wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework More...

#include <DnaInterfaceMultiStateDesign.hh>

Inheritance diagram for protocols::dna::DnaInterfaceMultiStateDesign:

Collaboration diagram for protocols::dna::DnaInterfaceMultiStateDesign:

Public Types
typedef multistate_design::PosType	PosType

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef genetic_algorithm::GeneticAlgorithmOP	GeneticAlgorithmOP

Public Types inherited from protocols::simple_moves::PackRotamersMover
typedef core::pack::interaction_graph::InteractionGraphBaseOP	InteractionGraphBaseOP
	please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here! More...

typedef core::pack::interaction_graph::InteractionGraphBaseCOP	InteractionGraphBaseCOP

typedef core::pack::rotamer_set::RotamerSetsOP	RotamerSetsOP

typedef core::pack::rotamer_set::RotamerSetsCOP	RotamerSetsCOP

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef core::pack::task::TaskFactoryCOP	TaskFactoryCOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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

Public Member Functions
	DnaInterfaceMultiStateDesign ()

virtual	~DnaInterfaceMultiStateDesign ()

virtual void	apply (Pose &)
	Performs side-chain packing based on the input PackerTask using the input ScoreFunction. More...

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

void	copy_dna_chains (DnaChainsOP)

void	copy_targeted_dna (DnaDesignDefOPs const &)

void	output_results (Pose &)

virtual void	parse_my_tag (TagPtr const, moves::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, Pose const &)
	parse XML (specifically in the context of the parser/scripting scheme) More...

virtual moves::MoverOP	fresh_instance () const
	required in the context of the parser/scripting scheme More...

virtual moves::MoverOP	clone () const
	required in the context of the parser/scripting scheme More...

Public Member Functions inherited from protocols::simple_moves::PackRotamersMover
	PackRotamersMover ()
	default constructor More...

	PackRotamersMover (std::string const &)
	constructor with typename More...

	PackRotamersMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task=0, core::Size nloop=1)
	Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn> More...

virtual	~PackRotamersMover ()

	PackRotamersMover (PackRotamersMover const &other)

bool	task_is_valid (Pose const &pose) const
	when the PackerTask was not generated locally, verify compatibility with pose More...

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

virtual void	parse_score_function (TagPtr const, protocols::moves::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...

virtual void	parse_task_operations (TagPtr const, protocols::moves::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...

void	score_function (ScoreFunctionCOP sf)
	Sets the ScoreFunction to <sf> More...

void	task_factory (TaskFactoryCOP tf)
	Sets the TaskFactory to <tf> More...

void	task (PackerTaskCOP t)
	Sets the PackerTask to <t> More...

void	nloop (core::Size nloop_in)

ScoreFunctionCOP	score_function () const
	Returns the ScoreFunction. More...

PackerTaskCOP	task () const
	Returns the PackerTask. More...

core::Size	nloop () const

TaskFactoryCOP	task_factory () const
	Returns the TaskFactory. More...

RotamerSetsCOP	rotamer_sets () const

InteractionGraphBaseCOP	ig () const

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	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)

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
	this function informs 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
	this function informs 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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	initialize (Pose &)

void	run ()

void	add_dna_states (Pose const &, PackerTaskCOP)

Additional Inherited Members
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Protected Member Functions inherited from protocols::simple_moves::PackRotamersMover
virtual void	setup (Pose &pose)
	get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask. More...

virtual core::PackerEnergy	run (Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const

virtual void	note_packertask_settings (Pose const &)
	note PackerTask's packable and designable residues as string info More...

Detailed Description

wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework

Definition at line 41 of file DnaInterfaceMultiStateDesign.hh.

Member Typedef Documentation

typedef genetic_algorithm::GeneticAlgorithmOP protocols::dna::DnaInterfaceMultiStateDesign::GeneticAlgorithmOP

Definition at line 45 of file DnaInterfaceMultiStateDesign.hh.

typedef core::pack::task::PackerTaskCOP protocols::dna::DnaInterfaceMultiStateDesign::PackerTaskCOP

Definition at line 44 of file DnaInterfaceMultiStateDesign.hh.

typedef multistate_design::PosType protocols::dna::DnaInterfaceMultiStateDesign::PosType

Definition at line 43 of file DnaInterfaceMultiStateDesign.hh.

Constructor & Destructor Documentation

protocols::dna::DnaInterfaceMultiStateDesign::DnaInterfaceMultiStateDesign ( )

Definition at line 100 of file DnaInterfaceMultiStateDesign.cc.

Referenced by clone(), and fresh_instance().

protocols::dna::DnaInterfaceMultiStateDesign::~DnaInterfaceMultiStateDesign ( )

virtual

Definition at line 122 of file DnaInterfaceMultiStateDesign.cc.

Member Function Documentation

void protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states	(	Pose const &	pose,
		PackerTaskCOP	ptask
	)

private

Definition at line 413 of file DnaInterfaceMultiStateDesign.cc.

References protocols::dna::DnaPosition::bottom(), core::pose::Pose::chain(), dna_chains_, protocols::dna::dna_comp_name_str(), multistate_packer_, protocols::moves::Mover::name(), protocols::dna::DnaPosition::paired(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::residue_type_set(), protocols::dna::substitute_residue(), protocols::dna::DnaPosition::top(), and protocols::dna::TR().

Referenced by initialize().

void protocols::dna::DnaInterfaceMultiStateDesign::apply ( Pose & pose)

virtual

Performs side-chain packing based on the input PackerTask using the input ScoreFunction.

example(s): packmover.apply(pose) See Also: PackerTask ScoreFunction

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 125 of file DnaInterfaceMultiStateDesign.cc.

References initialize(), output_results(), and run().

moves::MoverOP protocols::dna::DnaInterfaceMultiStateDesign::clone ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 407 of file DnaInterfaceMultiStateDesign.cc.

References DnaInterfaceMultiStateDesign().

void protocols::dna::DnaInterfaceMultiStateDesign::copy_dna_chains ( DnaChainsOP dna_chains)

Definition at line 133 of file DnaInterfaceMultiStateDesign.cc.

References dna_chains_.

void protocols::dna::DnaInterfaceMultiStateDesign::copy_targeted_dna ( DnaDesignDefOPs const & defs)

Definition at line 140 of file DnaInterfaceMultiStateDesign.cc.

References targeted_dna_.

moves::MoverOP protocols::dna::DnaInterfaceMultiStateDesign::fresh_instance ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 400 of file DnaInterfaceMultiStateDesign.cc.

References DnaInterfaceMultiStateDesign().

std::string protocols::dna::DnaInterfaceMultiStateDesign::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 360 of file DnaInterfaceMultiStateDesign.cc.

References protocols::dna::DnaInterfaceMultiStateDesignCreator::mover_name().

void protocols::dna::DnaInterfaceMultiStateDesign::initialize ( Pose & pose)

private

void protocols::dna::DnaInterfaceMultiStateDesign::output_results ( Pose & pose)

Definition at line 295 of file DnaInterfaceMultiStateDesign.cc.

References core::sequence::end, protocols::genetic_algorithm::Entity::fitness(), gen_alg_, protocols::moves::Mover::info(), multistate_packer_, numresults_, protocols::dna::TR(), and protocols::genetic_algorithm::Entity::traits().

Referenced by apply().

void protocols::dna::DnaInterfaceMultiStateDesign::parse_my_tag	(	TagPtr const	tag,
		moves::DataMap &	datamap,
		protocols::filters::Filters_map const &	filters,
		moves::Movers_map const &	movers,
		Pose const &	pose
	)

virtual

parse XML (specifically in the context of the parser/scripting scheme)

parse "XML" Tag (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 365 of file DnaInterfaceMultiStateDesign.cc.

References anchor_offset_, boltz_temp_, checkpoint_gz_, checkpoint_interval_, checkpoint_prefix_, checkpoint_rename_, fraction_by_recombination_, generations_, mutate_rate_, num_packs_, numresults_, protocols::simple_moves::PackRotamersMover::parse_score_function(), protocols::simple_moves::PackRotamersMover::parse_task_operations(), pop_from_ss_, and pop_size_.

void protocols::dna::DnaInterfaceMultiStateDesign::run ( )

private

Definition at line 283 of file DnaInterfaceMultiStateDesign.cc.

References gen_alg_, and protocols::dna::TR().

Referenced by apply().

Member Data Documentation

core::Real protocols::dna::DnaInterfaceMultiStateDesign::anchor_offset_

private

Definition at line 86 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

core::Real protocols::dna::DnaInterfaceMultiStateDesign::boltz_temp_

private

Definition at line 86 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

bool protocols::dna::DnaInterfaceMultiStateDesign::checkpoint_gz_

private

Definition at line 90 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::checkpoint_interval_

private

Definition at line 89 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

std::string protocols::dna::DnaInterfaceMultiStateDesign::checkpoint_prefix_

private

Definition at line 88 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

bool protocols::dna::DnaInterfaceMultiStateDesign::checkpoint_rename_

private

Definition at line 90 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

DnaChainsOP protocols::dna::DnaInterfaceMultiStateDesign::dna_chains_

private

Definition at line 81 of file DnaInterfaceMultiStateDesign.hh.

Referenced by add_dna_states(), copy_dna_chains(), and initialize().

core::Real protocols::dna::DnaInterfaceMultiStateDesign::fraction_by_recombination_

private

Definition at line 86 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

GeneticAlgorithmOP protocols::dna::DnaInterfaceMultiStateDesign::gen_alg_

private

Definition at line 77 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), output_results(), and run().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::generations_

private

Definition at line 85 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

multistate_design::MultiStatePackerOP protocols::dna::DnaInterfaceMultiStateDesign::multistate_packer_

private

Definition at line 80 of file DnaInterfaceMultiStateDesign.hh.

Referenced by add_dna_states(), initialize(), and output_results().

core::Real protocols::dna::DnaInterfaceMultiStateDesign::mutate_rate_

private

Definition at line 86 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::num_packs_

private

Definition at line 85 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::numresults_

private

Definition at line 85 of file DnaInterfaceMultiStateDesign.hh.

Referenced by output_results(), and parse_my_tag().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::pop_from_ss_

private

Definition at line 85 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::pop_size_

private

Definition at line 85 of file DnaInterfaceMultiStateDesign.hh.

Referenced by initialize(), and parse_my_tag().

DnaDesignDefOPs protocols::dna::DnaInterfaceMultiStateDesign::targeted_dna_

private

Definition at line 82 of file DnaInterfaceMultiStateDesign.hh.

Referenced by copy_targeted_dna(), and initialize().

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

src/protocols/dna/DnaInterfaceMultiStateDesign.hh
src/protocols/dna/DnaInterfaceMultiStateDesign.cc

Private Attributes
GeneticAlgorithmOP	gen_alg_

multistate_design::MultiStatePackerOP	multistate_packer_

DnaChainsOP	dna_chains_

DnaDesignDefOPs	targeted_dna_

core::Size	generations_

core::Size	pop_size_

core::Size	num_packs_

core::Size	pop_from_ss_

core::Size	numresults_

core::Real	fraction_by_recombination_

core::Real	mutate_rate_

core::Real	boltz_temp_

core::Real	anchor_offset_

std::string	checkpoint_prefix_

core::Size	checkpoint_interval_

bool	checkpoint_gz_

bool	checkpoint_rename_

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation