protocols::hybridization Namespace Reference

Classes
class	AllResiduesChanged
	(helper) functor class which keeps track of initial phi/psi values. calls of operator ( pose ) compare the initial phi/psi values More...
class	CartesianHybridize
class	CartesianSampler
class	ChunkTrialMover
class	DDomainParse
class	DomainAssembly
class	hConvergenceCheck
class	FoldTreeHybridize
class	HybridizeFoldtreeDynamic
class	HybridizeProtocol
class	HybridizeProtocolCreator
class	CartesianSamplerCreator
class	InsertChunkMover
class	TemplateHistory
class	TMalign
class	WeightedFragmentSmoothTrialMover
class	WeightedFragmentTrialMover

Typedefs
typedef utility::pointer::owning_ptr < CartesianHybridize >	CartesianHybridizeOP
typedef utility::pointer::owning_ptr < CartesianHybridize const >	CartesianHybridizeCOP
typedef utility::pointer::owning_ptr < CartesianSampler >	CartesianSamplerOP
typedef utility::pointer::owning_ptr < CartesianSampler const >	CartesianSamplerCOP
typedef utility::pointer::owning_ptr < ChunkTrialMover >	ChunkTrialMoverOP
typedef utility::pointer::owning_ptr < ChunkTrialMover const >	ChunkTrialMoverCOP
typedef utility::pointer::owning_ptr < TemlateAssembly >	TemlateAssemblyOP
typedef utility::pointer::owning_ptr < TemlateAssembly const >	TemlateAssemblyCOP
typedef utility::pointer::owning_ptr < hConvergenceCheck >	hConvergenceCheckOP
typedef utility::pointer::owning_ptr < FoldTreeHybridize >	FoldTreeHybridizeOP
typedef utility::pointer::owning_ptr < FoldTreeHybridize const >	FoldTreeHybridizeCOP
typedef utility::pointer::owning_ptr < HybridizeFoldtreeMover >	HybridizeFoldtreeMoverOP
typedef utility::pointer::owning_ptr < HybridizeFoldtreeMover const >	HybridizeFoldtreeMoverCOP
typedef utility::pointer::owning_ptr < HybridizeProtocol >	HybridizeProtocolOP
typedef utility::pointer::owning_ptr < HybridizeProtocol const >	HybridizeProtocolCOP
typedef utility::pointer::owning_ptr < TemplateHistory >	TemplateHistoryOP
typedef utility::pointer::owning_ptr < TemplateHistory const >	TemplateHistoryCOP
typedef utility::pointer::owning_ptr < WeightedFragmentSmoothTrialMover >	WeightedFragmentSmoothTrialMoverOP
typedef utility::pointer::owning_ptr < WeightedFragmentSmoothTrialMover const >	WeightedFragmentSmoothTrialMoverCOP
typedef utility::pointer::owning_ptr < WeightedFragmentTrialMover >	WeightedFragmentTrialMoverOP
typedef utility::pointer::owning_ptr < WeightedFragmentTrialMover const >	WeightedFragmentTrialMoverCOP

Enumerations
enum	AlignOption { all_chunks, random_chunk }

Functions
static basic::Tracer	TR ("protocols.hybridization.CartesianHybridize")
static basic::Tracer	TR ("protocols.hybridization.CartesianSampler")
static numeric::random::RandomGenerator	RG (8403155)
bool	TMalign_poses (core::pose::Pose &aligned_pose, core::pose::Pose const &ref_pose, std::list< Size > const &residue_list, std::list< Size > const &ref_residue_list)
void	remove_residues (core::pose::Pose &pose, utility::vector1< int > const resnum_list, utility::vector1< int > &remaining_resnum)
utility::vector1< Size >	find_uncovered_residues (core::pose::Pose const &pose, utility::vector1< Size > const covered_residues)
core::Real	gap_distance (Size Seq_gap)
static basic::Tracer	TZ ("protocols.hybridization.TemplateHistory")
core::Size	get_num_residues_nonvirt (core::pose::Pose const &pose)
void	setup_centroid_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > templates, utility::vector1< core::Real > template_weights, std::string cen_cst_file, std::set< core::Size > ignore_res_for_AUTO)
void	setup_fullatom_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > templates, utility::vector1< core::Real > template_weights, std::string cen_cst_file, std::string fa_cst_file)
void	generate_centroid_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > templates, utility::vector1< core::Real >, std::set< core::Size > ignore_res)
void	generate_fullatom_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > templates, utility::vector1< core::Real > template_weights)
void	add_strand_pairs_cst (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > const strand_pairs)
void	add_non_protein_cst (core::pose::Pose &pose, core::Real const cst_weight)
bool	discontinued_upper (core::pose::Pose const &pose, Size const seqpos)
bool	discontinued_lower (core::pose::Pose const &pose, Size const seqpos)
std::list< Size >	downstream_residues_from_jump (core::pose::Pose const &pose, Size const jump_number)
void	partial_align (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, bool iterate_convergence, utility::vector1< core::Real > distance_thresholds, core::Real min_coverage)
void	partial_align (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, std::list< Size > const &residue_list, bool iterate_convergence, utility::vector1< core::Real > distance_thresholds, core::Real min_coverage)
core::Size	atom_map_valid_size (core::pose::Pose const &pose, core::id::AtomID_Map< core::id::AtomID > const &atom_map)
core::id::AtomID_Map < core::id::AtomID >	update_atom_map (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, core::Real distance_squared_threshold)
Size	natom_aligned (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, core::Real distance_squared_threshold)
void	get_superposition_transformation (pose::Pose const &mod_pose, pose::Pose const &ref_pose, core::id::AtomID_Map< core::id::AtomID > const &atom_map, numeric::xyzMatrix< core::Real > &R, numeric::xyzVector< core::Real > &preT, numeric::xyzVector< core::Real > &postT)
void	apply_transformation (pose::Pose &mod_pose, std::list< Size > const &residue_list, numeric::xyzMatrix< core::Real > const &R, numeric::xyzVector< core::Real > const &preT, numeric::xyzVector< core::Real > const &postT)
core::fragment::FragSetOP	create_fragment_set (core::pose::Pose const &pose, core::Size len, core::Size nfrag)
protocols::loops::Loops	renumber_with_pdb_info (protocols::loops::Loops &template_chunk, core::pose::PoseCOP template_pose)
core::Real	get_gdtmm (core::pose::Pose &native, core::pose::Pose &pose, core::sequence::SequenceAlignmentOP &aln)

Variables
const core::Size	DEFAULT_NCYCLES =400

Typedef Documentation

typedef utility::pointer::owning_ptr< CartesianHybridize const > protocols::hybridization::CartesianHybridizeCOP

Definition at line 29 of file CartesianHybridize.fwd.hh.

typedef utility::pointer::owning_ptr< CartesianHybridize > protocols::hybridization::CartesianHybridizeOP

Definition at line 27 of file CartesianHybridize.fwd.hh.

typedef utility::pointer::owning_ptr< CartesianSampler const > protocols::hybridization::CartesianSamplerCOP

Definition at line 29 of file CartesianSampler.fwd.hh.

typedef utility::pointer::owning_ptr< CartesianSampler > protocols::hybridization::CartesianSamplerOP

Definition at line 27 of file CartesianSampler.fwd.hh.

typedef utility::pointer::owning_ptr< ChunkTrialMover const > protocols::hybridization::ChunkTrialMoverCOP

Definition at line 26 of file ChunkTrialMover.fwd.hh.

typedef utility::pointer::owning_ptr< ChunkTrialMover > protocols::hybridization::ChunkTrialMoverOP

Definition at line 24 of file ChunkTrialMover.fwd.hh.

typedef utility::pointer::owning_ptr< FoldTreeHybridize const > protocols::hybridization::FoldTreeHybridizeCOP

Definition at line 26 of file FoldTreeHybridize.fwd.hh.

typedef utility::pointer::owning_ptr< FoldTreeHybridize > protocols::hybridization::FoldTreeHybridizeOP

Definition at line 24 of file FoldTreeHybridize.fwd.hh.

typedef utility::pointer::owning_ptr< hConvergenceCheck > protocols::hybridization::hConvergenceCheckOP

Definition at line 1102 of file FoldTreeHybridize.cc.

typedef utility::pointer::owning_ptr<HybridizeFoldtreeMover const> protocols::hybridization::HybridizeFoldtreeMoverCOP

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

typedef utility::pointer::owning_ptr<HybridizeFoldtreeMover> protocols::hybridization::HybridizeFoldtreeMoverOP

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

typedef utility::pointer::owning_ptr< HybridizeProtocol const > protocols::hybridization::HybridizeProtocolCOP

Definition at line 26 of file HybridizeProtocol.fwd.hh.

typedef utility::pointer::owning_ptr< HybridizeProtocol > protocols::hybridization::HybridizeProtocolOP

Definition at line 24 of file HybridizeProtocol.fwd.hh.

typedef utility::pointer::owning_ptr< TemlateAssembly const > protocols::hybridization::TemlateAssemblyCOP

Definition at line 27 of file DomainAssembly.fwd.hh.

typedef utility::pointer::owning_ptr< TemlateAssembly > protocols::hybridization::TemlateAssemblyOP

Definition at line 25 of file DomainAssembly.fwd.hh.

typedef utility::pointer::owning_ptr< TemplateHistory const > protocols::hybridization::TemplateHistoryCOP

Definition at line 25 of file TemplateHistory.fwd.hh.

typedef utility::pointer::owning_ptr< TemplateHistory > protocols::hybridization::TemplateHistoryOP

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

typedef utility::pointer::owning_ptr< WeightedFragmentSmoothTrialMover const > protocols::hybridization::WeightedFragmentSmoothTrialMoverCOP

Definition at line 26 of file WeightedFragmentSmoothTrialMover.fwd.hh.

typedef utility::pointer::owning_ptr< WeightedFragmentSmoothTrialMover > protocols::hybridization::WeightedFragmentSmoothTrialMoverOP

Definition at line 24 of file WeightedFragmentSmoothTrialMover.fwd.hh.

typedef utility::pointer::owning_ptr< WeightedFragmentTrialMover const > protocols::hybridization::WeightedFragmentTrialMoverCOP

Definition at line 27 of file WeightedFragmentTrialMover.fwd.hh.

typedef utility::pointer::owning_ptr< WeightedFragmentTrialMover > protocols::hybridization::WeightedFragmentTrialMoverOP

Definition at line 25 of file WeightedFragmentTrialMover.fwd.hh.

Enumeration Type Documentation

enum protocols::hybridization::AlignOption

Enumerator
all_chunks
random_chunk

Definition at line 54 of file ChunkTrialMover.hh.

Function Documentation

void protocols::hybridization::add_non_protein_cst	(	core::pose::Pose &	pose,
		core::Real const	cst_weight
	)

Definition at line 213 of file util.cc.

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::has(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::hybridization::HybridizeProtocol::apply(), and protocols::hybridization::FoldTreeHybridize::apply().

void protocols::hybridization::add_strand_pairs_cst	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > const	strand_pairs
	)

Definition at line 196 of file util.cc.

References core::pose::Pose::add_constraint(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::hybridization::HybridizeProtocol::apply().

void protocols::hybridization::apply_transformation	(	pose::Pose &	mod_pose,
		std::list< Size > const &	residue_list,
		numeric::xyzMatrix< core::Real > const &	R,
		numeric::xyzVector< core::Real > const &	preT,
		numeric::xyzVector< core::Real > const &	postT
	)

Definition at line 518 of file util.cc.

References core::pose::Pose::batch_set_xyz(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::pose::Pose::xyz().

Referenced by partial_align().

core::Size protocols::hybridization::atom_map_valid_size	(	core::pose::Pose const &	pose,
		core::id::AtomID_Map< core::id::AtomID > const &	atom_map
	)

Definition at line 384 of file util.cc.

References core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::id::AtomID::valid().

Referenced by partial_align().

core::fragment::FragSetOP protocols::hybridization::create_fragment_set	(	core::pose::Pose const &	pose,
		core::Size	len,
		core::Size	nfrag
	)

Definition at line 541 of file util.cc.

References core::pose::Pose::fold_tree(), core::scoring::dssp::Dssp::get_dssp_secstruct(), get_num_residues_nonvirt(), core::kinematics::FoldTree::is_cutpoint(), core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), and core::pose::Pose::sequence().

Referenced by protocols::hybridization::CartesianSampler::apply(), and protocols::hybridization::CartesianSampler::parse_my_tag().

bool protocols::hybridization::discontinued_lower	(	core::pose::Pose const &	pose,
		Size const	seqpos
	)

Definition at line 277 of file util.cc.

References core::chemical::ResidueType::is_polymer(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::hybridization::InsertChunkMover::get_local_sequence_mapping().

bool protocols::hybridization::discontinued_upper	(	core::pose::Pose const &	pose,
		Size const	seqpos
	)

Definition at line 263 of file util.cc.

References core::chemical::ResidueType::is_polymer(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().

Referenced by protocols::hybridization::InsertChunkMover::get_local_sequence_mapping().

std::list< core::Size > protocols::hybridization::downstream_residues_from_jump	(	core::pose::Pose const &	pose,
		Size const	jump_number
	)

Definition at line 292 of file util.cc.

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_outgoing_edges(), core::kinematics::FoldTree::jump_edge(), protocols::loops::start, core::kinematics::Edge::stop(), and protocols::loops::stop.

Referenced by protocols::hybridization::InsertChunkMover::set_aligned_chunk().

utility::vector1<Size> protocols::hybridization::find_uncovered_residues	(	core::pose::Pose const &	pose,
		utility::vector1< Size > const	covered_residues
	)

Definition at line 170 of file DomainAssembly.cc.

References core::pose::Pose::pdb_info(), and core::pose::Pose::total_residue().

Referenced by protocols::hybridization::DomainAssembly::run().

core::Real protocols::hybridization::gap_distance

(

Size

Seq_gap)

Definition at line 191 of file DomainAssembly.cc.

Referenced by protocols::hybridization::DomainAssembly::run().

void protocols::hybridization::generate_centroid_constraints	(	core::pose::Pose &	pose,
		utility::vector1< core::pose::PoseCOP >	templates,
		utility::vector1< core::Real >	,
		std::set< core::Size >	ignore_res
	)

Definition at line 133 of file util.cc.

References core::pose::Pose::add_constraint(), get_num_residues_nonvirt(), core::pose::Pose::remove_constraints(), and protocols::kinmatch::xyz().

Referenced by generate_fullatom_constraints(), setup_centroid_constraints(), and setup_fullatom_constraints().

void protocols::hybridization::generate_fullatom_constraints	(	core::pose::Pose &	pose,
		utility::vector1< core::pose::PoseCOP >	templates,
		utility::vector1< core::Real >	template_weights
	)

Definition at line 188 of file util.cc.

References generate_centroid_constraints().

Referenced by setup_fullatom_constraints().

core::Real protocols::hybridization::get_gdtmm	(	core::pose::Pose &	native,
		core::pose::Pose &	pose,
		core::sequence::SequenceAlignmentOP &	aln
	)

Definition at line 588 of file util.cc.

References core::sequence::align_naive(), protocols::comparative_modeling::gather_coords(), core::pose::Pose::sequence(), core::pose::Pose::total_residue(), and core::scoring::xyz_gdtmm().

Referenced by protocols::hybridization::HybridizeProtocol::apply(), and protocols::hybridization::FoldTreeHybridize::apply().

core::Size protocols::hybridization::get_num_residues_nonvirt

(

core::pose::Pose const &

pose)

Definition at line 78 of file util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::conformation(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::pose::Pose::residue(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::pose::Pose::total_residue().

Referenced by create_fragment_set(), generate_centroid_constraints(), protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_1mers(), protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_big_frags(), protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_small_frags(), and protocols::hybridization::FoldTreeHybridize::setup_foldtree().

void protocols::hybridization::get_superposition_transformation	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		core::id::AtomID_Map< core::id::AtomID > const &	atom_map,
		numeric::xyzMatrix< core::Real > &	R,
		numeric::xyzVector< core::Real > &	preT,
		numeric::xyzVector< core::Real > &	postT
	)

Definition at line 448 of file util.cc.

References core::conformation::Residue::atom(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::id::AtomID::valid(), core::conformation::Atom::xyz(), and core::pose::Pose::xyz().

Referenced by partial_align().

core::Size protocols::hybridization::natom_aligned	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		id::AtomID_Map< id::AtomID > const &	atom_map,
		core::Real	distance_squared_threshold
	)

Definition at line 424 of file util.cc.

References core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::id::AtomID::valid(), and core::pose::Pose::xyz().

void protocols::hybridization::partial_align	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		id::AtomID_Map< id::AtomID > const &	atom_map,
		bool	iterate_convergence,
		utility::vector1< core::Real >	distance_thresholds,
		core::Real	min_coverage
	)

Definition at line 314 of file util.cc.

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

Referenced by protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::hybridization::DomainAssembly::run(), and TMalign_poses().

void protocols::hybridization::partial_align	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		id::AtomID_Map< id::AtomID > const &	atom_map,
		std::list< Size > const &	residue_list,
		bool	iterate_convergence,
		utility::vector1< core::Real >	distance_thresholds,
		core::Real	min_coverage
	)

Definition at line 332 of file util.cc.

References apply_transformation(), atom_map_valid_size(), get_superposition_transformation(), and update_atom_map().

void protocols::hybridization::remove_residues	(	core::pose::Pose &	pose,
		utility::vector1< int > const	resnum_list,
		utility::vector1< int > &	remaining_resnum
	)

Definition at line 145 of file DomainAssembly.cc.

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::pose::Pose::pdb_info(), and core::pose::Pose::total_residue().

Referenced by protocols::hybridization::DomainAssembly::run().

protocols::loops::Loops protocols::hybridization::renumber_with_pdb_info	(	protocols::loops::Loops &	template_chunk,
		core::pose::PoseCOP	template_pose
	)

Definition at line 571 of file util.cc.

References protocols::loops::Loops::num_loop().

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), and protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_big_frags().

static numeric::random::RandomGenerator protocols::hybridization::RG ( 8403155  )

static

Referenced by protocols::hybridization::WeightedFragmentTrialMover::apply(), protocols::hybridization::WeightedFragmentSmoothTrialMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::ChunkTrialMover::apply(), protocols::hybridization::InsertChunkMover::check_overlap(), protocols::hybridization::HybridizeFoldtreeDynamic::decide_cuts(), protocols::hybridization::DomainAssembly::DomainAssembly(), protocols::hybridization::HybridizeProtocol::expand_domains_to_full_length(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), protocols::hybridization::HybridizeProtocol::init(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::hybridization::ChunkTrialMover::pick_random_chunk(), protocols::hybridization::ChunkTrialMover::pick_random_template(), protocols::hybridization::HybridizeProtocol::pick_starting_template(), and protocols::hybridization::DomainAssembly::run().

void protocols::hybridization::setup_centroid_constraints	(	core::pose::Pose &	pose,
		utility::vector1< core::pose::PoseCOP >	templates,
		utility::vector1< core::Real >	template_weights,
		std::string	cen_cst_file,
		std::set< core::Size >	ignore_res_for_AUTO
	)

Definition at line 92 of file util.cc.

References core::pose::Pose::constraint_set(), generate_centroid_constraints(), core::scoring::constraints::ConstraintIO::get_instance(), and core::scoring::constraints::ConstraintIO::read_constraints_new().

Referenced by protocols::hybridization::HybridizeProtocol::apply(), and protocols::hybridization::FoldTreeHybridize::apply().

void protocols::hybridization::setup_fullatom_constraints	(	core::pose::Pose &	pose,
		utility::vector1< core::pose::PoseCOP >	templates,
		utility::vector1< core::Real >	template_weights,
		std::string	cen_cst_file,
		std::string	fa_cst_file
	)

Definition at line 107 of file util.cc.

References protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), core::pose::Pose::constraint_set(), generate_centroid_constraints(), generate_fullatom_constraints(), core::scoring::constraints::ConstraintIO::get_instance(), and core::scoring::constraints::ConstraintIO::read_constraints_new().

Referenced by protocols::hybridization::HybridizeProtocol::apply().

bool protocols::hybridization::TMalign_poses	(	core::pose::Pose &	aligned_pose,
		core::pose::Pose const &	ref_pose,
		std::list< Size > const &	residue_list,
		std::list< Size > const &	ref_residue_list
	)

Definition at line 54 of file DomainAssembly.cc.

References protocols::hybridization::TMalign::alignment2AtomMap(), protocols::hybridization::TMalign::alignment2strings(), protocols::hybridization::TMalign::apply(), core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), partial_align(), protocols::hybridization::TMalign::TMscore(), core::pose::Pose::total_residue(), and TR().

Referenced by protocols::hybridization::DomainAssembly::run().

static basic::Tracer protocols::hybridization::TR ( "protocols.hybridization.CartesianSampler"  )

static

static basic::Tracer protocols::hybridization::TR ( "protocols.hybridization.CartesianHybridize"  )

static

Referenced by protocols::hybridization::FoldTreeHybridize::add_gap_constraints_to_pose(), protocols::hybridization::HybridizeFoldtreeDynamic::add_overlapping_pair_chunks(), protocols::hybridization::FoldTreeHybridize::add_strand_pairing(), protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), protocols::hybridization::HybridizeProtocol::add_template(), protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::hybridization::WeightedFragmentSmoothTrialMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::ChunkTrialMover::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::hybridization::FoldTreeHybridize::auto_frag_insertion_weight(), protocols::hybridization::CartesianHybridize::CartesianHybridize(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), protocols::hybridization::HybridizeFoldtreeDynamic::decide_cuts(), protocols::hybridization::FoldTreeHybridize::filter_templates(), protocols::hybridization::ChunkTrialMover::get_alignment_from_template(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_1mers(), protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_big_frags(), protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_small_frags(), protocols::hybridization::HybridizeProtocol::init(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::hybridization::hConvergenceCheck::operator()(), protocols::hybridization::HybridizeProtocol::read_template_structures(), protocols::hybridization::DomainAssembly::run(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates(), TMalign_poses(), protocols::hybridization::FoldTreeHybridize::translate_virt_to_CoM(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

static basic::Tracer protocols::hybridization::TZ ( "protocols.hybridization.TemplateHistory"  )

static

core::id::AtomID_Map< core::id::AtomID > protocols::hybridization::update_atom_map	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		id::AtomID_Map< id::AtomID > const &	atom_map,
		core::Real	distance_squared_threshold
	)

Definition at line 401 of file util.cc.

References core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::id::AtomID::valid(), and core::pose::Pose::xyz().

Referenced by partial_align().

Variable Documentation

const core::Size protocols::hybridization::DEFAULT_NCYCLES =400

Definition at line 119 of file CartesianHybridize.cc.