protocols::seeded_abinitio Namespace Reference

Classes
class	CAcstGenerator
class	CAcstGeneratorCreator
class	CloseFold
class	CloseFoldCreator
class	CoordinateCst
class	CoordinateCstCreator
class	DefineMovableLoops
class	DefineMovableLoopsCreator
class	GrowPeptides
class	GrowPeptidesCreator
class	PlaceFragments
class	SeedFoldTree
class	SeedFoldTreeCreator
class	SeedSetupMover
class	SeedSetupMoverCreator
class	SegmentHybridizer
class	SegmentHybridizerCreator
class	SwapSegment
class	SwapSegmentCreator

Typedefs
typedef utility::pointer::owning_ptr < SeedFoldTree >	SeedFoldTreeOP
typedef utility::pointer::owning_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::constraints::HarmonicFuncOP &coord_cst_func)
static basic::Tracer	TR ("protocols.seeded_abinitio.PlaceFragments")
utility::vector1< core::Size >	parse_residues (pose::Pose &pose, std::string resid)
	adjustment since parse time specified residues are different numbered than run time residues More...
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 (Size start_resi, Size stop_resi, std::string secondarystruct_seq, core::Size start_fold_pose)
std::pair< Size, Size >	get_closest_residue_pair (Size seed_start, Size seed_stop, core::pose::PoseOP &target_seed_pose)
std::pair< Size, Size >	find_nearest_residue (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 numeric::random::RandomGenerator	RG (1245273)

Typedef Documentation

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

Definition at line 23 of file SeedFoldTree.fwd.hh.

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

Definition at line 21 of file SeedFoldTree.fwd.hh.

Function Documentation

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::constraints::HarmonicFuncOP &	coord_cst_func
	)

Definition at line 169 of file CoordinateCst.cc.

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(), and core::conformation::Residue::xyz().

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

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....

Definition at line 98 of file CAcstGenerator.cc.

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

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

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

Definition at line 314 of file SeedSetupMover.cc.

References core::pose::parse_resnum().

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

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

Definition at line 97 of file SeededAbinitio_util.cc.

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

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

Definition at line 135 of file CoordinateCst.cc.

References core::pose::parse_resnum().

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

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

residue parsing at runtime

Definition at line 155 of file CoordinateCst.cc.

References core::pose::parse_resnum().

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

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

Definition at line 167 of file SeededAbinitio_util.cc.

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

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

Definition at line 172 of file SeedFoldTree.cc.

References RG(), and TR().

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

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
	)

Definition at line 247 of file SeedSetupMover.cc.

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::total_residue(), and core::pose::Pose::update_residue_neighbors().

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

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

Definition at line 256 of file SeedFoldTree.cc.

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

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

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

Definition at line 209 of file SeedFoldTree.cc.

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

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

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

Definition at line 87 of file CAcstGenerator.cc.

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

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

Definition at line 138 of file SeedSetupMover.cc.

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

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

Definition at line 384 of file PlaceFragments.cc.

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

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

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

Definition at line 149 of file SeededAbinitio_util.cc.

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

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

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

Definition at line 112 of file CoordinateCst.cc.

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

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

static numeric::random::RandomGenerator protocols::seeded_abinitio::RG ( 1245273  )

static

Referenced by define_cut_point_stochasticly().

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

static

Referenced by adjust_mm_to_length(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::seeded_abinitio::SwapSegment::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), combine_two_poses(), protocols::seeded_abinitio::SwapSegment::copying_side_chains(), define_cut_point_stochasticly(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), find_nearest_residue(), get_closest_residue_pair(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::seeded_abinitio::PlaceFragments::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::seeded_abinitio::SeedFoldTree::parse_my_tag(), parse_residues(), parse_seeds(), protocols::seeded_abinitio::CloseFold::quick_closure(), protocols::seeded_abinitio::SeedFoldTree::set_foldtree(), protocols::seeded_abinitio::SwapSegment::swap_chain(), and protocols::seeded_abinitio::SwapSegment::swap_segment().

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

static

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

static

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

static

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

static

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

static

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

static