Namespaces
	picking_old

	rna

Classes
class	BaseCacheUnit

class	BBTorsionAndAnglesSRFD

class	BBTorsionSRFD

class	ConstantLengthFragSet
	A set of fragments that contains fragments of a constant length read in from a fragment file. More...

class	ConstantLengthFragSetIterator_

class	FragCache

class	MapCacheUnit

class	VectorCacheUnit

class	CacheWrapper

class	FragStore

class	FragData

class	AnnotatedFragData
	FragData that contains additional information. More...

class	FragID

class	FragID_Iterator

class	FragFactory

class	FragmentIO

class	FragmentRmsd

class	FragmentSetLoader
	FragmentSetLoader constructs a FragSet instance from data provided by the ResourceManager. More...

class	FragmentSetLoaderCreator
	FragmentSetLoaderCreator allows the ResourceLoaderFactory to create a FragmentSetLoader instance, which in turn can load a FragmentSet. More...

class	FragSet
	@detail The FragSet: (Interface Definition – Virtual BaseClass ) More...

class	FragSetCollection

class	Frame
	Frame couples a list of FragData-instances to a certain alignment frame, i.e., position in sequence space @detail A frame may be continous, i.e., its fragment data will be applied to all residues between start() and end() or ( in a specialized version inheriting this interface) may contain a loose list of sequence positions. More...

class	ConstFrameIterator

class	FrameIterator

class	FrameIteratorWorker_

class	FrameList

class	FrameListIterator_

class	IndependentBBTorsionSRFD
	A version of BBTorsionSRFD that considers each torsion independently during is_applicable() and apply() calls when passed a MoveMap (vs the all-torsions-must-be-moveable-or-nothing-is behavior in the original BBTorsionSRFD). More...

class	NonContinuousFrame
	JumpingFrame is a discontinuous frame i.e, the SRFDs stored in the FragData objects can be applied to residues anywhere a 5 7 9 Frame of a FragData containing three BBTorsionSRFDs would change torsions of 5 7 9 a 5 32 2 Frame of a FragData containing two BBTorsionSRFD and on JumpSRFD would change torsions of 5 and 32 and the RT of jump_nr 2 note that in the latter case the 2 is not coding for a residue number! More...

class	JumpingFrame
	JumpingFrame, so far there is nothing special about JumpingFrames. but I think we might want to have additionally information like the start and end residues that belong to a certain jump_nr.! okay: right now I require that the creator of a JumpingFrame sets start to the start-residue of the jump. More...

class	UpJumpSRFD

class	DownJumpSRFD

struct	torsions

class	MinimalFragSet

class	MinimalFragSetIterator_

class	OrderedFragSet

class	OrderedFragSetIterator_

class	SecondaryStructure
	tiny helper class that knows the relative fractions of secondary structure L,H,E @detail so far these fractions can be computed from a FragSet other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses, More...

class	SecstructSRFD

class	SingleResidueFragData
	Base class for SRFD classes @detail Instances of SRFD classes contain information on specific dofs in a single residue or a jump connected to a residue The classes' apply method will now how to implement the specified dofs in the give pose at the given residue position. More...

Typedefs
typedef utility::pointer::shared_ptr< BaseCacheUnit >	BaseCacheUnitOP

typedef utility::pointer::weak_ptr< BaseCacheUnit >	BaseCacheUnitAP

typedef utility::pointer::shared_ptr< BBTorsionSRFD >	BBTorsionSRFDOP

typedef utility::pointer::shared_ptr< BBTorsionSRFD const >	BBTorsionSRFDCOP

typedef utility::pointer::shared_ptr< ConstantLengthFragSet >	ConstantLengthFragSetOP

typedef utility::pointer::shared_ptr< ConstantLengthFragSet const >	ConstantLengthFragSetCOP

typedef utility::pointer::shared_ptr< FragData >	FragDataOP

typedef utility::pointer::shared_ptr< FragData const >	FragDataCOP

typedef utility::vector1< FragDataCOP >	FragDataCOPs

typedef utility::vector1< FragDataOP >	FragDataOPs

typedef utility::pointer::shared_ptr< AnnotatedFragData >	AnnotatedFragDataOP

typedef utility::pointer::shared_ptr< AnnotatedFragData const >	AnnotatedFragDataCOP

typedef utility::vector1< Size >	PositionList

typedef utility::vector1< FragID >	FragID_List

typedef utility::pointer::shared_ptr< FragmentRmsd >	FragmentRmsdOP

typedef utility::pointer::shared_ptr< FragmentRmsd const >	FragmentRmsdCOP

typedef utility::pointer::shared_ptr< FragmentSetLoader >	FragmentSetLoaderOP

typedef utility::pointer::shared_ptr< FragmentSetLoader const >	FragmentSetLoaderCOP

typedef utility::pointer::shared_ptr< FragSet >	FragSetOP

typedef utility::pointer::shared_ptr< FragSet const >	FragSetCOP

typedef std::pair< Size, Size >	Range

typedef utility::vector1< Size >	InsertMap

typedef utility::vector1< Size >	InsertSize

typedef utility::pointer::shared_ptr< FragSetCollection >	FragSetCollectionOP

typedef utility::pointer::shared_ptr< FragSetCollection const >	FragSetCollectionCOP

typedef utility::pointer::shared_ptr< Frame >	FrameOP

typedef utility::pointer::shared_ptr< Frame const >	FrameCOP

typedef utility::pointer::shared_ptr< FrameIteratorWorker_ >	FrameIteratorWorker_OP

typedef utility::pointer::weak_ptr< IndependentBBTorsionSRFD >	IndependentBBTorsionSRFD_AP
	access pointer for IndependentBBTorsionSRFD More...

typedef utility::pointer::weak_ptr< IndependentBBTorsionSRFD const >	IndependentBBTorsionSRFD_CAP
	const access pointer for IndependentBBTorsionSRFD More...

typedef utility::pointer::shared_ptr< IndependentBBTorsionSRFD >	IndependentBBTorsionSRFD_OP
	owning pointer for IndependentBBTorsionSRFD More...

typedef utility::pointer::shared_ptr< IndependentBBTorsionSRFD const >	IndependentBBTorsionSRFD_COP
	const owning pointer for IndependentBBTorsionSRFD More...

typedef utility::pointer::shared_ptr< JumpingFrame >	JumpingFrameOP

typedef utility::pointer::shared_ptr< JumpingFrame const >	JumpingFrameCOP

typedef utility::pointer::shared_ptr< NonContinuousFrame >	NonContinuousFrameOP

typedef utility::pointer::shared_ptr< NonContinuousFrame const >	NonContinuousFrameCOP

typedef utility::pointer::shared_ptr< UpJumpSRFD >	UpJumpSRFDOP

typedef utility::pointer::shared_ptr< UpJumpSRFD const >	UpJumpSRFDCOP

typedef utility::pointer::shared_ptr< DownJumpSRFD >	DownJumpSRFDOP

typedef utility::pointer::shared_ptr< DownJumpSRFD const >	DownJumpSRFDCOP

typedef utility::pointer::shared_ptr< MinimalFragSet >	MinimalFragSetOP

typedef utility::pointer::shared_ptr< MinimalFragSet const >	MinimalFragSetCOP

typedef utility::pointer::shared_ptr< OrderedFragSet >	OrderedFragSetOP

typedef utility::pointer::shared_ptr< OrderedFragSet const >	OrderedFragSetCOP

typedef utility::pointer::shared_ptr< SecondaryStructure >	SecondaryStructureOP

typedef utility::pointer::shared_ptr< SecondaryStructure const >	SecondaryStructureCOP

typedef utility::pointer::shared_ptr< SingleResidueFragData >	SingleResidueFragDataOP

typedef utility::pointer::shared_ptr< SingleResidueFragData const >	SingleResidueFragDataCOP

Functions
static basic::Tracer	tr ("core.fragment.BBTorsionAndAnglesSRFD")

static basic::Tracer	tr ("core.fragment")

static basic::Tracer	tr ("core.fragments.ConstantLengthFragSet")

void	make_pose_from_sequence_ (std::string sequence, chemical::ResidueTypeSet &residue_set, pose::Pose &pose)

std::ostream &	operator<< (std::ostream &out, FragData const &fr)

static basic::Tracer	tr ("core.io.fragments")

static basic::Tracer	tr ("core.fragment")

std::ostream &	operator<< (std::ostream &out, FragSet const &cfrags)

static basic::Tracer	tr ("core.fragment")

void	make_pose_from_sequence_ (std::string sequence, chemical::ResidueTypeSet const &residue_set, pose::Pose &pose)

std::ostream &	operator<< (std::ostream &out, Frame const &frame)

static basic::Tracer	tr ("core.fragment")

std::ostream &	operator<< (std::ostream &out, FrameList const &frags)

static basic::Tracer	tr ("core.fragment.JumpSRFD")

static basic::Tracer	tr ("core.fragments")

static basic::Tracer	tr ("core.fragments")

std::ostream &	operator<< (std::ostream &os, SecondaryStructure const &t)
	output operator More...

static basic::Tracer	tr ("core.fragment")

std::ostream &	operator<< (std::ostream &out, SingleResidueFragData const &srfd)

std::istream &	operator>> (std::istream &in, SingleResidueFragData &srfd)

static basic::Tracer	tr ("core.fragment")

void	retain_top (core::Size k, FragSetOP fragments)
	Removes all but the top <k> fragments from <fragments> More...

void	steal_constant_length_frag_set_from_pose (pose::Pose const &pose_in, ConstantLengthFragSet &fragset)

void	steal_frag_set_from_pose (pose::Pose const &pose_in, FragSet &fragset, core::fragment::FragDataCOP frag_type)

void	steal_frag_set_from_pose (pose::Pose const &pose_in, Size const begin, Size const end, FragSet &fragset, core::fragment::FragDataCOP frag_type)

void	steal_frag_set_from_pose (pose::Pose const &pose_in, FragSet &fragset, core::fragment::FragDataCOP frag_type, std::set< core::Size > const &selected_residues)

void	chop_fragments (core::fragment::FragSet &source, core::fragment::FragSet &dest)
	Function for chopping the X-sized fragments in source into fragments that go into N-sized fragments in dest. Sizes are encoded by the value of max_frag_length() in both source and dest. More...

void	compute_per_residue_coverage (core::fragment::FragSet const &_frags, utility::vector1< core::Size > &nr_frags)

void	flatten_list (FrameList &frames, FragID_List &frag_ids)

FragSetOP	merge_frags (FragSet const &good_frags, FragSet const &filling, Size min_nr_frags, bool bRandom)

void	apply_best_scoring_fragdata (pose::Pose &pose, Frame const &frame, scoring::ScoreFunction const &sfxn)
	goes through all frag_data in the frame and puts the best scoring one into the pose, i.e. quenches the frame More...

void	dump_frames_as_pdb (pose::Pose const &pose, utility::vector1< FrameOP > const &frames, std::string const &filename, core::Size start_frag=1)
	writes FragData in multimodel pdb format start_tag can be used to only write a subset of the contained frag data More...

bool	fill_template_frames_from_pdb (pose::Pose const &pose, utility::vector1< FrameOP > const &template_frames, std::string const &filename)
	filling a frameset from a multimodel pdb file More...

void	read_std_frags_from_cmd (FragSetOP &fragset_large, FragSetOP &fragset_small)

void	make_simple_fold_tree_from_jump_frame (Frame const &frame, Size total_residue, kinematics::FoldTree &new_fold_tree)
	given a JumpFrame with Up and DownJumpSRFDs as LAST SRFDs this will make a fold-tree compatible with the Frame... this is NOT GOOD for sampling, since it introduces cut-points outside of fragments later for sampling: one could probably write a routine that looks if it can move existing Jumps in Fold-tree to fit the FRAME ... if not it returns failure... More...

void	fragment_set_slice (ConstantLengthFragSetOP &fragset, Size const &min_res, Size const &max_res)

void	fragment_set_slice (core::fragment::ConstantLengthFragSetOP &fragset, utility::vector1< core::Size > const &slice_res)

void	FindBoundaries (const core::kinematics::FoldTree &tree, core::Size pos, core::Size left, core::Size right)
	Finds the fold tree boundaries to the left and right of <pos>. More...

core::kinematics::Stub	getxform (numeric::xyzVector< core::Real > m1, numeric::xyzVector< core::Real > m2, numeric::xyzVector< core::Real > m3, numeric::xyzVector< core::Real > f1, numeric::xyzVector< core::Real > f2, numeric::xyzVector< core::Real > f3)

void	xform_pose (core::pose::Pose &pose, const core::kinematics::Stub &s, core::Size sres, core::Size eres)

void	make_pose_from_frags (pose::Pose &pose, std::string sequence, utility::vector1< FragDataCOP > frags, bool chains)

Typedef Documentation

◆ AnnotatedFragDataCOP

typedef utility::pointer::shared_ptr< AnnotatedFragData const > core::fragment::AnnotatedFragDataCOP

◆ AnnotatedFragDataOP

typedef utility::pointer::shared_ptr< AnnotatedFragData > core::fragment::AnnotatedFragDataOP

◆ BaseCacheUnitAP

typedef utility::pointer::weak_ptr< BaseCacheUnit > core::fragment::BaseCacheUnitAP

◆ BaseCacheUnitOP

typedef utility::pointer::shared_ptr< BaseCacheUnit > core::fragment::BaseCacheUnitOP

◆ BBTorsionSRFDCOP

typedef utility::pointer::shared_ptr< BBTorsionSRFD const > core::fragment::BBTorsionSRFDCOP

◆ BBTorsionSRFDOP

typedef utility::pointer::shared_ptr< BBTorsionSRFD > core::fragment::BBTorsionSRFDOP

◆ ConstantLengthFragSetCOP

typedef utility::pointer::shared_ptr< ConstantLengthFragSet const > core::fragment::ConstantLengthFragSetCOP

◆ ConstantLengthFragSetOP

typedef utility::pointer::shared_ptr< ConstantLengthFragSet > core::fragment::ConstantLengthFragSetOP

◆ DownJumpSRFDCOP

typedef utility::pointer::shared_ptr< DownJumpSRFD const > core::fragment::DownJumpSRFDCOP

◆ DownJumpSRFDOP

typedef utility::pointer::shared_ptr< DownJumpSRFD > core::fragment::DownJumpSRFDOP

◆ FragDataCOP

typedef utility::pointer::shared_ptr< FragData const > core::fragment::FragDataCOP

◆ FragDataCOPs

typedef utility::vector1< FragDataCOP > core::fragment::FragDataCOPs

◆ FragDataOP

typedef utility::pointer::shared_ptr< FragData > core::fragment::FragDataOP

◆ FragDataOPs

typedef utility::vector1< FragDataOP > core::fragment::FragDataOPs

◆ FragID_List

typedef utility::vector1< FragID > core::fragment::FragID_List

◆ FragmentRmsdCOP

typedef utility::pointer::shared_ptr<FragmentRmsd const> core::fragment::FragmentRmsdCOP

◆ FragmentRmsdOP

typedef utility::pointer::shared_ptr<FragmentRmsd> core::fragment::FragmentRmsdOP

◆ FragmentSetLoaderCOP

typedef utility::pointer::shared_ptr< FragmentSetLoader const > core::fragment::FragmentSetLoaderCOP

◆ FragmentSetLoaderOP

typedef utility::pointer::shared_ptr< FragmentSetLoader > core::fragment::FragmentSetLoaderOP

◆ FragSetCollectionCOP

typedef utility::pointer::shared_ptr< FragSetCollection const > core::fragment::FragSetCollectionCOP

◆ FragSetCollectionOP

typedef utility::pointer::shared_ptr< FragSetCollection > core::fragment::FragSetCollectionOP

◆ FragSetCOP

typedef utility::pointer::shared_ptr< FragSet const > core::fragment::FragSetCOP

◆ FragSetOP

typedef utility::pointer::shared_ptr< FragSet > core::fragment::FragSetOP

◆ FrameCOP

typedef utility::pointer::shared_ptr< Frame const > core::fragment::FrameCOP

◆ FrameIteratorWorker_OP

typedef utility::pointer::shared_ptr< FrameIteratorWorker_ > core::fragment::FrameIteratorWorker_OP

◆ FrameOP

typedef utility::pointer::shared_ptr< Frame > core::fragment::FrameOP

◆ IndependentBBTorsionSRFD_AP

typedef utility::pointer::weak_ptr< IndependentBBTorsionSRFD > core::fragment::IndependentBBTorsionSRFD_AP

access pointer for IndependentBBTorsionSRFD

◆ IndependentBBTorsionSRFD_CAP

typedef utility::pointer::weak_ptr< IndependentBBTorsionSRFD const > core::fragment::IndependentBBTorsionSRFD_CAP

const access pointer for IndependentBBTorsionSRFD

◆ IndependentBBTorsionSRFD_COP

typedef utility::pointer::shared_ptr< IndependentBBTorsionSRFD const > core::fragment::IndependentBBTorsionSRFD_COP

const owning pointer for IndependentBBTorsionSRFD

◆ IndependentBBTorsionSRFD_OP

typedef utility::pointer::shared_ptr< IndependentBBTorsionSRFD > core::fragment::IndependentBBTorsionSRFD_OP

owning pointer for IndependentBBTorsionSRFD

◆ InsertMap

typedef utility::vector1< Size > core::fragment::InsertMap

◆ InsertSize

typedef utility::vector1< Size > core::fragment::InsertSize

◆ JumpingFrameCOP

typedef utility::pointer::shared_ptr< JumpingFrame const > core::fragment::JumpingFrameCOP

◆ JumpingFrameOP

typedef utility::pointer::shared_ptr< JumpingFrame > core::fragment::JumpingFrameOP

◆ MinimalFragSetCOP

typedef utility::pointer::shared_ptr< MinimalFragSet const > core::fragment::MinimalFragSetCOP

◆ MinimalFragSetOP

typedef utility::pointer::shared_ptr< MinimalFragSet > core::fragment::MinimalFragSetOP

◆ NonContinuousFrameCOP

typedef utility::pointer::shared_ptr< NonContinuousFrame const > core::fragment::NonContinuousFrameCOP

◆ NonContinuousFrameOP

typedef utility::pointer::shared_ptr< NonContinuousFrame > core::fragment::NonContinuousFrameOP

◆ OrderedFragSetCOP

typedef utility::pointer::shared_ptr< OrderedFragSet const > core::fragment::OrderedFragSetCOP

◆ OrderedFragSetOP

typedef utility::pointer::shared_ptr< OrderedFragSet > core::fragment::OrderedFragSetOP

◆ PositionList

typedef utility::vector1< Size > core::fragment::PositionList

◆ Range

typedef std::pair< Size, Size > core::fragment::Range

◆ SecondaryStructureCOP

typedef utility::pointer::shared_ptr< SecondaryStructure const > core::fragment::SecondaryStructureCOP

◆ SecondaryStructureOP

typedef utility::pointer::shared_ptr< SecondaryStructure > core::fragment::SecondaryStructureOP

◆ SingleResidueFragDataCOP

typedef utility::pointer::shared_ptr< SingleResidueFragData const > core::fragment::SingleResidueFragDataCOP

◆ SingleResidueFragDataOP

typedef utility::pointer::shared_ptr< SingleResidueFragData > core::fragment::SingleResidueFragDataOP

◆ UpJumpSRFDCOP

typedef utility::pointer::shared_ptr< UpJumpSRFD const > core::fragment::UpJumpSRFDCOP

◆ UpJumpSRFDOP

typedef utility::pointer::shared_ptr< UpJumpSRFD > core::fragment::UpJumpSRFDOP

Function Documentation

◆ apply_best_scoring_fragdata()

void core::fragment::apply_best_scoring_fragdata	(	pose::Pose &	pose,
		Frame const &	frame,
		scoring::ScoreFunction const &	sfxn
	)

goes through all frag_data in the frame and puts the best scoring one into the pose, i.e. quenches the frame

References core::fragment::Frame::apply(), and core::fragment::Frame::nr_frags().

◆ chop_fragments()

void core::fragment::chop_fragments	(	core::fragment::FragSet &	source,
		core::fragment::FragSet &	dest
	)

Function for chopping the X-sized fragments in source into fragments that go into N-sized fragments in dest. Sizes are encoded by the value of max_frag_length() in both source and dest.

References core::fragment::FragSet::add(), core::fragment::Frame::add_fragment(), core::fragment::FragSet::begin(), core::fragment::Frame::end(), core::fragment::FragSet::end(), core::fragment::Frame::fragment(), core::fragment::FragData::generate_sub_fragment(), core::fragment::FragSet::max_frag_length(), core::fragment::FragSet::max_pos(), core::fragment::Frame::nr_frags(), and core::fragment::Frame::start().

Referenced by protocols::loop_grower::LoopGrower::apply(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize(), protocols::loops::read_loop_fragments(), and protocols::rbsegment_relax::OptimizeThreadingMover::rebuild_unaligned().

◆ compute_per_residue_coverage()

void core::fragment::compute_per_residue_coverage	(	core::fragment::FragSet const &	_frags,
		utility::vector1< core::Size > &	nr_frags
	)

References core::fragment::FragSet::begin(), core::fragment::FragSet::end(), core::fragment::FragSet::max_pos(), and protocols::loops::stop.

Referenced by merge_frags().

◆ dump_frames_as_pdb()

void core::fragment::dump_frames_as_pdb	(	pose::Pose const &	pose,
		utility::vector1< FrameOP > const &	frames,
		std::string const &	filename,
		Size const	start_frag
	)

writes FragData in multimodel pdb format start_tag can be used to only write a subset of the contained frag data

References core::io::pdb::dump_pdb_residue(), core::sequence::end, protocols::abinitio::filename(), core::chemical::element::I, and core::pose::Pose::residue().

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::apply().

◆ fill_template_frames_from_pdb()

bool core::fragment::fill_template_frames_from_pdb	(	pose::Pose const &	pose,
		utility::vector1< FrameOP > const &	template_frames,
		std::string const &	filename
	)

filling a frameset from a multimodel pdb file

this is a little tricky: this should support functionality for both creating a frameset entirely from

the input pdb (i.e. with no prior information about frag data length or srfds ), but it should also

be possible to pass in non_empty frames such that the information in the pdb will generate FragData

objects that are compatible to the ones already in the passed in frames. hmpf

returns true if no error occured

References core::pose::Pose::copy_segment(), protocols::abinitio::filename(), core::import_pose::PDB_file, core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), and protocols::loops::start.

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::recover_loops_from_file().

◆ FindBoundaries()

void core::fragment::FindBoundaries	(	const core::kinematics::FoldTree &	tree,
		core::Size	pos,
		core::Size *	left,
		core::Size *	right
	)

Finds the fold tree boundaries to the left and right of <pos>.

References core::kinematics::FoldTree::cutpoint(), core::sequence::left, core::kinematics::FoldTree::nres(), and core::kinematics::FoldTree::num_cutpoint().

Referenced by make_pose_from_frags().

◆ flatten_list()

void core::fragment::flatten_list	(	FrameList &	frames,
		FragID_List &	frag_ids
	)

References core::fragment::FrameList::flat_size().

Referenced by merge_frags().

◆ fragment_set_slice() [1/2]

void core::fragment::fragment_set_slice	(	ConstantLengthFragSetOP &	fragset,
		Size const &	min_res,
		Size const &	max_res
	)

Referenced by protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler::initialize().

◆ fragment_set_slice() [2/2]

void core::fragment::fragment_set_slice	(	core::fragment::ConstantLengthFragSetOP &	fragset,
		utility::vector1< core::Size > const &	slice_res
	)

References tr().

◆ getxform()

core::kinematics::Stub core::fragment::getxform	(	numeric::xyzVector< core::Real >	m1,
		numeric::xyzVector< core::Real >	m2,
		numeric::xyzVector< core::Real >	m3,
		numeric::xyzVector< core::Real >	f1,
		numeric::xyzVector< core::Real >	f2,
		numeric::xyzVector< core::Real >	f3
	)

References core::kinematics::Stub::M, and core::kinematics::Stub::v.

Referenced by make_pose_from_frags().

◆ make_pose_from_frags()

void core::fragment::make_pose_from_frags	(	pose::Pose &	pose,
		std::string	sequence,
		utility::vector1< FragDataCOP >	frags,
		bool	chains
	)

◆ make_pose_from_sequence_() [1/2]

void core::fragment::make_pose_from_sequence_	(	std::string	sequence,
		chemical::ResidueTypeSet &	residue_set,
		pose::Pose &	pose
	)

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::pose::Pose::clear(), core::conformation::ResidueFactory::create_residue(), and core::chemical::ResidueTypeSet::get_representative_type_aa().

Referenced by core::fragment::Frame::fragment_as_pose().

◆ make_pose_from_sequence_() [2/2]

void core::fragment::make_pose_from_sequence_	(	std::string	sequence,
		chemical::ResidueTypeSet const &	residue_set,
		pose::Pose &	pose
	)

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clear(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueTypeSet::get_representative_type_aa(), and tr().

◆ make_simple_fold_tree_from_jump_frame()

void core::fragment::make_simple_fold_tree_from_jump_frame	(	Frame const &	frame,
		Size	total_residue,
		kinematics::FoldTree &	new_fold_tree
	)

given a JumpFrame with Up and DownJumpSRFDs as LAST SRFDs this will make a fold-tree compatible with the Frame... this is NOT GOOD for sampling, since it introduces cut-points outside of fragments later for sampling: one could probably write a routine that looks if it can move existing Jumps in Fold-tree to fit the FRAME ... if not it returns failure...

one little assumption: create frames always like this: contigues piece JUMP contig. piec JUMP contig. piece. then good candidates for cutpoints are the last contig.piece residue before a jump

References protocols::loops::cut_point, core::fragment::Frame::fragment(), core::fragment::FragData::get_residue(), core::fragment::Frame::length(), core::fragment::Frame::nr_frags(), core::fragment::Frame::seqpos(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

◆ merge_frags()

FragSetOP core::fragment::merge_frags	(	FragSet const &	good_frags,
		FragSet const &	filling,
		Size	min_nr_frags,
		bool	bRandom
	)

References core::fragment::FragSet::clone(), compute_per_residue_coverage(), flatten_list(), core::fragment::FragSet::frames(), core::fragment::FragSet::max_pos(), core::scoring::rg, protocols::loops::stop, and tr().

Referenced by protocols::abinitio::AbrelaxApplication::setup_fragments().

◆ operator<<() [1/6]

std::ostream& core::fragment::operator<<	(	std::ostream &	os,
		SecondaryStructure const &	t
	)

inline

output operator

References protocols::hybridization::t.

◆ operator<<() [2/6]

std::ostream& core::fragment::operator<<	(	std::ostream &	out,
		FragData const &	fr
	)

inline

References core::conformation::membrane::out, and core::fragment::FragData::show().

◆ operator<<() [3/6]

std::ostream& core::fragment::operator<<	(	std::ostream &	out,
		FragSet const &	cfrags
	)

◆ operator<<() [4/6]

std::ostream& core::fragment::operator<<	(	std::ostream &	out,
		Frame const &	frame
	)

inline

References core::conformation::membrane::out, and core::fragment::Frame::show().

◆ operator<<() [5/6]

std::ostream & core::fragment::operator<<	(	std::ostream &	out,
		FrameList const &	frags
	)

References core::conformation::membrane::out.

◆ operator<<() [6/6]

std::ostream& core::fragment::operator<<	(	std::ostream &	out,
		SingleResidueFragData const &	srfd
	)

inline

References core::conformation::membrane::out, and core::fragment::SingleResidueFragData::show().

◆ operator>>()

std::istream& core::fragment::operator>>	(	std::istream &	in,
		SingleResidueFragData &	srfd
	)

inline

References core::conformation::membrane::in, and core::fragment::SingleResidueFragData::read_data().

◆ read_std_frags_from_cmd()

void core::fragment::read_std_frags_from_cmd	(	FragSetOP &	fragset_large,
		FragSetOP &	fragset_small
	)

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::fragment::FragmentIO::read_data(), core::pose::set_ss_from_phipsi(), steal_frag_set_from_pose(), and tr().

Referenced by protocols::topology_broker::add_cmdline_claims().

◆ retain_top()

void core::fragment::retain_top	(	core::Size	k,
		FragSetOP	fragments
	)

Removes all but the top <k> fragments from <fragments>

References core::fragment::Frame::add_fragment(), and protocols::mean_field::min().

Referenced by protocols::nonlocal::PolicyFactory::get_policy().

◆ steal_constant_length_frag_set_from_pose()

void core::fragment::steal_constant_length_frag_set_from_pose	(	pose::Pose const &	pose_in,
		ConstantLengthFragSet &	fragset
	)

References core::fragment::FragSet::add(), core::kinematics::FoldTree::cutpoint(), core::pose::Pose::fold_tree(), core::fragment::FragSet::max_frag_length(), core::kinematics::FoldTree::num_cutpoint(), core::pose::set_ss_from_phipsi(), and core::pose::Pose::size().

Referenced by protocols::abinitio::IterativeBase::gen_resample_fragments().

◆ steal_frag_set_from_pose() [1/3]

void core::fragment::steal_frag_set_from_pose	(	pose::Pose const &	pose_in,
		FragSet &	fragset,
		core::fragment::FragDataCOP	frag_type
	)

References core::fragment::FragSet::add(), core::pose::set_ss_from_phipsi(), and core::pose::Pose::size().

Referenced by protocols::legacy_sewing::LegacyAddStartnodeFragments::apply(), protocols::topology_broker::StartStructClaimer::generate_init_frags(), protocols::loops::read_loop_fragments(), read_std_frags_from_cmd(), protocols::parser::FragmentReader::set_fragments(), and protocols::abinitio::AbrelaxApplication::setup_fragments().

◆ steal_frag_set_from_pose() [2/3]

void core::fragment::steal_frag_set_from_pose	(	pose::Pose const &	pose_in,
		FragSet &	fragset,
		core::fragment::FragDataCOP	frag_type,
		std::set< core::Size > const &	selected_residues
	)

References core::fragment::FragSet::add(), and core::pose::set_ss_from_phipsi().