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

#include <DnaInterfaceMultiStateDesign.hh>

Inheritance diagram for protocols::dna::DnaInterfaceMultiStateDesign:

[legend]

Public Types
typedef multistate_design::PosType	PosType

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

typedef genetic_algorithm::GeneticAlgorithmOP	GeneticAlgorithmOP

Public Types inherited from protocols::minimization_packing::PackRotamersMover
typedef core::pack::interaction_graph::AnnealableGraphBaseOP	AnnealableGraphBaseOP

typedef core::pack::interaction_graph::AnnealableGraphBaseCOP	AnnealableGraphBaseCOP

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::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

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

Public Member Functions
	DnaInterfaceMultiStateDesign ()

	~DnaInterfaceMultiStateDesign () override

void	apply (Pose &) override
	Main Method. More...

void	copy_dna_chains (DnaChainsOP)

void	copy_targeted_dna (DnaDesignDefOPs const &)

void	output_results (Pose &)

void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	parse XML (specifically in the context of the parser/scripting scheme) More...

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

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

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

Public Member Functions inherited from protocols::minimization_packing::PackRotamersMover
	PackRotamersMover ()
	default constructor; reads the nloop_ value from the global options system. More...

	PackRotamersMover (utility::options::OptionCollection const &options)
	constructor that reads from the (possibly local) options collection object More...

	PackRotamersMover (std::string const &)
	constructor with typename; reads the nloop_ value from the global options system. More...

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

	~PackRotamersMover () override

	PackRotamersMover (PackRotamersMover const &other)

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

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

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

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

void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	parse XML (specifically in the context of the parser/scripting scheme) More...

virtual void	parse_score_function (TagCOP, basic::datacache::DataMap const &)
	parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...

virtual void	parse_task_operations (TagCOP, basic::datacache::DataMap const &)
	parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...

void	initialize_task_factory_with_operations (std::list< core::pack::task::operation::TaskOperationCOP > const &)

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

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

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

virtual 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
	Returns the RotamerSets object being used for packing. More...

void	set_annealer_observer (core::pack::annealer::AnnealerObserverOP observer)

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

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

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

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...

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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::minimization_packing::PackRotamersMover
static std::string	mover_name ()

static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_pack_rotamers_mover (utility::tag::XMLSchemaDefinition &xsd)

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static void	list_options_read (utility::options::OptionKeyList &opts)

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...

Private Member Functions
void	initialize (Pose &)

void	run ()

void	add_dna_states (Pose const &, PackerTaskCOP)

Additional Inherited Members
Protected Member Functions inherited from protocols::minimization_packing::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	cleanup (core::pose::Pose &pose)
	Clean up cached pose and mover data after the fact. More...

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

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

Member Typedef Documentation

◆ GeneticAlgorithmOP

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

◆ PackerTaskCOP

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

◆ PosType

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

Constructor & Destructor Documentation

◆ DnaInterfaceMultiStateDesign()

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

◆ ~DnaInterfaceMultiStateDesign()

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

overridedefault

Member Function Documentation

◆ add_dna_states()

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

private

References core::chemical::ResidueTypeFinder::base_property(), protocols::dna::DnaPosition::bottom(), core::pose::Pose::chain(), core::chemical::DNA, dna_chains_, protocols::dna::dna_comp_name_str(), core::chemical::ResidueTypeFinder::get_possible_base_residue_types(), multistate_packer_, protocols::moves::Mover::name(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name3(), protocols::dna::DnaPosition::paired(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), protocols::dna::substitute_residue(), protocols::dna::DnaPosition::top(), and protocols::dna::TR().

Referenced by initialize().

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

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

◆ clone()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ copy_dna_chains()

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

References dna_chains_.

◆ copy_targeted_dna()

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

References targeted_dna_.

◆ fresh_instance()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ initialize()

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

private

References protocols::cluster::calibur::aa, add_dna_states(), core::pack::task::ResidueLevelTask::allowed_residue_types(), anchor_offset_, core::pack::task::ResidueLevelTask::being_designed(), boltz_temp_, checkpoint_gz_, checkpoint_interval_, checkpoint_prefix_, checkpoint_rename_, core::scoring::ScoreFunctionFactory::create_score_function(), dna_chains_, core::sequence::end, protocols::dna::find_basepairs(), fraction_by_recombination_, gen_alg_, generations_, protocols::moves::Mover::info(), core::chemical::ResidueTypeBase::is_protein(), multistate_packer_, mutate_rate_, num_packs_, pop_from_ss_, pop_size_, core::pose::Pose::residue_type(), protocols::minimization_packing::PackRotamersMover::score_function(), protocols::hybridization::t, targeted_dna_, protocols::minimization_packing::PackRotamersMover::task_factory(), and protocols::dna::TR().

Referenced by apply().

◆ mover_name()

std::string protocols::dna::DnaInterfaceMultiStateDesign::mover_name ( )

static

Referenced by get_name(), protocols::dna::DnaInterfaceMultiStateDesignCreator::keyname(), and provide_xml_schema().

◆ output_results()

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

References core::sequence::end, core::chemical::element::F, 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().

◆ parse_my_tag()

void protocols::dna::DnaInterfaceMultiStateDesign::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

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::moves::Mover.

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

◆ provide_xml_schema()

void protocols::dna::DnaInterfaceMultiStateDesign::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::dna::DnaInterfaceMultiStateDesignCreator::provide_xml_schema().

◆ run()

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

private

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

Referenced by apply().

Member Data Documentation

◆ anchor_offset_

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

private

Referenced by initialize(), and parse_my_tag().

◆ boltz_temp_

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

private

Referenced by initialize(), and parse_my_tag().

◆ checkpoint_gz_

bool protocols::dna::DnaInterfaceMultiStateDesign::checkpoint_gz_

private

Referenced by initialize(), and parse_my_tag().

◆ checkpoint_interval_

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

private

Referenced by initialize(), and parse_my_tag().

◆ checkpoint_prefix_

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

private

Referenced by initialize(), and parse_my_tag().

◆ checkpoint_rename_

bool protocols::dna::DnaInterfaceMultiStateDesign::checkpoint_rename_

private

Referenced by initialize(), and parse_my_tag().

◆ dna_chains_

DnaChainsOP protocols::dna::DnaInterfaceMultiStateDesign::dna_chains_

private

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

◆ fraction_by_recombination_

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

private

Referenced by initialize(), and parse_my_tag().

◆ gen_alg_

GeneticAlgorithmOP protocols::dna::DnaInterfaceMultiStateDesign::gen_alg_

private

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

◆ generations_

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

private

Referenced by initialize(), and parse_my_tag().

◆ multistate_packer_

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

private

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

◆ mutate_rate_

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

private

Referenced by initialize(), and parse_my_tag().

◆ num_packs_

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

private

Referenced by initialize(), and parse_my_tag().

◆ numresults_

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

private

Referenced by output_results(), and parse_my_tag().

◆ pop_from_ss_

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

private

Referenced by initialize(), and parse_my_tag().

◆ pop_size_

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

private

Referenced by initialize(), and parse_my_tag().

◆ targeted_dna_

DnaDesignDefOPs protocols::dna::DnaInterfaceMultiStateDesign::targeted_dna_

private

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

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ GeneticAlgorithmOP

◆ PackerTaskCOP

◆ PosType

Constructor & Destructor Documentation

◆ DnaInterfaceMultiStateDesign()

◆ ~DnaInterfaceMultiStateDesign()

Member Function Documentation

◆ add_dna_states()

◆ apply()

◆ clone()

◆ copy_dna_chains()

◆ copy_targeted_dna()

◆ fresh_instance()

◆ get_name()

◆ initialize()

◆ mover_name()

◆ output_results()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ run()

Member Data Documentation

◆ anchor_offset_

◆ boltz_temp_

◆ checkpoint_gz_

◆ checkpoint_interval_

◆ checkpoint_prefix_

◆ checkpoint_rename_

◆ dna_chains_

◆ fraction_by_recombination_

◆ gen_alg_

◆ generations_

◆ multistate_packer_

◆ mutate_rate_

◆ num_packs_

◆ numresults_

◆ pop_from_ss_

◆ pop_size_

◆ targeted_dna_