Classes
class	CAcstGenerator

class	CAcstGeneratorCreator

class	CloseFold

class	CloseFoldCreator

class	CoordinateCst

class	CoordinateCstCreator

class	DefineMovableLoops

class	DefineMovableLoopsCreator

struct	GrowPeptidesSegment

class	GrowPeptides

class	GrowPeptidesCreator

class	SeedFoldTree

class	SeedFoldTreeCreator

class	SeedSetupMover

class	SeedSetupMoverCreator

class	SegmentHybridizer

class	SegmentHybridizerCreator

struct	SegmentSpec

class	SwapSegment

class	SwapSegmentCreator

Typedefs
using	GrowPeptidesSegmentOP = utility::pointer::shared_ptr< GrowPeptidesSegment >

typedef utility::pointer::shared_ptr< SeedFoldTree >	SeedFoldTreeOP

typedef utility::pointer::shared_ptr< SeedFoldTree const >	SeedFoldTreeCOP

Functions
static basic::Tracer	TR ("protocols.seeded_abinitio.CAcstGenerator")

bool	is_part (utility::vector1< core::Size > &cut_points, core::Size &residue)

void	add_dist_constraints (pose::Pose &pose, pose::PoseOP &pose_of_int, core::Size start_relevant_chain, core::scoring::constraints::ConstraintSetOP &cst, protocols::loops::Loops &seeds, protocols::loops::Loops &clear_area, utility::vector1< core::Size > cut_points, utility::vector1< core::Size > seed_exceptions, bool add_cst_seed, core::Real stddev, core::Size seq_separation, core::Real distance_cutoff)
	this method will get de-convoluted soon.... More...

static basic::Tracer	TR ("protocols.seeded_abinitio.CoordinateCst")

static basic::Tracer	TR_debug ("CoordinateCst.Debug")

void	parse_spans (pose::Pose &pose, utility::vector1< std::pair< std::string, std::string > > const span_vector, std::set< core::Size > resi_collection)
	parse residues at run time, in case there was a lenght change More...

utility::vector1< core::Size >	adjust_residues (pose::Pose &pose, std::string design_residues)

void	adjust_single_residues (pose::Pose &pose, std::string single_residues, std::set< core::Size > resi_collection)
	residue parsing at runtime More...

void	add_coordinate_constraints (pose::Pose &pose, std::set< core::Size > const &constrain_residues, core::Size const anchor_resnum, core::Real const coord_sdev, std::string anchor_atom_name, std::string atom_name, core::scoring::func::HarmonicFuncOP &coord_cst_func)

void	adjust_mm_to_length (core::pose::Pose const &pose, core::kinematics::MoveMapOP &mm)
	method to update numbering of a movemap if the pose length was changed previously only works if a LengthEventCollector is set in the pose's observer cache default behavior is to set everything new to be movable and adjust the numbering of the residues that were previously not allowed to move to the appropriate new numbering More...

protocols::loops::Loops	parse_seeds (core::pose::Pose const &pose, utility::vector1< std::pair< std::string, std::string > > seed_vector)
	for runtime parsing of seeds More...

void	combine_two_poses (core::pose::Pose design_pose, core::pose::PoseOP target_chain)

Size	define_cut_point_stochasticly (core::Size start_resi, core::Size stop_resi, std::string secondarystruct_seq, core::Size start_fold_pose)

std::pair< core::Size, core::Size >	get_closest_residue_pair (core::Size seed_start, core::Size seed_stop, core::pose::PoseOP &target_seed_pose)

std::pair< core::Size, core::Size >	find_nearest_residue (core::Size anchor, pose::PoseOP &target_seed_pose)

static basic::Tracer	TR ("protocols.seeded_abinitio.SeedSetupMover")

bool	is_part (utility::vector1< core::Size > vec, core::Size pos)

void	define_movemap_chains (core::pose::Pose &pose, core::kinematics::MoveMapOP &movemap, protocols::loops::Loops &seeds, bool chi_chain1, bool chi_chain2, bool interface_chi1, bool, core::Real interface_distance_cutoff)

utility::vector1< core::Size >	adjust_des_residues (pose::Pose &pose, std::string design_residues)
	adjustment since parse time specified residues are different numbered than run time residues More...

static basic::Tracer	TR ("protocols.seeded_abinitio.movers.SegmentHybridizer")

static basic::Tracer	TR_ccd ("protocols.seeded_abinitio.movers.SegmentHybridizer_ccd")

static basic::Tracer	TR ("protocols.seeded_abinitio.util")

void	superposition_transform (utility::vector1< numeric::xyzVector< numeric::Real > > &init_coords, utility::vector1< numeric::xyzVector< numeric::Real > > &ref_coords, numeric::xyzMatrix< numeric::Real > &rotation, numeric::xyzVector< numeric::Real > &toCenter, numeric::xyzVector< numeric::Real > &toFitCenter)

template<typename T >
void	vector_vector_to_FArray2 (utility::vector1< numeric::xyzVector< T > > &from, ObjexxFCL::FArray2D< T > &to)

Typedef Documentation

◆ GrowPeptidesSegmentOP

using protocols::seeded_abinitio::GrowPeptidesSegmentOP = typedef utility::pointer::shared_ptr< GrowPeptidesSegment >

◆ SeedFoldTreeCOP

typedef utility::pointer::shared_ptr<SeedFoldTree const> protocols::seeded_abinitio::SeedFoldTreeCOP

◆ SeedFoldTreeOP

typedef utility::pointer::shared_ptr<SeedFoldTree> protocols::seeded_abinitio::SeedFoldTreeOP

Function Documentation

◆ add_coordinate_constraints()

void protocols::seeded_abinitio::add_coordinate_constraints	(	pose::Pose &	pose,
		std::set< core::Size > const &	constrain_residues,
		core::Size const	anchor_resnum,
		core::Real const	coord_sdev,
		std::string	anchor_atom_name,
		std::string	atom_name,
		core::scoring::func::HarmonicFuncOP &	coord_cst_func
	)

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::pose::Pose::add_constraints(), core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::id::to_string(), TR(), and core::conformation::Residue::xyz().

Referenced by protocols::seeded_abinitio::CoordinateCst::apply().

◆ add_dist_constraints()

void protocols::seeded_abinitio::add_dist_constraints	(	pose::Pose &	pose,
		pose::PoseOP &	pose_of_int,
		core::Size	start_relevant_chain,
		core::scoring::constraints::ConstraintSetOP &	cst,
		protocols::loops::Loops &	seeds,
		protocols::loops::Loops &	clear_area,
		utility::vector1< core::Size >	cut_points,
		utility::vector1< core::Size >	seed_exceptions,
		bool	add_cst_seed,
		core::Real	stddev,
		core::Size	seq_separation,
		core::Real	distance_cutoff
	)

this method will get de-convoluted soon....

References core::conformation::Residue::atom_index(), protocols::loops::Loops::is_loop_residue(), is_part(), core::pose::Pose::residue(), protocols::loops::Loops::size(), TR(), and core::conformation::Residue::xyz().

Referenced by protocols::seeded_abinitio::CAcstGenerator::apply().

◆ adjust_des_residues()

utility::vector1< core::Size > protocols::seeded_abinitio::adjust_des_residues	(	pose::Pose &	pose,
		std::string	design_residues
	)

adjustment since parse time specified residues are different numbered than run time residues

References core::pose::parse_resnum(), and TR().

Referenced by protocols::seeded_abinitio::SeedSetupMover::apply().

◆ adjust_mm_to_length()

void protocols::seeded_abinitio::adjust_mm_to_length	(	core::pose::Pose const &	pose,
		core::kinematics::MoveMapOP &	mm
	)

method to update numbering of a movemap if the pose length was changed previously only works if a LengthEventCollector is set in the pose's observer cache default behavior is to set everything new to be movable and adjust the numbering of the residues that were previously not allowed to move to the appropriate new numbering

to readjust the move map after length changes

References core::id::combine_sequence_mappings(), core::pose::datacache::LENGTH_EVENT_COLLECTOR, core::pose::Pose::observer_cache(), core::pose::Pose::size(), and TR().

◆ adjust_residues()

utility::vector1< core::Size > protocols::seeded_abinitio::adjust_residues	(	pose::Pose &	pose,
		std::string	design_residues
	)

References core::pose::parse_resnum(), and TR().

Referenced by protocols::seeded_abinitio::CoordinateCst::apply().

◆ adjust_single_residues()

void protocols::seeded_abinitio::adjust_single_residues	(	pose::Pose &	pose,
		std::string	single_residues,
		std::set< core::Size >	resi_collection
	)

residue parsing at runtime

References core::pose::parse_resnum().

Referenced by protocols::seeded_abinitio::CoordinateCst::apply().

◆ combine_two_poses()

void protocols::seeded_abinitio::combine_two_poses	(	core::pose::Pose	design_pose,
		core::pose::PoseOP	target_chain
	)

References core::conformation::Residue::clone(), core::pose::Pose::residue(), core::pose::Pose::size(), and TR().

◆ define_cut_point_stochasticly()

Size protocols::seeded_abinitio::define_cut_point_stochasticly	(	core::Size	start_resi,
		core::Size	stop_resi,
		std::string	secondarystruct_seq,
		core::Size	start_fold_pose
	)

References core::scoring::rg, and TR().

Referenced by protocols::seeded_abinitio::SeedFoldTree::set_foldtree().

◆ define_movemap_chains()

void protocols::seeded_abinitio::define_movemap_chains	(	core::pose::Pose &	pose,
		core::kinematics::MoveMapOP &	movemap,
		protocols::loops::Loops &	seeds,
		bool	chi_chain1,
		bool	chi_chain2,
		bool	interface_chi1,
		bool	,
		core::Real	interface_distance_cutoff
	)

References protocols::scoring::Interface::calculate(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::scoring::Interface::distance(), protocols::scoring::Interface::is_interface(), protocols::loops::Loops::is_loop_residue(), core::conformation::Conformation::num_chains(), core::pose::Pose::size(), TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::seeded_abinitio::SeedSetupMover::apply().

◆ find_nearest_residue()

std::pair< core::Size, core::Size > protocols::seeded_abinitio::find_nearest_residue	(	core::Size	anchor,
		pose::PoseOP &	target_seed_pose
	)

References core::kinematics::distance(), core::conformation::Residue::name3(), TR(), and core::conformation::Residue::xyz().

Referenced by protocols::seeded_abinitio::SeedFoldTree::set_foldtree().

◆ get_closest_residue_pair()

std::pair< core::Size, core::Size > protocols::seeded_abinitio::get_closest_residue_pair	(	core::Size	seed_start,
		core::Size	seed_stop,
		core::pose::PoseOP &	target_seed_pose
	)

References core::kinematics::distance(), and TR().

Referenced by protocols::seeded_abinitio::SeedFoldTree::set_foldtree().

◆ is_part() [1/2]

bool protocols::seeded_abinitio::is_part	(	utility::vector1< core::Size > &	cut_points,
		core::Size &	residue
	)

Referenced by add_dist_constraints(), and protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds().

◆ is_part() [2/2]

bool protocols::seeded_abinitio::is_part	(	utility::vector1< core::Size >	vec,
		core::Size	pos
	)

◆ parse_seeds()

protocols::loops::Loops protocols::seeded_abinitio::parse_seeds	(	core::pose::Pose const &	pose,
		utility::vector1< std::pair< std::string, std::string > >	seed_vector
	)

for runtime parsing of seeds

References protocols::loops::Loops::add_loop(), core::sequence::end, core::pose::parse_resnum(), and TR().

Referenced by protocols::seeded_abinitio::CloseFold::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), and protocols::seeded_abinitio::SeedSetupMover::apply().

◆ parse_spans()

void protocols::seeded_abinitio::parse_spans	(	pose::Pose &	pose,
		utility::vector1< std::pair< std::string, std::string > > const	span_vector,
		std::set< core::Size >	resi_collection
	)

parse residues at run time, in case there was a lenght change

References core::sequence::end, core::pose::parse_resnum(), and TR().

Referenced by protocols::seeded_abinitio::CoordinateCst::apply().

◆ superposition_transform()

void protocols::seeded_abinitio::superposition_transform	(	utility::vector1< numeric::xyzVector< numeric::Real > > &	init_coords,
		utility::vector1< numeric::xyzVector< numeric::Real > > &	ref_coords,
		numeric::xyzMatrix< numeric::Real > &	rotation,
		numeric::xyzVector< numeric::Real > &	toCenter,
		numeric::xyzVector< numeric::Real > &	toFitCenter
	)

References protocols::toolbox::superposition_transform(), and vector_vector_to_FArray2().

Referenced by protocols::pose_length_moves::PossibleLoop::add_coordinate_csts_from_lookback(), protocols::backbone_moves::local_backbone_mover::FreePeptide::align(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::apply(), protocols::simple_moves::AlignChainMover::apply(), protocols::splice::AlignEndsMover::apply(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::simple_filters::SSMotifFinder::superimpose_pose_on_template(), protocols::splice::Splice::superimpose_source_on_pose(), protocols::splice::SpliceOut::superimpose_source_on_pose(), protocols::splice::SpliceOutTail::superimpose_source_on_pose(), protocols::splice::RBOutMover::superimpose_source_on_pose(), and protocols::simple_moves::AddChainMover::swap_chain().

◆ TR() [1/5]

static basic::Tracer protocols::seeded_abinitio::TR ( "protocols.seeded_abinitio.CAcstGenerator" )

static

◆ TR() [2/5]

static basic::Tracer protocols::seeded_abinitio::TR ( "protocols.seeded_abinitio.CoordinateCst" )

static

◆ TR() [3/5]

static basic::Tracer protocols::seeded_abinitio::TR ( "protocols.seeded_abinitio.movers.SegmentHybridizer" )

static

◆ TR() [4/5]

static basic::Tracer protocols::seeded_abinitio::TR ( "protocols.seeded_abinitio.SeedSetupMover" )

static

◆ TR() [5/5]

static basic::Tracer protocols::seeded_abinitio::TR ( "protocols.seeded_abinitio.util" )

static

◆ TR_ccd()

static basic::Tracer protocols::seeded_abinitio::TR_ccd ( "protocols.seeded_abinitio.movers.SegmentHybridizer_ccd" )

static

◆ TR_debug()

static basic::Tracer protocols::seeded_abinitio::TR_debug ( "CoordinateCst.Debug" )

static

◆ vector_vector_to_FArray2()

template<typename T >

void protocols::seeded_abinitio::vector_vector_to_FArray2	(	utility::vector1< numeric::xyzVector< T > > &	from,
		ObjexxFCL::FArray2D< T > &	to
	)

Referenced by superposition_transform().

Classes

Typedefs

Functions

Typedef Documentation

◆ GrowPeptidesSegmentOP

◆ SeedFoldTreeCOP

◆ SeedFoldTreeOP

Function Documentation

◆ add_coordinate_constraints()

◆ add_dist_constraints()

◆ adjust_des_residues()

◆ adjust_mm_to_length()

◆ adjust_residues()

◆ adjust_single_residues()

◆ combine_two_poses()

◆ define_cut_point_stochasticly()

◆ define_movemap_chains()

◆ find_nearest_residue()

◆ get_closest_residue_pair()

◆ is_part() [1/2]

◆ is_part() [2/2]

◆ parse_seeds()

◆ parse_spans()

◆ superposition_transform()

◆ TR() [1/5]

◆ TR() [2/5]

◆ TR() [3/5]

◆ TR() [4/5]

◆ TR() [5/5]

◆ TR_ccd()

◆ TR_debug()

◆ vector_vector_to_FArray2()