#include <BluePrintBDR.hh>

Inheritance diagram for protocols::fldsgn::BluePrintBDR:

[legend]

Public Types
typedef std::string	String

typedef core::Real	Real

typedef core::Size	Size

typedef core::scoring::dssp::Dssp	Dssp

typedef core::pose::Pose	Pose

typedef core::pose::PoseOP	PoseOP

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef protocols::parser::BluePrint	BluePrint

typedef protocols::parser::BluePrintOP	BluePrintOP

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

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

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

typedef protocols::forge::components::VarLengthBuild	VarLengthBuild

typedef protocols::forge::components::VarLengthBuildOP	VarLengthBuildOP

typedef protocols::moves::MoverOP	MoverOP

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

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
	BluePrintBDR ()
	default constructor More...

	BluePrintBDR (String const &filename, bool const ss_from_blueprint=true)
	value constructor More...

	BluePrintBDR (BluePrintOP blueprintOP, bool const ss_from_blueprint=true)
	moves the BluePrintOP More...

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

	~BluePrintBDR () override
	default destructor More...

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

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

ScoreFunction const &	scorefunction () const
	the centroid level score function, default "fldsgn_cen" More...

core::Size	instruction_size () const

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

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

core::Size	num_fragpick () const
	the number of fragments to pick at each position More...

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

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

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

bool	is_initialized () const
	define secondary structrue by blueprint More...

void	add_instruction (BuildInstructionOP bi)
	add instruction to the manager of this BluePrintBDR (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	use_abego_bias (bool const flag)
	use abego biased fragments when building the loop? (default false) More...

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

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

void	num_fragpick (core::Size const num)
	the number of fragments to pick at each position More...

void	ss_from_blueprint (bool const flag)
	define secondary structrue by blueprint More...

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

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

void	set_blueprint (String const &filename)
	set blueprint file by filename More...

void	set_blueprint (BluePrintOP const &blp)
	set blueprint file More...

void	set_constraints_NtoC (Real const &weight)
	set constraints between N- and C- Ca atoms More...

void	set_constraint_file (String const &constraint_file)
	set constraint file More...

void	dump_pdb_when_fail (String const &dump_pdb_when_fail)
	dump pdb when this protocol failed More...

void	set_rcgs (utility::vector1< protocols::forge::remodel::RemodelConstraintGeneratorOP > const &rcgs)
	set list of remodel constraint generators More...

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

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	parse xml file More...

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

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 Types
typedef protocols::moves::Mover	Super

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

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

bool	set_instruction_blueprint (Pose const &pose)
	set instruction by blueprint More...

void	setup_invrot_tree_in_vlb (VarLengthBuild &vlb, Pose &pose) const
	set up folding aroung theozyme in a vlb More...

Private Attributes
BluePrintOP	blueprint_
	bluerprint file for setting build instruction More...

BuildManager	manager_
	the BuildManager More...

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

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

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

core::Size	num_fragpick_
	the number of fragments to pick at each position More...

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

bool	use_abego_bias_
	use abego biased fragments when building the loop? (default false) More...

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

bool	initialized_
	vlb_ is intialized or not More...

bool	ss_from_blueprint_
	define secondary structure by blueprint More...

Real	constraints_NtoC_
	add constraints between N- and C- terminal Ca atoms More...

Real	constraints_sheet_
	add constraints betwee Ca atoms in sheet More...

String	constraint_file_
	constraint file More...

String	dump_pdb_when_fail_
	dump pdb when this protocol failed More...

String	loop_mover_
	loop mover for loop building, default RemodelLoopMover More...

core::Size	rmdl_attempts_
	number of allowed_closure_attempts_ of RemodelLoopMover More...

bool	use_poly_val_
	Entire sequence except for rebuilding regions become poly Val. More...

bool	tell_vlb_to_not_touch_fold_tree_
	if we a fold tree has already been set up prior More...

protocols::toolbox::match_enzdes_util::InvrotTreeOP	invrot_tree_
	in case we're folding up around a ligand More...

toolbox::match_enzdes_util::EnzConstraintIOCOP	enzcst_io_

utility::vector1< protocols::forge::remodel::RemodelConstraintGeneratorOP >	rcgs_
	User-specified constraint generators which will be called from the VarLengthBuild. 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

◆ BluePrint

typedef protocols::parser::BluePrint protocols::fldsgn::BluePrintBDR::BluePrint

◆ BluePrintOP

typedef protocols::parser::BluePrintOP protocols::fldsgn::BluePrintBDR::BluePrintOP

◆ BuildInstructionOP

typedef protocols::forge::build::BuildInstructionOP protocols::fldsgn::BluePrintBDR::BuildInstructionOP

◆ BuildManager

typedef protocols::forge::build::BuildManager protocols::fldsgn::BluePrintBDR::BuildManager

◆ DataMap

typedef basic::datacache::DataMap protocols::fldsgn::BluePrintBDR::DataMap

◆ Dssp

typedef core::scoring::dssp::Dssp protocols::fldsgn::BluePrintBDR::Dssp

◆ Interval

typedef protocols::forge::build::Interval protocols::fldsgn::BluePrintBDR::Interval

◆ MoverOP

typedef protocols::moves::MoverOP protocols::fldsgn::BluePrintBDR::MoverOP

◆ Pose

typedef core::pose::Pose protocols::fldsgn::BluePrintBDR::Pose

◆ PoseOP

typedef core::pose::PoseOP protocols::fldsgn::BluePrintBDR::PoseOP

◆ Real

typedef core::Real protocols::fldsgn::BluePrintBDR::Real

◆ ScoreFunction

typedef core::scoring::ScoreFunction protocols::fldsgn::BluePrintBDR::ScoreFunction

◆ ScoreFunctionOP

typedef core::scoring::ScoreFunctionOP protocols::fldsgn::BluePrintBDR::ScoreFunctionOP

◆ Size

typedef core::Size protocols::fldsgn::BluePrintBDR::Size

◆ String

typedef std::string protocols::fldsgn::BluePrintBDR::String

◆ Super

typedef protocols::moves::Mover protocols::fldsgn::BluePrintBDR::Super

private

◆ TagCOP

typedef utility::tag::TagCOP protocols::fldsgn::BluePrintBDR::TagCOP

◆ VarLengthBuild

typedef protocols::forge::components::VarLengthBuild protocols::fldsgn::BluePrintBDR::VarLengthBuild

◆ VarLengthBuildOP

typedef protocols::forge::components::VarLengthBuildOP protocols::fldsgn::BluePrintBDR::VarLengthBuildOP

Constructor & Destructor Documentation

◆ BluePrintBDR() [1/4]

protocols::fldsgn::BluePrintBDR::BluePrintBDR ( )

default constructor

References rcgs_.

◆ BluePrintBDR() [2/4]

protocols::fldsgn::BluePrintBDR::BluePrintBDR	(	String const &	filename,
		bool const	ss_from_blueprint = `true`
	)

value constructor

References protocols::abinitio::filename(), rcgs_, and set_blueprint().

◆ BluePrintBDR() [3/4]

protocols::fldsgn::BluePrintBDR::BluePrintBDR	(	BluePrintOP	blueprintOP,
		bool const	ss_from_blueprint = `true`
	)

moves the BluePrintOP

value constructor

References rcgs_.

◆ BluePrintBDR() [4/4]

protocols::fldsgn::BluePrintBDR::BluePrintBDR ( BluePrintBDR const & rval )

copy constructor

@Brief copy constructor

References vlb_.

◆ ~BluePrintBDR()

protocols::fldsgn::BluePrintBDR::~BluePrintBDR ( )

overridedefault

default destructor

Member Function Documentation

◆ add_instruction()

void protocols::fldsgn::BluePrintBDR::add_instruction ( BuildInstructionOP bi )

add instruction to the manager of this BluePrintBDR (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

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

Referenced by set_instruction_blueprint().

◆ apply()

void protocols::fldsgn::BluePrintBDR::apply ( Pose & pose )

overridevirtual

◆ centroid_build()

bool protocols::fldsgn::BluePrintBDR::centroid_build ( Pose & pose )

private

run the centroid level build stage

Returns: true if loop closed, false otherwise

References core::scoring::atom_pair_constraint, blueprint_, core::scoring::Energies::clear(), protocols::forge::components::VLB_VallMemoryUsage::CLEAR_IF_CACHING_FRAGMENTS, constraint_file_, core::pose::Pose::constraint_set(), constraints_NtoC_, constraints_sheet_, protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), core::pose::Pose::energies(), core::chemical::FULL_ATOM_t, invrot_tree_, core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), loop_mover_str_, manager_, max_linear_chainbreak_, core::chemical::ResidueTypeBase::mode(), protocols::forge::build::BuildManager::modify(), protocols::moves::MS_SUCCESS, num_fragpick_, protocols::forge::build::BuildManager::original2modified(), rcgs_, core::pose::Pose::residue(), protocols::forge::methods::restore_residues(), core::pose::Pose::sequence(), setup_invrot_tree_in_vlb(), sfx_, core::scoring::constraints::ConstraintSet::show(), core::pose::Pose::size(), core::util::switch_to_residue_type_set(), tell_vlb_to_not_touch_fold_tree_, protocols::fldsgn::TR(), core::conformation::Residue::type(), use_abego_bias_, use_fullmer_, use_poly_val_, use_sequence_bias_, and vlb_.

Referenced by apply().

◆ clone()

BluePrintBDR::MoverOP protocols::fldsgn::BluePrintBDR::clone ( ) const

overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

◆ create_directed_dependency()

void protocols::fldsgn::BluePrintBDR::create_directed_dependency	(	BuildInstructionOP	u,
		BuildInstructionOP	v
	)

create directed dependency between two instructions

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

◆ dump_pdb_when_fail()

void protocols::fldsgn::BluePrintBDR::dump_pdb_when_fail ( String const & dump_pdb_when_fail )

dump pdb when this protocol failed

References dump_pdb_when_fail_.

◆ fresh_instance()

BluePrintBDR::MoverOP protocols::fldsgn::BluePrintBDR::fresh_instance ( ) const

overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::fldsgn::BluePrintBDR::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ instruction_size()

core::Size protocols::fldsgn::BluePrintBDR::instruction_size ( ) const

inline

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

Referenced by set_instruction_blueprint().

◆ is_initialized()

bool protocols::fldsgn::BluePrintBDR::is_initialized ( ) const

inline

define secondary structrue by blueprint

References initialized_.

◆ loop_mover_str() [1/2]

String const& protocols::fldsgn::BluePrintBDR::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 loop_mover_str_.

◆ loop_mover_str() [2/2]

void protocols::fldsgn::BluePrintBDR::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 loop_mover_str(), and loop_mover_str_.

Referenced by loop_mover_str().

◆ max_linear_chainbreak() [1/2]

Real protocols::fldsgn::BluePrintBDR::max_linear_chainbreak ( ) const

inline

the maximum allowed linear chainbreak (default 0.07)

References max_linear_chainbreak_.

◆ max_linear_chainbreak() [2/2]

void protocols::fldsgn::BluePrintBDR::max_linear_chainbreak ( Real const threshold )

inline

the maximum allowed linear chainbreak

References max_linear_chainbreak_.

◆ mover_name()

std::string protocols::fldsgn::BluePrintBDR::mover_name ( )

static

Referenced by get_name(), protocols::fldsgn::BluePrintBDRCreator::keyname(), and provide_xml_schema().

◆ num_fragpick() [1/2]

core::Size protocols::fldsgn::BluePrintBDR::num_fragpick ( ) const

inline

the number of fragments to pick at each position

References num_fragpick_.

◆ num_fragpick() [2/2]

void protocols::fldsgn::BluePrintBDR::num_fragpick ( core::Size const num )

inline

the number of fragments to pick at each position

References num_fragpick_.

◆ operator=()

BluePrintBDR& protocols::fldsgn::BluePrintBDR::operator= ( BluePrintBDR const & rval )

private

copy assignment

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

◆ parse_my_tag()

void protocols::fldsgn::BluePrintBDR::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

◆ provide_xml_schema()

void protocols::fldsgn::BluePrintBDR::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::fldsgn::BluePrintBDRCreator::provide_xml_schema().

◆ scorefunction() [1/3]

BluePrintBDR::ScoreFunction const & protocols::fldsgn::BluePrintBDR::scorefunction ( ) const

the centroid level score function, default "fldsgn_cen"

the centroid level score function, default "remodel_cen"

References sfx_.

◆ scorefunction() [2/3]

void protocols::fldsgn::BluePrintBDR::scorefunction ( ScoreFunction const & sfx )

set the centroid level score function

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

◆ scorefunction() [3/3]

void protocols::fldsgn::BluePrintBDR::scorefunction ( ScoreFunctionOP sfx )

set the centroid level score function

References sfx_.

◆ set_blueprint() [1/2]

void protocols::fldsgn::BluePrintBDR::set_blueprint ( BluePrintOP const & blp )

set blueprint file

use blueprint

References blueprint_.

◆ set_blueprint() [2/2]

void protocols::fldsgn::BluePrintBDR::set_blueprint ( String const & filename )

set blueprint file by filename

use blueprint

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

Referenced by BluePrintBDR(), and parse_my_tag().

◆ set_constraint_file()

void protocols::fldsgn::BluePrintBDR::set_constraint_file ( String const & constraint_file )

set constraint file

References constraint_file_.

◆ set_constraints_NtoC()

void protocols::fldsgn::BluePrintBDR::set_constraints_NtoC ( Real const & weight )

set constraints between N- and C- Ca atoms

set constraint between N- and C- terminal residues, need to set the weight

References constraints_NtoC_.

◆ set_instruction_blueprint()

bool protocols::fldsgn::BluePrintBDR::set_instruction_blueprint ( Pose const & pose )

private

set instruction by blueprint

References protocols::cluster::calibur::aa, add_instruction(), blueprint_, protocols::simple_filters::dssp(), instruction_size(), core::sequence::left, core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), and protocols::fldsgn::TR().

Referenced by apply().

◆ set_rcgs()

void protocols::fldsgn::BluePrintBDR::set_rcgs ( utility::vector1< protocols::forge::remodel::RemodelConstraintGeneratorOP > const & rcgs )

set list of remodel constraint generators

References rcgs_.

◆ setup_invrot_tree_in_vlb()

void protocols::fldsgn::BluePrintBDR::setup_invrot_tree_in_vlb	(	VarLengthBuild &	vlb,
		Pose &	pose
	)		const

private

set up folding aroung theozyme in a vlb

References protocols::forge::components::VarLengthBuild::add_rcg(), protocols::forge::components::VarLengthBuild::add_setup_mover(), protocols::forge::components::VarLengthBuild::add_user_provided_mover(), blueprint_, protocols::forge::components::VarLengthBuild::clear_setup_movers(), protocols::forge::components::VarLengthBuild::clear_user_provided_movers(), enzcst_io_, invrot_tree_, protocols::forge::components::VarLengthBuild::loop_mover_fold_tree_constant(), use_abego_bias_, and vlb_.

Referenced by centroid_build().

◆ ss_from_blueprint()

void protocols::fldsgn::BluePrintBDR::ss_from_blueprint ( bool const flag )

inline

define secondary structrue by blueprint

References ss_from_blueprint_.

◆ use_abego_bias() [1/2]

bool protocols::fldsgn::BluePrintBDR::use_abego_bias ( ) const

inline

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

References use_abego_bias_.

◆ use_abego_bias() [2/2]

void protocols::fldsgn::BluePrintBDR::use_abego_bias ( bool const flag )

inline

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

References use_abego_bias_.

◆ use_fullmer() [1/2]

bool protocols::fldsgn::BluePrintBDR::use_fullmer ( ) const

inline

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

References use_fullmer_.

◆ use_fullmer() [2/2]

void protocols::fldsgn::BluePrintBDR::use_fullmer ( bool const flag )

inline

use full-mer fragments when building the loop?

References use_fullmer_.

◆ use_sequence_bias() [1/2]

bool protocols::fldsgn::BluePrintBDR::use_sequence_bias ( ) const

inline

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

References use_sequence_bias_.

◆ use_sequence_bias() [2/2]

void protocols::fldsgn::BluePrintBDR::use_sequence_bias ( bool const flag )

inline

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

References use_sequence_bias_.

Member Data Documentation

◆ blueprint_

BluePrintOP protocols::fldsgn::BluePrintBDR::blueprint_

private

bluerprint file for setting build instruction

Referenced by apply(), centroid_build(), set_blueprint(), set_instruction_blueprint(), and setup_invrot_tree_in_vlb().

◆ constraint_file_

String protocols::fldsgn::BluePrintBDR::constraint_file_

private

constraint file

Referenced by centroid_build(), parse_my_tag(), and set_constraint_file().

◆ constraints_NtoC_

Real protocols::fldsgn::BluePrintBDR::constraints_NtoC_

private

add constraints between N- and C- terminal Ca atoms

Referenced by centroid_build(), parse_my_tag(), and set_constraints_NtoC().

◆ constraints_sheet_

Real protocols::fldsgn::BluePrintBDR::constraints_sheet_

private

add constraints betwee Ca atoms in sheet

Referenced by centroid_build(), and parse_my_tag().

◆ dump_pdb_when_fail_

String protocols::fldsgn::BluePrintBDR::dump_pdb_when_fail_

private

dump pdb when this protocol failed

Referenced by apply(), dump_pdb_when_fail(), and parse_my_tag().

◆ enzcst_io_

toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::fldsgn::BluePrintBDR::enzcst_io_

private

Referenced by parse_my_tag(), and setup_invrot_tree_in_vlb().

◆ initialized_

bool protocols::fldsgn::BluePrintBDR::initialized_

private

vlb_ is intialized or not

Referenced by apply(), and is_initialized().

◆ invrot_tree_

protocols::toolbox::match_enzdes_util::InvrotTreeOP protocols::fldsgn::BluePrintBDR::invrot_tree_

private

in case we're folding up around a ligand

Referenced by centroid_build(), parse_my_tag(), and setup_invrot_tree_in_vlb().

◆ loop_mover_

String protocols::fldsgn::BluePrintBDR::loop_mover_

private

loop mover for loop building, default RemodelLoopMover

◆ loop_mover_str_

String protocols::fldsgn::BluePrintBDR::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(), loop_mover_str(), and parse_my_tag().

◆ manager_

BuildManager protocols::fldsgn::BluePrintBDR::manager_

private

the BuildManager

Referenced by add_instruction(), centroid_build(), create_directed_dependency(), and instruction_size().

◆ max_linear_chainbreak_

Real protocols::fldsgn::BluePrintBDR::max_linear_chainbreak_

private

the maximum allowed linear chainbreak (default 0.07)

Referenced by centroid_build(), and max_linear_chainbreak().

◆ num_fragpick_

core::Size protocols::fldsgn::BluePrintBDR::num_fragpick_

private

the number of fragments to pick at each position

Referenced by centroid_build(), and num_fragpick().

◆ rcgs_

utility::vector1< protocols::forge::remodel::RemodelConstraintGeneratorOP > protocols::fldsgn::BluePrintBDR::rcgs_

private

User-specified constraint generators which will be called from the VarLengthBuild.

Referenced by BluePrintBDR(), centroid_build(), parse_my_tag(), and set_rcgs().

◆ rmdl_attempts_

core::Size protocols::fldsgn::BluePrintBDR::rmdl_attempts_

private

number of allowed_closure_attempts_ of RemodelLoopMover

Referenced by parse_my_tag().

◆ sfx_

ScoreFunctionOP protocols::fldsgn::BluePrintBDR::sfx_

private

the centroid scorefunction to use, default "remodel_cen"

Referenced by apply(), centroid_build(), parse_my_tag(), and scorefunction().

◆ ss_from_blueprint_

bool protocols::fldsgn::BluePrintBDR::ss_from_blueprint_

private

define secondary structure by blueprint

Referenced by apply(), parse_my_tag(), and ss_from_blueprint().

◆ tell_vlb_to_not_touch_fold_tree_

bool protocols::fldsgn::BluePrintBDR::tell_vlb_to_not_touch_fold_tree_

private

if we a fold tree has already been set up prior

Referenced by centroid_build(), and parse_my_tag().

◆ use_abego_bias_

bool protocols::fldsgn::BluePrintBDR::use_abego_bias_

private

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

Referenced by centroid_build(), parse_my_tag(), setup_invrot_tree_in_vlb(), and use_abego_bias().

◆ use_fullmer_

bool protocols::fldsgn::BluePrintBDR::use_fullmer_

private

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

Referenced by centroid_build(), and use_fullmer().

◆ use_poly_val_

bool protocols::fldsgn::BluePrintBDR::use_poly_val_

private

Entire sequence except for rebuilding regions become poly Val.

Referenced by centroid_build(), and parse_my_tag().

◆ use_sequence_bias_

bool protocols::fldsgn::BluePrintBDR::use_sequence_bias_

private

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

Referenced by centroid_build(), parse_my_tag(), and use_sequence_bias().

◆ vlb_

VarLengthBuildOP protocols::fldsgn::BluePrintBDR::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(), BluePrintBDR(), centroid_build(), and setup_invrot_tree_in_vlb().

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

src/protocols/fldsgn/BluePrintBDR.hh
src/protocols/fldsgn/BluePrintBDR.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ BluePrint

◆ BluePrintOP

◆ BuildInstructionOP

◆ BuildManager

◆ DataMap

◆ Dssp

◆ Interval

◆ MoverOP

◆ Pose

◆ PoseOP

◆ Real

◆ ScoreFunction

◆ ScoreFunctionOP

◆ Size

◆ String

◆ Super

◆ TagCOP

◆ VarLengthBuild

◆ VarLengthBuildOP

Constructor & Destructor Documentation

◆ BluePrintBDR() [1/4]

◆ BluePrintBDR() [2/4]

◆ BluePrintBDR() [3/4]

◆ BluePrintBDR() [4/4]

◆ ~BluePrintBDR()

Member Function Documentation

◆ add_instruction()

◆ apply()

◆ centroid_build()

◆ clone()

◆ create_directed_dependency()

◆ dump_pdb_when_fail()

◆ fresh_instance()

◆ get_name()

◆ instruction_size()

◆ is_initialized()

◆ loop_mover_str() [1/2]

◆ loop_mover_str() [2/2]

◆ max_linear_chainbreak() [1/2]

◆ max_linear_chainbreak() [2/2]

◆ mover_name()

◆ num_fragpick() [1/2]

◆ num_fragpick() [2/2]

◆ operator=()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ scorefunction() [1/3]

◆ scorefunction() [2/3]

◆ scorefunction() [3/3]

◆ set_blueprint() [1/2]

◆ set_blueprint() [2/2]

◆ set_constraint_file()

◆ set_constraints_NtoC()

◆ set_instruction_blueprint()

◆ set_rcgs()

◆ setup_invrot_tree_in_vlb()

◆ ss_from_blueprint()

◆ use_abego_bias() [1/2]

◆ use_abego_bias() [2/2]

◆ use_fullmer() [1/2]

◆ use_fullmer() [2/2]

◆ use_sequence_bias() [1/2]

◆ use_sequence_bias() [2/2]

Member Data Documentation

◆ blueprint_

◆ constraint_file_

◆ constraints_NtoC_

◆ constraints_sheet_

◆ dump_pdb_when_fail_

◆ enzcst_io_

◆ initialized_

◆ invrot_tree_