protocols::denovo_design::movers Namespace Reference

Classes
class	AddSegmentDataMover
	Adds a segment to the structuredata. More...
class	AddSegmentDataMoverCreator
class	AlignResiduesMover
	Aligns one residue onto another. More...
class	AlignResiduesMoverCreator
class	BridgeChainsMover
	Creates a bridge connection between two chains using remodel. More...
class	BridgeChainsMoverCreator
class	BridgeChainsCreator
class	DeclareStructureDataCovalentBondMover
	declares covalent bond More...
class	DeclareStructureDataCovalentBondMoverCreator
class	ExtendChainMover
class	ExtendChainMoverCreator
struct	RelaxScriptCommand
class	FastDesign
class	FastDesignCreator
class	FoldArchitectMover
	Mover that builds and folds a structure via fragment insertion. More...
class	SetPoseSecstructFromStructureDataMover
class	EXCN_FilterFailed
class	EXCN_NothingToFold
class	BuildDeNovoBackboneMover
class	FoldArchitectMoverCreator
class	BuildDeNovoBackboneMoverCreator
struct	CutAndJump
class	FoldTreeFromFoldGraphMover
	Creates and sets a new fold tree for the pose by traversing a FoldGraph. More...
class	FoldTreeFromFoldGraphMoverCreator
class	MakeAsymmetricStructureDataMover
	Converts a StructureData for a symmetric pose into an asymmetric representation. More...
class	MakeAsymmetricStructureDataMoverCreator
class	RotationRange
class	RotateSegmentMover
	Rotates a segment in the pose. More...
class	RotateSegmentMoverCreator
class	SealFoldTreeMover
	Creates a sealed foldtree, and removes all cutpoints from the pose. More...
class	SealFoldTreeMoverCreator
class	SetResidueAliasMover
	Sets a residue alias in the StructureData. More...
class	SetResidueAliasMoverCreator

Typedefs
typedef utility::pointer::shared_ptr< AddSegmentDataMover >	AddSegmentDataMoverOP
typedef utility::pointer::shared_ptr< AddSegmentDataMover const >	AddSegmentDataMoverCOP
typedef utility::pointer::shared_ptr< AlignResiduesMover >	AlignResiduesMoverOP
typedef utility::pointer::shared_ptr< AlignResiduesMover const >	AlignResiduesMoverCOP
typedef utility::pointer::shared_ptr< BridgeChainsMover >	BridgeChainsMoverOP
typedef utility::pointer::shared_ptr< BridgeChainsMover const >	BridgeChainsMoverCOP
typedef utility::pointer::shared_ptr< DeclareStructureDataCovalentBondMover >	DeclareStructureDataCovalentBondMoverOP
typedef utility::pointer::shared_ptr< DeclareStructureDataCovalentBondMover const >	DeclareStructureDataCovalentBondMoverCOP
typedef utility::pointer::shared_ptr< ExtendChainMover >	ExtendChainMoverOP
typedef utility::pointer::shared_ptr< ExtendChainMover const >	ExtendChainMoverCOP
typedef utility::pointer::weak_ptr< ExtendChainMover >	ExtendChainMoverAP
typedef utility::pointer::weak_ptr< ExtendChainMover const >	ExtendChainMoverCAP
typedef utility::pointer::shared_ptr< FastDesign >	FastDesignOP
typedef utility::pointer::shared_ptr< FastDesign const >	FastDesignCOP
typedef utility::pointer::weak_ptr< FastDesign >	FastDesignAP
typedef utility::pointer::weak_ptr< FastDesign const >	FastDesignCAP
typedef utility::pointer::shared_ptr< FoldArchitectMover >	FoldArchitectMoverOP
typedef utility::pointer::shared_ptr< FoldArchitectMover const >	FoldArchitectMoverCOP
typedef utility::pointer::shared_ptr< BuildDeNovoBackboneMover >	BuildDeNovoBackboneMoverOP
typedef utility::pointer::shared_ptr< BuildDeNovoBackboneMover const >	BuildDeNovoBackboneMoverCOP
typedef utility::pointer::shared_ptr< FoldTreeFromFoldGraphMover >	FoldTreeFromFoldGraphMoverOP
typedef utility::pointer::shared_ptr< FoldTreeFromFoldGraphMover const >	FoldTreeFromFoldGraphMoverCOP
typedef utility::vector1< CutAndJump >	JumpInfo
typedef utility::pointer::shared_ptr< MakeAsymmetricStructureDataMover >	MakeAsymmetricStructureDataMoverOP
typedef utility::pointer::shared_ptr< MakeAsymmetricStructureDataMover const >	MakeAsymmetricStructureDataMoverCOP
typedef utility::pointer::shared_ptr< RotateSegmentMover >	RotateSegmentMoverOP
typedef utility::pointer::shared_ptr< RotateSegmentMover const >	RotateSegmentMoverCOP
typedef utility::pointer::shared_ptr< SealFoldTreeMover >	SealFoldTreeMoverOP
typedef utility::pointer::shared_ptr< SealFoldTreeMover const >	SealFoldTreeMoverCOP
typedef utility::pointer::shared_ptr< SetResidueAliasMover >	SetResidueAliasMoverOP
typedef utility::pointer::shared_ptr< SetResidueAliasMover const >	SetResidueAliasMoverCOP

Functions
std::ostream &	operator<< (std::ostream &os, AddSegmentDataMover const &mover)
AlignResiduesMover::ResidueSelectorCOPs	parse_residue_selectors (std::string const &selector_name_str, basic::datacache::DataMap const &data)
std::ostream &	operator<< (std::ostream &os, AlignResiduesMover const &mover)
AlignResiduesMover::ResidueVectors	compute_residues_from_selectors (core::pose::Pose const &pose, AlignResiduesMover::ResidueSelectorCOPs const &selectors)
std::ostream &	operator<< (std::ostream &os, BridgeChainsMover const &mover)
std::ostream &	operator<< (std::ostream &os, DeclareStructureDataCovalentBondMover const &mover)
std::string	pdb_filename (core::Size const phase_num)
	given an build phase number, returns a pdb filename for checkpointing Example filename: iter_01_20160718133800.pdb More...
core::scoring::ScoreFunctionOP	get_score_function (core::pose::Pose const &)
utility::tag::XMLSchemaSimpleSubelementList	pre_and_post_fold_mover_subelements ()
FoldArchitectMover::ResidueVector	add_overlap_to_loops (protocols::loops::Loops &loops, core::Size const overlap, core::pose::Pose const &pose)
	goes through loops and adds overlapping residues More...
std::ostream &	operator<< (std::ostream &os, FoldTreeFromFoldGraphMover const &mover)
int	new_jump_and_cutpoint (core::pose::Pose &pose, core::Size const saferes1, core::Size const saferes2, core::Size const cutres)
std::ostream &	operator<< (std::ostream &os, MakeAsymmetricStructureDataMover const &mover)
std::string	new_id (core::Size const subunit, std::string const &orig_name)
core::Real	calc_dihedral (core::Vector const &p1, core::Vector const &p2, core::Vector const &p3, core::Vector const &p4)
std::ostream &	operator<< (std::ostream &os, SealFoldTreeMover const &mover)
std::ostream &	operator<< (std::ostream &os, SetResidueAliasMover const &mover)

Typedef Documentation

AddSegmentDataMoverCOP

typedef utility::pointer::shared_ptr< AddSegmentDataMover const > protocols::denovo_design::movers::AddSegmentDataMoverCOP

AddSegmentDataMoverOP

typedef utility::pointer::shared_ptr< AddSegmentDataMover > protocols::denovo_design::movers::AddSegmentDataMoverOP

AlignResiduesMoverCOP

typedef utility::pointer::shared_ptr< AlignResiduesMover const > protocols::denovo_design::movers::AlignResiduesMoverCOP

AlignResiduesMoverOP

typedef utility::pointer::shared_ptr< AlignResiduesMover > protocols::denovo_design::movers::AlignResiduesMoverOP

BridgeChainsMoverCOP

typedef utility::pointer::shared_ptr< BridgeChainsMover const > protocols::denovo_design::movers::BridgeChainsMoverCOP

BridgeChainsMoverOP

typedef utility::pointer::shared_ptr< BridgeChainsMover > protocols::denovo_design::movers::BridgeChainsMoverOP

BuildDeNovoBackboneMoverCOP

typedef utility::pointer::shared_ptr< BuildDeNovoBackboneMover const > protocols::denovo_design::movers::BuildDeNovoBackboneMoverCOP

BuildDeNovoBackboneMoverOP

typedef utility::pointer::shared_ptr< BuildDeNovoBackboneMover > protocols::denovo_design::movers::BuildDeNovoBackboneMoverOP

DeclareStructureDataCovalentBondMoverCOP

typedef utility::pointer::shared_ptr< DeclareStructureDataCovalentBondMover const > protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCOP

DeclareStructureDataCovalentBondMoverOP

typedef utility::pointer::shared_ptr< DeclareStructureDataCovalentBondMover > protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverOP

ExtendChainMoverAP

typedef utility::pointer::weak_ptr< ExtendChainMover > protocols::denovo_design::movers::ExtendChainMoverAP

ExtendChainMoverCAP

typedef utility::pointer::weak_ptr< ExtendChainMover const > protocols::denovo_design::movers::ExtendChainMoverCAP

ExtendChainMoverCOP

typedef utility::pointer::shared_ptr< ExtendChainMover const > protocols::denovo_design::movers::ExtendChainMoverCOP

ExtendChainMoverOP

typedef utility::pointer::shared_ptr< ExtendChainMover > protocols::denovo_design::movers::ExtendChainMoverOP

FastDesignAP

typedef utility::pointer::weak_ptr< FastDesign > protocols::denovo_design::movers::FastDesignAP

FastDesignCAP

typedef utility::pointer::weak_ptr< FastDesign const > protocols::denovo_design::movers::FastDesignCAP

FastDesignCOP

typedef utility::pointer::shared_ptr< FastDesign const > protocols::denovo_design::movers::FastDesignCOP

FastDesignOP

typedef utility::pointer::shared_ptr< FastDesign > protocols::denovo_design::movers::FastDesignOP

FoldArchitectMoverCOP

typedef utility::pointer::shared_ptr< FoldArchitectMover const > protocols::denovo_design::movers::FoldArchitectMoverCOP

FoldArchitectMoverOP

typedef utility::pointer::shared_ptr< FoldArchitectMover > protocols::denovo_design::movers::FoldArchitectMoverOP

FoldTreeFromFoldGraphMoverCOP

typedef utility::pointer::shared_ptr< FoldTreeFromFoldGraphMover const > protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCOP

FoldTreeFromFoldGraphMoverOP

typedef utility::pointer::shared_ptr< FoldTreeFromFoldGraphMover > protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverOP

JumpInfo

typedef utility::vector1< CutAndJump > protocols::denovo_design::movers::JumpInfo

MakeAsymmetricStructureDataMoverCOP

typedef utility::pointer::shared_ptr< MakeAsymmetricStructureDataMover const > protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCOP

MakeAsymmetricStructureDataMoverOP

typedef utility::pointer::shared_ptr< MakeAsymmetricStructureDataMover > protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverOP

RotateSegmentMoverCOP

typedef utility::pointer::shared_ptr< RotateSegmentMover const > protocols::denovo_design::movers::RotateSegmentMoverCOP

RotateSegmentMoverOP

typedef utility::pointer::shared_ptr< RotateSegmentMover > protocols::denovo_design::movers::RotateSegmentMoverOP

SealFoldTreeMoverCOP

typedef utility::pointer::shared_ptr< SealFoldTreeMover const > protocols::denovo_design::movers::SealFoldTreeMoverCOP

SealFoldTreeMoverOP

typedef utility::pointer::shared_ptr< SealFoldTreeMover > protocols::denovo_design::movers::SealFoldTreeMoverOP

SetResidueAliasMoverCOP

typedef utility::pointer::shared_ptr< SetResidueAliasMover const > protocols::denovo_design::movers::SetResidueAliasMoverCOP

SetResidueAliasMoverOP

typedef utility::pointer::shared_ptr< SetResidueAliasMover > protocols::denovo_design::movers::SetResidueAliasMoverOP

Function Documentation

add_overlap_to_loops()

FoldArchitectMover::ResidueVector protocols::denovo_design::movers::add_overlap_to_loops	(	protocols::loops::Loops &	loops,
		core::Size const	overlap,
		core::pose::Pose const &	pose
	)

goes through loops and adds overlapping residues

References core::pose::is_lower_terminus(), core::pose::is_upper_terminus(), core::scoring::packstat::overlap(), protocols::TR(), protocols::loops::Loops::v_begin(), and protocols::loops::Loops::v_end().

Referenced by protocols::denovo_design::movers::FoldArchitectMover::create_loops().

calc_dihedral()

core::Real protocols::denovo_design::movers::calc_dihedral	(	core::Vector const &	p1,
		core::Vector const &	p2,
		core::Vector const &	p3,
		core::Vector const &	p4
	)

Referenced by protocols::denovo_design::movers::RotateSegmentMover::apply().

compute_residues_from_selectors()

AlignResiduesMover::ResidueVectors protocols::denovo_design::movers::compute_residues_from_selectors	(	core::pose::Pose const &	pose,
		AlignResiduesMover::ResidueSelectorCOPs const &	selectors
	)

Referenced by protocols::denovo_design::movers::AlignResiduesMover::compute_target_residues(), and protocols::denovo_design::movers::AlignResiduesMover::compute_template_residues().

get_score_function()

core::scoring::ScoreFunctionOP protocols::denovo_design::movers::get_score_function

(

core::pose::Pose const &

)

References core::scoring::get_score_function().

Referenced by protocols::denovo_design::movers::FoldArchitectMover::fold_attempt().

new_id()

std::string protocols::denovo_design::movers::new_id	(	core::Size const	subunit,
		std::string const &	orig_name
	)

Referenced by core::fragment::FragSet::add(), protocols::sewing::data_storage::SmartAssembly::add_segment_and_neighbors_to_local_segments(), protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), protocols::grafting::combine_movemaps_post_insertion(), core::sequence::Sequence::id(), core::fragment::MapCacheUnit< T >::remap_value(), core::fragment::VectorCacheUnit< T >::remap_value(), protocols::constraints_additional::COMCoordinateConstraint::remapped_clone(), core::scoring::constraints::AtomToAxisConstraint::remapped_clone(), and protocols::denovo_design::architects::StructureArchitect::set_id().

new_jump_and_cutpoint()

int protocols::denovo_design::movers::new_jump_and_cutpoint	(	core::pose::Pose &	pose,
		core::Size const	saferes1,
		core::Size const	saferes2,
		core::Size const	cutres
	)

References core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom_name(), core::pose::Pose::chain(), core::conformation::Conformation::chains_from_termini(), core::kinematics::FoldTree::check_fold_tree(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), core::pose::Pose::fold_tree(), core::conformation::Residue::lower_connect_atom(), core::conformation::Residue::name(), core::kinematics::FoldTree::new_jump(), protocols::denovo_design::rebuild_missing_atoms(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::TR(), and core::conformation::Residue::upper_connect_atom().

Referenced by protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::prepare_termini_for_remodel().

operator<<() [1/8]

std::ostream & protocols::denovo_design::movers::operator<<	(	std::ostream &	os,
		AddSegmentDataMover const &	mover
	)

References protocols::denovo_design::movers::AddSegmentDataMover::show().

operator<<() [2/8]

std::ostream & protocols::denovo_design::movers::operator<<	(	std::ostream &	os,
		AlignResiduesMover const &	mover
	)

References protocols::denovo_design::movers::AlignResiduesMover::show().

operator<<() [3/8]

std::ostream & protocols::denovo_design::movers::operator<<	(	std::ostream &	os,
		BridgeChainsMover const &	mover
	)

References protocols::denovo_design::movers::BridgeChainsMover::show().

operator<<() [4/8]

std::ostream & protocols::denovo_design::movers::operator<<	(	std::ostream &	os,
		DeclareStructureDataCovalentBondMover const &	mover
	)

References protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::show().

operator<<() [5/8]

std::ostream & protocols::denovo_design::movers::operator<<	(	std::ostream &	os,
		FoldTreeFromFoldGraphMover const &	mover
	)

References protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::show().

operator<<() [6/8]

std::ostream & protocols::denovo_design::movers::operator<<	(	std::ostream &	os,
		MakeAsymmetricStructureDataMover const &	mover
	)

References protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::show().

operator<<() [7/8]

std::ostream & protocols::denovo_design::movers::operator<<	(	std::ostream &	os,
		SealFoldTreeMover const &	mover
	)

References protocols::denovo_design::movers::SealFoldTreeMover::show().

operator<<() [8/8]

std::ostream & protocols::denovo_design::movers::operator<<	(	std::ostream &	os,
		SetResidueAliasMover const &	mover
	)

References protocols::denovo_design::movers::SetResidueAliasMover::show().

parse_residue_selectors()

AlignResiduesMover::ResidueSelectorCOPs protocols::denovo_design::movers::parse_residue_selectors	(	std::string const &	selector_name_str,
		basic::datacache::DataMap const &	data
	)

References core::select::residue_selector::get_residue_selector().

Referenced by protocols::denovo_design::movers::AlignResiduesMover::parse_my_tag().

pdb_filename()

std::string protocols::denovo_design::movers::pdb_filename

(

core::Size const

phase_num

)

given an build phase number, returns a pdb filename for checkpointing Example filename: iter_01_20160718133800.pdb

Parameters

[in]

phase_num

Build phase number

References protocols::abinitio::filename().

Referenced by protocols::denovo_design::movers::FoldArchitectMover::build_in_phases(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::create_segment_file(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), protocols::stepwise::legacy::modeler::rna::get_tag_from_pdb_filename(), protocols::optimize_weights::IterativeOptEDriver::make_simple_ssd_from_pdb(), and protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs().

pre_and_post_fold_mover_subelements()

utility::tag::XMLSchemaSimpleSubelementList protocols::denovo_design::movers::pre_and_post_fold_mover_subelements

(

)

Referenced by protocols::denovo_design::movers::FoldArchitectMover::define_postfold_movers_ct(), and protocols::denovo_design::movers::FoldArchitectMover::define_prefold_movers_ct().