Designs antibody CDR structures using a variety of different methods. Main methods involve using cluster-based sequence probability statistics and conservative design strategies to limit unknown structural effects caused by aggressive design. Uses North_AHO numbering and cluster-based design. Part of Rosetta Antibody Designer. More...

#include <AntibodySeqDesignMover.hh>

Public Member Functions
	AntibodySeqDesignMover (AntibodyInfoOP ab_info)

	AntibodySeqDesignMover (AntibodyInfoOP ab_info, std::string instruction_path)

virtual	~AntibodySeqDesignMover ()

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

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

void	set_cdr_only (CDRNameEnum const cdr, bool const 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 const setting)
	Set a range of CDRs. More...

void	set_neighbor_detection_dis (core::Real const neighbor_distance)
	Repack neighbors of CDR's being designed within this distance. More...

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

void	set_rounds (core::Size const rounds)

void	set_use_conservative_design (CDRNameEnum const cdr, bool const setting)
	Set a conservative method for design, including only using general conserved aminoacids, and specific amino acids for identified turn types. Default true for H3. Any probabilities not found for a particular cluster will result in conservative design. More...

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

void	set_use_turn_conservation (bool const setting)
	Try to conserve turn structure using known turn-based conservative mutations during conservative design. More...

void	set_probability_data_cutoff (core::Size const cutoff)
	Use conservative mutations (or alternative method) instead of using cluster sequence probabilities for design if the number of sequences in the particular CDR's cluster probability data is lower than this cutoff. Default is 10. This is why we try and stay in type 1 clusters during graft. More...

void	set_zero_prob_weight_at (core::Real const weight)
	Use these weights during probabilistic design for data that is normally zero. More...

void	no_design_proline (bool const setting)
	keep proline fixed. Maybe should be not an option - and just do it. More...

void	set_design_method (DesignTypeEnum const design_method)
	Type of design method used. Acceptable options - relaxed_design, fixbb, flxbb. More...

void	set_basic_design (bool const setting)
	Sets the designer to not use our fancy taskops and statistics. Only use basic design with all residues turned on. Use for benchmarking. More...

void	set_use_cluster_constraints (bool const setting)
	Should we use the cdr cluster CircularHarmonic constraints? Default true - this is mainly used for benchmarking. More...

virtual void	apply (core::pose::Pose &pose)

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

void	set_type (std::string const &setting)

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
std::map< core::Size, std::map < core::chemical::AA, core::Real > >	setup_probability_data (core::pose::Pose &pose)
	Reads from database, gets prob_set for ResidueProbDesignOperation + sets cdrs_wo_prob_data_. More...

core::pack::task::TaskFactoryOP	setup_task_factory (core::pose::Pose &pose)
	Setup the Designer's taskfactory. More...

vector1< core::Size >	get_conservative_design_residues (core::pose::Pose &pose)
	Get a list of residues where conservative design will be used. More...

void	disable_design_cdrs (core::pack::task::TaskFactoryOP tf, core::pose::Pose &pose)
	Turns off CDRs for design that are set to off. More...

void	disable_design_cdr (CDRNameEnum cdr, core::pack::task::TaskFactoryOP tf, core::pose::Pose &pose)

void	setup_constraints (core::pose::Pose &pose)
	Set cluster-based harmonic dihedral constraints if known cluster or set coordinate constraints. More...

bool	cdr_has_constraints (core::pose::Pose const &pose, CDRNameEnum const cdr, std::string const constraint_type)

void	read_command_line_options ()

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

void	remove_conservative_design_residues_from_prob_set (vector1< core::Size > const &positions, std::map< core::Size, std::map< core::chemical::AA, core::Real > > &prob_set)
	Removes residues from prob_set from instruction settings. Used so that we speed task generation instead of overwriting these residues. More...

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

Designs antibody CDR structures using a variety of different methods. Main methods involve using cluster-based sequence probability statistics and conservative design strategies to limit unknown structural effects caused by aggressive design. Uses North_AHO numbering and cluster-based design. Part of Rosetta Antibody Designer.

Constructor & Destructor Documentation

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

References protocols::antibody::CDRNameEnum_start, protocols::antibody::CDRNameEnum_total, core::scoring::get_score_function(), and utility_exit_with_message.

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

References protocols::antibody::CDRNameEnum_start, protocols::antibody::CDRNameEnum_total, core::scoring::get_score_function(), and utility_exit_with_message.

protocols::antibody::design::AntibodySeqDesignMover::~AntibodySeqDesignMover ( )

virtual

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

References protocols::antibody::CDRNameEnum_total, chainbreak, protocols::antibody::clusters::check_if_pose_renumbered_for_clusters(), design, dihedral_constraint, protocols::antibody::design::docked_design, protocols::antibody::design::fixbb, protocols::antibody::design::flxbb, mc, movemap, protocols::antibody::design::relaxed_design, protocols::medal::setup_constraints(), protocols::antibody::TR, and utility_exit_with_message.

bool protocols::antibody::design::AntibodySeqDesignMover::cdr_has_constraints	(	core::pose::Pose const &	pose,
		CDRNameEnum const	cdr,
		std::string const	constraint_type
	)

private

The CDR have constraints of this type. A bit hacky. Used for going form graftdesigner to this, without regenerating the 'wrong' constraints.

probably only works 'correctly' for dihedral/coordinate constraints. THe function assumes that constraints were set for the whole CDR.

References core::pose::Pose::constraint_set(), residues, and type.

void protocols::antibody::design::AntibodySeqDesignMover::disable_design_cdr	(	CDRNameEnum	cdr,
		core::pack::task::TaskFactoryOP	tf,
		core::pose::Pose &	pose
	)

private

References end, core::pack::task::operation::RestrictResidueToRepacking::include_residue(), core::pack::task::TaskFactory::push_back(), and protocols::loops::start.

void protocols::antibody::design::AntibodySeqDesignMover::disable_design_cdrs	(	core::pack::task::TaskFactoryOP	tf,
		core::pose::Pose &	pose
	)

private

Turns off CDRs for design that are set to off.

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

vector1< core::Size > protocols::antibody::design::AntibodySeqDesignMover::get_conservative_design_residues ( core::pose::Pose & pose )

private

Get a list of residues where conservative design will be used.

References protocols::antibody::CDRNameEnum_start, protocols::antibody::CDRNameEnum_total, end, and protocols::loops::start.

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

virtual

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

Implements protocols::moves::Mover.

void protocols::antibody::design::AntibodySeqDesignMover::no_design_proline ( bool const setting )

keep proline fixed. Maybe should be not an option - and just do it.

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

private

References protocols::antibody::design::design_type_from_string(), protocols::antibody::h3, basic::options::OptionKeys::antibody::design::instructions, basic::options::option, option, and basic::options::OptionKeys::antibody::design::sample_zero_probs_at.

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

private

Call DesignInstructionParser to determine settings for the design run.

References parser, and protocols::antibody::design::DesignInstructionsParser::read_cdr_design_instructions().

void protocols::antibody::design::AntibodySeqDesignMover::remove_conservative_design_residues_from_prob_set	(	vector1< core::Size > const &	positions,
		std::map< core::Size, std::map< core::chemical::AA, core::Real > > &	prob_set
	)

private

Removes residues from prob_set from instruction settings. Used so that we speed task generation instead of overwriting these residues.

References protocols::antibody::TR.

void protocols::antibody::design::AntibodySeqDesignMover::set_basic_design ( bool const setting )

Sets the designer to not use our fancy taskops and statistics. Only use basic design with all residues turned on. Use for benchmarking.

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

Set to design CDRs. Default is all of them true.

void protocols::antibody::design::AntibodySeqDesignMover::set_cdr_only	(	CDRNameEnum const	cdr,
		bool const	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::AntibodySeqDesignMover::set_cdr_range	(	CDRNameEnum const	cdr_start,
		CDRNameEnum const	cdr_end,
		bool const	setting
	)

Set a range of CDRs.

References protocols::antibody::cdr_end.

void protocols::antibody::design::AntibodySeqDesignMover::set_design_method ( DesignTypeEnum const design_method )

Type of design method used. Acceptable options - relaxed_design, fixbb, flxbb.

void protocols::antibody::design::AntibodySeqDesignMover::set_neighbor_detection_dis ( core::Real const neighbor_distance )

Repack neighbors of CDR's being designed within this distance.

void protocols::antibody::design::AntibodySeqDesignMover::set_probability_data_cutoff ( core::Size const cutoff )

Use conservative mutations (or alternative method) instead of using cluster sequence probabilities for design if the number of sequences in the particular CDR's cluster probability data is lower than this cutoff. Default is 10. This is why we try and stay in type 1 clusters during graft.

void protocols::antibody::design::AntibodySeqDesignMover::set_rounds ( core::Size const rounds )

void protocols::antibody::design::AntibodySeqDesignMover::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn )

void protocols::antibody::design::AntibodySeqDesignMover::set_use_cluster_constraints ( bool const setting )

Should we use the cdr cluster CircularHarmonic constraints? Default true - this is mainly used for benchmarking.

void protocols::antibody::design::AntibodySeqDesignMover::set_use_conservative_design	(	CDRNameEnum const	cdr,
		bool const	setting
	)

Set a conservative method for design, including only using general conserved aminoacids, and specific amino acids for identified turn types. Default true for H3. Any probabilities not found for a particular cluster will result in conservative design.

void protocols::antibody::design::AntibodySeqDesignMover::set_use_conservative_design_range	(	CDRNameEnum const	cdr_start,
		CDRNameEnum const	cdr_end,
		bool const	setting
	)

References protocols::antibody::cdr_end.

void protocols::antibody::design::AntibodySeqDesignMover::set_use_turn_conservation ( bool const setting )

Try to conserve turn structure using known turn-based conservative mutations during conservative design.

void protocols::antibody::design::AntibodySeqDesignMover::set_zero_prob_weight_at ( core::Real const weight )

Use these weights during probabilistic design for data that is normally zero.

void protocols::antibody::design::AntibodySeqDesignMover::setup_constraints ( core::pose::Pose & pose )

private

Set cluster-based harmonic dihedral constraints if known cluster or set coordinate constraints.

References core::scoring::constraints::add_coordinate_constraints(), protocols::antibody::add_harmonic_cluster_constraint(), protocols::antibody::CDRNameEnum_total, and protocols::antibody::TR.

std::map< core::Size, std::map< core::chemical::AA, core::Real > > protocols::antibody::design::AntibodySeqDesignMover::setup_probability_data ( core::pose::Pose & pose )

private

Reads from database, gets prob_set for ResidueProbDesignOperation + sets cdrs_wo_prob_data_.

References protocols::antibody::design::AntibodyDatabaseManager::load_cdr_design_data().

core::pack::task::TaskFactoryOP protocols::antibody::design::AntibodySeqDesignMover::setup_task_factory ( core::pose::Pose & pose )

private

Setup the Designer's taskfactory.

References protocols::antibody::CDRNameEnum_total, design, core::pack::task::TaskFactory::push_back(), protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors::set_cutoff_distance(), protocols::toolbox::task_operations::RestrictToLoops::set_design_loop(), protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors::set_include_neighbors(), protocols::toolbox::task_operations::RestrictToLoops::set_loops(), and protocols::antibody::TR.

Member Data Documentation

AntibodyInfoOP protocols::antibody::design::AntibodySeqDesignMover::ab_info_

private

bool protocols::antibody::design::AntibodySeqDesignMover::basic_design_

private

DesignTypeEnum protocols::antibody::design::AntibodySeqDesignMover::design_method_

private

std::string protocols::antibody::design::AntibodySeqDesignMover::instruction_path_

private

std::map<CDRNameEnum, CDRDesignInstructions> protocols::antibody::design::AntibodySeqDesignMover::instructions_

private

core::Real protocols::antibody::design::AntibodySeqDesignMover::neighbor_dis_

private

bool protocols::antibody::design::AntibodySeqDesignMover::no_design_proline_

private

core::Size protocols::antibody::design::AntibodySeqDesignMover::prob_cutoff_

private

core::Size protocols::antibody::design::AntibodySeqDesignMover::rounds_

private

ScoreFunctionOP protocols::antibody::design::AntibodySeqDesignMover::scorefxn_

private

bool protocols::antibody::design::AntibodySeqDesignMover::turn_conservation_

private

bool protocols::antibody::design::AntibodySeqDesignMover::use_cluster_constraints_

private

core::Real protocols::antibody::design::AntibodySeqDesignMover::zero_prob_weight_

private

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

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

Private Attributes
AntibodyInfoOP	ab_info_

DesignTypeEnum	design_method_

ScoreFunctionOP	scorefxn_

core::Real	zero_prob_weight_

core::Real	neighbor_dis_

core::Size	prob_cutoff_

core::Size	rounds_

bool	turn_conservation_

bool	no_design_proline_

bool	basic_design_

bool	use_cluster_constraints_

std::map< CDRNameEnum, CDRDesignInstructions >	instructions_

std::string	instruction_path_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation