#include <BDR.hh>

Inheritance diagram for protocols::forge::components::BDR:

Public Types
typedef std::string	String

typedef core::Real	Real

typedef core::Size	Size

typedef core::pack::task::TaskFactoryOP	TaskFactoryOP

typedef core::pose::Pose	Pose

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef protocols::forge::build::BuildInstructionOP	BuildInstructionOP

typedef protocols::forge::build::BuildManager	BuildManager

typedef protocols::forge::build::BuildManager::Original2Modified	Original2Modified

typedef protocols::forge::build::Interval	Interval

typedef protocols::moves::MoverOP	MoverOP

typedef std::pair< Interval, String >	OriginalInterval2DesignString
	A pair storing a instruction's original interval and a string denoting the sequence during design. More...

typedef utility::vector1 < OriginalInterval2DesignString >	DesignInfo

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

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
	BDR ()
	default constructor More...

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

virtual	~BDR ()
	default destructor More...

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

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

bool	use_fullmer () const
	use full-mer fragments when building the loop? (default false) More...

bool	use_sequence_bias () const
	use sequence biased fragments when building the loop? (default false) More...

Real	max_linear_chainbreak () const
	the maximum allowed linear chainbreak (default 0.07) More...

String const &	centroid_loop_mover_str () const
	the loop mover string to use during centroid build (default "RemodelLoopMover") More...

bool	redesign_loop_neighborhood () const
	redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true) More...

String const &	resfile () const
	name of the resfile to use during design-refine; empty string implies no resfile More...

Size	dr_cycles () const
	the number of design-refine cycles to perform, default 3 More...

ScoreFunction const &	centroid_scorefunction () const
	the centroid level score function, default "remodel_cen" More...

ScoreFunction const &	fullatom_scorefunction () const
	the full-atom level score function, default score12 More...

void	add_instruction (BuildInstructionOP bi, String const &aa_during_design_refine=String())
	add instruction to the manager of this BDR (no copy) More...

void	create_directed_dependency (BuildInstructionOP u, BuildInstructionOP v)
	create directed dependency between two instructions More...

void	use_fullmer (bool const flag)
	use full-mer fragments when building the loop? More...

void	use_sequence_bias (bool const flag)
	use sequence biased fragments when building the loop? (default false) More...

void	max_linear_chainbreak (Real const threshold)
	the maximum allowed linear chainbreak More...

void	centroid_loop_mover_str (String const &loop_mover_str)
	the loop mover string to use during centroid build More...

void	redesign_loop_neighborhood (bool const flag)
	redesign the neighborhood around the loop? if false, then just repacks during the design phase More...

void	resfile (String const &filename)
	name of the resfile to use during design-refine; empty string implies no resfile More...

void	dr_cycles (Size const cycles)
	set the number of design-refine cycles to perform More...

void	centroid_scorefunction (ScoreFunction const &sfx)
	set the centroid level score function More...

void	centroid_scorefunction (ScoreFunctionOP sfx)
	set the centroid level score function More...

void	fullatom_scorefunction (ScoreFunction const &sfx)
	set the full-atom level score function More...

void	fullatom_scorefunction (ScoreFunctionOP sfx)
	set the full-atom level score function More...

virtual void	apply (Pose &pose)
	apply defined moves to given Pose More...

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

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

virtual	~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...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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	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 (TagCOP tag, basic::datacache::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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

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

Static Public Member Functions
static String	neighborhood_calc_name ()
	the name for the loops' neighborhood calculator More...

static String	loops_buns_polar_calc_name ()
	the name for the loops' buried unsatisfied polars calculator More...

static String	neighborhood_buns_polar_calc_name ()
	the name for the loops' neighborhood buried unsatisfied polars calculator 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. More...

Private Types
typedef protocols::moves::Mover	Super

Private Member Functions
BDR &	operator= (BDR const &rval)
	copy assignment More...

bool	centroid_build (Pose &pose)
	run the centroid level build stage More...

bool	design_refine (Pose &pose)
	run the design-refine stage More...

TaskFactoryOP	generic_taskfactory ()
	return a TaskFactory useable as a starting point for either design or refinement More...

void	process_continuous_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf)
	process a continuous design string, adding appropriate operations to the TaskFactory More...

void	process_insert_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf)
	process a design string containing an insert, adding appropriate operations to the TaskFactory More...

Static Private Member Functions
static utility::vector1< bool > const &	allowed_surface_aa ()
	return a boolean vector specifying allowed a.a. when designing on the surface More...

Private Attributes
BuildManager	manager_
	the BuildManager More...

DesignInfo	design_info_
	Stores instructions' original interval and a string denoting the sequence during design. More...

bool	use_fullmer_
	use full-mer fragments when building the loop? (default false) More...

bool	use_sequence_bias_
	use sequence biased fragments when building the loop? (default false) More...

Real	max_linear_chainbreak_
	the maximum allowed linear chainbreak (default 0.07) More...

String	centroid_loop_mover_str_
	the loop mover string to use during centroid build (default "RemodelLoopMover") More...

bool	redesign_loop_neighborhood_
	redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true) More...

String	resfile_
	name of the resfile to use during design-refine; empty string implies no resfile More...

Size	dr_cycles_
	the number of design-refine cycles to perform, default 3 More...

ScoreFunctionOP	centroid_sfx_
	the centroid scorefunction to use, default "remodel_cen" More...

ScoreFunctionOP	fullatom_sfx_
	the full-atom scorefunction to use, default score12 More...

VarLengthBuildOP	vlb_
	VLB for centroid_build. More...

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...

Member Typedef Documentation

typedef protocols::forge::build::BuildInstructionOP protocols::forge::components::BDR::BuildInstructionOP

typedef protocols::forge::build::BuildManager protocols::forge::components::BDR::BuildManager

typedef utility::vector1< OriginalInterval2DesignString > protocols::forge::components::BDR::DesignInfo

typedef protocols::forge::build::Interval protocols::forge::components::BDR::Interval

typedef protocols::moves::MoverOP protocols::forge::components::BDR::MoverOP

typedef protocols::forge::build::BuildManager::Original2Modified protocols::forge::components::BDR::Original2Modified

typedef std::pair< Interval, String > protocols::forge::components::BDR::OriginalInterval2DesignString

A pair storing a instruction's original interval and a string denoting the sequence during design.

Remarks: This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.

typedef core::pose::Pose protocols::forge::components::BDR::Pose

typedef core::Real protocols::forge::components::BDR::Real

typedef core::scoring::ScoreFunction protocols::forge::components::BDR::ScoreFunction

typedef core::scoring::ScoreFunctionOP protocols::forge::components::BDR::ScoreFunctionOP

typedef core::Size protocols::forge::components::BDR::Size

typedef std::string protocols::forge::components::BDR::String

typedef protocols::moves::Mover protocols::forge::components::BDR::Super

private

typedef core::pack::task::TaskFactoryOP protocols::forge::components::BDR::TaskFactoryOP

Constructor & Destructor Documentation

protocols::forge::components::BDR::BDR ( )

default constructor

Referenced by clone(), and fresh_instance().

protocols::forge::components::BDR::BDR ( BDR const & rval )

copy constructor

References vlb_.

protocols::forge::components::BDR::~BDR ( )

virtual

default destructor

Member Function Documentation

void protocols::forge::components::BDR::add_instruction	(	BuildInstructionOP	bi,
		String const &	aa_during_design_refine = `String()`
	)

add instruction to the manager of this BDR (no copy)

Parameters

[in]	bi	BuildInstruction
[in]	aa_during_design_refine	The allowed amino acid sequence during design. Only applicable to BuildInstructions like SegmentRebuild and SegmentInsert. Make sure the length of this string matches up properly, and remember to use any special characters, e.g. the insertion character for SegmentInsert
[in]	bi	BuildInstruction
[in]	aa_during_design_refine	The allowed amino acid sequence during design. Only applicable to BuildInstructions like SegmentRebuild and SegmentInsert. Make sure the length of this string matches up properly. Default empty string.

References protocols::forge::build::BuildManager::add(), design_info_, manager_, and vlb_.

utility::vector1< bool > const & protocols::forge::components::BDR::allowed_surface_aa ( )

staticprivate

return a boolean vector specifying allowed a.a. when designing on the surface

References core::chemical::aa_from_oneletter_code().

Referenced by process_continuous_design_string(), and process_insert_design_string().

void protocols::forge::components::BDR::apply ( Pose & pose )

virtual

apply defined moves to given Pose

Implements protocols::moves::Mover.

References centroid_build(), design_refine(), dr_cycles_, protocols::simple_filters::dssp(), protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, loops_buns_polar_calc_name(), manager_, core::pose::Pose::metric(), protocols::moves::MS_SUCCESS, neighborhood_buns_polar_calc_name(), neighborhood_calc_name(), protocols::moves::Mover::set_last_move_status(), and protocols::forge::build::BuildManager::union_of_intervals_containing_undefined_positions().

bool protocols::forge::components::BDR::centroid_build ( Pose & pose )

private

run the centroid level build stage

Returns: true if loop closed, false otherwise

References centroid_loop_mover_str_, centroid_sfx_, core::scoring::Energies::clear(), protocols::forge::components::VLB_VallMemoryUsage::CLEAR_IF_CACHING_FRAGMENTS, protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), protocols::denovo_design::construct_poly_ala_pose(), core::pose::Pose::energies(), core::chemical::FA_STANDARD, core::conformation::Residue::is_protein(), manager_, max_linear_chainbreak_, protocols::forge::build::BuildManager::modify(), protocols::moves::MS_SUCCESS, core::pose::Pose::n_residue(), protocols::forge::build::BuildManager::original2modified(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), protocols::forge::methods::restore_residues(), core::pose::Pose::sequence(), core::util::switch_to_residue_type_set(), use_fullmer_, use_sequence_bias_, and vlb_.

Referenced by apply().

String const& protocols::forge::components::BDR::centroid_loop_mover_str ( ) const

inline

the loop mover string to use during centroid build (default "RemodelLoopMover")

Remarks: set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"

References centroid_loop_mover_str_.

void protocols::forge::components::BDR::centroid_loop_mover_str ( String const & loop_mover_str )

inline

the loop mover string to use during centroid build

Remarks: set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"

References centroid_loop_mover_str_.

BDR::ScoreFunction const & protocols::forge::components::BDR::centroid_scorefunction ( ) const

the centroid level score function, default "remodel_cen"

References centroid_sfx_.

void protocols::forge::components::BDR::centroid_scorefunction ( ScoreFunction const & sfx )

set the centroid level score function

References centroid_sfx_, and core::scoring::ScoreFunction::clone().

void protocols::forge::components::BDR::centroid_scorefunction ( ScoreFunctionOP sfx )

set the centroid level score function

References centroid_sfx_.

BDR::MoverOP protocols::forge::components::BDR::clone ( ) const

virtual

clone this object

Reimplemented from protocols::moves::Mover.

References BDR().

void protocols::forge::components::BDR::create_directed_dependency	(	BuildInstructionOP	u,
		BuildInstructionOP	v
	)

create directed dependency between two instructions

References protocols::forge::build::BuildManager::create_directed_dependency(), and manager_.

bool protocols::forge::components::BDR::design_refine ( Pose & pose )

private

run the design-refine stage

Returns: currently always true

References core::pose::annotated_to_oneletter_sequence(), core::pack::dunbrack::c, core::scoring::Energies::clear(), design_info_, dr_cycles_, core::pose::Pose::energies(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), fullatom_sfx_, generic_taskfactory(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, manager_, max_linear_chainbreak_, protocols::forge::build::BuildManager::movemap_as_OP(), core::pose::Pose::n_residue(), neighborhood_calc_name(), protocols::forge::build::BuildManager::new_positions(), protocols::forge::build::BuildManager::original2modified_interval_endpoints(), process_continuous_design_string(), process_insert_design_string(), redesign_loop_neighborhood_, core::util::remove_cutpoint_variants(), and protocols::loops::remove_cutpoint_variants().

Referenced by apply().

Size protocols::forge::components::BDR::dr_cycles ( ) const

inline

the number of design-refine cycles to perform, default 3

References dr_cycles_.

void protocols::forge::components::BDR::dr_cycles ( Size const cycles )

inline

set the number of design-refine cycles to perform

Remarks: set this to 0 to skip design-refine

References dr_cycles_.

BDR::MoverOP protocols::forge::components::BDR::fresh_instance ( ) const

virtual

create this type of object

Reimplemented from protocols::moves::Mover.

References BDR().

BDR::ScoreFunction const & protocols::forge::components::BDR::fullatom_scorefunction ( ) const

the full-atom level score function, default score12

the full-atom level score function

References fullatom_sfx_.

void protocols::forge::components::BDR::fullatom_scorefunction ( ScoreFunction const & sfx )

set the full-atom level score function

References core::scoring::ScoreFunction::clone(), and fullatom_sfx_.

void protocols::forge::components::BDR::fullatom_scorefunction ( ScoreFunctionOP sfx )

set the full-atom level score function

References fullatom_sfx_.

BDR::TaskFactoryOP protocols::forge::components::BDR::generic_taskfactory ( )

private

return a TaskFactory useable as a starting point for either design or refinement

References resfile_.

Referenced by design_refine().

std::string protocols::forge::components::BDR::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

static String protocols::forge::components::BDR::loops_buns_polar_calc_name ( )

inlinestatic

the name for the loops' buried unsatisfied polars calculator

Referenced by apply().

Real protocols::forge::components::BDR::max_linear_chainbreak ( ) const

inline

the maximum allowed linear chainbreak (default 0.07)

References max_linear_chainbreak_.

void protocols::forge::components::BDR::max_linear_chainbreak ( Real const threshold )

inline

the maximum allowed linear chainbreak

References max_linear_chainbreak_.

static String protocols::forge::components::BDR::neighborhood_buns_polar_calc_name ( )

inlinestatic

the name for the loops' neighborhood buried unsatisfied polars calculator

Referenced by apply().

static String protocols::forge::components::BDR::neighborhood_calc_name ( )

inlinestatic

the name for the loops' neighborhood calculator

Referenced by apply(), and design_refine().

BDR& protocols::forge::components::BDR::operator= ( BDR const & rval )

private

copy assignment

Remarks: Mover base class prevents this from working properly...

void protocols::forge::components::BDR::process_continuous_design_string	(	Interval const &	original_interval,
		String const &	design_str,
		Original2Modified const &	original2modified_interval_endpoints,
		TaskFactoryOP	design_tf
	)

private

process a continuous design string, adding appropriate operations to the TaskFactory

References core::chemical::aa_from_oneletter_code(), allowed_surface_aa(), and protocols::forge::build::Interval::left.

Referenced by design_refine().

void protocols::forge::components::BDR::process_insert_design_string	(	Interval const &	original_interval,
		String const &	design_str,
		Original2Modified const &	original2modified_interval_endpoints,
		TaskFactoryOP	design_tf
	)

private

process a design string containing an insert, adding appropriate operations to the TaskFactory

References core::chemical::aa_from_oneletter_code(), allowed_surface_aa(), protocols::forge::build::Interval::left, protocols::forge::build::Interval::length(), and protocols::forge::build::Interval::right.

Referenced by design_refine().

bool protocols::forge::components::BDR::redesign_loop_neighborhood ( ) const

inline

redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true)

References redesign_loop_neighborhood_.

void protocols::forge::components::BDR::redesign_loop_neighborhood ( bool const flag )

inline

redesign the neighborhood around the loop? if false, then just repacks during the design phase

References redesign_loop_neighborhood_.

String const& protocols::forge::components::BDR::resfile ( ) const

inline

name of the resfile to use during design-refine; empty string implies no resfile

References resfile_.

void protocols::forge::components::BDR::resfile ( String const & filename )

inline

name of the resfile to use during design-refine; empty string implies no resfile

References protocols::abinitio::filename(), and resfile_.

bool protocols::forge::components::BDR::use_fullmer ( ) const

inline

use full-mer fragments when building the loop? (default false)

References use_fullmer_.

void protocols::forge::components::BDR::use_fullmer ( bool const flag )

inline

use full-mer fragments when building the loop?

References use_fullmer_.

bool protocols::forge::components::BDR::use_sequence_bias ( ) const

inline

use sequence biased fragments when building the loop? (default false)

References use_sequence_bias_.

void protocols::forge::components::BDR::use_sequence_bias ( bool const flag )

inline

use sequence biased fragments when building the loop? (default false)

References use_sequence_bias_.

Member Data Documentation

String protocols::forge::components::BDR::centroid_loop_mover_str_

private

the loop mover string to use during centroid build (default "RemodelLoopMover")

Remarks: set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"

Referenced by centroid_build(), and centroid_loop_mover_str().

ScoreFunctionOP protocols::forge::components::BDR::centroid_sfx_

private

the centroid scorefunction to use, default "remodel_cen"

Referenced by centroid_build(), and centroid_scorefunction().

DesignInfo protocols::forge::components::BDR::design_info_

private

Stores instructions' original interval and a string denoting the sequence during design.

Remarks: This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.

Referenced by add_instruction(), and design_refine().

Size protocols::forge::components::BDR::dr_cycles_

private

the number of design-refine cycles to perform, default 3

Referenced by apply(), design_refine(), and dr_cycles().

ScoreFunctionOP protocols::forge::components::BDR::fullatom_sfx_

private

the full-atom scorefunction to use, default score12

Referenced by design_refine(), and fullatom_scorefunction().

BuildManager protocols::forge::components::BDR::manager_

private

the BuildManager

Referenced by add_instruction(), apply(), centroid_build(), create_directed_dependency(), and design_refine().

Real protocols::forge::components::BDR::max_linear_chainbreak_

private

the maximum allowed linear chainbreak (default 0.07)

Referenced by centroid_build(), design_refine(), and max_linear_chainbreak().

bool protocols::forge::components::BDR::redesign_loop_neighborhood_

private

redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true)

Referenced by design_refine(), and redesign_loop_neighborhood().

String protocols::forge::components::BDR::resfile_

private

name of the resfile to use during design-refine; empty string implies no resfile

Referenced by generic_taskfactory(), and resfile().

bool protocols::forge::components::BDR::use_fullmer_

private

use full-mer fragments when building the loop? (default false)

Referenced by centroid_build(), and use_fullmer().

bool protocols::forge::components::BDR::use_sequence_bias_

private

use sequence biased fragments when building the loop? (default false)

Referenced by centroid_build(), and use_sequence_bias().

VarLengthBuildOP protocols::forge::components::BDR::vlb_

private

VLB for centroid_build.

Remarks: Store it here instead of re-instantiation each centroid_build() call so fragment caching works.

Warning: Remember to set this to null if the BuildManager changes.

Referenced by add_instruction(), BDR(), and centroid_build().

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

src/protocols/forge/components/BDR.hh
src/protocols/forge/components/BDR.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation