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	BackboneTorsionPerturbation
class	BackboneTorsionPerturbationCreator
class	BackboneTorsionSampler
class	BackboneTorsionSamplerCreator
class	CartesianHybridize
class	CartesianSampler
class	CartesianSamplerCreator
class	ChunkTrialMover
class	DDomainParse
class	DomainAssembly
class	FoldTreeHybridize
class	FragmentBiasAssigner
class	hConvergenceCheck
class	HybridizeFoldtreeDynamic
class	HybridizeProtocol
class	HybridizeProtocolCreator
class	InsertChunkMover
class	MRMover
class	TemplateHistory
class	TMalign
class	WeightedFragmentSmoothTrialMover
class	WeightedFragmentTrialMover

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

Enumerations
enum	AlignOption { all_chunks, random_chunk }

Functions
void	add_constraints (core::pose::Pose &pose, Size rsd1, Size rsd2)
void	optimize (core::pose::Pose &pose, Size rsd1, Size rsd2, core::scoring::ScoreFunctionOP scorefxn, Size ncycles, core::Real max_delta_torsion)
void	pick_pivots (core::pose::Pose &pose, Size &rsd1, Size &torsion1, Size &rsd2, Size &torsion2, Size variance=5)
static THREAD_LOCAL basic::Tracer	TR ("protocols.hybridization.CartesianHybridize")
static THREAD_LOCAL basic::Tracer	TR ("protocols.hybridization.CartesianSampler")
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 THREAD_LOCAL basic::Tracer	fragbias_tr ("protocols.hybridization.FragmentBiasAssigner")
static THREAD_LOCAL basic::Tracer	TR ("protocols.electron_density.util")
core::Size	parse_res (core::pose::Pose const &pose, std::string resnum)
static THREAD_LOCAL basic::Tracer	TZ ("protocols.hybridization.TemplateHistory")
core::Size	get_num_residues_nonvirt (core::pose::Pose const &pose)
core::Size	get_num_residues_prot (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	setup_user_coordinate_constraints (core::pose::Pose &pose, utility::vector1< Size > reses)
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::pose::Pose &tmpl, core::Real const self_cst_weight, core::Real const het_prot_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)
core::fragment::FragSetOP	create_fragment_set_no_ssbias (core::pose::Pose const &pose, core::Size len, core::Size nfrag, char force_ss)
core::fragment::FragSetOP	create_fragment_set_no_ssbias (core::pose::Pose const &pose, std::set< core::Size > user_pos, core::Size len, core::Size nfrag, char force_ss)
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)
void	setup_user_coordinate_constraints (core::pose::Pose &pose, utility::vector1< core::Size > reses_to_cst)

Variables
const core::Size	DEFAULT_NCYCLES =400
double	D0_MIN
double	Lnorm
double	score_d8
double	d0
double	d0_search
double	dcu0
std::vector< std::vector < double > >	score
std::vector< std::vector< bool > >	path
std::vector< std::vector < double > >	val
int	xlen
int	ylen
int	minlen
std::vector < numeric::xyzVector < core::Real > >	xa
std::vector < numeric::xyzVector < core::Real > >	ya
std::vector< int >	xresno
std::vector< int >	yresno
std::vector < numeric::xyzVector < core::Real > >	xtm
std::vector < numeric::xyzVector < core::Real > >	ytm
std::vector < numeric::xyzVector < core::Real > >	xt
std::string	seqx
std::string	seqy
std::vector< int >	secx
std::vector< int >	secy
std::vector < numeric::xyzVector < core::Real > >	r1
std::vector < numeric::xyzVector < core::Real > >	r2
numeric::xyzVector< core::Real >	t
numeric::xyzMatrix< core::Real >	u
int	n_ali8_
std::vector< int >	m1_
std::vector< int >	m2_
double	d0_out_
double	d0A
double	d0B

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::shared_ptr< MRMover > protocols::hybridization::MRMoverOP

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

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

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

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

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

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

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

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

Enumeration Type Documentation

enum protocols::hybridization::AlignOption

Enumerator
all_chunks
random_chunk

Function Documentation

void protocols::hybridization::add_constraints	(	core::pose::Pose &	pose,
		Size	rsd1,
		Size	rsd2
	)

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

Referenced by protocols::hybridization::BackboneTorsionPerturbation::perturb(), setup_fullatom_constraints(), and protocols::protein_interface_design::movers::PlaceStubMover::stub_based_atom_tree().

void protocols::hybridization::add_non_protein_cst	(	core::pose::Pose &	pose,
		core::pose::Pose &	tmpl,
		core::Real const	self_cst_weight,
		core::Real const	het_prot_cst_weight
	)

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::chemical::aa_vrt, core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), core::pose::Pose::conformation(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), 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
	)

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
	)

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
	)

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
	)

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

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

References core::pose::Pose::fold_tree(), get_num_residues_nonvirt(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_protein(), core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), core::pose::Pose::residue(), and core::pose::Pose::sequence().

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

core::fragment::FragSetOP protocols::hybridization::create_fragment_set_no_ssbias	(	core::pose::Pose const &	pose,
		std::set< core::Size >	user_pos,
		core::Size	len,
		core::Size	nfrag,
		char	force_ss
	)

References core::pose::Pose::fold_tree(), get_num_residues_nonvirt(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_protein(), core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), core::pose::Pose::residue(), core::pose::Pose::sequence(), and TR().

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

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
	)

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
	)

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

Referenced by protocols::hybridization::ChunkTrialMover::apply(), protocols::hybridization::ChunkTrialMover::pick_random_chunk(), and 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
	)

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

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

static THREAD_LOCAL basic::Tracer protocols::hybridization::fragbias_tr ( "protocols.hybridization.FragmentBiasAssigner"  )

static

Referenced by protocols::hybridization::FragmentBiasAssigner::assign_fragprobs(), protocols::hybridization::FragmentBiasAssigner::assign_prob_with_rsd_wdw(), protocols::hybridization::FragmentBiasAssigner::automode(), protocols::hybridization::FragmentBiasAssigner::bfactors(), protocols::hybridization::FragmentBiasAssigner::cal_perrsd_score(), protocols::hybridization::FragmentBiasAssigner::chainbreak(), protocols::hybridization::FragmentBiasAssigner::compute_frag_bias(), protocols::hybridization::FragmentBiasAssigner::density(), protocols::hybridization::FragmentBiasAssigner::density_nbr(), protocols::hybridization::FragmentBiasAssigner::fragbias_reporter(), protocols::hybridization::FragmentBiasAssigner::geometry(), protocols::hybridization::FragmentBiasAssigner::init(), protocols::hybridization::FragmentBiasAssigner::old_rama(), protocols::hybridization::FragmentBiasAssigner::rama(), protocols::hybridization::FragmentBiasAssigner::uniform(), and protocols::hybridization::FragmentBiasAssigner::user().

core::Real protocols::hybridization::gap_distance

(

Size

Seq_gap

)

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
	)

References core::pose::Pose::add_constraint(), core::pose::Pose::conformation(), get_num_residues_nonvirt(), core::pose::symmetry::is_symmetric(), core::pose::Pose::remove_constraints(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), 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
	)

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
	)

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::BackboneTorsionSampler::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::hybridization::HybridizeProtocol::apply(), and protocols::hybridization::FoldTreeHybridize::apply().

core::Size protocols::hybridization::get_num_residues_nonvirt

(

core::pose::Pose const &

pose

)

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

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::hybridization::CartesianSampler::apply_constraints(), create_fragment_set(), create_fragment_set_no_ssbias(), generate_centroid_constraints(), protocols::hybridization::FoldTreeHybridize::get_residue_weights(), protocols::hybridization::HybridizeProtocol::parse_my_tag(), protocols::rbsegment_relax::SequenceShiftMover::SequenceShiftMover(), and protocols::hybridization::FoldTreeHybridize::setup_foldtree().

core::Size protocols::hybridization::get_num_residues_prot

(

core::pose::Pose const &

pose

)

References 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().

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
	)

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
	)

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::optimize	(	core::pose::Pose &	pose,
		Size	rsd1,
		Size	rsd2,
		core::scoring::ScoreFunctionOP	scorefxn,
		Size	ncycles,
		core::Real	max_delta_torsion
	)

References core::pose::Pose::phi(), core::pose::Pose::psi(), core::scoring::rg, core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by protocols::hybridization::BackboneTorsionPerturbation::perturb().

core::Size protocols::hybridization::parse_res	(	core::pose::Pose const &	pose,
		std::string	resnum
	)

References core::pose::Pose::pdb_info().

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

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
	)

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
	)

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

void protocols::hybridization::pick_pivots	(	core::pose::Pose &	pose,
		Size &	rsd1,
		Size &	torsion1,
		Size &	rsd2,
		Size &	torsion2,
		Size	variance = 5
	)

References core::scoring::rg, core::pose::Pose::total_residue(), and TR().

Referenced by protocols::hybridization::BackboneTorsionPerturbation::perturb().

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

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
	)

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

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings().

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
	)

References core::pose::Pose::constraint_set(), and generate_centroid_constraints().

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
	)

References add_constraints(), protocols::moves::ConstraintGenerator::apply(), core::pose::Pose::constraint_set(), generate_centroid_constraints(), and generate_fullatom_constraints().

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

void protocols::hybridization::setup_user_coordinate_constraints	(	core::pose::Pose &	pose,
		utility::vector1< core::Size >	reses_to_cst
	)

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

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

void protocols::hybridization::setup_user_coordinate_constraints	(	core::pose::Pose &	pose,
		utility::vector1< Size >	reses
	)

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

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

References protocols::hybridization::TMalign::alignment2AtomMap(), protocols::hybridization::TMalign::alignment2strings(), protocols::hybridization::TMalign::apply(), core::id::BOGUS_ATOM_ID, core::chemical::element::F, 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 THREAD_LOCAL basic::Tracer protocols::hybridization::TR ( "protocols.electron_density.util"  )

static

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

static

Referenced by add_constraints(), protocols::hybridization::HybridizeProtocol::add_fragment_csts(), 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::CartesianSampler::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::ChunkTrialMover::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::hybridization::FoldTreeHybridize::auto_frag_insertion_weight(), protocols::hybridization::CartesianHybridize::CartesianHybridize(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), create_fragment_set_no_ssbias(), protocols::hybridization::HybridizeFoldtreeDynamic::decide_cuts(), protocols::hybridization::HybridizeProtocol::domain_parse_templates(), downstream_residues_from_jump(), protocols::hybridization::FoldTreeHybridize::filter_templates(), protocols::hybridization::ChunkTrialMover::get_alignment_from_template(), protocols::hybridization::HybridizeProtocol::init(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::hybridization::hConvergenceCheck::operator()(), protocols::hybridization::CartesianSampler::parse_my_tag(), protocols::hybridization::HybridizeProtocol::parse_my_tag(), pick_pivots(), protocols::hybridization::DomainAssembly::run(), protocols::hybridization::InsertChunkMover::set_aligned_chunk(), 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(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), and protocols::hybridization::HybridizeProtocol::validate_template().

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

static

static THREAD_LOCAL 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
	)

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

double protocols::hybridization::d0

Referenced by core::scoring::TMscoreStore::add_residue_dis(), core::scoring::packstat::cavity_distance_constraint(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::scoring::magnesium::get_gaussian_deriv(), core::scoring::magnesium::get_gaussian_score(), core::scoring::methods::IdealParametersDatabase::lookup_length(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), and protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths().

double protocols::hybridization::D0_MIN

double protocols::hybridization::d0_out_

double protocols::hybridization::d0_search

double protocols::hybridization::d0A

double protocols::hybridization::d0B

double protocols::hybridization::dcu0

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

double protocols::hybridization::Lnorm

std::vector< int > protocols::hybridization::m1_

std::vector< int > protocols::hybridization::m2_

int protocols::hybridization::minlen

Referenced by core::scoring::motif::HACK_dump_helices().

int protocols::hybridization::n_ali8_

std::vector< std::vector < bool > > protocols::hybridization::path

Referenced by protocols::antibody::ModelCDRH3::apply(), protocols::jobdist::AtomTreeDiffJobDistributor::AtomTreeDiffJobDistributor(), protocols::jd2::AtomTreeDiffJobOutputter::AtomTreeDiffJobOutputter(), protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_init_pose(), core::chemical::ChemicalManager::create_residue_type_set(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), protocols::jd2::FileSystemJobDistributor::FileSystemJobDistributor(), core::io::NomenclatureManager::find_alternate_codes_file(), protocols::abinitio::AbrelaxApplication::fold(), protocols::antibody::constraints::CDRDihedralConstraintMover::get_harmonic_cluster_constraint_filename(), protocols::antibody::constraints::CDRDihedralConstraintMover::get_number_of_struct_used_for_csts(), protocols::jobdist::PlainPdbJobDistributor::get_output_filename(), protocols::jobdist::PlainRawJobDistributor::get_output_filename(), core::init::init_paths(), protocols::farna::options::RNA_FragmentMonteCarloOptions::initialize_from_command_line(), protocols::canonical_sampling::jobname_dirhash(), protocols::features::DatabaseJobOutputter::load_options_from_option_system(), protocols::optimize_weights::IterativeOptEDriver::load_pose(), core::init::locate_rosetta_database(), core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_path(), protocols::membrane::MPMutateRelaxMover::output_filename(), protocols::sewing::AssemblyMover::output_stats(), protocols::antibody::CDRSetOptionsParser::parse_default_and_user_options(), protocols::antibody::design::CDRSeqDesignOptionsParser::parse_default_and_user_options(), protocols::antibody::design::CDRGraftDesignOptionsParser::parse_default_and_user_options(), protocols::antibody::CDRSetOptionsParser::parse_options(), protocols::antibody::design::CDRSeqDesignOptionsParser::parse_options(), protocols::antibody::design::CDRGraftDesignOptionsParser::parse_options(), core::chemical::patch_operation_from_patch_file_line(), protocols::jd2::PDBJobOutputter::PDBJobOutputter(), core::chemical::rotamers::PeptoidRotamerLibrarySpecification::peptoid_rotlib_path(), core::scoring::cryst::PhenixInterface::PhenixInterface(), protocols::jobdist::PlainPdbJobDistributor::PlainPdbJobDistributor(), protocols::jobdist::PlainRawJobDistributor::PlainRawJobDistributor(), core::chemical::read_topology_file(), protocols::canonical_sampling::CanonicalSamplingMover::register_options(), protocols::features::DatabaseJobOutputter::register_options(), protocols::analysis::PeptideDeriverFilter::report(), core::scoring::rna::RNA_SuitePotential::RNA_SuitePotential(), protocols::toolbox::KClusterData::save_cluster_tree(), protocols::jd2::FileJobOutputter::set_defaults(), protocols::jd2::SilentFileJobOutputter::set_defaults(), protocols::match::MatcherTask::set_upstream_pose(), and core::chemical::carbohydrates::CarbohydrateInfoManager::short_name_to_iupac_strings_map().

std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::r1

Referenced by protocols::fldsgn::topology::StrandPairing::add_pair(), core::select::residue_selector::NeighborhoodResidueSelector::apply(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), protocols::fldsgn::topology::HelixPairing::calc_geometry(), protocols::sparta::PDB::calc_HN_S2(), protocols::sparta::PDB::calcSurface(), protocols::simple_moves::BBConRotMover::closure(), protocols::sparta::PDB::collect_HN_S2_and_EF(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::pack::rotamers::SingleResiduePeptoidLibraryCreator::create(), core::pack::create_minimization_graph(), core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib(), core::pack::dunbrack::RotamerLibrary::create_semi_rotameric_dunlib(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), protocols::fldsgn::topology::StrandPairing::elongate(), core::scoring::GenBornPotential::eval_atom_derivative(), protocols::sparta::Sparta::SpartaLib::get_ANN_data(), protocols::kinematic_closure::ClosureSolution::get_jacobian(), core::scoring::GenBornPotential::get_res_res_elecE(), protocols::sparta::PDB::getOrbitalShift(), protocols::sparta::Sparta::SpartaLib::getResInfo(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_backbone_backbone(), protocols::sparta::PDB::loadPDB(), protocols::simple_moves::BBConRotMover::make_move(), protocols::helical_bundle::FitSimpleHelixMultiFunc::operator()(), core::scoring::packstat::Circle::overlap(), core::scoring::packstat::overlap(), protocols::motifs::MotifSearch::override_option_input(), protocols::motifs::LigandMotifSearch::override_option_input(), protocols::sparta::PDB::PDB(), protocols::frag_picker::FragmentCandidate::print_fragment_seq(), protocols::simple_filters::res_rmsd(), protocols::protein_interface_design::filters::res_rmsd(), protocols::motifs::MotifSearch::reset_option_input(), protocols::motifs::LigandMotifSearch::reset_option_input(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), protocols::farna::movers::RNA_LoopCloser::rna_ccd_close(), core::pack::RTMin::rtmin(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), protocols::fldsgn::potentials::sspot::spherical(), core::scoring::SecondaryStructurePotential::spherical(), and protocols::canonical_sampling::SimulatedTempering::temperature_move().

std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::r2

Referenced by protocols::fldsgn::topology::StrandPairing::add_pair(), core::select::residue_selector::NeighborhoodResidueSelector::apply(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), protocols::fldsgn::topology::HelixPairing::calc_geometry(), protocols::normalmode::NormalMode::calc_inertia_tensor(), protocols::denovo_design::components::StructureData::check_residues(), core::scoring::sc::MolecularSurfaceCalculator::CheckProbeCollision(), protocols::simple_moves::BBConRotMover::closure(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::pack::rotamers::SingleResiduePeptoidLibraryCreator::create(), core::pack::create_minimization_graph(), core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib(), protocols::denovo_design::components::StructureData::delete_segment(), protocols::denovo_design::components::StructureData::delete_segment_nopose(), protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1::dfunc(), protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3::dfunc(), protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4::dfunc(), protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2::dfunc(), protocols::scoring::methods::pcs::TensorsOptimizer::dfunc(), protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerSvd::dfunc_exact(), protocols::fldsgn::topology::StrandPairing::elongate(), core::scoring::GenBornPotential::eval_atom_derivative(), protocols::scoring::methods::pcsTs2::fill_A_line(), protocols::scoring::methods::pcsTs1::fill_A_line(), protocols::scoring::methods::pcsTs3::fill_A_line(), protocols::scoring::methods::pcsTs4::fill_A_line(), protocols::scoring::methods::pcs::fill_A_line(), protocols::scoring::methods::pcs2::fill_A_line_fast(), protocols::scoring::methods::pcs2::fill_A_line_slow(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::frdc(), core::scoring::frdcDa(), core::scoring::frdcDaR(), core::scoring::frdcR(), protocols::kinematic_closure::ClosureSolution::get_jacobian(), core::scoring::GenBornPotential::get_res_res_elecE(), core::scoring::rna::StackElecEnergy::get_stack_elec_deriv(), protocols::sparta::PDB::getOrbitalShift(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_backbone_backbone(), protocols::simple_moves::BBConRotMover::make_move(), protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2::next_center(), protocols::scoring::methods::pcs::GridSearchIterator::next_center(), protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1::next_center(), protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4::next_center(), protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3::next_center(), core::scoring::packstat::overlap(), protocols::motifs::MotifSearch::override_option_input(), protocols::motifs::LigandMotifSearch::override_option_input(), protocols::denovo_design::components::StructureData::rename_segment(), protocols::simple_filters::res_rmsd(), protocols::protein_interface_design::filters::res_rmsd(), protocols::motifs::MotifSearch::reset_option_input(), protocols::motifs::LigandMotifSearch::reset_option_input(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), protocols::farna::movers::RNA_LoopCloser::rna_ccd_close(), core::pack::RTMin::rtmin(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), and core::scoring::sc::ShapeComplementarityCalculator::TrimPeripheralBandCheckDot().

std::vector< std::vector < double > > protocols::hybridization::score

Referenced by protocols::abinitio::Templates::_get_scored_list(), protocols::loops::addScoresForLoopParts(), protocols::qsar::scoring_grid::GridManager::append_cached_scores(), protocols::simple_filters::PredictedBurialEvaluator::apply(), protocols::qsar::qsarMover::apply(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::star::StarAbinitio::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::simple_filters::JScoreEvaluator::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::toolbox::task_operations::SelectByDensityFitOperation::apply(), protocols::medal::MedalMover::apply(), protocols::cluster::GatherPosesMover::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::topology_broker::ConstraintEvaluatorWrapper::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::simple_filters::MotifScoreFilter::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::constraints_additional::ConstraintEvaluator::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::forge::remodel::RemodelAccumulator::apply(), protocols::relax::FastRelax::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), protocols::cluster::AssignToClustersMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::apply_solutions(), protocols::coarse_rna::CoarseRNA_LoopCloser::apply_solutions(), protocols::hybridization::FragmentBiasAssigner::automode(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::scoring::dna::DNA_BasePotential::base_score(), protocols::relax::FastRelax::batch_apply(), protocols::protein_interface_design::best_bbcst_residues(), protocols::boinc::boincOutputFilter(), protocols::sewing::MonteCarloAssemblyMover::boltzman(), protocols::canonical_sampling::BiasedMonteCarlo::boltzmann(), protocols::moves::MonteCarlo::boltzmann(), protocols::denovo_design::DisulfidizeMover::build_and_score_disulfide(), protocols::forge::remodel::build_and_score_disulfide(), protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors(), protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors_with_svd(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::calc_dipscore(), protocols::sparta::calc_per_residue_scores(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_cost_only_with_svd(), core::scoring::rna::data::RNA_ChemicalMappingEnergy::calculate_energy(), protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::dna::DnaInterfacePacker::calculate_specificity(), protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1::calculate_tensor_and_cost_with_svd(), protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2::calculate_tensor_and_cost_with_svd(), protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3::calculate_tensor_and_cost_with_svd(), protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4::calculate_tensor_and_cost_with_svd(), protocols::scoring::methods::pcs::PCS_data_per_lanthanides::calculate_tensor_and_cost_with_svd(), protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_tensor_and_cost_with_svd(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), protocols::relax::CentroidRelax::CentroidRelax(), protocols::antibody::design::AntibodyDesignMover::check_for_top_designs(), protocols::stepwise::modeler::check_scores_from_parts(), protocols::nonlocal::SmoothPolicy::choose(), protocols::frag_picker::scores::FragmentScoreManager::clean_up(), protocols::hotspot_hashing::HotspotStubSet::cluster(), protocols::toolbox::KCluster::cluster(), protocols::relax::FastRelax::cmd_accept_to_best(), core::scoring::dna::TorsionFourierComponent::compute(), protocols::simple_filters::MotifScoreFilter::compute(), core::scoring::func::SoedingFunc::compute_func(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::abinitio::PairingStatistics::compute_model_weights(), protocols::scoring::ResidualDipolarCouplingRigidSegments::compute_pairwise_score(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::scoring::ResidualDipolarCouplingRigidSegments::compute_total_score(), protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzSum(), protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzWeight(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::convert_silent_file_to_pose_data_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::sewing::RepeatAssemblyMover::dfs_cycle_finder(), protocols::electron_density::BfactorMultifunc::dfunc(), core::scoring::func::USOGFunc::dfunc(), protocols::optimize_weights::OptEMultifunc::dfunc(), protocols::frag_picker::scores::FragmentScoreManager::do_caching(), protocols::frag_picker::scores::ProfileScoreDistWeight::do_caching(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::do_some_clustering(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::do_some_clustering(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::do_some_clustering(), protocols::toolbox::sample_around::do_xy_scan(), protocols::electron_density::BfactorMultifunc::dump(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::methods::ChemicalShiftAnisotropyEnergy::eval_csa(), core::scoring::methods::DipolarCouplingEnergy::eval_dc(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::eval_dipolar(), protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments::eval_dipolar(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_dipolar(), core::scoring::methods::DNA_DihedralEnergy::eval_dof_derivative(), core::scoring::membrane::FaMPEnvEnergy::eval_fa_mbenv(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::elec::FA_GrpElecEnergy::eval_intrares_energy(), protocols::moves::MonteCarlo::eval_lowest_score_pose(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy_deriv(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::rna::data::RNA_DMS_Potential::evaluate(), protocols::pack_daemon::MultistateFitnessFunction::evaluate(), protocols::pack_daemon::DynamicAggregateFunction::evaluate(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), core::io::extract_scores(), protocols::hotspot_hashing::HotspotStubSet::fill(), protocols::jd2::AtomTreeDiffJobInputter::fill_jobs(), core::scoring::motif::ResPairMotif::filter(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::filter_score(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), core::scoring::methods::CenPairMotifEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation(), core::scoring::func::TopOutFunc::func(), core::scoring::func::SoedingFunc::func(), core::scoring::func::USOGFunc::func(), core::scoring::func::SOGFunc_Impl::func(), protocols::scoring::methods::pcs2::TensorsOptimizerSvd::func(), protocols::scoring::methods::pcs2::TensorsOptimizer::func(), core::scoring::func::MixtureFunc::func(), protocols::scoring::methods::pcs2::TensorsOptimizerFix::func(), core::scoring::disulfides::Cb_Distance_Func::func(), core::scoring::func::MixtureFunc::func_(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::sewing::EnumerateAssemblyMover::generate_assembly(), protocols::sewing::RepeatAssemblyMover::generate_assembly(), core::scoring::methods::GoapEnergy::get_angle_score(), protocols::frags::VallData::get_cheating_frags(), core::scoring::Ramachandran::get_custom_rama_table_filename(), core::scoring::rna::RNA_FullAtomStackingEnergy::get_fa_stack_score(), protocols::frags::RMSVallData::get_frags(), protocols::frags::VallData::get_frags(), core::scoring::magnesium::get_gaussian_score(), protocols::magnesium::MgWaterHydrogenPacker::get_heuristic_water_hydrogen_score(), protocols::magnesium::MgOrbitalFrameFinder::get_orbital_frame_score_upon_rotation(), protocols::trajectory::DbTrajectoryReader::get_pose(), core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential_RNA(), core::scoring::membrane::FaMPSolvEnergy::get_residue_pair_energy(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), protocols::magnesium::MgScanner::get_score(), core::scoring::rna::StackElecEnergy::get_stack_elec_score(), core::scoring::rna::data::RNA_DataBackboneEnergy::get_sugar_env_score(), core::scoring::cryst::PhenixInterface::getScore(), core::scoring::cryst::PhenixInterface::getScoreAndDerivs(), protocols::ligand_docking::grid_score(), core::scoring::lkball::lkbtrie::LKBTrieEvaluator::heavyatom_heavyatom_energy(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), protocols::match::output::BestMatchesCollection::index_for_new_match(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::canonical_sampling::HamiltonianExchange::initialize_from_file(), core::scoring::ResidualDipolarCoupling::iterate_tensor_weights(), protocols::simple_moves::GenericMonteCarloMover::last_accepted_score(), protocols::simple_moves::GenericMonteCarloMover::lowest_score(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::rotamer_recovery::RRProtocol::measure_rotamer_recovery(), protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_mode_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fullatom_mode_perturbation(), core::scoring::methods::DirectReadoutEnergy::my_residue_pair_energy(), protocols::canonical_sampling::TemperatureController::observe_after_metropolis(), protocols::pockets::PocketExemplarMultifunc::operator()(), core::optimization::AtomTreeMultifunc::operator()(), core::optimization::CartesianMultifunc::operator()(), protocols::pockets::FingerprintMultifunc::operator()(), protocols::normalmode::NormalModeMultifunc::operator()(), core::optimization::SingleResidueMultifunc::operator()(), core::optimization::symmetry::SymAtomTreeMultifunc::operator()(), protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1::operator()(), protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3::operator()(), protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2::operator()(), protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4::operator()(), protocols::scoring::methods::pcs::TensorsOptimizer::operator()(), protocols::optimize_weights::OptEMultifunc::operator()(), protocols::optimize_weights::WrapperOptEMultifunc::operator()(), core::sequence::operator<<(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), protocols::magnesium::MgWaterHydrogenPacker::pack_mg_water_hydrogens_in_pose(), protocols::mpi_refinement::Scheduler::pick_enrich_methods(), protocols::simple_moves::LookupResultPlus::print(), protocols::cluster::ClusterBase::print_summary(), core::scoring::func::SOGFunc_Impl::prob_sum_of_gaussians(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), protocols::match::output::MatchConsolidator::process_match(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_line(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_VECTOR_line(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::electron_density::RBfitResult::RBfitResult(), core::scoring::motif::XformScore::read_binary(), protocols::hotspot_hashing::HotspotStubSet::read_data(), core::fragment::ConstantLengthFragSet::read_fragment_stream(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), core::sequence::SequenceProfile::read_from_file(), core::sequence::read_general_aln(), core::sequence::read_grishin_aln_file(), core::pack::interaction_graph::SurfacePotential::read_hASA_score_database_file(), core::pack::interaction_graph::SurfacePotential::read_hpatch_score_database_file(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm(), protocols::anchored_design::AnchoredDesignMover::read_options(), core::scoring::P_AA::read_P_AA_pp(), core::scoring::carbon_hbonds::CarbonHBondPotential::read_potential(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::toolbox::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::electron_density::RefinementResult::RefinementResult(), protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group(), protocols::simple_filters::MotifScoreFilter::report(), protocols::simple_filters::MotifScoreFilter::report_sm(), protocols::hotspot_hashing::HotspotStubSet::rescore(), protocols::canonical_sampling::BiasedMonteCarlo::reset(), protocols::simple_moves::GenericMonteCarloMover::reset(), protocols::moves::MonteCarlo::reset(), core::scoring::methods::BurialEnergy::residue_energy(), core::scoring::methods::SymmetricLigandEnergy::residue_energy(), core::scoring::methods::DNA_DihedralEnergy::residue_energy(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::residue_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), core::scoring::rna::StackElecEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy(), core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::scoring::elec::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy_ext(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy_ext(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::fragment::CacheWrapper< protocols::simple_moves::GunnTuple, MapCacheUnit< protocols::simple_moves::GunnTuple > >::retrieve(), protocols::dna::DnaInterfacePacker::reversion_scan(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_axis_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_pair_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stagger_pairwise_pair_energy(), core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >::rotamer_energy_deriv(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::sparta::Sparta::run_A_ANN_Prediction(), protocols::toolbox::sample_around::sample_all_rotations_at_jump(), protocols::magnesium::MgOrbitalFrameFinder::sample_orbital_frame(), protocols::magnesium::MgScanner::scan_magnesiums(), core::scoring::ScoreFunction::score_by_scoretype(), protocols::frag_picker::scores::FragmentScoreManager::score_fragment(), protocols::frag_picker::scores::FragmentScoreManager::score_fragment_from_cache(), protocols::canonical_sampling::BiasedMonteCarlo::score_function(), protocols::medal::MedalMover::score_function(), core::io::pose_from_sfr::score_mapping(), core::fragment::CacheWrapper< protocols::simple_moves::GunnTuple, MapCacheUnit< protocols::simple_moves::GunnTuple > >::scored_frag_ids(), protocols::simple_moves::GenericMonteCarloMover::scoring(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_five_prime_phosphate(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_three_prime_phosphate(), protocols::multistate_design::SingleState::set_best_score(), protocols::relax::CentroidRelax::set_cartesian(), protocols::jd2::FileJobOutputter::set_defaults(), protocols::relax::CentroidRelax::set_fa_score_function(), protocols::moves::MonteCarlo::set_last_accepted_pose(), protocols::moves::MonteCarlo::set_last_accepted_score(), protocols::moves::MonteCarlo::set_lowest_score_pose(), protocols::relax::CentroidRelax::set_score_function(), core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), core::scoring::membrane::FaMPEnvSmoothEnergy::setup_for_derivatives(), protocols::star::setup_score(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), protocols::multistate_design::MultiStatePacker::single_state_design(), protocols::simple_moves::symmetry::SymmetrySlider::slide(), protocols::cryst::DockLatticeMover::slide_lattice(), protocols::toolbox::ClusterBase::sort_each_group_by_energy(), protocols::cluster::ClusterBase::sort_each_group_by_energy(), protocols::cluster::ClusterBase::sort_groups_by_energy(), core::scoring::motif::MotifHits::stat_motifs(), core::fragment::CacheWrapper< protocols::simple_moves::GunnTuple, MapCacheUnit< protocols::simple_moves::GunnTuple > >::store(), protocols::canonical_sampling::ParallelTempering::temperature_move(), protocols::abinitio::Templates::Templates(), protocols::ligand_docking::Translate::translate_ligand(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::trilinear_gradient(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::trilinear_interpolation(), protocols::stepwise::setup::StepWiseCSA_JobDistributor::update_bank(), core::io::silent::SilentStruct::update_score(), protocols::mpi_refinement::StructAvrgMover::weighted_average(), protocols::trajectory::DbTrajectoryWriter::write_cache_to_db(), protocols::canonical_sampling::DbTrajectoryRecorder::write_cache_to_db(), protocols::rotamer_recovery::RRReporterSQLite::write_rotamer_recovery_full_table_schema(), protocols::features::ResidueGridScoresFeatures::write_schema_to_db(), protocols::trajectory::DbTrajectoryWriter::write_schema_to_db(), protocols::features::TotalScoreFeatures::write_schema_to_db(), and protocols::canonical_sampling::DbTrajectoryRecorder::write_schema_to_db().

double protocols::hybridization::score_d8

std::vector< int > protocols::hybridization::secx

std::vector< int > protocols::hybridization::secy

std::string protocols::hybridization::seqx

std::string protocols::hybridization::seqy

numeric::xyzVector<core::Real> protocols::hybridization::t

Referenced by protocols::frag_picker::quota::ABEGO_SS_Config::ABEGO_SS_Config(), protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::protein_interface_design::movers::PatchdockTransform::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::matdes::SymDofMover::apply(), protocols::simple_moves::MinMover::apply_dof_tasks_to_movemap(), protocols::loophash::LoopHashLibrary::apply_random(), core::scoring::ScoreFunctionFactory::apply_user_defined_reweighting_(), protocols::cartesian::MolecularDynamics::applyForces_BeeMan(), protocols::cartesian::MolecularDynamics::applyForces_LangevinIntegration(), core::pose::PDBInfo::bfactor(), protocols::frag_picker::scores::GunnCostScore::cached_score(), protocols::simple_filters::RepeatParameterFilter::calculate_helical_parameters_helper(), core::scoring::ScoreFunction::check_methods(), protocols::denovo_design::components::FoldGraph::compute_best_solution(), core::scoring::packstat::Slice::compute_surface(), protocols::features::LoopAnchorFeatures::compute_transform_and_write_to_db(), protocols::denovo_design::components::StructureData::create_from_xml(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), protocols::moves::PyMolMover::energy_type(), core::io::HeaderInformation::experimental_technique_to_string(), protocols::loophash::LoopHashLibrary::extract_data_from_pose(), core::io::HeaderInformation::fill_compound_records(), core::scoring::packstat::LeeRichards::find_first_slice(), core::kinematics::find_stub_transform(), protocols::simple_moves::rational_mc::RationalMonteCarlo::fire_all_triggers(), protocols::simple_moves::GenericMonteCarloMover::fire_all_triggers(), protocols::sic_dock::flood_fill3D(), protocols::helical_bundle::generate_atom_positions(), core::kinematics::MoveMap::get(), protocols::loophash::LoopHashLibrary::get_all(), protocols::forge::remodel::RemodelGlobalFrame::get_helical_params(), core::scoring::packstat::old::get_orientation(), protocols::jumping::PairingLibrary::get_random_beta_sheet_jump(), protocols::jumping::PairingLibrary::get_random_tmh_jump(), core::scoring::ScoreFunction::get_weight(), protocols::frags::has_element(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::HPool_RMSD(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), core::kinematics::AtomTree::insert_single_fragment(), core::io::HeaderInformation::is_experimental_technique(), protocols::moves::PyMolMover::is_it_time(), protocols::evaluation::PCA::jacobi(), protocols::toolbox::jacobi(), core::scoring::jacobi(), core::scoring::jacobi3(), protocols::multistate_design::list_amino_acid_options(), protocols::antibody::AntibodyDatabaseManager::load_cdr_poses(), protocols::features::PoseConformationFeatures::load_fold_tree(), protocols::features::PoseConformationFeatures::load_jumps(), protocols::loophash::MPI_LoopHashRefine_Master::load_sample_weight(), protocols::mpi_refinement::MPI_Refine_Master::load_sample_weight(), core::optimization::GA_Minimizer::loop(), protocols::helical_bundle::FitSimpleHelixMultiFunc::operator()(), core::kinematics::operator>>(), core::scoring::ScoreFunction::operator[](), core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log(), protocols::residue_selectors::TaskSelector::parse_my_tag(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::parse_my_tag(), core::io::external::PsiPredInterface::parse_psipred_horiz_output(), protocols::electron_density::DockIntoDensityMover::poseSphericalSamples(), core::optimization::GA_Minimizer::randomize(), protocols::frag_picker::CSTalosIO::read(), protocols::frag_picker::PhiPsiTalosIO::read(), core::fragment::BBTorsionSRFD::read_data(), protocols::loophash::LoopHashMap::read_db(), core::chemical::Metapatch::read_file(), core::chemical::Patch::read_file(), core::fragment::MinimalFragSet::read_fragment_file(), protocols::jumping::DisulfPairingLibrary::read_from_file(), protocols::jumping::PairingLibrary::read_from_file(), protocols::jumping::PairingLibrary::read_from_file_no_filters(), protocols::protein_interface_design::PatchdockReader::read_patchdock_entry(), protocols::protein_interface_design::PatchdockReader::read_poses(), protocols::jd2::JD2ResourceManager::read_resource_options_table_tag(), core::scoring::motif::real6_to_rt(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), core::chemical::retype_is_aromatic(), core::chemical::rosetta_retype_fullatom(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::round(), core::io::external::PsiPredInterface::run_psipred(), core::scoring::ScoreFunction::score_by_scoretype(), core::scoring::ScoreFunction::score_types_by_method_type(), core::kinematics::MoveMap::set(), protocols::pockets::SmallMol::set_size(), protocols::toolbox::KMedoid::set_threshold(), protocols::jumping::PairingLibrary::set_tmh_jump(), core::kinematics::RT::set_translation(), core::scoring::ScoreFunction::set_weight(), protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_jump(), protocols::sic_dock::SICFast::slide_into_contact(), protocols::cartesian::sqr(), core::sequence::SequenceCoupling::temp(), protocols::protein_interface_design::filters::BoltzmannFilter::temperature(), core::pose::PDBInfo::temperature(), protocols::loophash::LoopHashLibrary::test_loop_sample(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::test_round(), protocols::loophash::LoopHashLibrary::test_saving_library(), protocols::simple_filters::RelativePoseFilter::thread(), protocols::simple_filters::MultipleSigmoids::threshold(), protocols::simple_filters::Operator::threshold(), protocols::protein_interface_design::filters::AverageDegreeFilter::threshold(), protocols::simple_filters::Sigmoid::threshold(), protocols::protein_interface_design::filters::BindingStrainFilter::threshold(), protocols::matdes::ClashCheckFilter::threshold(), protocols::simple_filters::TaskAwareSASAFilter::threshold(), protocols::matdes::OligomericAverageDegreeFilter::threshold(), protocols::protein_interface_design::PatchdockReader::to_entry(), protocols::protein_interface_design::filters::Torsion::torsion(), protocols::protein_interface_design::filters::BoltzmannFilter::triage_threshold(), protocols::protein_interface_design::movers::SetAtomTree::two_parts_chain1(), protocols::moves::PyMolMover::update_interval(), protocols::frag_picker::VallProvider::vallChunksFromLibrary(), core::scoring::vector1_remove(), and protocols::features::HBondFeatures::write_hbond_chem_types_table_schema().

numeric::xyzMatrix<core::Real> protocols::hybridization::u

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::frag_picker::CS2ndShift::also_check_fix_disulf(), protocols::evaluation::PCA::calc_fit_R(), protocols::toolbox::calc_fit_R(), protocols::sic_dock::Rose::clashes_naive(), protocols::sic_dock::Rose::contacts_naive(), protocols::pockets::dD_dv1(), protocols::pockets::dD_dv2(), protocols::pockets::dD_dv3(), core::scoring::dna::find_basepairs(), protocols::forge::build::BuildManager::find_instruction(), protocols::pockets::SmallMol::findRoot(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz(), core::scoring::motif::MotifHashManager::init(), core::chemical::RerootRestypeVisitor::initialize_vertex(), protocols::denovo_design::components::StructureData::insert_after_residue_in_pose(), protocols::frag_picker::scores::MakeDisulfideDistance::make(), protocols::moves::ResId::modifiable(), core::io::raw_data::DisulfideFile::parse_disulf_file(), protocols::simple_filters::DeltaFilter::relax_unbound(), core::scoring::MembranePotential::rigid_perturb_vector(), core::scoring::MembranePotential::rot_perturb_vector(), core::scoring::MembranePotential::search_memb_normal(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::svbksb(), protocols::simple_filters::DeltaFilter::unbound(), protocols::simple_filters::RotamerBoltzmannWeight::unbound(), protocols::protein_interface_design::filters::FilterScanFilter::unbound(), protocols::protein_interface_design::filters::Torsion::upper(), protocols::simple_filters::DeltaFilter::upper(), protocols::protein_interface_design::filters::DesignableResiduesFilter::upper_threshold(), and protocols::matdes::InterfacePackingFilter::upper_threshold().

std::vector< std::vector < double > > protocols::hybridization::val

Referenced by core::optimization::SimpleDerivCheckResult::abs_deriv_dev(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::add(), core::pose::add_comment(), core::pose::add_score_line_string(), protocols::generalized_kinematic_closure::GeneralizedKIC::add_value_to_perturber_value_list(), protocols::simple_filters::PoseComment::apply(), protocols::simple_filters::Operator::apply(), protocols::simple_filters::MultipleSigmoids::apply(), protocols::simple_filters::Sigmoid::apply(), protocols::simple_filters::ScoreEvaluator::apply(), protocols::constraints_additional::CombinedConstraintEvaluator::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::simple_moves::TaskAwareMinMover::bb(), core::optimization::SimpleDerivCheckResult::best_abs_log_norm_ratio(), core::optimization::SimpleDerivCheckResult::best_cos_theta(), core::optimization::SimpleDerivCheckResult::best_norm_analytic(), core::optimization::SimpleDerivCheckResult::best_norm_numeric(), protocols::frag_picker::VallResidue::bF(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::blanket_set(), protocols::denovo_design::components::StructureData::cached_remarks(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::calc_orderparam(), protocols::frag_picker::VallResidue::cbx(), protocols::frag_picker::VallResidue::cby(), protocols::frag_picker::VallResidue::cbz(), protocols::frag_picker::VallResidue::cenx(), protocols::frag_picker::VallResidue::ceny(), protocols::frag_picker::VallResidue::cenz(), protocols::simple_moves::TaskAwareMinMover::chi(), core::scoring::func::CircularGeneral1D_Func::CircularGeneral1D_Func(), protocols::dna::DnaNeighbor::close(), core::io::silent::SilentStruct::comment_from_line(), core::chemical::gasteiger::compact_enum_set(), protocols::simple_filters::PoseComment::compute(), protocols::simple_filters::Operator::compute(), protocols::simple_filters::MultipleSigmoids::compute(), protocols::simple_filters::Sigmoid::compute(), protocols::simple_filters::DdgFilter::compute(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), core::scoring::packing::compute_holes_surfs(), protocols::dna::DnaNeighbor::contact(), protocols::helical_bundle::MakeBundle::convert_angle(), protocols::helical_bundle::PerturbBundle::convert_angle(), protocols::ligand_docking::count_buried_unsat_Hbonds(), protocols::toolbox::match_enzdes_util::GeomSampleInfo::create_sample_vector(), protocols::relax::FastRelax::dualspace(), core::import_pose::atom_tree_diffs::dump_score_line(), protocols::design_opt::PointMutationCalculator::eval_filters(), protocols::matdes::MatDesPointMutationCalculator::eval_filters(), protocols::denovo_design::extract_int(), core::pose::metrics::StructureDependentCalculator::get(), core::pose::metrics::EnergyDependentCalculator::get(), core::scoring::dna::get_mean_median_and_sdev(), core::io::silent::SilentStruct::get_parent_remark_from_line(), core::scoring::fiber_diffraction::gnl_R_qfht(), protocols::ligand_docking::grid_score_atr_rep(), core::scoring::hbonds::HBondOptions::hb_env_dep_new_high_nneigh(), core::scoring::hbonds::HBondOptions::hb_env_dep_new_low_nneigh(), core::scoring::hbonds::HBondOptions::hb_env_dep_new_low_scale(), protocols::frags::heap_insert(), protocols::frags::heap_replace(), protocols::match::Matcher::increment_upstream_only_hit_combination(), core::scoring::SigmoidWeightedCenList< T >::initialize(), protocols::comparative_modeling::LoopRelaxMover::intermedrelax(), core::optimization::MinimizerOptions::linmin_deriv_cutoff(), protocols::denovo_design::components::StructureData::load_pdb_info_old(), protocols::forge::remodel::RemodelLoopMover::max_linear_chainbreak(), protocols::frag_picker::VallResidue::nali(), core::scoring::EMapVector::norm_squared(), core::fragment::picking_old::vall::VallResidue::omega(), protocols::frag_picker::VallResidue::omega(), protocols::pack_daemon::InSetExpression::operator()(), core::chemical::gasteiger::parse_enum_set(), protocols::helical_bundle::BackboneGridSampler::parse_my_tag(), protocols::helical_bundle::PerturbBundle::parse_my_tag(), protocols::helical_bundle::BundleGridSampler::parse_my_tag(), core::fragment::picking_old::vall::VallResidue::phi(), protocols::frag_picker::VallResidue::phi(), protocols::optimize_weights::IterativeOptEDriver::print_energies(), core::fragment::picking_old::vall::VallResidue::psi(), protocols::frag_picker::VallResidue::psi(), protocols::toolbox::pose_metric_calculators::FragQualCalculator::ratio_cutoff(), protocols::frag_picker::JCouplingIO::read(), core::scoring::methods::NMerSVMEnergy::read_aa_encoding_matrix(), protocols::noesy_assign::PeakFileFormat::read_assignments(), protocols::jd2::JD2ResourceManagerJobInputter::read_BooleanOption_subtag_for_job(), core::scoring::SplitUnfoldedTwoBodyPotential::read_database_file(), core::scoring::UnfoldedStatePotential::read_database_file(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), protocols::optimize_weights::PNatAAOptEPositionData::read_from_file(), protocols::noesy_assign::PeakFileFormat::read_header(), protocols::jd2::JD2ResourceManagerJobInputter::read_IntegerOption_subtag_for_job(), protocols::jd2::JD2ResourceManagerJobInputter::read_Option_subtag_for_job(), protocols::jd2::JD2ResourceManagerJobInputter::read_RealOption_subtag_for_job(), protocols::noesy_assign::PeakFileFormat::read_resonances(), protocols::noesy_assign::PeakFileFormat::read_strength(), protocols::comparative_modeling::LoopRelaxMover::refine(), core::optimization::SimpleDerivCheckResult::rel_deriv_dev(), protocols::comparative_modeling::LoopRelaxMover::relax(), protocols::comparative_modeling::LoopRelaxMover::remodel(), protocols::simple_filters::PoseComment::report(), protocols::simple_filters::Operator::report(), protocols::simple_filters::MultipleSigmoids::report(), protocols::simple_filters::Sigmoid::report(), protocols::simple_filters::Operator::report_sm(), core::fragment::CacheWrapper< protocols::simple_moves::GunnTuple, MapCacheUnit< protocols::simple_moves::GunnTuple > >::retrieve(), protocols::toolbox::pose_metric_calculators::FragQualCalculator::rmsd_cutoff(), core::scoring::SecondaryStructurePotential::rsigma_dot_initializer(), protocols::frag_picker::VallResidue::sa(), core::chemical::gasteiger::safe_read(), core::chemical::gasteiger::safe_write(), protocols::frag_picker::scores::JCoupling::score(), protocols::sic_dock::XfoxmScore::score(), protocols::frag_picker::DiversifyCrmsdByClustering::select_fragments(), core::scoring::EMapVector::set(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< core::PackerEnergy >::set(), protocols::helical_bundle::parameters::BundleParameters::set_allow_bondangles(), protocols::helical_bundle::parameters::BundleParameters::set_allow_bondlengths(), protocols::helical_bundle::parameters::BundleParameters::set_allow_dihedrals(), core::select::util::SelectResiduesByLayer::set_angle_exponent(), core::select::util::SelectResiduesByLayer::set_angle_shift_factor(), protocols::protein_interface_design::filters::HbondsToResidueFilter::set_backbone(), protocols::protein_interface_design::filters::HbondsToResidueFilter::set_bb_bb(), core::pack::interaction_graph::SimpleEdge::set_bb_bbE(), protocols::helical_bundle::parameters::BundleParametersSet::set_bundle_symmetry(), protocols::helical_bundle::parameters::BundleParametersSet::set_bundle_symmetry_copies(), protocols::helical_bundle::PerturbBundle::set_bundleparametersset_index(), core::select::residue_selector::LayerSelector::set_cache_selection(), protocols::denovo_design::connection::Connection::set_check_abego(), protocols::denovo_design::connection::Connection::set_connecting_bond_dist(), protocols::denovo_design::components::StructureData::set_data_int(), protocols::denovo_design::components::StructureData::set_data_real(), protocols::denovo_design::components::StructureData::set_data_str(), protocols::helical_bundle::MakeBundle::set_default_allow_bondangles(), protocols::helical_bundle::MakeBundle::set_default_allow_bondlengths(), protocols::helical_bundle::MakeBundle::set_default_allow_dihedrals(), protocols::helical_bundle::MakeBundle::set_default_delta_t(), protocols::helical_bundle::MakeBundle::set_default_helix_length(), protocols::helical_bundle::MakeBundle::set_default_invert(), protocols::helical_bundle::MakeBundle::set_default_r0(), protocols::helical_bundle::PerturbBundleOptions::set_default_value(), protocols::helical_bundle::MakeBundle::set_default_z0_offset(), protocols::helical_bundle::MakeBundle::set_default_z1(), protocols::helical_bundle::MakeBundle::set_default_z1_offset(), protocols::helical_bundle::parameters::BundleParameters::set_delta_omega0(), protocols::helical_bundle::parameters::BundleParameters::set_delta_omega1_all(), protocols::helical_bundle::parameters::BundleParameters::set_delta_t(), core::optimization::BrentLineMinimization::set_deriv_cutoff(), protocols::cryst::DockLatticeMover::set_design(), core::select::util::SelectResiduesByLayer::set_dist_exponent(), core::select::util::SelectResiduesByLayer::set_dist_midpoint(), protocols::denovo_design::connection::Connection::set_do_remodel(), protocols::relax::FastRelax::set_enable_design(), protocols::protein_interface_design::filters::HbondsToResidueFilter::set_energy_cutoff(), protocols::LoopRebuild::set_extended_loop(), protocols::genetic_algorithm::Entity::set_fitness(), protocols::jd2::JobsContainer::set_force_job_purging(), protocols::relax::FastRelax::set_force_nonideal(), protocols::protein_interface_design::filters::HbondsToResidueFilter::set_from_other_chains(), protocols::protein_interface_design::filters::HbondsToResidueFilter::set_from_same_chain(), protocols::cryst::DockLatticeMover::set_fullatom(), protocols::helical_bundle::PerturbBundleOptions::set_helix_index(), protocols::denovo_design::connection::Connection::set_idealized_abego(), protocols::flxbb::LayerDesignOperation::set_ignore_pikaa_natro(), protocols::helical_bundle::parameters::BundleParameters::set_invert_helix(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_iterations(), protocols::helical_bundle::MakeBundleHelix::set_last_apply_failed(), protocols::helical_bundle::MakeBundle::set_last_apply_failed(), protocols::make_rot_lib::RotData::set_lib_chi_val(), protocols::helical_bundle::PerturbBundleOptions::set_lower_value(), core::scoring::bin_transitions::BinTransitionData::set_matrix_entry(), core::scoring::Energies::set_max_context_neighbor_cutoff(), protocols::helical_bundle::BackboneGridSampler::set_max_samples(), protocols::helical_bundle::BundleGridSampler::set_max_samples(), protocols::cyclic_peptide::TryDisulfPermutations::set_mintolerance(), core::conformation::symmetry::VirtualCoordinate::set_mirror_z(), core::conformation::symmetry::SymmetryTransform::set_mirror_z(), protocols::cryst::MakeLayerMover::set_moving_lattice(), protocols::simple_moves::bin_transitions::PerturbByBins::set_must_switch_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_must_switch_bins(), protocols::helical_bundle::parameters::BundleParametersSet::set_n_helices(), core::scoring::bin_transitions::BinTransitionData::set_n_mainchain_torsions_i(), core::scoring::bin_transitions::BinTransitionData::set_n_mainchain_torsions_iplus1(), protocols::helical_bundle::BackboneGridSampler::set_nstruct_mode(), protocols::helical_bundle::BundleGridSampler::set_nstruct_mode(), protocols::helical_bundle::BackboneGridSampler::set_nstruct_repeats(), protocols::helical_bundle::BundleGridSampler::set_nstruct_repeats(), protocols::helical_bundle::parameters::BundleParameters::set_omega0(), protocols::helical_bundle::parameters::BundleParameters::set_omega1(), protocols::protein_interface_design::filters::HbondsToResidueFilter::set_partners(), protocols::helical_bundle::BackboneGridSampler::set_pdb_output(), protocols::helical_bundle::BundleGridSampler::set_pdb_output(), protocols::noesy_assign::CrossPeak::set_peak_id(), protocols::helical_bundle::PerturbBundleOptions::set_perturbable(), protocols::helical_bundle::PerturbBundleOptions::set_perturbation_magnitude(), protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_iterations(), protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_must_switch_bins(), protocols::simple_moves::MutateResidue::set_preserve_atom_coords(), protocols::helical_bundle::parameters::BundleParameters::set_r0(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_rama_cutoff_energy(), protocols::cryst::MakeLatticeMover::set_refinable_lattice(), protocols::helical_bundle::parameters::BundleParameters::set_repeating_unit_offset(), protocols::helical_bundle::BundleReporterFilter::set_report_sequence(), protocols::helical_bundle::BundleGridSampler::set_reset_mode(), protocols::helical_bundle::parameters::BundleParameters::set_residues_per_repeat(), protocols::helical_bundle::BackboneGridSampler::set_residues_per_repeat(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_resnum(), protocols::protein_interface_design::filters::HbondsToResidueFilter::set_resnum(), core::select::util::SelectResiduesByLayer::set_rsd_neighbor_denominator(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_sampler_values(), protocols::helical_bundle::PerturbBundleOptions::set_samples(), protocols::helical_bundle::BundleReporterFilter::set_score_type_threshold(), protocols::helical_bundle::BackboneGridSampler::set_selection_low(), protocols::helical_bundle::BundleGridSampler::set_selection_low(), protocols::jd2::MPIWorkPoolJobDistributor::set_sequential_distribution(), protocols::protein_interface_design::filters::HbondsToResidueFilter::set_sidechain(), core::scoring::methods::ProClosureEnergy::set_skip_ring_closure(), protocols::jd2::MPIWorkPoolJobDistributor::set_starter_for_sequential_distribution(), core::scoring::dna::DNA_BasePotential::set_stiffness(), core::scoring::packing::PoseBalls::set_surf(), protocols::cryst::DockLatticeMover::set_temp(), core::io::ResidueInformation::set_temp(), protocols::canonical_sampling::BiasEnergy::set_temperature(), protocols::filters::CombinedFilter::set_threshold(), protocols::helical_bundle::PerturbBundleOptions::set_upper_value(), protocols::helical_bundle::PerturbBundleOptions::set_use_defaults(), protocols::helical_bundle::PerturbBundle::set_use_degrees(), protocols::helical_bundle::MakeBundle::set_use_degrees(), protocols::flxbb::LayerDesignOperation::set_use_symmetry(), protocols::helical_bundle::BundleReporterFilter::set_use_threeletter(), core::scoring::methods::GoapRsdType::set_using(), protocols::noesy_assign::CrossPeak::set_volume(), protocols::helical_bundle::parameters::BundleParameters::set_z0_offset(), protocols::helical_bundle::parameters::BundleParameters::set_z1(), protocols::helical_bundle::parameters::BundleParameters::set_z1_offset(), protocols::electron_density::DockIntoDensityMover::setCenterOnMiddleCA(), core::scoring::EMapVector::show_if_nonzero_weight(), core::scoring::EMapVector::show_nonzero(), core::scoring::EMapVector::show_weighted(), protocols::simple_moves::symmetry::SetupForSymmetryMover::slide_into_contact(), protocols::match::Matcher::test_upstream_only_hit_incompatibility(), protocols::optimize_weights::IterativeOptEDriver::test_weight_sensitivity(), protocols::simple_filters::RelativePoseFilter::thread_seq(), protocols::loops::Loops::transfer_to_residue_vector(), core::scoring::hbonds::HBondOptions::use_hb_env_dep_new(), protocols::noesy_assign::PeakFileFormat_xpk::write_assignment(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), protocols::noesy_assign::PeakFileFormat::write_assignment(), protocols::noesy_assign::PeakFileFormat::write_assignment_stats(), protocols::noesy_assign::PeakFileFormat::write_assignments(), protocols::noesy_assign::PeakFileFormat::write_resonances(), core::fragment::picking_old::vall::VallResidue::x(), protocols::frag_picker::VallResidue::x(), core::fragment::picking_old::vall::VallResidue::y(), protocols::frag_picker::VallResidue::y(), core::fragment::picking_old::vall::VallResidue::z(), and protocols::frag_picker::VallResidue::z().

std::vector< numeric::xyzVector<core::Real> > protocols::hybridization::xa

int protocols::hybridization::xlen

std::vector< int > protocols::hybridization::xresno

std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::xt

std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::xtm

std::vector< numeric::xyzVector<core::Real> > protocols::hybridization::ya

int protocols::hybridization::ylen

std::vector< int > protocols::hybridization::yresno

std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::ytm