be used for any docking or minimization on the jump. (LH_A, L_H, etc. - A for antigen) More...

void	set_min_interface (bool min_interface)
	Set to minimize the set interface (during minimization/relax) Not implemented while minimizing CDRs as well. More...

void	set_min_sc (bool min_sc)
	Set to minimize sidechains (add to movemap) More...

void	set_include_neighbor_sc (bool include_neighbor_sc)
	Set to include neighbor side chains during any regional repacking. More...

void	set_cartmin (bool cartmin)
	Use cartesian minimization for MinMovers Setup appropriate scorefunction and min settings. More...

void	set_dualspace (bool dualspace)
	Use DualSpace relax during FastRelax Setup appropriate scorefunction and settings. More...

void	set_start_coord_csts (bool coord_csts)
	Set to use starting coordinate constraints during relax. More...

void	set_dock_low_res_scorefunction (core::scoring::ScoreFunctionCOP scorefxn)

void	set_dock_high_res_scorefunction (core::scoring::ScoreFunctionCOP scorefxn)

void	set_high_res_dock_outer_cycles (core::Size first_cycle=3)
	Set the outer cycles for DockMCM. Normal in docking is 4. More...

void	set_high_res_dock_inner_cycles (core::Size second_cycle=10)
	Set the inner cycles for DockMCM. Normal in docking is 45. More...

void	setup_general_min_foldtree (core::pose::Pose const &pose, protocols::moves::ChangeFoldTreeMover &ft_mover)

void	setup_dock_foldtree (core::pose::Pose const &pose, protocols::moves::ChangeFoldTreeMover &ft_mover)

minimization_packing::PackRotamersMoverOP	generate_repack_cdrs (core::pose::Pose const &pose)
	Generate a packer and optionally set as the current mover. More...

void	setup_repack_cdrs (core::pose::Pose const &pose, minimization_packing::PackRotamersMoverOP packer)

protocols::minimization_packing::PackRotamersMoverOP	generate_repack_antigen_ab_interface (Pose const &pose)
	Get a pre-configured Packer to repack the interface between Antibody and Antigen. If set_as_mover is true, will set the needed ab-ag foldtree to this class which the task op will use. More...

void	setup_repack_antigen_ab_interface (core::pose::Pose const &pose, minimization_packing::PackRotamersMoverOP packer)
	Configure a packer to repack the interface between Antibody and Antigen If set_as_mover is true, will set the needed ab-ag foldtree to this class which the task op will use. More...

minimization_packing::MinMoverOP	generate_minimizer (core::pose::Pose &pose)
	Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin). If set_as_mover is true, will set the appropriate FoldTree to this class. More...

void	setup_minimizer (core::pose::Pose &pose, minimization_packing::MinMoverOP min_mover)
	Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin). If set_as_mover is true, will set the appropriate FoldTree to this class. More...

relax::FastRelaxOP	generate_relax (core::pose::Pose &pose)
	Generate FastRelax of CDRs +/or Interface. More...

void	setup_relax (core::pose::Pose &pose, relax::FastRelaxOP rel)
	Setup FastRelax of CDRs +/or Interface. More...

docking::DockingLowResOP	generate_dock_low_res (core::pose::Pose const &pose)
	Configure a low-res docking mover. No repacking, but will switch chains. Using A for designation of Antigen chains. Not full antigen chains. (L_A, LH_A, L_H, etc.) More...

void	setup_dock_low_res (core::pose::Pose const &pose, docking::DockingLowResOP docker)

docking::DockMCMProtocolOP	generate_dock_high_res (core::pose::Pose const &pose)
	Configure a high-res, DockMCMProtocol for docking. More...

void	setup_dock_high_res (core::pose::Pose const &pose, docking::DockMCMProtocolOP docker)

void	set_cdr_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, bool setting)
	Set a range of CDRs. More...

core::kinematics::MoveMapOP	get_cdrs_movemap_with_overhang (core::pose::Pose &pose, bool min_bb=true, bool min_sc=true, bool include_neighbor_sc=true, bool include_neighbor_bb=false) const

core::kinematics::MoveMapOP	get_movemap_from_task (core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task) const

virtual std::string	get_name () const

Private Member Functions
void	read_command_line_options ()

void	setup_scorefxns ()

void	setup_task_operations ()

core::pack::task::TaskFactoryOP	get_dock_tf ()

Private Attributes
AntibodyInfoCOP	ab_info_

protocols::moves::MoverOP	mover_

protocols::moves::ChangeFoldTreeMoverOP	ft_mover_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	docking_scorefxn_low_

core::scoring::ScoreFunctionOP	docking_scorefxn_high_

core::pack::task::TaskFactoryOP	interface_tf_

core::pack::task::TaskFactoryOP	tf_

core::pack::task::TaskFactoryOP	set_tf_

protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP	loops_operation_

core::pack::task::operation::InitializeFromCommandlineOP	cmd_line_operation_

core::pack::task::operation::RestrictToRepackingOP	restrict_design_operation_

core::Real	interface_dis_

core::Real	neighbor_dis_

std::string	ab_dock_chains_

utility::vector1< bool >	model_cdrs_

core::Size	overhang_

bool	min_interface_

bool	min_sc_

bool	include_neighbor_sc_

bool	cartmin_

bool	dualspace_

bool	start_coord_csts_

core::Size	high_res_dock_outer_cycles_

core::Size	high_res_dock_inner_cycles_

bool	set_as_mover_

bool	use_ft_mover_

Detailed Description

Generates pre-configured general MoverOPs for use in AntibodyDesign and modeling Helper functions for setting up FoldTrees. Can set the generated mover to apply, which will include the needed FoldTree and any changing of typeset. FoldTree stuff will eventually be refactored in favor of the TopologyBroker/Environment system.

Way too complicated for its own good. Should have used separate setup movers.

Constructor & Destructor Documentation

◆ AntibodyDesignMoverGenerator() [1/2]

protocols::antibody::design::AntibodyDesignMoverGenerator::AntibodyDesignMoverGenerator ( )

Default constructor for RosettaScripts. Do not use.

References ft_mover_, read_command_line_options(), set_defaults(), setup_scorefxns(), and setup_task_operations().

◆ AntibodyDesignMoverGenerator() [2/2]

protocols::antibody::design::AntibodyDesignMoverGenerator::AntibodyDesignMoverGenerator ( AntibodyInfoCOP ab_info )

References ft_mover_, read_command_line_options(), set_defaults(), setup_scorefxns(), and setup_task_operations().

◆ ~AntibodyDesignMoverGenerator()

protocols::antibody::design::AntibodyDesignMoverGenerator::~AntibodyDesignMoverGenerator ( )

virtual

Member Function Documentation

◆ ab_dock_chains()

void protocols::antibody::design::AntibodyDesignMoverGenerator::ab_dock_chains ( std::string ab_dock_chains )

Set the ab_dock chains, which will be used for any docking or minimization on the jump. (LH_A, L_H, etc. - A for antigen)

References ab_dock_chains_.

◆ apply()

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

virtual

Apply the last mover generated or run the set mover. Will do the following: 1) Run any set ChangeFoldTreeMover. This is set by any generated class if needed. 2) Will call set_cutpoint_variants. If there are none, no harm done. 3) Call the set mover's apply function. 4) Remove cutpoint variants and any coord csts left over from [ relax ]. Foldtree calls will eventually be replaced with the Environment/Topology Broker system.

References cartmin_, ft_mover_, mover_, beta_nonlocal::pose, scorefxn_, start_coord_csts_, TR, use_ft_mover_, and utility_exit_with_message.

Referenced by pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase::__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_keys_from_sm_data(), pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute(), and protocols::antibody::model_cdrs().

◆ ft_mover()

moves::ChangeFoldTreeMoverCOP protocols::antibody::design::AntibodyDesignMoverGenerator::ft_mover ( ) const

References ft_mover_.

Referenced by set_ft_mover(), setup_dock_foldtree(), and setup_general_min_foldtree().

◆ generate_dock_high_res()

protocols::docking::DockMCMProtocolOP protocols::antibody::design::AntibodyDesignMoverGenerator::generate_dock_high_res ( core::pose::Pose const & pose )

Configure a high-res, DockMCMProtocol for docking.

References docking_scorefxn_high_, beta_nonlocal::pose, scorefxn_, and setup_dock_high_res().

◆ generate_dock_low_res()

DockingLowResOP protocols::antibody::design::AntibodyDesignMoverGenerator::generate_dock_low_res ( core::pose::Pose const & pose )

Configure a low-res docking mover. No repacking, but will switch chains. Using A for designation of Antigen chains. Not full antigen chains. (L_A, LH_A, L_H, etc.)

References beta_nonlocal::pose, and setup_dock_low_res().

◆ generate_minimizer()

MinMoverOP protocols::antibody::design::AntibodyDesignMoverGenerator::generate_minimizer ( core::pose::Pose & pose )

Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin). If set_as_mover is true, will set the appropriate FoldTree to this class.

References vancomycin::min_mover, beta_nonlocal::pose, and setup_minimizer().

◆ generate_protocol_mover()

simple_moves::ChangeAndResetFoldTreeMoverOP protocols::antibody::design::AntibodyDesignMoverGenerator::generate_protocol_mover ( ) const

Generate a ChangeAndResetFoldTreeMover from any set mover, FoldTree mover, and ScoreFunction. Be careful of needed cutpoint variants. If needed, generate everything manually!!

References ft_mover_, mover_, and scorefxn_.

◆ generate_relax()

FastRelaxOP protocols::antibody::design::AntibodyDesignMoverGenerator::generate_relax ( core::pose::Pose & pose )

Generate FastRelax of CDRs +/or Interface.

Any Cluster Constraints should already be set. Optionally use start_coordinate constraints. All coordinate constraints on the pose will then be removed in this classes apply.

References beta_nonlocal::pose, test.G200_Module_Region::rel, and setup_relax().

Referenced by protocols::antibody::model_cdrs().

◆ generate_repack_antigen_ab_interface()

PackRotamersMoverOP protocols::antibody::design::AntibodyDesignMoverGenerator::generate_repack_antigen_ab_interface ( Pose const & pose )

Get a pre-configured Packer to repack the interface between Antibody and Antigen. If set_as_mover is true, will set the needed ab-ag foldtree to this class which the task op will use.

References ab_info_, beta_nonlocal::pose, setup_repack_antigen_ab_interface(), and TR.

◆ generate_repack_cdrs()

PackRotamersMoverOP protocols::antibody::design::AntibodyDesignMoverGenerator::generate_repack_cdrs ( core::pose::Pose const & pose )

Generate a packer and optionally set as the current mover.

References beta_nonlocal::pose, scorefxn_, setup_repack_cdrs(), and basic::options::OptionKeys::task_operations::task_operations.

Referenced by protocols::antibody::model_cdrs().

◆ get_cdrs_movemap_with_overhang()

MoveMapOP protocols::antibody::design::AntibodyDesignMoverGenerator::get_cdrs_movemap_with_overhang	(	core::pose::Pose &	pose,
		bool	min_bb = `true`,
		bool	min_sc = `true`,
		bool	include_neighbor_sc = `true`,
		bool	include_neighbor_bb = `false`
	)		const

References ab_info_, create_a3b_hbs::i, beta_nonlocal::mm, model_cdrs_, neighbor_dis_, overhang_, beta_nonlocal::pose, select_loop_residues(), and x.

Referenced by setup_minimizer(), and setup_relax().

◆ get_dock_tf()

core::pack::task::TaskFactoryOP protocols::antibody::design::AntibodyDesignMoverGenerator::get_dock_tf ( )

private

References cmd_line_operation_, interface_dis_, restrict_design_operation_, and test.G200_Module_Region::tf.

Referenced by setup_dock_high_res().

◆ get_movemap_from_task()

MoveMapOP protocols::antibody::design::AntibodyDesignMoverGenerator::get_movemap_from_task	(	core::pose::Pose const &	pose,
		core::pack::task::PackerTaskCOP	task
	)		const

References create_a3b_hbs::i, beta_nonlocal::mm, beta_nonlocal::pose, and vancomycin::task.

◆ get_name()

virtual std::string protocols::antibody::design::AntibodyDesignMoverGenerator::get_name ( ) const

inlinevirtual

◆ interface_detection_dis() [1/2]

core::Real protocols::antibody::design::AntibodyDesignMoverGenerator::interface_detection_dis ( ) const

inline

References interface_dis_.

Referenced by read_command_line_options().

◆ interface_detection_dis() [2/2]

void protocols::antibody::design::AntibodyDesignMoverGenerator::interface_detection_dis ( core::Real interface_distance )

Set a value for interface detection across the class.

References interface_dis_, and basic::options::OptionKeys::carbohydrates::glycopeptide_docking::interface_distance.

◆ mover()

protocols::moves::MoverOP protocols::antibody::design::AntibodyDesignMoverGenerator::mover ( ) const

virtual

Get the currently set mover.

References mover_.

Referenced by set_mover().

◆ neighbor_detection_dis() [1/2]

core::Real protocols::antibody::design::AntibodyDesignMoverGenerator::neighbor_detection_dis ( ) const

inline

References neighbor_dis_.

Referenced by read_command_line_options().

◆ neighbor_detection_dis() [2/2]

void protocols::antibody::design::AntibodyDesignMoverGenerator::neighbor_detection_dis ( core::Real neighbor_distance )

Set a value for neighbor detection across the class.

References neighbor_dis_.

Referenced by protocols::antibody::model_cdrs().

◆ read_command_line_options()

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

private

References interface_detection_dis(), basic::options::OptionKeys::antibody::design::interface_dis, neighbor_detection_dis(), basic::options::OptionKeys::antibody::design::neighbor_dis, and basic::options::option.

Referenced by AntibodyDesignMoverGenerator().

◆ set_as_mover()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_as_mover ( bool setting )

Set the last setup mover as the current mover to call during apply. Default is True. See apply for more details.

References set_as_mover_.

◆ set_cartmin()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_cartmin ( bool cartmin )

Use cartesian minimization for MinMovers Setup appropriate scorefunction and min settings.

References basic::options::OptionKeys::carbohydrates::glycan_sampler::cartmin, and cartmin_.

◆ set_cdr()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_cdr	(	CDRNameEnum const	cdr,
		bool	setting
	)

Set to model CDRs. Default is all of them false.

References ab_info_, model_cdrs_, and TR.

Referenced by set_cdr_only(), and set_cdr_range().

◆ set_cdr_only()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_cdr_only	(	CDRNameEnum const	cdr,
		bool	setting
	)

Set to model only one cdr, or all others but one.

References set_cdr(), and set_cdr_range().

◆ set_cdr_range()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_cdr_range	(	CDRNameEnum const	cdr_start,
		CDRNameEnum const	cdr_end,
		bool	setting
	)

Set a range of CDRs.

References create_a3b_hbs::i, and set_cdr().

Referenced by protocols::antibody::model_cdrs(), and set_cdr_only().

◆ set_cdrs()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_cdrs ( utility::vector1< bool > cdrs )

References ab_info_, test.G201_Module_Structure::cdrs, create_a3b_hbs::i, and model_cdrs_.

◆ set_defaults()

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

References cartmin_, dualspace_, high_res_dock_inner_cycles_, high_res_dock_outer_cycles_, include_neighbor_sc_, min_interface_, min_sc_, model_cdrs_, overhang_, set_as_mover_, start_coord_csts_, and use_ft_mover_.

Referenced by AntibodyDesignMoverGenerator().

◆ set_dock_high_res_scorefunction()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_dock_high_res_scorefunction ( core::scoring::ScoreFunctionCOP scorefxn )

References docking_scorefxn_high_, and oop_conformations::scorefxn.

◆ set_dock_low_res_scorefunction()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_dock_low_res_scorefunction ( core::scoring::ScoreFunctionCOP scorefxn )

References docking_scorefxn_low_, and oop_conformations::scorefxn.

◆ set_dualspace()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_dualspace ( bool dualspace )

Use DualSpace relax during FastRelax Setup appropriate scorefunction and settings.

References basic::options::OptionKeys::relax::dualspace, and dualspace_.

◆ set_ft_mover()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_ft_mover ( protocols::moves::ChangeFoldTreeMoverOP ft_mover )

Set the particular ChangeFoldTreeMover to use. Generator functions will set this themselves or to NULL, but can be changed before apply.

References ft_mover(), and ft_mover_.

◆ set_high_res_dock_inner_cycles()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_high_res_dock_inner_cycles ( core::Size second_cycle = 10 )

Set the inner cycles for DockMCM. Normal in docking is 45.

References high_res_dock_inner_cycles_.

◆ set_high_res_dock_outer_cycles()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_high_res_dock_outer_cycles ( core::Size first_cycle = 3 )

Set the outer cycles for DockMCM. Normal in docking is 4.

References high_res_dock_outer_cycles_.

◆ set_include_neighbor_sc()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_include_neighbor_sc ( bool include_neighbor_sc )

Set to include neighbor side chains during any regional repacking.

References include_neighbor_sc_.

Referenced by protocols::antibody::model_cdrs().

◆ set_min_interface()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_min_interface ( bool min_interface )

Set to minimize the set interface (during minimization/relax) Not implemented while minimizing CDRs as well.

References min_interface_.

◆ set_min_sc()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_min_sc ( bool min_sc )

Set to minimize sidechains (add to movemap)

References min_sc_.

Referenced by protocols::antibody::model_cdrs().

◆ set_mover()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_mover ( protocols::moves::MoverOP mover )

virtual

Set the mover for apply Generator functions will set this themselves, but can be changed before apply.

References mover(), and mover_.

◆ set_scorefunction()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_scorefunction ( core::scoring::ScoreFunctionCOP scorefxn )

References oop_conformations::scorefxn, and scorefxn_.

◆ set_start_coord_csts()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_start_coord_csts ( bool coord_csts )

Set to use starting coordinate constraints during relax.

References start_coord_csts_.

◆ set_task_factory()

void protocols::antibody::design::AntibodyDesignMoverGenerator::set_task_factory ( core::pack::task::TaskFactoryOP tf )

Override the TaskFactory that will be created and use this instead (for everything that uses a task!)

Hack for graft cdrs extremely specialized tf for design and to limit the amount of casting that would be done otherwise. Use of AntibodySeqDesignTFCreator or helper utility functions for TF creation are recommended. A better way here is preferred.

References set_tf_, and test.G200_Module_Region::tf.

◆ setup_dock_foldtree()

void protocols::antibody::design::AntibodyDesignMoverGenerator::setup_dock_foldtree	(	core::pose::Pose const &	pose,
		protocols::moves::ChangeFoldTreeMover &	ft_mover
	)

References ab_dock_chains_, ab_info_, test.T020_Pose_Bindings::ft, ft_mover(), beta_nonlocal::pose, and TR.

Referenced by setup_dock_high_res(), setup_dock_low_res(), and setup_repack_antigen_ab_interface().

◆ setup_dock_high_res()

void protocols::antibody::design::AntibodyDesignMoverGenerator::setup_dock_high_res	(	core::pose::Pose const &	pose,
		docking::DockMCMProtocolOP	docker
	)

References docking_scorefxn_high_, ft_mover_, get_dock_tf(), high_res_dock_inner_cycles_, high_res_dock_outer_cycles_, mover_, scorefxn_, set_as_mover_, set_tf_, setup_dock_foldtree(), and use_ft_mover_.

Referenced by generate_dock_high_res().

◆ setup_dock_low_res()

void protocols::antibody::design::AntibodyDesignMoverGenerator::setup_dock_low_res	(	core::pose::Pose const &	pose,
		docking::DockingLowResOP	docker
	)

References docking_scorefxn_low_, ft_mover_, mover_, beta_nonlocal::pose, test.Workshop5test::seq_mover, set_as_mover_, setup_dock_foldtree(), and use_ft_mover_.

Referenced by generate_dock_low_res().

◆ setup_general_min_foldtree()

void protocols::antibody::design::AntibodyDesignMoverGenerator::setup_general_min_foldtree	(	core::pose::Pose const &	pose,
		protocols::moves::ChangeFoldTreeMover &	ft_mover
	)

References ab_dock_chains_, ab_info_, fold_tree_from_loops(), test.T020_Pose_Bindings::ft, ft_mover(), create_a3b_hbs::i, min_interface_, model_cdrs_, overhang_, beta_nonlocal::pose, TR, and utility_exit_with_message.

Referenced by setup_minimizer(), and setup_relax().

◆ setup_minimizer()

void protocols::antibody::design::AntibodyDesignMoverGenerator::setup_minimizer	(	core::pose::Pose &	pose,
		minimization_packing::MinMoverOP	min_mover
	)

Vanilla minimizer using dfpmin_armijo_nonmonotone at .001 tolerance (or lfbgs for cartmin). If set_as_mover is true, will set the appropriate FoldTree to this class.

References cartmin_, ft_mover_, get_cdrs_movemap_with_overhang(), include_neighbor_sc_, min_interface_, vancomycin::min_mover, min_sc_, beta_nonlocal::mm, mover_, beta_nonlocal::pose, scorefxn_, set_as_mover_, setup_general_min_foldtree(), and use_ft_mover_.

Referenced by generate_minimizer().

◆ setup_relax()

void protocols::antibody::design::AntibodyDesignMoverGenerator::setup_relax	(	core::pose::Pose &	pose,
		relax::FastRelaxOP	rel
	)

Setup FastRelax of CDRs +/or Interface.

Any Cluster Constraints should already be set. Optionally use start_coordinate constraints. All coordinate constraints on the pose will then be removed in this classes apply.

References ab_info_, cartmin_, cmd_line_operation_, dualspace_, ft_mover_, get_cdrs_movemap_with_overhang(), include_neighbor_sc_, loops_operation_, min_sc_, beta_nonlocal::mm, model_cdrs_, mover_, neighbor_dis_, overhang_, beta_nonlocal::pose, test.G200_Module_Region::rel, restrict_design_operation_, scorefxn_, set_as_mover_, set_tf_, setup_general_min_foldtree(), start_coord_csts_, tf_, and use_ft_mover_.

Referenced by generate_relax().

◆ setup_repack_antigen_ab_interface()

void protocols::antibody::design::AntibodyDesignMoverGenerator::setup_repack_antigen_ab_interface	(	core::pose::Pose const &	pose,
		minimization_packing::PackRotamersMoverOP	packer
	)

Configure a packer to repack the interface between Antibody and Antigen If set_as_mover is true, will set the needed ab-ag foldtree to this class which the task op will use.

References ab_dock_chains_, ab_info_, ft_mover_, interface_tf_, mover_, scorefxn_, set_as_mover_, set_tf_, setup_dock_foldtree(), TR, and use_ft_mover_.

Referenced by generate_repack_antigen_ab_interface().

◆ setup_repack_cdrs()

void protocols::antibody::design::AntibodyDesignMoverGenerator::setup_repack_cdrs	(	core::pose::Pose const &	pose,
		minimization_packing::PackRotamersMoverOP	packer
	)

References ab_info_, cmd_line_operation_, include_neighbor_sc_, loops_operation_, model_cdrs_, mover_, neighbor_dis_, overhang_, beta_nonlocal::pose, restrict_design_operation_, set_as_mover_, set_tf_, tf_, and use_ft_mover_.

Referenced by generate_repack_cdrs().

◆ setup_scorefxns()

void protocols::antibody::design::AntibodyDesignMoverGenerator::setup_scorefxns ( )

private

References pyrosetta.io::create_score_function, docking_scorefxn_high_, docking_scorefxn_low_, pyrosetta.distributed.io::get_score_function(), and scorefxn_.

Referenced by AntibodyDesignMoverGenerator().

◆ setup_task_operations()

void protocols::antibody::design::AntibodyDesignMoverGenerator::setup_task_operations ( )

private

References cmd_line_operation_, interface_dis_, interface_tf_, loops_operation_, restrict_design_operation_, and tf_.

Referenced by AntibodyDesignMoverGenerator().

◆ stem_size()

void protocols::antibody::design::AntibodyDesignMoverGenerator::stem_size ( core::Size overhang )

How many residues on either side of the CDR to include in CDR - modeling? (2 is a good number - more if not North)

References overhang_.

Referenced by protocols::antibody::model_cdrs().

Member Data Documentation

◆ ab_dock_chains_

std::string protocols::antibody::design::AntibodyDesignMoverGenerator::ab_dock_chains_

private

Referenced by ab_dock_chains(), setup_dock_foldtree(), setup_general_min_foldtree(), and setup_repack_antigen_ab_interface().

◆ ab_info_

AntibodyInfoCOP protocols::antibody::design::AntibodyDesignMoverGenerator::ab_info_

private

Referenced by generate_repack_antigen_ab_interface(), get_cdrs_movemap_with_overhang(), set_cdr(), set_cdrs(), setup_dock_foldtree(), setup_general_min_foldtree(), setup_relax(), setup_repack_antigen_ab_interface(), and setup_repack_cdrs().

◆ cartmin_

bool protocols::antibody::design::AntibodyDesignMoverGenerator::cartmin_

private

Referenced by apply(), set_cartmin(), set_defaults(), setup_minimizer(), and setup_relax().

◆ cmd_line_operation_

core::pack::task::operation::InitializeFromCommandlineOP protocols::antibody::design::AntibodyDesignMoverGenerator::cmd_line_operation_

private

Referenced by get_dock_tf(), setup_relax(), setup_repack_cdrs(), and setup_task_operations().

◆ docking_scorefxn_high_

core::scoring::ScoreFunctionOP protocols::antibody::design::AntibodyDesignMoverGenerator::docking_scorefxn_high_

private

Referenced by generate_dock_high_res(), set_dock_high_res_scorefunction(), setup_dock_high_res(), and setup_scorefxns().

◆ docking_scorefxn_low_

core::scoring::ScoreFunctionOP protocols::antibody::design::AntibodyDesignMoverGenerator::docking_scorefxn_low_

private

Referenced by set_dock_low_res_scorefunction(), setup_dock_low_res(), and setup_scorefxns().

◆ dualspace_

bool protocols::antibody::design::AntibodyDesignMoverGenerator::dualspace_

private

Referenced by set_defaults(), set_dualspace(), and setup_relax().

◆ ft_mover_

protocols::moves::ChangeFoldTreeMoverOP protocols::antibody::design::AntibodyDesignMoverGenerator::ft_mover_

private

Referenced by AntibodyDesignMoverGenerator(), apply(), ft_mover(), generate_protocol_mover(), set_ft_mover(), setup_dock_high_res(), setup_dock_low_res(), setup_minimizer(), setup_relax(), and setup_repack_antigen_ab_interface().

◆ high_res_dock_inner_cycles_

core::Size protocols::antibody::design::AntibodyDesignMoverGenerator::high_res_dock_inner_cycles_

private

Referenced by set_defaults(), set_high_res_dock_inner_cycles(), and setup_dock_high_res().

◆ high_res_dock_outer_cycles_

core::Size protocols::antibody::design::AntibodyDesignMoverGenerator::high_res_dock_outer_cycles_

private

Referenced by set_defaults(), set_high_res_dock_outer_cycles(), and setup_dock_high_res().

◆ include_neighbor_sc_

bool protocols::antibody::design::AntibodyDesignMoverGenerator::include_neighbor_sc_

private

Referenced by set_defaults(), set_include_neighbor_sc(), setup_minimizer(), setup_relax(), and setup_repack_cdrs().

◆ interface_dis_

core::Real protocols::antibody::design::AntibodyDesignMoverGenerator::interface_dis_

private

Referenced by get_dock_tf(), interface_detection_dis(), and setup_task_operations().

◆ interface_tf_

core::pack::task::TaskFactoryOP protocols::antibody::design::AntibodyDesignMoverGenerator::interface_tf_

private

Referenced by setup_repack_antigen_ab_interface(), and setup_task_operations().

◆ loops_operation_

protocols::simple_task_operations::RestrictToLoopsAndNeighborsOP protocols::antibody::design::AntibodyDesignMoverGenerator::loops_operation_

private

Referenced by setup_relax(), setup_repack_cdrs(), and setup_task_operations().

◆ min_interface_

bool protocols::antibody::design::AntibodyDesignMoverGenerator::min_interface_

private

Referenced by set_defaults(), set_min_interface(), setup_general_min_foldtree(), and setup_minimizer().

◆ min_sc_

bool protocols::antibody::design::AntibodyDesignMoverGenerator::min_sc_

private

Referenced by set_defaults(), set_min_sc(), setup_minimizer(), and setup_relax().

◆ model_cdrs_

utility::vector1<bool> protocols::antibody::design::AntibodyDesignMoverGenerator::model_cdrs_

private

Referenced by get_cdrs_movemap_with_overhang(), set_cdr(), set_cdrs(), set_defaults(), setup_general_min_foldtree(), setup_relax(), and setup_repack_cdrs().

◆ mover_

protocols::moves::MoverOP protocols::antibody::design::AntibodyDesignMoverGenerator::mover_

private

Referenced by apply(), generate_protocol_mover(), mover(), set_mover(), setup_dock_high_res(), setup_dock_low_res(), setup_minimizer(), setup_relax(), setup_repack_antigen_ab_interface(), and setup_repack_cdrs().

◆ neighbor_dis_

core::Real protocols::antibody::design::AntibodyDesignMoverGenerator::neighbor_dis_

private

Referenced by get_cdrs_movemap_with_overhang(), neighbor_detection_dis(), setup_relax(), and setup_repack_cdrs().

◆ overhang_

core::Size protocols::antibody::design::AntibodyDesignMoverGenerator::overhang_

private

Referenced by get_cdrs_movemap_with_overhang(), set_defaults(), setup_general_min_foldtree(), setup_relax(), setup_repack_cdrs(), and stem_size().

◆ restrict_design_operation_

core::pack::task::operation::RestrictToRepackingOP protocols::antibody::design::AntibodyDesignMoverGenerator::restrict_design_operation_

private

Referenced by get_dock_tf(), setup_relax(), setup_repack_cdrs(), and setup_task_operations().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::antibody::design::AntibodyDesignMoverGenerator::scorefxn_

private

Referenced by apply(), generate_dock_high_res(), generate_protocol_mover(), generate_repack_cdrs(), set_scorefunction(), setup_dock_high_res(), setup_minimizer(), setup_relax(), setup_repack_antigen_ab_interface(), and setup_scorefxns().

◆ set_as_mover_

bool protocols::antibody::design::AntibodyDesignMoverGenerator::set_as_mover_

private

Referenced by set_as_mover(), set_defaults(), setup_dock_high_res(), setup_dock_low_res(), setup_minimizer(), setup_relax(), setup_repack_antigen_ab_interface(), and setup_repack_cdrs().

◆ set_tf_

core::pack::task::TaskFactoryOP protocols::antibody::design::AntibodyDesignMoverGenerator::set_tf_

private

Referenced by set_task_factory(), setup_dock_high_res(), setup_relax(), setup_repack_antigen_ab_interface(), and setup_repack_cdrs().

◆ start_coord_csts_

bool protocols::antibody::design::AntibodyDesignMoverGenerator::start_coord_csts_

private

Referenced by apply(), set_defaults(), set_start_coord_csts(), and setup_relax().

◆ tf_

core::pack::task::TaskFactoryOP protocols::antibody::design::AntibodyDesignMoverGenerator::tf_

private

Referenced by setup_relax(), setup_repack_cdrs(), and setup_task_operations().

◆ use_ft_mover_

bool protocols::antibody::design::AntibodyDesignMoverGenerator::use_ft_mover_

private

Referenced by apply(), set_defaults(), setup_dock_high_res(), setup_dock_low_res(), setup_minimizer(), setup_relax(), setup_repack_antigen_ab_interface(), and setup_repack_cdrs().

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

src/apps/pilot/jadolfbr/AntibodyDesignMoverGenerator.hh
src/apps/pilot/jadolfbr/AntibodyDesignMoverGenerator.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AntibodyDesignMoverGenerator() [1/2]

◆ AntibodyDesignMoverGenerator() [2/2]

◆ ~AntibodyDesignMoverGenerator()

Member Function Documentation

◆ ab_dock_chains()

◆ apply()

◆ ft_mover()

◆ generate_dock_high_res()

◆ generate_dock_low_res()

◆ generate_minimizer()

◆ generate_protocol_mover()

◆ generate_relax()

◆ generate_repack_antigen_ab_interface()

◆ generate_repack_cdrs()

◆ get_cdrs_movemap_with_overhang()

◆ get_dock_tf()

◆ get_movemap_from_task()

◆ get_name()

◆ interface_detection_dis() [1/2]

◆ interface_detection_dis() [2/2]

◆ mover()

◆ neighbor_detection_dis() [1/2]

◆ neighbor_detection_dis() [2/2]

◆ read_command_line_options()

◆ set_as_mover()

◆ set_cartmin()

◆ set_cdr()

◆ set_cdr_only()

◆ set_cdr_range()

◆ set_cdrs()

◆ set_defaults()

◆ set_dock_high_res_scorefunction()

◆ set_dock_low_res_scorefunction()

◆ set_dualspace()

◆ set_ft_mover()

◆ set_high_res_dock_inner_cycles()

◆ set_high_res_dock_outer_cycles()

◆ set_include_neighbor_sc()

◆ set_min_interface()

◆ set_min_sc()

◆ set_mover()

◆ set_scorefunction()

◆ set_start_coord_csts()

◆ set_task_factory()

◆ setup_dock_foldtree()

◆ setup_dock_high_res()

◆ setup_dock_low_res()

◆ setup_general_min_foldtree()

◆ setup_minimizer()

◆ setup_relax()

◆ setup_repack_antigen_ab_interface()

◆ setup_repack_cdrs()

◆ setup_scorefxns()

◆ setup_task_operations()

◆ stem_size()

Member Data Documentation

◆ ab_dock_chains_

◆ ab_info_

◆ cartmin_

◆ cmd_line_operation_

◆ docking_scorefxn_high_

◆ docking_scorefxn_low_

◆ dualspace_

◆ ft_mover_

◆ high_res_dock_inner_cycles_

◆ high_res_dock_outer_cycles_

◆ include_neighbor_sc_

◆ interface_dis_

◆ interface_tf_

◆ loops_operation_

◆ min_interface_

◆ min_sc_

◆ model_cdrs_

◆ mover_

◆ neighbor_dis_