#include <MotifDnaPacker.hh>

Inheritance diagram for protocols::motifs::MotifDnaPacker:

Collaboration diagram for protocols::motifs::MotifDnaPacker:

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

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

virtual	~MotifDnaPacker ()
	destructor More...

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

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

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

virtual void	apply (core::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

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 void	parse_my_tag (TagPtr const tag, 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
	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	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)

Additional Inherited Members
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

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::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

Definition at line 41 of file MotifDnaPacker.hh.

Constructor & Destructor Documentation

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

lightweight default constructor

Definition at line 146 of file MotifDnaPacker.cc.

References init_options().

Referenced by clone(), and fresh_instance().

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

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

virtual

destructor

Definition at line 190 of file MotifDnaPacker.cc.

Member Function Documentation

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

virtual

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

Definition at line 696 of file MotifDnaPacker.cc.

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

Referenced by apply().

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

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Definition at line 201 of file MotifDnaPacker.cc.

References MotifDnaPacker().

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

Definition at line 595 of file MotifDnaPacker.cc.

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

Referenced by apply().

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

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Definition at line 194 of file MotifDnaPacker.cc.

References MotifDnaPacker().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 207 of file MotifDnaPacker.cc.

References protocols::motifs::MotifDnaPackerCreator::mover_name().

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

private

Definition at line 501 of file MotifDnaPacker.cc.

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

Referenced by MotifDnaPacker().

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

private

Definition at line 398 of file MotifDnaPacker.cc.

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().

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

Definition at line 515 of file MotifDnaPacker.cc.

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

bool protocols::motifs::MotifDnaPacker::aromatic_motifs_

private

Definition at line 112 of file MotifDnaPacker.hh.

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

bool protocols::motifs::MotifDnaPacker::dna_design_

private

Definition at line 118 of file MotifDnaPacker.hh.

Referenced by apply(), and init_options().

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

private

Definition at line 102 of file MotifDnaPacker.hh.

Referenced by apply(), aromatic_motifs(), expand_motifs(), init_standard(), and run_motifs().

bool protocols::motifs::MotifDnaPacker::expand_motifs_

private

Definition at line 111 of file MotifDnaPacker.hh.

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

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

private

Definition at line 117 of file MotifDnaPacker.hh.

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

bool protocols::motifs::MotifDnaPacker::flex_dna_sugar_

private

Definition at line 116 of file MotifDnaPacker.hh.

Referenced by init_options().

bool protocols::motifs::MotifDnaPacker::minimize_dna_

private

Definition at line 113 of file MotifDnaPacker.hh.

Referenced by init_options().

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

private

Definition at line 103 of file MotifDnaPacker.hh.

Referenced by apply(), and run_motifs().

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

private

Definition at line 115 of file MotifDnaPacker.hh.

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

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

private

Definition at line 105 of file MotifDnaPacker.hh.

Referenced by apply(), aromatic_motifs(), expand_motifs(), init_standard(), and run_motifs().

bool protocols::motifs::MotifDnaPacker::run_motifs_

private

Definition at line 110 of file MotifDnaPacker.hh.

Referenced by apply(), and init_options().

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

private

Definition at line 104 of file MotifDnaPacker.hh.

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

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

private

Definition at line 114 of file MotifDnaPacker.hh.

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

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

private

Definition at line 106 of file MotifDnaPacker.hh.

Referenced by apply(), aromatic_motifs(), expand_motifs(), init_standard(), and run_motifs().

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

private

Definition at line 107 of file MotifDnaPacker.hh.

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

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_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation