Class that runs the modeling for AntibodyDesign protocols. Could be moved to antibody. More...

#include <AntibodyDesignModeler.hh>

Public Member Functions
	AntibodyDesignModeler (AntibodyInfoOP ab_info)

virtual	~AntibodyDesignModeler ()

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

void	set_scorefunction (ScoreFunctionCOP scorefxn)

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

void	set_neighbor_detection_dis (core::Real neighbor_distance)

void	set_ab_dock_chains (std::string ab_dock_chains)
	Override the command line default of LH to L or H or something strange. Used primarily for bivalent antibody design, or if you are designing an antibody to primarily bind light or heavy chain. This is only used by docking and rigid-body jump minimization functions. More...

std::string	get_ab_dock_chains ()
	Get the ab_dock_chains string, set via command line. More...

void	relax_cdrs (Pose &pose, bool centroid_mode, bool starting_coordinate_constraints=false, bool min_interface=false, std::string dock_chains="L_H") const
	Relax CDRs only either using FastRelax or CentroidRelax. More...

void	relax_cdrs_and_neighbor_sc (Pose &pose, bool starting_coordinate_constraints=false, bool min_interface=false, std::string dock_chains="L_H") const

void	relax_interface (Pose &pose, std::string dock_chains, bool min_interface_sc=true) const

void	minimize_cdrs (Pose &pose, bool min_interface=false, std::string dock_chains="L_H") const
	Vanilla minimizer using dfpmin_armijo_nonmonotone at .01 tolerance. More...

void	minimize_cdrs_and_neighbor_sc (Pose &pose, bool min_interface=false, std::string dock_chains="L_H") const

void	minimize_interface (Pose &pose, std::string dock_chains, bool min_interface_sc=true) const

void	repack_antigen_ab_interface (Pose &pose) const
	Repack the interface between Antibody and Antigen. Foldtree for docking (LH_A/etc.) must be set. More...

void	repack_antigen_interface (Pose &pose) const
	Repack the interface between antibody and antigen, but only pack antigen. More...

void	repack_antibody_interface (Pose &pose) const
	Repack the interface between antibody and antigen, but only pack antibody. More...

void	repack_CDRs (Pose &pose)
	Repack the CDRs given. Nothing special. More...

void	repack_CDRs_and_neighbors (Pose &pose)
	Repack CDRs and their neighbors within distance. More...

void	dock_LH_A_low_res (Pose &pose, bool pack_interface=false) const

void	dock_LH_A_high_res (Pose &pose, int first_cycle=4, int second_cycle=45) const

void	dock_A_LH_low_res (Pose &pose, bool pack_interface=false) const

void	dock_A_LH_high_res (Pose &pose, int first_cycle=4, int second_cycle=45) const

void	dock_L_H_low_res (Pose &pose, bool pack_interface=false) const

void	dock_L_H_high_res (Pose &pose, int first_cycle=4, int second_cycle=45) const

void	dock_H_L_low_res (Pose &pose, bool pack_interface=false) const

void	dock_H_L_high_res (Pose &pose, int first_cycle=4, int second_cycle=45) const

void	extend_CDR (Pose &pose, CDRNameEnum cdr) const
	Randomizes the dihedrals of the CDR. More...

Protected Member Functions
void	read_command_line_options ()

void	apply_LH_A_foldtree (core::pose::Pose &pose) const
	Applies an LH-A Foldtree. Forked from AbInfo - Its version uses hardcoded order of the PDB. Need to refactor that using this. Need to find out if they are exactly the same first. More...

void	dock_high_res (core::pose::Pose &pose, std::string dock_chains, int first_cycle=4, int second_cycle=45) const
	Main High-res docker. More...

void	dock_low_res (core::pose::Pose &pose, std::string dock_chains, bool pack_interface=false) const
	Main Low-res docker. More...

protocols::loops::LoopsOP	get_cdr_loops (Pose &pose) const
	AntibodyInfo has this function. Need to refactor more to get single loop on the fly. More...

Detailed Description

Class that runs the modeling for AntibodyDesign protocols. Could be moved to antibody.

Constructor & Destructor Documentation

protocols::antibody::design::AntibodyDesignModeler::AntibodyDesignModeler ( AntibodyInfoOP ab_info )

References protocols::antibody::CDRNameEnum_start, protocols::antibody::CDRNameEnum_total, core::scoring::ScoreFunctionFactory::create_score_function(), and getScoreFunction().

protocols::antibody::design::AntibodyDesignModeler::~AntibodyDesignModeler ( )

virtual

Member Function Documentation

void protocols::antibody::design::AntibodyDesignModeler::apply_LH_A_foldtree ( core::pose::Pose & pose ) const

protected

Applies an LH-A Foldtree. Forked from AbInfo - Its version uses hardcoded order of the PDB. Need to refactor that using this. Need to find out if they are exactly the same first.

References protocols::docking::setup_foldtree().

void protocols::antibody::design::AntibodyDesignModeler::dock_A_LH_high_res	(	Pose &	pose,
		int	first_cycle = `4`,
		int	second_cycle = `45`
	)		const

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::dock_A_LH_low_res	(	Pose &	pose,
		bool	pack_interface = `false`
	)		const

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::dock_H_L_high_res	(	Pose &	pose,
		int	first_cycle = `4`,
		int	second_cycle = `45`
	)		const

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::dock_H_L_low_res	(	Pose &	pose,
		bool	pack_interface = `false`
	)		const

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::dock_high_res	(	core::pose::Pose &	pose,
		std::string	dock_chains,
		int	first_cycle = `4`,
		int	second_cycle = `45`
	)		const

protected

Main High-res docker.

References core::pose::Pose::fold_tree(), protocols::docking::setup_foldtree(), and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::dock_L_H_high_res	(	Pose &	pose,
		int	first_cycle = `4`,
		int	second_cycle = `45`
	)		const

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::dock_L_H_low_res	(	Pose &	pose,
		bool	pack_interface = `false`
	)		const

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::dock_LH_A_high_res	(	Pose &	pose,
		int	first_cycle = `4`,
		int	second_cycle = `45`
	)		const

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::dock_LH_A_low_res	(	Pose &	pose,
		bool	pack_interface = `false`
	)		const

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::dock_low_res	(	core::pose::Pose &	pose,
		std::string	dock_chains,
		bool	pack_interface = `false`
	)		const

protected

Main Low-res docker.

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), core::pose::Pose::fold_tree(), protocols::docking::setup_foldtree(), and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::extend_CDR	(	Pose &	pose,
		CDRNameEnum	cdr
	)		const

Randomizes the dihedrals of the CDR.

References protocols::loops::Loops::add_loop(), end, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::loops::set_extended_torsions_and_idealize_loops(), and protocols::loops::start.

std::string protocols::antibody::design::AntibodyDesignModeler::get_ab_dock_chains ( )

Get the ab_dock_chains string, set via command line.

protocols::loops::LoopsOP protocols::antibody::design::AntibodyDesignModeler::get_cdr_loops ( Pose & pose ) const

protected

AntibodyInfo has this function. Need to refactor more to get single loop on the fly.

References protocols::antibody::CDRNameEnum_total, protocols::loops::start, and protocols::loops::stop.

void protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs	(	Pose &	pose,
		bool	min_interface = `false`,
		std::string	dock_chains = `"L_H"`
	)		const

Vanilla minimizer using dfpmin_armijo_nonmonotone at .01 tolerance.

References protocols::simple_moves::MinMover::apply(), protocols::antibody::CDRNameEnum_total, chainbreak, core::scoring::ScoreFunction::clone(), core::pose::Pose::fold_tree(), protocols::docking::setup_foldtree(), and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::minimize_cdrs_and_neighbor_sc	(	Pose &	pose,
		bool	min_interface = `false`,
		std::string	dock_chains = `"L_H"`
	)		const

References protocols::simple_moves::MinMover::apply(), protocols::antibody::CDRNameEnum_total, chainbreak, core::scoring::ScoreFunction::clone(), core::pose::Pose::fold_tree(), protocols::docking::setup_foldtree(), and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::minimize_interface	(	Pose &	pose,
		std::string	dock_chains,
		bool	min_interface_sc = `true`
	)		const

References protocols::simple_moves::MinMover::apply(), core::scoring::ScoreFunction::clone(), core::pose::Pose::fold_tree(), core::pack::task::PackerTask::pack_residue(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), protocols::docking::setup_foldtree(), core::pose::Pose::total_residue(), and protocols::antibody::TR.

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

protected

References basic::options::OptionKeys::antibody::design::ab_dock_chains, basic::options::OptionKeys::antibody::design::interface_dis, basic::options::OptionKeys::antibody::design::neighbor_dis, and basic::options::option.

void protocols::antibody::design::AntibodyDesignModeler::relax_cdrs	(	Pose &	pose,
		bool	centroid_mode,
		bool	starting_coordinate_constraints = `false`,
		bool	min_interface = `false`,
		std::string	dock_chains = `"L_H"`
	)		const

Relax CDRs only either using FastRelax or CentroidRelax.

Cluster Constraints should already be set. Optionally use start_coordinate constraints. All coordinate constraints on the pose will then be removed.

References protocols::antibody::CDRNameEnum_total, chainbreak, core::scoring::ScoreFunction::clone(), core::pose::Pose::fold_tree(), core::scoring::constraints::remove_constraints_of_type(), protocols::docking::setup_foldtree(), and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::relax_cdrs_and_neighbor_sc	(	Pose &	pose,
		bool	starting_coordinate_constraints = `false`,
		bool	min_interface = `false`,
		std::string	dock_chains = `"L_H"`
	)		const

References protocols::antibody::CDRNameEnum_total, chainbreak, core::scoring::ScoreFunction::clone(), core::pose::Pose::fold_tree(), core::scoring::constraints::remove_constraints_of_type(), protocols::docking::setup_foldtree(), and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::relax_interface	(	Pose &	pose,
		std::string	dock_chains,
		bool	min_interface_sc = `true`
	)		const

References core::scoring::ScoreFunction::clone(), utility::options::StringOptionKey::clone(), core::pose::Pose::fold_tree(), core::pack::task::PackerTask::pack_residue(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), protocols::docking::setup_foldtree(), tf, core::pose::Pose::total_residue(), and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::repack_antibody_interface ( Pose & pose ) const

Repack the interface between antibody and antigen, but only pack antibody.

References protocols::simple_moves::PackRotamersMover::apply(), chain, utility::options::StringOptionKey::clone(), core::pose::Pose::fold_tree(), core::pose::get_chain_id_from_chain(), tf, and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::repack_antigen_ab_interface ( Pose & pose ) const

Repack the interface between Antibody and Antigen. Foldtree for docking (LH_A/etc.) must be set.

References protocols::simple_moves::PackRotamersMover::apply(), core::pose::Pose::fold_tree(), and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::repack_antigen_interface ( Pose & pose ) const

Repack the interface between antibody and antigen, but only pack antigen.

References protocols::simple_moves::PackRotamersMover::apply(), utility::options::StringOptionKey::clone(), core::pose::Pose::fold_tree(), core::pose::get_chain_id_from_chain(), tf, and protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::repack_CDRs ( Pose & pose )

Repack the CDRs given. Nothing special.

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::repack_CDRs_and_neighbors ( Pose & pose )

Repack CDRs and their neighbors within distance.

References protocols::antibody::TR.

void protocols::antibody::design::AntibodyDesignModeler::set_ab_dock_chains ( std::string ab_dock_chains )

Override the command line default of LH to L or H or something strange. Used primarily for bivalent antibody design, or if you are designing an antibody to primarily bind light or heavy chain. This is only used by docking and rigid-body jump minimization functions.

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

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

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

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

References protocols::antibody::CDRNameEnum_start, and protocols::antibody::CDRNameEnum_total.

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

Set a range of CDRs.

References protocols::antibody::cdr_end.

void protocols::antibody::design::AntibodyDesignModeler::set_interface_detection_dis ( core::Real interface_distance )

Set a value for interface detection across the class.

void protocols::antibody::design::AntibodyDesignModeler::set_neighbor_detection_dis ( core::Real neighbor_distance )

void protocols::antibody::design::AntibodyDesignModeler::set_scorefunction ( ScoreFunctionCOP scorefxn )

Member Data Documentation

std::string protocols::antibody::design::AntibodyDesignModeler::ab_dock_chains_

protected

AntibodyInfoOP protocols::antibody::design::AntibodyDesignModeler::ab_info_

protected

TaskFactoryOP protocols::antibody::design::AntibodyDesignModeler::antigen_interface_tf_

protected

vector1<bool> protocols::antibody::design::AntibodyDesignModeler::cdrs_

protected

operation::InitializeFromCommandlineOP protocols::antibody::design::AntibodyDesignModeler::cmd_line_operation_

protected

ScoreFunctionOP protocols::antibody::design::AntibodyDesignModeler::docking_scorefxn_high_

protected

core::Real protocols::antibody::design::AntibodyDesignModeler::interface_dis_

protected

protocols::toolbox::task_operations::RestrictToLoopsAndNeighborsOP protocols::antibody::design::AntibodyDesignModeler::loops_operation_

protected

core::Real protocols::antibody::design::AntibodyDesignModeler::neighbor_dis_

protected

operation::RestrictToRepackingOP protocols::antibody::design::AntibodyDesignModeler::restrict_design_operation_

protected

ScoreFunctionOP protocols::antibody::design::AntibodyDesignModeler::scorefxn_

protected

TaskFactoryOP protocols::antibody::design::AntibodyDesignModeler::tf_

protected

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

symlinks/rosetta/src/protocols/antibody/design/AntibodyDesignModeler.hh
symlinks/rosetta/src/protocols/antibody/design/AntibodyDesignModeler.cc

Protected Attributes
AntibodyInfoOP	ab_info_

ScoreFunctionOP	scorefxn_

ScoreFunctionOP	docking_scorefxn_high_

TaskFactoryOP	antigen_interface_tf_

TaskFactoryOP	tf_

protocols::toolbox::task_operations::RestrictToLoopsAndNeighborsOP	loops_operation_

operation::InitializeFromCommandlineOP	cmd_line_operation_

operation::RestrictToRepackingOP	restrict_design_operation_

core::Real	interface_dis_

core::Real	neighbor_dis_

std::string	ab_dock_chains_

vector1< bool >	cdrs_

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation