#include <FlxbbDesign.hh>

Inheritance diagram for protocols::flxbb::FlxbbDesign:

Collaboration diagram for protocols::flxbb::FlxbbDesign:

Public Types
typedef protocols::moves::Mover	Super

typedef std::string	String

typedef core::Size	Size

typedef core::Real	Real

typedef core::kinematics::MoveMapOP	MoveMapOP

typedef core::pose::Pose	Pose

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::pack::task::operation::TaskOperation	TaskOperation

typedef core::pack::task::operation::TaskOperationOP	TaskOperationOP

typedef protocols::moves::MoverOP	MoverOP

typedef protocols::jd2::parser::BluePrint	BluePrint

typedef protocols::jd2::parser::BluePrintOP	BluePrintOP

typedef protocols::flxbb::DesignTaskOP	DesignTaskOP

typedef protocols::flxbb::DesignTaskSet	DesignTaskSet

typedef utility::tag::TagPtr	TagPtr

typedef protocols::filters::Filters_map	Filters_map

typedef protocols::moves::DataMap	DataMap

typedef protocols::moves::Movers_map	Movers_map

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
	FlxbbDesign ()
	default constructor More...

	FlxbbDesign (ScoreFunctionOP const sfxnd, ScoreFunctionOP const sfxnr, Size const ncycle=3, String const layer_mode="", bool const use_origseq_for_not_dsgned_layer=true, bool const no_relax=false)
	value constructor More...

	FlxbbDesign (FlxbbDesign const &rval)
	copy constructor More...

virtual	~FlxbbDesign ()
	destructor More...

virtual MoverOP	clone () const
	clone this object More...

virtual MoverOP	fresh_instance () const
	create this type of object More...

void	read_options ()
	read parameters More...

void	initialize_filter (Size const filter_trial, String const &filter_type)
	initialize filter parameters More...

virtual void	apply (Pose &pose)
	mover apply More...

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

void	set_scorefxn_design (ScoreFunctionOP const scorefxn)
	set the score function for fixbb design More...

void	set_scorefxn_relax (ScoreFunctionOP const scorefxn)
	set the score function for relax More...

void	set_ncycles (Size const ncycles)
	the number of cycles of fixbb and relax More...

void	set_layer_mode (String const &layer_mode)
	set layer mode More...

void	use_origseq_for_not_dsgned_layer (bool const use)
	use original sequence for not designed region in layer_mode, otherwise the residues of the region turned into Ala ( default true ) More...

void	no_relax (bool const no_relax)
	relax is not performed after design (default false) More...

void	no_design (bool const no_design)
	design protocol will not be performed (default false) More...

void	set_blueprint (BluePrintOP const blueprint)
	set BluePrintOP More...

void	set_weight_constraints_sheet (Real const value)
	set weight of constraints_sheet which constrains between Ca atoms in beta-sheets if this weight > 0.0, the constraints is applied ( default = -1.0 ) More...

void	set_weight_constraints_NtoC (Real const value)
	set weight of constraints_NtoC which constrain between Ca atoms of C- and N-terminal if this weight > 0.0, the constraints is applied ( default = -1.0 ) More...

void	movemap_from_blueprint (bool const value)
	set movemap for relax More...

void	set_movemap (MoveMapOP const movemap)
	set movemap for relax More...

void	set_design_taskset (DesignTaskSet const &design_taskset)
	set DesignTaskSet Once you set DesignTaskSet, this controls almost every setups of this class More...

void	add_design_task (DesignTaskOP const design_task)
	add the design task which cotrols the iteration of fixbb design and relax More...

void	set_filter_during_design (FilterStructsOP const filter_during_design)
	filtering during design More...

void	clear_design_taskset ()
	clear DesignTaskSet More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &, Movers_map const &, Pose const &)
	parse xml More...

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)

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

Static Public Member Functions
static void	register_options ()
	register options More...

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...

Private Member Functions
DesignTaskSet	build_design_taskset (Pose const &pose)
	build design_task_set More...

MoveMapOP	get_movemap_from_blueprint (Pose const &pose, BluePrintOP const blueprint)
	make movemap from blueprint for relax More...

Private Attributes
ScoreFunctionOP	scorefxn_design_
	score function for design More...

ScoreFunctionOP	scorefxn_relax_
	score function for relax More...

Size	nflxbb_cycles_
	the number of cycles of fixbb and relax More...

String	layer_mode_
	perform fixbb in layer mode More...

bool	use_origseq_for_not_dsgned_layer_
	use original sequence for not designed region in layer_mode, otherwise the residues of the region turned into Ala More...

bool	no_relax_
	relax is not performed after design (default false) More...

bool	no_design_
	design protocol will not be performed (default false) More...

DesignTaskSet	design_taskset_
	control the method of design with filter and relax More...

FilterStructsOP	filter_during_design_
	filter during design More...

BluePrintOP	blueprint_
	blueprint for setting up constraints of beta sheet More...

String	resfile_
	resfile More...

Real	constraints_sheet_
	weight of constraints_sheet which constrains between Ca atoms in beta-sheets if this weight > 0.0, the constraints is applied ( default = -1.0 ) More...

Real	constraints_NtoC_
	weight of constraints_NtoC which constrains between Ca atoms of C- and N-terminal if this weight > 0.0, the constraints is applied ( default = -1.0 ) More...

bool	movemap_from_blueprint_
	set movemap from blueprint ( default false ) More...

MoveMapOP	movemap_
	mavemap for relax ( defalut NULL ) More...

utility::vector1< TaskOperationOP >	task_operations_
	task operations More...

bool	use_fast_relax_
	use fast relax or not More...

bool	clear_all_residues_
	clear all residues before design More...

bool	relax_constraint_to_design_

bool	limit_aroma_chi2_

Additional Inherited Members
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 57 of file FlxbbDesign.hh.

Member Typedef Documentation

typedef protocols::jd2::parser::BluePrint protocols::flxbb::FlxbbDesign::BluePrint

Definition at line 73 of file FlxbbDesign.hh.

typedef protocols::jd2::parser::BluePrintOP protocols::flxbb::FlxbbDesign::BluePrintOP

Definition at line 74 of file FlxbbDesign.hh.

typedef protocols::moves::DataMap protocols::flxbb::FlxbbDesign::DataMap

Definition at line 80 of file FlxbbDesign.hh.

typedef protocols::flxbb::DesignTaskOP protocols::flxbb::FlxbbDesign::DesignTaskOP

Definition at line 75 of file FlxbbDesign.hh.

typedef protocols::flxbb::DesignTaskSet protocols::flxbb::FlxbbDesign::DesignTaskSet

Definition at line 76 of file FlxbbDesign.hh.

typedef protocols::filters::Filters_map protocols::flxbb::FlxbbDesign::Filters_map

Definition at line 79 of file FlxbbDesign.hh.

typedef core::kinematics::MoveMapOP protocols::flxbb::FlxbbDesign::MoveMapOP

Definition at line 65 of file FlxbbDesign.hh.

typedef protocols::moves::MoverOP protocols::flxbb::FlxbbDesign::MoverOP

Definition at line 72 of file FlxbbDesign.hh.

typedef protocols::moves::Movers_map protocols::flxbb::FlxbbDesign::Movers_map

Definition at line 81 of file FlxbbDesign.hh.

typedef core::pose::Pose protocols::flxbb::FlxbbDesign::Pose

Definition at line 66 of file FlxbbDesign.hh.

typedef core::Real protocols::flxbb::FlxbbDesign::Real

Definition at line 64 of file FlxbbDesign.hh.

typedef core::scoring::ScoreFunction protocols::flxbb::FlxbbDesign::ScoreFunction

Definition at line 67 of file FlxbbDesign.hh.

typedef core::scoring::ScoreFunctionOP protocols::flxbb::FlxbbDesign::ScoreFunctionOP

Definition at line 68 of file FlxbbDesign.hh.

typedef core::Size protocols::flxbb::FlxbbDesign::Size

Definition at line 63 of file FlxbbDesign.hh.

typedef std::string protocols::flxbb::FlxbbDesign::String

Definition at line 62 of file FlxbbDesign.hh.

typedef protocols::moves::Mover protocols::flxbb::FlxbbDesign::Super

Definition at line 61 of file FlxbbDesign.hh.

typedef utility::tag::TagPtr protocols::flxbb::FlxbbDesign::TagPtr

Definition at line 78 of file FlxbbDesign.hh.

typedef core::pack::task::operation::TaskOperation protocols::flxbb::FlxbbDesign::TaskOperation

Definition at line 69 of file FlxbbDesign.hh.

typedef core::pack::task::operation::TaskOperationOP protocols::flxbb::FlxbbDesign::TaskOperationOP

Definition at line 70 of file FlxbbDesign.hh.

Constructor & Destructor Documentation

protocols::flxbb::FlxbbDesign::FlxbbDesign ( )

default constructor

Definition at line 130 of file FlxbbDesign.cc.

References design_taskset_, read_options(), and task_operations_.

Referenced by clone(), and fresh_instance().

protocols::flxbb::FlxbbDesign::FlxbbDesign	(	ScoreFunctionOP const	sfxnd,
		ScoreFunctionOP const	sfxnr,
		Size const	ncycle = `3`,
		String const	layer_mode = `""`,
		bool const	use_origseq_for_not_dsgned_layer = `true`,
		bool const	no_relax = `false`
	)

value constructor

Definition at line 157 of file FlxbbDesign.cc.

References design_taskset_, read_options(), and task_operations_.

protocols::flxbb::FlxbbDesign::FlxbbDesign ( FlxbbDesign const & rval)

copy constructor

Definition at line 191 of file FlxbbDesign.cc.

protocols::flxbb::FlxbbDesign::~FlxbbDesign ( )

virtual

destructor

Definition at line 217 of file FlxbbDesign.cc.

Member Function Documentation

void protocols::flxbb::FlxbbDesign::add_design_task ( DesignTaskOP const design_task)

add the design task which cotrols the iteration of fixbb design and relax

set DesignTask

Definition at line 357 of file FlxbbDesign.cc.

References design_taskset_.

void protocols::flxbb::FlxbbDesign::apply ( pose::Pose & pose)

virtual

DesignTaskSet protocols::flxbb::FlxbbDesign::build_design_taskset ( Pose const & pose)

private

build design_task_set

Definition at line 377 of file FlxbbDesign.cc.

References filter_during_design_, layer_mode_, limit_aroma_chi2_, movemap_, nflxbb_cycles_, relax_constraint_to_design_, resfile_, scorefxn_design_, scorefxn_relax_, core::scoring::surface, task_operations_, protocols::TR(), use_fast_relax_, and use_origseq_for_not_dsgned_layer_.

Referenced by apply().

void protocols::flxbb::FlxbbDesign::clear_design_taskset ( )

clear DesignTaskSet

Definition at line 369 of file FlxbbDesign.cc.

References design_taskset_.

FlxbbDesign::MoverOP protocols::flxbb::FlxbbDesign::clone ( ) const

virtual

clone this object

Reimplemented from protocols::moves::Mover.

Definition at line 220 of file FlxbbDesign.cc.

References FlxbbDesign().

FlxbbDesign::MoverOP protocols::flxbb::FlxbbDesign::fresh_instance ( ) const

virtual

create this type of object

Reimplemented from protocols::moves::Mover.

Definition at line 226 of file FlxbbDesign.cc.

References FlxbbDesign().

MoveMapOP protocols::flxbb::FlxbbDesign::get_movemap_from_blueprint	(	Pose const &	pose,
		BluePrintOP const	blueprint
	)

private

make movemap from blueprint for relax

std::string protocols::flxbb::FlxbbDesign::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 604 of file FlxbbDesign.cc.

References protocols::flxbb::FlxbbDesignCreator::mover_name().

void protocols::flxbb::FlxbbDesign::initialize_filter	(	Size const	filter_trial,
		String const &	filter_type
	)

initialize filter parameters

Definition at line 251 of file FlxbbDesign.cc.

References filter_during_design_, and protocols::TR().

Referenced by parse_my_tag(), and read_options().

void protocols::flxbb::FlxbbDesign::movemap_from_blueprint ( bool const value)

set movemap for relax

Definition at line 339 of file FlxbbDesign.cc.

References movemap_from_blueprint_.

void protocols::flxbb::FlxbbDesign::no_design ( bool const no_design)

design protocol will not be performed (default false)

Definition at line 313 of file FlxbbDesign.cc.

References no_design_.

void protocols::flxbb::FlxbbDesign::no_relax ( bool const no_relax)

relax is not performed after design (default false)

Definition at line 307 of file FlxbbDesign.cc.

References no_relax_.

void protocols::flxbb::FlxbbDesign::parse_my_tag	(	TagPtr const	tag,
		DataMap &	data,
		Filters_map const &	,
		Movers_map const &	,
		Pose const &	pose
	)

virtual

parse xml

Reimplemented from protocols::moves::Mover.

Definition at line 610 of file FlxbbDesign.cc.

References blueprint_, clear_all_residues_, constraints_NtoC_, constraints_sheet_, protocols::moves::DataMap::get(), protocols::rosetta_scripts::get_task_operations(), initialize_filter(), layer_mode_, limit_aroma_chi2_, movemap_, movemap_from_blueprint_, nflxbb_cycles_, no_design_, no_relax_, protocols::rosetta_scripts::parse_movemap(), read_options(), relax_constraint_to_design_, resfile_, scorefxn_design_, scorefxn_relax_, task_operations_, protocols::TR(), use_fast_relax_, and use_origseq_for_not_dsgned_layer_.

void protocols::flxbb::FlxbbDesign::read_options ( )

read parameters

initialize setups

Definition at line 232 of file FlxbbDesign.cc.

References blueprint_, protocols::flxbb::constraints_NtoC(), constraints_NtoC_, protocols::flxbb::constraints_sheet(), constraints_sheet_, initialize_filter(), layer_mode_, movemap_from_blueprint_, and nflxbb_cycles_.

Referenced by FlxbbDesign(), and parse_my_tag().

void protocols::flxbb::FlxbbDesign::register_options ( )

static

register options

registering of options that are relevant for FlxbbDesign

Definition at line 263 of file FlxbbDesign.cc.

References protocols::flxbb::constraints_NtoC(), and protocols::flxbb::constraints_sheet().

void protocols::flxbb::FlxbbDesign::set_blueprint ( BluePrintOP const blueprint)

set BluePrintOP

set BlueprintOP

Definition at line 319 of file FlxbbDesign.cc.

References blueprint_.

void protocols::flxbb::FlxbbDesign::set_design_taskset ( DesignTaskSet const & design_taskset)

set DesignTaskSet Once you set DesignTaskSet, this controls almost every setups of this class

clear DesignTaskSet

Definition at line 351 of file FlxbbDesign.cc.

References design_taskset_.

void protocols::flxbb::FlxbbDesign::set_filter_during_design ( FilterStructsOP const filter_during_design)

filtering during design

Definition at line 363 of file FlxbbDesign.cc.

References filter_during_design_.

void protocols::flxbb::FlxbbDesign::set_layer_mode ( String const & layer_mode)

set layer mode

Definition at line 294 of file FlxbbDesign.cc.

References layer_mode_.

void protocols::flxbb::FlxbbDesign::set_movemap ( MoveMapOP const movemap)

set movemap for relax

Definition at line 345 of file FlxbbDesign.cc.

References movemap_.

void protocols::flxbb::FlxbbDesign::set_ncycles ( Size const ncycles)

the number of cycles of fixbb and relax

Definition at line 288 of file FlxbbDesign.cc.

References nflxbb_cycles_.

void protocols::flxbb::FlxbbDesign::set_scorefxn_design ( ScoreFunctionOP const scorefxn)

set the score function for fixbb design

set scorefxn for fixbb design

Definition at line 276 of file FlxbbDesign.cc.

References scorefxn_design_.

void protocols::flxbb::FlxbbDesign::set_scorefxn_relax ( ScoreFunctionOP const scorefxn)

set the score function for relax

set scorefxn for relax

Definition at line 282 of file FlxbbDesign.cc.

References scorefxn_relax_.

void protocols::flxbb::FlxbbDesign::set_weight_constraints_NtoC ( Real const value)

set weight of constraints_NtoC which constrain between Ca atoms of C- and N-terminal if this weight > 0.0, the constraints is applied ( default = -1.0 )

Definition at line 333 of file FlxbbDesign.cc.

References constraints_NtoC_.

void protocols::flxbb::FlxbbDesign::set_weight_constraints_sheet ( Real const value)

set weight of constraints_sheet which constrains between Ca atoms in beta-sheets if this weight > 0.0, the constraints is applied ( default = -1.0 )

Definition at line 326 of file FlxbbDesign.cc.

References constraints_sheet_.

void protocols::flxbb::FlxbbDesign::use_origseq_for_not_dsgned_layer ( bool const use)

use original sequence for not designed region in layer_mode, otherwise the residues of the region turned into Ala ( default true )

Definition at line 301 of file FlxbbDesign.cc.

References use_origseq_for_not_dsgned_layer_.