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. The Antibody Database that this class uses will be available online (Too large for the rosetta_database) Till then, email me for access to the github repository. More...

#include <AntibodyGraftDesigner.hh>

Public Member Functions
	AntibodyGraftDesigner (AntibodyInfoOP ab_info)

	AntibodyGraftDesigner (AntibodyInfoOP &ab_info, std::string instruction_path)

virtual	~AntibodyGraftDesigner ()

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

virtual void	apply (pose::Pose &pose)

void	set_cdr_set (CDRSet &cdr_set, CDRClusterMap &cdr_cluster_map, core::Size overhang)
	Will not initialize CDRs from the AntibodyDatabase. Use if you have your own CDR's you are interested in grafting. More...

void	set_scorefunction (ScoreFunctionOP scorefxn)

void	set_graft_rounds (core::Size graft_rounds)

void	set_mintype (CDRNameEnum const cdr_name, MinTypeEnum mintype)
	Options are: relax, minimize, repack. Default is minimize. More...

void	set_mintype_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, MinTypeEnum mintype)

void	set_min_rb (CDRNameEnum const cdr_name, bool const setting)
	Use rigid body optimization during minimization of the CDR (Minimize jump bt antigen and antibody)? More...

void	set_min_rb_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, bool const setting)

void	set_min_neighbor_sc (CDRNameEnum const cdr_name, bool const setting)
	Use Neighbor sidechains during minimization of this CDR post-graft? More...

void	set_min_neighbor_sc_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, bool const setting)

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_pack_post_graft (bool pack_post_graft)
	Set the algorithm to run a packing step with neighbor detection post graft. Before any minimization or docking. More...

void	set_rb_min_post_graft (bool rb_min_post_graft)
	Set the algorithm to run a final rigid-body minimization of antigen/antibody interface post graft. Useful if not docking - quicker, but less reliable then full dock. 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...

vector1< 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_cluster (CDRNameEnum const cdr, CDRClusterEnum const cluster, bool const setting)
	Leave out or include only clusters added here. More...

void	set_cluster_range (CDRNameEnum const cdr, CDRClusterEnum const cluster_start, CDRClusterEnum const cluster_end, bool const setting)
	Leave out or include only clusters added here. More...

void	set_cdr (CDRNameEnum const cdr, bool const setting)
	Use this CDR during design. More...

void	set_cdr_range (CDRNameEnum const cdr_start, CDRNameEnum cdr_end, bool const setting)
	Use this range of CDRs during design. Default is all of them. More...

void	set_cdr_stay_in_native_cluster (CDRNameEnum const cdr, bool const setting)
	Set to only sample within the native cluster of this CDR. More...

void	set_cdr_range_stay_in_native_cluster (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, bool const setting)
	Set a range of CDRs for which to only sample their native clusters. More...

void	set_cdr_stay_in_type (CDRNameEnum const cdr, core::Size const type, bool const setting)
	Set to only sample with clusters of the given type for this CDR. Default is to only use type 1. More...

void	set_cdr_range_stay_in_type (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, core::Size const type, bool const setting)
	set a range of CDRs for which to stay within a particular type. Default is to only use type 1. More...

void	set_cdr_min_length (CDRNameEnum const cdr, core::Size length)
	set the minimum cdr length to sample. Nothing shorter then this will be used during graft. More...

void	set_cdr_min_length_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, core::Size length)

void	set_cdr_max_length (CDRNameEnum const cdr, core::Size length)
	set the maximum cdr length to sample. Nothing longer then this will be used. Useful for H3. More...

void	set_cdr_max_length_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, core::Size length)

void	set_cdr_cluster_centers_only (CDRNameEnum const cdr, bool setting)
	Only sample cluster centers for this CDR. More...

void	set_cdr_cluster_centers_only_range (CDRNameEnum const cdr_start, CDRNameEnum const cdr_end, bool setting)

virtual string	get_name () const
	Leave out these PDBs from sampling. Mainly for testing, but who knows. More...

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

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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

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...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

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...

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

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...

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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

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

jobdist::BasicJobCOP	get_current_job () const

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

Private Member Functions
void	read_command_line_options ()

void	read_instructions (std::string instruction_path)
	Call DesignInstructionParser to determine settings for the design run. More...

void	setup_native_clusters (pose::Pose &pose)

void	initialize_cdr_set ()
	Uses instructions to Query the AntibodyDatabase and load poses. More...

void	check_for_top_designs (pose::Pose &pose)

bool	graft_cdr (pose::Pose &pose, CDRNameEnum cdr, core::Size index)
	Grafts a single CDR. Index is the vector index of CDRSet/CDRClusterMap. More...

void	run_deterministic_graft_algorithm (pose::Pose &pose, vector1< CDRNameEnum > &cdrs_to_design)
	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_basic_mc_algorithm (pose::Pose &pose, vector1< CDRNameEnum > &cdrs_to_design)
	Basic mc algorithm that randomly samples from the cdr set. More...

void	fix_pdb_info (pose::Pose &pose, CDRNameEnum cdr, CDRClusterEnum cluster, core::Size original_start, core::Size original_pdb_end)
	Fix PDB info as somehow the code for pdbinfo changed and my other method no longer works. No idea why. More...

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

void	set_default_graft_settings ()

vector1< vector1< 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...

Private Attributes
map< CDRNameEnum, CDRClusterOP >	native_clusters_

map< CDRNameEnum, CDRGraftInstructions >	cdr_instructions_

map< CDRNameEnum, SamplingWeights >	sampling_instructions_

map< CDRNameEnum, utility::vector1 < core::scoring::constraints::ConstraintCOP > >	constraint_map_

std::string	instruction_path_

CDRSet	cdr_set_

CDRClusterMap	cdr_cluster_map_

PDBMap	pdbmap_

AntibodyInfoOP	ab_info_

AnchoredGraftMoverOP	graft_mover_

ScoreFunctionOP	scorefxn_

AntibodyDesignModelerOP	modeler_

protocols::moves::MonteCarloOP	mc_

core::Size	overhang_

core::Size	graft_rounds_

core::Size	dock_rounds_

core::Size	num_top_designs_

vector1< pose::PoseOP >	top_designs_

vector1< core::Real >	top_scores_

core::Size	total_permutations_

bool	dock_post_graft_

bool	pack_post_graft_

bool	rb_min_post_graft_

bool	initial_perturb_

bool	use_deterministic_algorithm_

core::Real	max_linear_chainbreak_

bool	extend_native_cdrs_

bool	benchmark_

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 protocols::filters::Filters_map	Filters_map

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

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...

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. The Antibody Database that this class uses will be available online (Too large for the rosetta_database) Till then, email me for access to the github repository.

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

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

References ab_info_, protocols::antibody::AntibodyInfo::get_current_AntibodyNumberingScheme(), protocols::antibody::AntibodyInfo::get_current_CDRDefinition(), max_linear_chainbreak_, modeler_, overhang_, read_command_line_options(), set_defaults(), and utility_exit_with_message.

protocols::antibody::design::AntibodyGraftDesigner::AntibodyGraftDesigner	(	AntibodyInfoOP &	ab_info,
		std::string	instruction_path
	)

References ab_info_, protocols::antibody::AntibodyInfo::get_current_AntibodyNumberingScheme(), protocols::antibody::AntibodyInfo::get_current_CDRDefinition(), instruction_path_, max_linear_chainbreak_, modeler_, overhang_, read_command_line_options(), set_defaults(), and utility_exit_with_message.

protocols::antibody::design::AntibodyGraftDesigner::~AntibodyGraftDesigner ( )

virtual

Member Function Documentation

void protocols::antibody::design::AntibodyGraftDesigner::apply ( pose::Pose & pose )

virtual

Implements protocols::moves::Mover.

References ab_info_, cdr_instructions_, cdr_set_, protocols::antibody::CDRNameEnum_total, check_for_top_designs(), protocols::antibody::clusters::check_if_pose_renumbered_for_clusters(), core::scoring::dihedral_constraint, extend_native_cdrs(), extend_native_cdrs_, protocols::antibody::AntibodyInfo::get_CDR_end(), protocols::antibody::AntibodyInfo::get_CDR_name(), protocols::antibody::AntibodyInfo::get_CDR_start(), core::scoring::getScoreFunction(), graft_mover_, protocols::antibody::h3, initialize_cdr_set(), mc_, modeler_, run_basic_mc_algorithm(), run_deterministic_graft_algorithm(), scorefxn_, set_default_graft_settings(), setup_native_clusters(), size(), top_designs_, top_scores_, total_permutations_, protocols::antibody::TR, use_deterministic_algorithm_, and utility_exit_with_message.

void protocols::antibody::design::AntibodyGraftDesigner::check_for_top_designs ( pose::Pose & pose )

private

References num_top_designs_, score, top_designs_, and top_scores_.

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

void protocols::antibody::design::AntibodyGraftDesigner::extend_native_cdrs	(	pose::Pose &	pose,
		vector1< CDRNameEnum > &	cdrs_to_design
	)

private

Extend the native CDRs to be designed for benchmarking.

References ab_info_, protocols::antibody::AntibodyInfo::get_CDR_name(), modeler_, and protocols::antibody::TR.

Referenced by apply().

void protocols::antibody::design::AntibodyGraftDesigner::fix_pdb_info	(	pose::Pose &	pose,
		CDRNameEnum	cdr,
		CDRClusterEnum	cluster,
		core::Size	original_start,
		core::Size	original_pdb_end
	)

private

Fix PDB info as somehow the code for pdbinfo changed and my other method no longer works. No idea why.

References ab_info_, chain, protocols::antibody::AntibodyInfo::get_CDR_chain(), protocols::antibody::AntibodyInfo::get_cluster_length(), core::pose::Pose::pdb_info(), and protocols::antibody::TR.

vector1< vector1< Size > > protocols::antibody::design::AntibodyGraftDesigner::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().

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

virtual

Leave out these PDBs from sampling. Mainly for testing, but who knows.

Implements protocols::moves::Mover.

vector1< pose::PoseOP> protocols::antibody::design::AntibodyGraftDesigner::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.

bool protocols::antibody::design::AntibodyGraftDesigner::graft_cdr	(	pose::Pose &	pose,
		CDRNameEnum	cdr,
		core::Size	index
	)

private

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

Return success or failure

References ab_info_, core::scoring::constraints::add_coordinate_constraints(), protocols::antibody::add_harmonic_cluster_constraint(), protocols::grafting::AnchoredGraftMover::apply(), cdr_cluster_map_, cdr_instructions_, cdr_set_, protocols::antibody::design::centroid_relax, constraint_map_, dock_post_graft_, dock_rounds_, end, core::pose::Pose::fold_tree(), protocols::antibody::AntibodyInfo::get_antigen_chains(), protocols::antibody::AntibodyInfo::get_CDR_end(), protocols::antibody::AntibodyInfo::get_CDR_name(), protocols::antibody::AntibodyInfo::get_CDR_start(), protocols::antibody::AntibodyInfo::get_cluster_name(), protocols::grafting::AnchoredGraftMover::get_cterm_scaffold_flexibility(), protocols::grafting::AnchoredGraftMover::get_nterm_scaffold_flexibility(), graft_mover_, protocols::antibody::h3, initial_perturb_, protocols::forge::methods::linear_chainbreak(), max_linear_chainbreak_, protocols::antibody::design::minimize, modeler_, protocols::antibody::design::no_min, overhang_, pack_post_graft_, core::pose::Pose::pdb_info(), pdbmap_, rb_min_post_graft_, protocols::antibody::design::relax, core::pose::Pose::remove_constraints(), core::scoring::constraints::remove_constraints_of_type(), protocols::antibody::design::repack, protocols::grafting::AnchoredGraftMover::repack_connection_and_residues_in_movemap(), protocols::grafting::AnchoredGraftMover::repack_connection_and_residues_in_movemap_and_piece(), scorefxn_, protocols::grafting::AnchoredGraftMover::set_cycles(), set_default_graft_settings(), protocols::grafting::AnchoredGraftMover::set_insert_flexibility(), protocols::grafting::GraftMoverBase::set_insert_region(), protocols::grafting::GraftMoverBase::set_piece(), protocols::grafting::AnchoredGraftMover::set_scaffold_flexibility(), protocols::docking::setup_foldtree(), protocols::loops::start, protocols::grafting::GraftMoverBase::superimpose_overhangs_heavy(), and protocols::antibody::TR.

Referenced by run_basic_mc_algorithm(), and run_deterministic_graft_algorithm().

void protocols::antibody::design::AntibodyGraftDesigner::initialize_cdr_set ( )

private

Uses instructions to Query the AntibodyDatabase and load poses.

References ab_info_, cdr_cluster_map_, cdr_instructions_, cdr_set_, and pdbmap_.

Referenced by apply().

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

private

Referenced by AntibodyGraftDesigner().

void protocols::antibody::design::AntibodyGraftDesigner::read_instructions ( std::string instruction_path )

private

Call DesignInstructionParser to determine settings for the design run.

References ab_info_, cdr_instructions_, parser, and protocols::antibody::design::DesignInstructionsParser::read_cdr_graft_instructions().

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesigner::run_basic_mc_algorithm	(	pose::Pose &	pose,
		vector1< CDRNameEnum > &	cdrs_to_design
	)

private

Basic mc algorithm that randomly samples from the cdr set.

References protocols::moves::MonteCarlo::boltzmann(), cdr_set_, check_for_top_designs(), graft_cdr(), graft_rounds_, protocols::moves::MonteCarlo::last_accepted_pose(), mc_, numeric::random::RandomGenerator::random_range(), protocols::moves::MonteCarlo::recover_low(), protocols::RG, scorefxn_, protocols::moves::MonteCarlo::set_last_accepted_pose(), protocols::moves::MonteCarlo::show_counters(), size(), top_designs_, top_scores_, and protocols::antibody::TR.

Referenced by apply().

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

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.

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

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

References cdr_set_, check_for_top_designs(), protocols::moves::MonteCarlo::eval_lowest_score_pose(), graft_cdr(), mc_, protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::show_counters(), and protocols::antibody::TR.

Referenced by apply().

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

Use this CDR during design.

References cdr_instructions_.

void protocols::antibody::design::AntibodyGraftDesigner::set_cdr_cluster_centers_only	(	CDRNameEnum const	cdr,
		bool	setting
	)

Only sample cluster centers for this CDR.

References cdr_instructions_.

Referenced by set_cdr_cluster_centers_only_range().

void protocols::antibody::design::AntibodyGraftDesigner::set_cdr_cluster_centers_only_range	(	CDRNameEnum const	cdr_start,
		CDRNameEnum const	cdr_end,
		bool	setting
	)

References protocols::antibody::cdr_end, and set_cdr_cluster_centers_only().

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesigner::set_cdr_max_length	(	CDRNameEnum const	cdr,
		core::Size	length
	)

set the maximum cdr length to sample. Nothing longer then this will be used. Useful for H3.

References cdr_instructions_.

Referenced by set_cdr_max_length_range().

void protocols::antibody::design::AntibodyGraftDesigner::set_cdr_max_length_range	(	CDRNameEnum const	cdr_start,
		CDRNameEnum const	cdr_end,
		core::Size	length
	)

References protocols::antibody::cdr_end, and set_cdr_max_length().

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesigner::set_cdr_min_length	(	CDRNameEnum const	cdr,
		core::Size	length
	)

set the minimum cdr length to sample. Nothing shorter then this will be used during graft.

References cdr_instructions_.

Referenced by set_cdr_min_length_range().

void protocols::antibody::design::AntibodyGraftDesigner::set_cdr_min_length_range	(	CDRNameEnum const	cdr_start,
		CDRNameEnum const	cdr_end,
		core::Size	length
	)

References protocols::antibody::cdr_end, and set_cdr_min_length().

Referenced by set_defaults().

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

Use this range of CDRs during design. Default is all of them.

References protocols::antibody::cdr_end, and cdr_instructions_.

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesigner::set_cdr_range_stay_in_native_cluster	(	CDRNameEnum const	cdr_start,
		CDRNameEnum const	cdr_end,
		bool const	setting
	)

Set a range of CDRs for which to only sample their native clusters.

References protocols::antibody::cdr_end, and cdr_instructions_.

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesigner::set_cdr_range_stay_in_type	(	CDRNameEnum const	cdr_start,
		CDRNameEnum const	cdr_end,
		core::Size const	type,
		bool const	setting
	)

set a range of CDRs for which to stay within a particular type. Default is to only use type 1.

References protocols::antibody::cdr_end, cdr_instructions_, and protocols::moves::Mover::type().

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesigner::set_cdr_set	(	CDRSet &	cdr_set,
		CDRClusterMap &	cdr_cluster_map,
		core::Size	overhang
	)

Will not initialize CDRs from the AntibodyDatabase. Use if you have your own CDR's you are interested in grafting.

Overhang residues will be used for superposition. To identify your CDRs, use the functions in AntibodyInfo or the pilot app identify_cdr_clusters in pilot/jadolfbr/cluster_utils

References cdr_cluster_map_, cdr_set_, and overhang_.

void protocols::antibody::design::AntibodyGraftDesigner::set_cdr_stay_in_native_cluster	(	CDRNameEnum const	cdr,
		bool const	setting
	)

Set to only sample within the native cluster of this CDR.

References cdr_instructions_.

void protocols::antibody::design::AntibodyGraftDesigner::set_cdr_stay_in_type	(	CDRNameEnum const	cdr,
		core::Size const	type,
		bool const	setting
	)

Set to only sample with clusters of the given type for this CDR. Default is to only use type 1.

References cdr_instructions_, and protocols::moves::Mover::type().

void protocols::antibody::design::AntibodyGraftDesigner::set_cluster	(	CDRNameEnum const	cdr,
		CDRClusterEnum const	cluster,
		bool const	setting
	)

Leave out or include only clusters added here.

References cdr_instructions_.

void protocols::antibody::design::AntibodyGraftDesigner::set_cluster_range	(	CDRNameEnum const	cdr,
		CDRClusterEnum const	cluster_start,
		CDRClusterEnum const	cluster_end,
		bool const	setting
	)

Leave out or include only clusters added here.

References cdr_instructions_, and cluster.

void protocols::antibody::design::AntibodyGraftDesigner::set_default_graft_settings ( )

private

References graft_mover_, protocols::grafting::AnchoredGraftMover::set_cycles(), protocols::grafting::AnchoredGraftMover::set_insert_flexibility(), protocols::grafting::AnchoredGraftMover::set_scaffold_flexibility(), protocols::grafting::AnchoredGraftMover::set_use_double_loop_double_CCD_arms(), and protocols::grafting::AnchoredGraftMover::set_use_smooth_centroid_settings().

Referenced by apply(), and graft_cdr().

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

Reads default CDRGraftInstruction file and creates structs.

References protocols::antibody::CDRNameEnum_start, protocols::antibody::CDRNameEnum_total, instruction_path_, protocols::antibody::design::minimize, read_instructions(), set_cdr_cluster_centers_only_range(), set_cdr_max_length_range(), set_cdr_min_length_range(), set_cdr_range(), set_cdr_range_stay_in_native_cluster(), set_cdr_range_stay_in_type(), set_min_neighbor_sc_range(), set_min_rb_range(), and set_mintype_range().

Referenced by AntibodyGraftDesigner().

void protocols::antibody::design::AntibodyGraftDesigner::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().

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

References dock_rounds_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodyGraftDesigner::set_graft_rounds ( core::Size graft_rounds )

References graft_rounds_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodyGraftDesigner::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().

void protocols::antibody::design::AntibodyGraftDesigner::set_min_neighbor_sc	(	CDRNameEnum const	cdr_name,
		bool const	setting
	)

Use Neighbor sidechains during minimization of this CDR post-graft?

References cdr_instructions_.

Referenced by set_min_neighbor_sc_range().

void protocols::antibody::design::AntibodyGraftDesigner::set_min_neighbor_sc_range	(	CDRNameEnum const	cdr_start,
		CDRNameEnum const	cdr_end,
		bool const	setting
	)

References protocols::antibody::cdr_end, and set_min_neighbor_sc().

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesigner::set_min_rb	(	CDRNameEnum const	cdr_name,
		bool const	setting
	)

Use rigid body optimization during minimization of the CDR (Minimize jump bt antigen and antibody)?

dock_chains is LH_antigen. Does nothing if repacking the cdr. Default False.

References cdr_instructions_.

Referenced by set_min_rb_range().

void protocols::antibody::design::AntibodyGraftDesigner::set_min_rb_range	(	CDRNameEnum const	cdr_start,
		CDRNameEnum const	cdr_end,
		bool const	setting
	)

References protocols::antibody::cdr_end, and set_min_rb().

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesigner::set_mintype	(	CDRNameEnum const	cdr_name,
		MinTypeEnum	mintype
	)

Options are: relax, minimize, repack. Default is minimize.

References cdr_instructions_.

Referenced by set_mintype_range().

void protocols::antibody::design::AntibodyGraftDesigner::set_mintype_range	(	CDRNameEnum const	cdr_start,
		CDRNameEnum const	cdr_end,
		MinTypeEnum	mintype
	)

References protocols::antibody::cdr_end, and set_mintype().

Referenced by set_defaults().

void protocols::antibody::design::AntibodyGraftDesigner::set_pack_post_graft ( bool pack_post_graft )

Set the algorithm to run a packing step with neighbor detection post graft. Before any minimization or docking.

References pack_post_graft_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodyGraftDesigner::set_rb_min_post_graft ( bool rb_min_post_graft )

Set the algorithm to run a final rigid-body minimization of antigen/antibody interface post graft. Useful if not docking - quicker, but less reliable then full dock.

References rb_min_post_graft_.

Referenced by read_command_line_options().

void protocols::antibody::design::AntibodyGraftDesigner::set_scorefunction ( ScoreFunctionOP scorefxn )

References core::scoring::ScoreFunction::clone(), core::scoring::dihedral_constraint, and scorefxn_.

void protocols::antibody::design::AntibodyGraftDesigner::setup_native_clusters ( pose::Pose & pose )

private

References ab_info_, protocols::antibody::CDRNameEnum_total, protocols::antibody::AntibodyInfo::get_CDR_cluster(), native_clusters_, and protocols::antibody::AntibodyInfo::setup_CDR_clusters().

Referenced by apply().

Member Data Documentation

AntibodyInfoOP protocols::antibody::design::AntibodyGraftDesigner::ab_info_

private

Referenced by AntibodyGraftDesigner(), apply(), extend_native_cdrs(), fix_pdb_info(), graft_cdr(), initialize_cdr_set(), read_instructions(), and setup_native_clusters().

bool protocols::antibody::design::AntibodyGraftDesigner::benchmark_

private

CDRClusterMap protocols::antibody::design::AntibodyGraftDesigner::cdr_cluster_map_

private

Referenced by graft_cdr(), initialize_cdr_set(), and set_cdr_set().

map< CDRNameEnum, CDRGraftInstructions > protocols::antibody::design::AntibodyGraftDesigner::cdr_instructions_

private

Referenced by apply(), graft_cdr(), initialize_cdr_set(), read_instructions(), set_cdr(), set_cdr_cluster_centers_only(), set_cdr_max_length(), set_cdr_min_length(), set_cdr_range(), set_cdr_range_stay_in_native_cluster(), set_cdr_range_stay_in_type(), set_cdr_stay_in_native_cluster(), set_cdr_stay_in_type(), set_cluster(), set_cluster_range(), set_min_neighbor_sc(), set_min_rb(), and set_mintype().

CDRSet protocols::antibody::design::AntibodyGraftDesigner::cdr_set_

private

Referenced by apply(), get_cdr_set_index_list(), graft_cdr(), initialize_cdr_set(), run_basic_mc_algorithm(), run_deterministic_graft_algorithm(), and set_cdr_set().

map< CDRNameEnum, utility::vector1< core::scoring::constraints::ConstraintCOP > > protocols::antibody::design::AntibodyGraftDesigner::constraint_map_

private

Referenced by graft_cdr().

bool protocols::antibody::design::AntibodyGraftDesigner::dock_post_graft_

private

Referenced by graft_cdr(), and set_dock_post_graft().

core::Size protocols::antibody::design::AntibodyGraftDesigner::dock_rounds_

private

Referenced by graft_cdr(), and set_dock_rounds().

bool protocols::antibody::design::AntibodyGraftDesigner::extend_native_cdrs_

private

Referenced by apply(), and read_command_line_options().

AnchoredGraftMoverOP protocols::antibody::design::AntibodyGraftDesigner::graft_mover_

private

Referenced by apply(), graft_cdr(), and set_default_graft_settings().

core::Size protocols::antibody::design::AntibodyGraftDesigner::graft_rounds_

private

Referenced by run_basic_mc_algorithm(), and set_graft_rounds().

bool protocols::antibody::design::AntibodyGraftDesigner::initial_perturb_

private

Referenced by graft_cdr(), and read_command_line_options().

std::string protocols::antibody::design::AntibodyGraftDesigner::instruction_path_

private

Referenced by AntibodyGraftDesigner(), read_command_line_options(), and set_defaults().

core::Real protocols::antibody::design::AntibodyGraftDesigner::max_linear_chainbreak_

private

Referenced by AntibodyGraftDesigner(), and graft_cdr().

protocols::moves::MonteCarloOP protocols::antibody::design::AntibodyGraftDesigner::mc_

private

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

AntibodyDesignModelerOP protocols::antibody::design::AntibodyGraftDesigner::modeler_

private

Referenced by AntibodyGraftDesigner(), apply(), extend_native_cdrs(), and graft_cdr().

map< CDRNameEnum, CDRClusterOP> protocols::antibody::design::AntibodyGraftDesigner::native_clusters_

private

Referenced by setup_native_clusters().

core::Size protocols::antibody::design::AntibodyGraftDesigner::num_top_designs_

private

Referenced by check_for_top_designs(), and set_keep_top_designs().

core::Size protocols::antibody::design::AntibodyGraftDesigner::overhang_

private

Referenced by AntibodyGraftDesigner(), graft_cdr(), and set_cdr_set().

bool protocols::antibody::design::AntibodyGraftDesigner::pack_post_graft_

private

Referenced by graft_cdr(), and set_pack_post_graft().

PDBMap protocols::antibody::design::AntibodyGraftDesigner::pdbmap_

private

Referenced by graft_cdr(), and initialize_cdr_set().

bool protocols::antibody::design::AntibodyGraftDesigner::rb_min_post_graft_

private

Referenced by graft_cdr(), and set_rb_min_post_graft().

map< CDRNameEnum, SamplingWeights > protocols::antibody::design::AntibodyGraftDesigner::sampling_instructions_

private

ScoreFunctionOP protocols::antibody::design::AntibodyGraftDesigner::scorefxn_

private

Referenced by apply(), graft_cdr(), run_basic_mc_algorithm(), and set_scorefunction().

vector1< pose::PoseOP > protocols::antibody::design::AntibodyGraftDesigner::top_designs_

private

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

vector1< core::Real> protocols::antibody::design::AntibodyGraftDesigner::top_scores_

private

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

core::Size protocols::antibody::design::AntibodyGraftDesigner::total_permutations_

private

Referenced by apply().

bool protocols::antibody::design::AntibodyGraftDesigner::use_deterministic_algorithm_

private

Referenced by apply(), and read_command_line_options().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation