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	SeedFoldTree
class	SeedFoldTreeCreator
class	SeedSetupMover
class	SeedSetupMoverCreator
class	SegmentHybridizer
class	SegmentHybridizerCreator
class	SwapSegment
class	SwapSegmentCreator

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

Functions
static thread_local 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 thread_local basic::Tracer	TR ("protocols.seeded_abinitio.CoordinateCst")
static thread_local 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 (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 thread_local 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 thread_local basic::Tracer	TR ("protocols.seeded_abinitio.movers.SegmentHybridizer")
static thread_local basic::Tracer	TR_ccd ("protocols.seeded_abinitio.movers.SegmentHybridizer_ccd")
static thread_local 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

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

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

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::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(), utility::to_string(), TR(), utility_exit_with_message, 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....

References core::conformation::Residue::atom_index(), 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

References key, core::pose::parse_resnum(), utility::string_split(), and TR().

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

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
	)

References key, core::pose::parse_resnum(), utility::string_split(), and TR().

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

References key, core::pose::parse_resnum(), and utility::string_split().

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

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::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
	)

References numeric::random::RandomGenerator::random_range(), numeric::random::rg(), TR(), and utility_exit_with_message.

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
	)

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(), TR(), 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
	)

References distance(), runtime_assert, TR(), and utility_exit_with_message.

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
	)

References distance(), runtime_assert, TR(), and utility_exit_with_message.

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

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().

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

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(), begin, 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

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

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

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

Referenced by protocols::simple_moves::AlignChainMover::apply(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::simple_filters::SSMotifFinder::superimpose_pose_on_template(), and protocols::simple_moves::AddChainMover::swap_chain().

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

static

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

static

Referenced by add_coordinate_constraints(), adjust_des_residues(), adjust_mm_to_length(), adjust_residues(), protocols::seeded_abinitio::CoordinateCst::apply(), protocols::seeded_abinitio::SwapSegment::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::seeded_abinitio::SeedSetupMover::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), combine_two_poses(), protocols::seeded_abinitio::SwapSegment::copying_side_chains(), define_cut_point_stochasticly(), define_movemap_chains(), 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::CoordinateCst::parse_my_tag(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::seeded_abinitio::SeedSetupMover::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::seeded_abinitio::SegmentHybridizer::parse_my_tag(), protocols::seeded_abinitio::SeedFoldTree::parse_my_tag(), parse_seeds(), parse_spans(), protocols::seeded_abinitio::CloseFold::quick_closure(), protocols::seeded_abinitio::SeedFoldTree::set_foldtree(), protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds(), protocols::seeded_abinitio::SwapSegment::swap_chain(), and protocols::seeded_abinitio::SwapSegment::swap_segment().

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

static

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

static

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

static

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

static

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

static

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().