#include <MotifDnaPacker.hh>

Inheritance diagram for protocols::motifs::MotifDnaPacker:

[legend]

Public Member Functions
	MotifDnaPacker ()
	lightweight default constructor More...

	MotifDnaPacker (core::scoring::ScoreFunctionOP, bool minimize=false, std::string filename_root="dnapacker")
	functional constructor More...

	~MotifDnaPacker () override
	destructor More...

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	apply (core::pose::Pose &) override

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

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

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

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 void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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::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	init_standard (core::pose::Pose &)

void	init_options ()

void	run_motifs (core::pose::Pose &pose, utility::vector1< core::Size > &design_positions, std::set< core::Size > &src_pos, std::map< core::Size, core::pack::rotamer_set::Rotamers > &rotamer_map, std::map< core::Size, std::set< std::string > > &types_map, std::list< std::string > &info_lines, core::pack::task::TaskFactoryOP taskfactory)

void	expand_motifs (core::pose::Pose &pose, utility::vector1< core::Size > &design_positions, std::set< core::Size > &src_pos, std::map< core::Size, core::pack::rotamer_set::Rotamers > &rotamer_map, std::map< core::Size, std::set< std::string > > &types_map, std::list< std::string > &info_lines, core::pack::task::TaskFactoryOP taskfactory)

void	aromatic_motifs (core::pose::Pose &pose, utility::vector1< core::Size > &design_positions, std::set< core::Size > &src_pos, std::map< core::Size, core::pack::rotamer_set::Rotamers > &rotamer_map, std::map< core::Size, std::set< std::string > > &types_map, std::list< std::string > &info_lines, core::pack::task::TaskFactoryOP taskfactory)

void	motif_expansion_inner_loop (core::pose::Pose &pose, std::set< core::Size > current_pos, std::map< core::Size, core::pack::rotamer_set::Rotamers >::const_iterator it, std::set< std::string >::const_iterator it2, std::map< core::Size, core::pack::rotamer_set::Rotamers > &rotamer_map, std::list< std::string > &info_lines, core::pack::task::TaskFactoryOP taskfactory)

Private Attributes
protocols::dna::DnaInterfacePackerOP	dna_packer_

protocols::motifs::MotifSearchOP	motif_search_

core::scoring::ScoreFunctionOP	scorefxn_

protocols::dna::PDBOutputOP	pdboutput_

core::pose::PoseCOP	starting_pose_

protocols::dna::DnaDesignDefOPs	targeted_dna_

bool	run_motifs_

bool	expand_motifs_

bool	aromatic_motifs_

bool	minimize_dna_

core::Real	special_rotweight_

core::Real	num_repacks_

bool	flex_dna_sugar_

std::string	filename_root_

bool	dna_design_

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 std::list< std::string >	Strings

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...

Constructor & Destructor Documentation

◆ MotifDnaPacker() [1/2]

protocols::motifs::MotifDnaPacker::MotifDnaPacker ( )

lightweight default constructor

References init_options().

◆ MotifDnaPacker() [2/2]

protocols::motifs::MotifDnaPacker::MotifDnaPacker	(	core::scoring::ScoreFunctionOP	scorefxn_in,
		bool	minimize = `false`,
		std::string	filename_root = `"dnapacker"`
	)

functional constructor

References dna_packer_, filename_root_, init_options(), protocols::antibody::design::minimize, motif_search_, and pdboutput_.

◆ ~MotifDnaPacker()

protocols::motifs::MotifDnaPacker::~MotifDnaPacker ( )

overridedefault

destructor

Member Function Documentation

◆ apply()

void protocols::motifs::MotifDnaPacker::apply ( core::pose::Pose & pose )

overridevirtual

◆ aromatic_motifs()

void protocols::motifs::MotifDnaPacker::aromatic_motifs	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > &	design_positions,
		std::set< core::Size > &	src_pos,
		std::map< core::Size, core::pack::rotamer_set::Rotamers > &	rotamer_map,
		std::map< core::Size, std::set< std::string > > &	types_map,
		std::list< std::string > &	info_lines,
		core::pack::task::TaskFactoryOP	taskfactory
	)

private

References aromatic_motifs_, core::sequence::end, motif_expansion_inner_loop(), and run_motifs().

Referenced by apply().

◆ clone()

protocols::moves::MoverOP protocols::motifs::MotifDnaPacker::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ expand_motifs()

void protocols::motifs::MotifDnaPacker::expand_motifs	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > &	design_positions,
		std::set< core::Size > &	src_pos,
		std::map< core::Size, core::pack::rotamer_set::Rotamers > &	rotamer_map,
		std::map< core::Size, std::set< std::string > > &	types_map,
		std::list< std::string > &	info_lines,
		core::pack::task::TaskFactoryOP	taskfactory
	)

private

References core::sequence::end, and motif_expansion_inner_loop().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::motifs::MotifDnaPacker::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::motifs::MotifDnaPacker::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ init_options()

void protocols::motifs::MotifDnaPacker::init_options ( )

private

References aromatic_motifs_, dna_design_, expand_motifs_, flex_dna_sugar_, minimize_dna_, num_repacks_, run_motifs_, and special_rotweight_.

Referenced by MotifDnaPacker().

◆ init_standard()

void protocols::motifs::MotifDnaPacker::init_standard ( core::pose::Pose & pose )

private

References dna_packer_, protocols::dna::load_dna_design_defs_from_options(), protocols::dna::load_dna_design_defs_from_strings(), pdboutput_, starting_pose_, and targeted_dna_.

Referenced by apply().

◆ motif_expansion_inner_loop()

void protocols::motifs::MotifDnaPacker::motif_expansion_inner_loop	(	core::pose::Pose &	pose,
		std::set< core::Size >	current_pos,
		std::map< core::Size, core::pack::rotamer_set::Rotamers >::const_iterator	it,
		std::set< std::string >::const_iterator	it2,
		std::map< core::Size, core::pack::rotamer_set::Rotamers > &	rotamer_map,
		std::list< std::string > &	info_lines,
		core::pack::task::TaskFactoryOP	taskfactory
	)

private

References core::chemical::aa_from_name(), dna_packer_, protocols::abinitio::filename(), filename_root_, core::chemical::num_canonical_aas, num_repacks_, core::pose::Pose::pdb_info(), pdboutput_, protocols::jumping::rot2, scorefxn_, core::scoring::special_rot, special_rotweight_, and starting_pose_.

Referenced by aromatic_motifs(), and expand_motifs().

◆ mover_name()

std::string protocols::motifs::MotifDnaPacker::mover_name ( )

static

Referenced by get_name(), protocols::motifs::MotifDnaPackerCreator::keyname(), and provide_xml_schema().

◆ provide_xml_schema()

void protocols::motifs::MotifDnaPacker::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::motifs::MotifDnaPackerCreator::provide_xml_schema().

◆ run_motifs()

void protocols::motifs::MotifDnaPacker::run_motifs	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > &	design_positions,
		std::set< core::Size > &	src_pos,
		std::map< core::Size, core::pack::rotamer_set::Rotamers > &	rotamer_map,
		std::map< core::Size, std::set< std::string > > &	types_map,
		std::list< std::string > &	info_lines,
		core::pack::task::TaskFactoryOP	taskfactory
	)

private

References core::pose::add_variant_type_to_residue(), aromatic_motifs_, dna_packer_, expand_motifs_, protocols::abinitio::filename(), filename_root_, motif_search_, num_repacks_, pdboutput_, rot(), scorefxn_, core::chemical::SPECIAL_ROT, core::scoring::special_rot, special_rotweight_, and starting_pose_.

Referenced by apply(), and aromatic_motifs().

Member Data Documentation

◆ aromatic_motifs_

bool protocols::motifs::MotifDnaPacker::aromatic_motifs_

private

Referenced by apply(), aromatic_motifs(), init_options(), and run_motifs().

◆ dna_design_

bool protocols::motifs::MotifDnaPacker::dna_design_

private

Referenced by apply(), and init_options().

◆ dna_packer_

protocols::dna::DnaInterfacePackerOP protocols::motifs::MotifDnaPacker::dna_packer_

private

Referenced by apply(), init_standard(), motif_expansion_inner_loop(), MotifDnaPacker(), and run_motifs().

◆ expand_motifs_

bool protocols::motifs::MotifDnaPacker::expand_motifs_

private

Referenced by apply(), init_options(), and run_motifs().

◆ filename_root_

std::string protocols::motifs::MotifDnaPacker::filename_root_

private

Referenced by apply(), motif_expansion_inner_loop(), MotifDnaPacker(), and run_motifs().

◆ flex_dna_sugar_

bool protocols::motifs::MotifDnaPacker::flex_dna_sugar_

private

Referenced by init_options().

◆ minimize_dna_

bool protocols::motifs::MotifDnaPacker::minimize_dna_

private

Referenced by init_options().

◆ motif_search_

protocols::motifs::MotifSearchOP protocols::motifs::MotifDnaPacker::motif_search_

private

Referenced by apply(), MotifDnaPacker(), and run_motifs().

◆ num_repacks_

core::Real protocols::motifs::MotifDnaPacker::num_repacks_

private

Referenced by init_options(), motif_expansion_inner_loop(), and run_motifs().

◆ pdboutput_

protocols::dna::PDBOutputOP protocols::motifs::MotifDnaPacker::pdboutput_

private

Referenced by apply(), init_standard(), motif_expansion_inner_loop(), MotifDnaPacker(), and run_motifs().

◆ run_motifs_

bool protocols::motifs::MotifDnaPacker::run_motifs_

private

Referenced by apply(), and init_options().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::motifs::MotifDnaPacker::scorefxn_

private

Referenced by apply(), motif_expansion_inner_loop(), and run_motifs().

◆ special_rotweight_

core::Real protocols::motifs::MotifDnaPacker::special_rotweight_

private

Referenced by init_options(), motif_expansion_inner_loop(), and run_motifs().

◆ starting_pose_

core::pose::PoseCOP protocols::motifs::MotifDnaPacker::starting_pose_

private

Referenced by apply(), init_standard(), motif_expansion_inner_loop(), and run_motifs().

◆ targeted_dna_

protocols::dna::DnaDesignDefOPs protocols::motifs::MotifDnaPacker::targeted_dna_

private

Referenced by apply(), and init_standard().

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

src/protocols/motifs/MotifDnaPacker.hh
src/protocols/motifs/MotifDnaPacker.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MotifDnaPacker() [1/2]

◆ MotifDnaPacker() [2/2]

◆ ~MotifDnaPacker()

Member Function Documentation

◆ apply()

◆ aromatic_motifs()

◆ clone()

◆ expand_motifs()

◆ fresh_instance()

◆ get_name()

◆ init_options()

◆ init_standard()

◆ motif_expansion_inner_loop()

◆ mover_name()

◆ provide_xml_schema()

◆ run_motifs()

Member Data Documentation

◆ aromatic_motifs_

◆ dna_design_

◆ dna_packer_

◆ expand_motifs_

◆ filename_root_

◆ flex_dna_sugar_

◆ minimize_dna_

◆ motif_search_

◆ num_repacks_

◆ pdboutput_

◆ run_motifs_

◆ scorefxn_

◆ special_rotweight_

◆ starting_pose_

◆ targeted_dna_