protocols::hybridization Namespace Reference

Classes
class	AllResiduesChanged
	(helper) functor class which keeps track of initial phi/psi values. @detail calls of operator ( pose ) compare the initial phi/psi values More...
class	BackboneTorsionPerturbation
class	BackboneTorsionPerturbationCreator
class	BackboneTorsionSampler
class	BackboneTorsionSamplerCreator
class	CartesianHybridize
class	CartesianSampler
class	ChunkTrialMover
class	DDomainParse
class	DomainAssembly
class	hConvergenceCheck
class	FoldTreeHybridize
class	FragmentBiasAssigner
class	HybridizeFoldtreeDynamic
struct	detailedControlsTagSetting
class	HybridizeProtocol
class	HybridizeProtocolCreator
class	CartesianSamplerCreator
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::shared_ptr< TemlateAssembly >	TemlateAssemblyOP
typedef utility::pointer::shared_ptr< TemlateAssembly const >	TemlateAssemblyCOP
using	hConvergenceCheckOP = utility::pointer::shared_ptr< hConvergenceCheck >
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 }
enum	sampleEnum { off = 0 , on , unset }

Functions
void	add_constraints (core::pose::Pose &pose, core::Size rsd1, core::Size rsd2)
void	optimize (core::pose::Pose &pose, core::Size rsd1, core::Size rsd2, core::scoring::ScoreFunctionOP scorefxn, core::Size ncycles, core::Real max_delta_torsion)
void	pick_pivots (core::pose::Pose &pose, core::Size &rsd1, core::Size &torsion1, core::Size &rsd2, core::Size &torsion2, core::Size variance=5)
static basic::Tracer	TR ("protocols.hybridization.CartesianHybridize")
static basic::Tracer	TR ("protocols.hybridization.CartesianSampler")
std::string	CartesianSampler_subelement_ct_name (std::string const &name)
bool	TMalign_poses (core::pose::Pose &aligned_pose, core::pose::Pose const &ref_pose, std::list< core::Size > const &residue_list, std::list< core::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< core::Size >	find_uncovered_residues (core::pose::Pose const &pose, utility::vector1< core::Size > const covered_residues)
core::Real	gap_distance (core::Size Seq_gap)
static basic::Tracer	fragbias_tr ("protocols.hybridization.FragmentBiasAssigner")
std::string	hybridize_subelement_ct_name (std::string const &name)
static basic::Tracer	TR ("protocols.electron_density.util")
core::Size	parse_res (core::pose::Pose const &pose, std::string resnum)
static 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 > const &templates, utility::vector1< core::Real > const &template_weights, std::string const &cen_cst_file, std::set< core::Size > const &ignore_res_for_AUTO)
void	setup_fullatom_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > const &templates, utility::vector1< core::Real > const &template_weights, std::string const &cen_cst_file, std::string const &fa_cst_file)
void	setup_constraints (core::pose::Pose &pose, std::string &cst_in)
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< core::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, core::Size const seqpos)
bool	discontinued_lower (core::pose::Pose const &pose, core::Size const seqpos)
std::list< core::Size >	downstream_residues_from_jump (core::pose::Pose const &pose, core::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< core::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< core::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)
core::fragment::FragSetOP	create_fragment_set_no_ssbias (std::string tgt_seq, 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)

Variables
const core::Size	DEFAULT_NCYCLES =400
core::Real	D0_MIN
core::Real	Lnorm
core::Real	score_d8
core::Real	d0
core::Real	d0_search
core::Real	dcu0
std::vector< std::vector< core::Real > >	score
std::vector< std::vector< bool > >	path
std::vector< std::vector< core::Real > >	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_
core::Real	d0_out_
core::Real	d0A
core::Real	d0B

Typedef Documentation

CartesianHybridizeCOP

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

CartesianHybridizeOP

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

CartesianSamplerCOP

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

CartesianSamplerOP

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

ChunkTrialMoverCOP

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

ChunkTrialMoverOP

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

FoldTreeHybridizeCOP

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

FoldTreeHybridizeOP

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

hConvergenceCheckOP

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

HybridizeFoldtreeMoverCOP

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

HybridizeFoldtreeMoverOP

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

HybridizeProtocolCOP

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

HybridizeProtocolOP

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

MRMoverOP

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

TemlateAssemblyCOP

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

TemlateAssemblyOP

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

TemplateHistoryCOP

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

TemplateHistoryOP

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

WeightedFragmentSmoothTrialMoverCOP

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

WeightedFragmentSmoothTrialMoverOP

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

WeightedFragmentTrialMoverCOP

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

WeightedFragmentTrialMoverOP

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

Enumeration Type Documentation

AlignOption

enum protocols::hybridization::AlignOption

Enumerator
all_chunks
random_chunk

sampleEnum

enum protocols::hybridization::sampleEnum

Enumerator
off
on
unset

Function Documentation

add_constraints()

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

References core::pose::Pose::add_constraint(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), 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().

add_non_protein_cst()

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::pose::Pose::size(), and core::conformation::Residue::xyz().

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

add_strand_pairs_cst()

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().

apply_transformation()

void protocols::hybridization::apply_transformation	(	pose::Pose &	mod_pose,
		std::list< core::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::pose::Pose::residue_type(), and core::pose::Pose::xyz().

Referenced by partial_align().

atom_map_valid_size()

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::pose::Pose::residue(), core::pose::Pose::size(), and core::id::AtomID::valid().

Referenced by partial_align().

CartesianSampler_subelement_ct_name()

std::string protocols::hybridization::CartesianSampler_subelement_ct_name

(

std::string const &

name

)

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

create_fragment_set()

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(), 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().

create_fragment_set_no_ssbias() [1/3]

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(), and protocols::loop_grower::FragmentExtension::apply().

create_fragment_set_no_ssbias() [2/3]

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().

create_fragment_set_no_ssbias() [3/3]

core::fragment::FragSetOP protocols::hybridization::create_fragment_set_no_ssbias	(	std::string	tgt_seq,
		core::Size	len,
		core::Size	nfrag,
		char	force_ss
	)

References core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa().

discontinued_lower()

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

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

Referenced by protocols::fold_from_loops::movers::SplitAndMixPoseMover::fix_ranges(), and protocols::hybridization::InsertChunkMover::get_local_sequence_mapping().

discontinued_upper()

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

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

Referenced by protocols::fold_from_loops::movers::SplitAndMixPoseMover::fix_ranges(), and protocols::hybridization::InsertChunkMover::get_local_sequence_mapping().

downstream_residues_from_jump()

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

find_uncovered_residues()

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

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

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

fragbias_tr()

static 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_scores(), protocols::hybridization::FragmentBiasAssigner::bfactors(), 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::init(), protocols::hybridization::FragmentBiasAssigner::uniform(), and protocols::hybridization::FragmentBiasAssigner::user().

gap_distance()

core::Real protocols::hybridization::gap_distance

(

core::Size

Seq_gap

)

Referenced by protocols::loophash::FastGapMover::find_next_gap(), and protocols::hybridization::DomainAssembly::run().

generate_centroid_constraints()

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(), and core::pose::Pose::remove_constraints().

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

generate_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().

get_gdtmm()

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::size(), and core::scoring::xyz_gdtmm().

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

get_num_residues_nonvirt()

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(), and core::pose::Pose::size().

Referenced by protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::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::rbsegment_relax::SequenceShiftMover::SequenceShiftMover(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), and protocols::hybridization::HybridizeProtocol::setup_templates_and_sampling_options().

get_num_residues_prot()

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(), and core::pose::Pose::size().

get_superposition_transformation()

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::pose::Pose::residue(), core::pose::Pose::size(), core::id::AtomID::valid(), core::conformation::Atom::xyz(), and core::pose::Pose::xyz().

Referenced by partial_align().

hybridize_subelement_ct_name()

std::string protocols::hybridization::hybridize_subelement_ct_name

(

std::string const &

name

)

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

natom_aligned()

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::pose::Pose::residue(), core::pose::Pose::size(), core::id::AtomID::valid(), and core::pose::Pose::xyz().

optimize()

void protocols::hybridization::optimize	(	core::pose::Pose &	pose,
		core::Size	rsd1,
		core::Size	rsd2,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::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().

parse_res()

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().

partial_align() [1/2]

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::size().

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

partial_align() [2/2]

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< core::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().

pick_pivots()

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

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

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

remove_residues()

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::size().

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

renumber_with_pdb_info()

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().

setup_centroid_constraints()

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

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

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

setup_constraints()

void protocols::hybridization::setup_constraints	(	core::pose::Pose &	pose,
		std::string &	cst_in
	)

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

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

setup_fullatom_constraints()

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

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

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

setup_user_coordinate_constraints()

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

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

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

TMalign_poses()

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

References protocols::hybridization::TMalign::alignment2AtomMap(), protocols::hybridization::TMalign::alignment2strings(), protocols::hybridization::TMalign::apply(), core::id::AtomID::BOGUS_ATOM_ID(), core::chemical::element::F, core::pose::initialize_atomid_map(), partial_align(), core::pose::Pose::size(), protocols::hybridization::TMalign::TMscore(), and TR().

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

TR() [1/3]

static basic::Tracer protocols::hybridization::TR ( "protocols.electron_density.util"  )

static

TR() [2/3]

static 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::BackboneTorsionPerturbation::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::hybridization::ChunkTrialMover::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::hybridization::WeightedFragmentSmoothTrialMover::apply(), protocols::hybridization::HybridizeProtocol::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::FoldTreeHybridize::get_residue_weights(), protocols::hybridization::HybridizeProtocol::init(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::hybridization::hConvergenceCheck::operator()(), protocols::hybridization::BackboneTorsionPerturbation::parse_my_tag(), protocols::hybridization::BackboneTorsionSampler::parse_my_tag(), protocols::hybridization::HybridizeProtocol::parse_my_tag(), protocols::hybridization::CartesianSampler::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().

TR() [3/3]

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

static

TZ()

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

static

update_atom_map()

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::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::pose::Pose::size(), core::id::AtomID::valid(), and core::pose::Pose::xyz().

Referenced by partial_align().

Variable Documentation

d0

core::Real protocols::hybridization::d0

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

D0_MIN

core::Real protocols::hybridization::D0_MIN

d0_out_

core::Real protocols::hybridization::d0_out_

d0_search

core::Real protocols::hybridization::d0_search

d0A

core::Real protocols::hybridization::d0A

d0B

core::Real protocols::hybridization::d0B

dcu0

core::Real protocols::hybridization::dcu0

Referenced by protocols::hybridization::TMalign::find_max_frag().

DEFAULT_NCYCLES

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

Lnorm

core::Real protocols::hybridization::Lnorm

m1_

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

m2_

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

minlen

int protocols::hybridization::minlen

Referenced by protocols::aa_composition::AddHelixSequenceConstraintsMover::check_lengths_sensible(), protocols::rbsegment_relax::AutoRBMover::grow_flexible(), and core::scoring::motif::HACK_dump_helices().

n_ali8_

int protocols::hybridization::n_ali8_

path

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

Referenced by protocols::design_opt::Supercharge::apply(), protocols::loop_grower::DensSkeleton::breadth_first_connect(), core::import_pose::RNA_HelixAssembler::build_init_pose(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), core::chemical::NCAARotlibPathCreator::create_operation(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_command_line_legacy(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_options(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), protocols::jd3::pose_outputters::ScoreFileOutputter::filename_for_job(), protocols::jd3::pose_outputters::SilentFilePoseOutputter::filename_for_output_job(), 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::kinematics::tree::Atom_::get_path_from_root(), core::environment::FoldTreeSketch::Node::has_cycle(), core::init::init_paths(), protocols::recces::options::RECCES_Options::initialize_from_command_line(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::initialize_from_options(), core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_options(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::is_canonical_beta_nov16_library(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::is_canonical_talaris_library(), protocols::canonical_sampling::jobname_dirhash(), core::import_pose::options::RNA_FragmentMonteCarloOptions::list_options_read(), core::import_pose::RNA_DeNovoSetup::list_options_read(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::list_options_read(), protocols::jd3::pose_outputters::mmTFPoseOutputter::list_options_read(), protocols::jd3::pose_outputters::PDBPoseOutputter::list_options_read(), protocols::jd3::pose_outputters::ScoreFileOutputter::list_options_read(), protocols::jd3::pose_outputters::SilentFilePoseOutputter::list_options_read(), protocols::features::DatabaseJobOutputter::load_options_from_option_system(), protocols::optimize_weights::IterativeOptEDriver::load_pose(), protocols::antibody::AntibodyDatabaseManager::load_structure_loading_info(), core::chemical::bcl::locate_bcl(), core::init::locate_rosetta_database(), protocols::kinematic_closure::perturbers::LogFilePerturber::LogFilePerturber(), protocols::jd2::mmCIFJobOutputter::mmCIFJobOutputter(), protocols::jd2::mmtfJobOutputter::mmtfJobOutputter(), core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_path(), protocols::membrane::MPMutateRelaxMover::output_filename(), protocols::jd3::pose_outputters::PDBPoseOutputter::output_name(), protocols::jd3::pose_outputters::mmTFPoseOutputter::output_name(), protocols::legacy_sewing::LegacyAssemblyMover::output_stats(), core::chemical::GlobalResidueTypeSet::params_files_from_commandline(), protocols::antibody::CDRSetOptionsParser::parse_default_and_user_options(), protocols::antibody::design::CDRGraftDesignOptionsParser::parse_default_and_user_options(), protocols::antibody::design::CDRSeqDesignOptionsParser::parse_default_and_user_options(), protocols::antibody::CDRSetOptionsParser::parse_options(), protocols::antibody::design::CDRGraftDesignOptionsParser::parse_options(), protocols::antibody::design::CDRSeqDesignOptionsParser::parse_options(), protocols::loop_grower::DensSkeleton::path_length(), protocols::jd2::PDBJobOutputter::PDBJobOutputter(), core::scoring::cryst::PhenixInterface::PhenixInterface(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::populate_from_segment_file_and_get_random_vector_set(), core::chemical::read_topology_file(), protocols::canonical_sampling::CanonicalSamplingMover::register_options(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::register_options(), protocols::features::DatabaseJobOutputter::register_options(), protocols::peptide_deriver::PeptideDeriverFilter::report(), core::scoring::rna::RNA_SuitePotential::RNA_SuitePotential(), protocols::toolbox::KClusterData::save_cluster_tree(), protocols::jd2::RNA_DeNovoJobOutputter::set_defaults(), protocols::jd2::SilentFileJobOutputter::set_defaults(), protocols::jd2::wwPDBJobOutputter::set_path(), protocols::match::MatcherTask::set_upstream_pose(), core::chemical::carbohydrates::CarbohydrateInfoManager::short_name_to_iupac_strings_map(), core::chemical::shortest_path(), protocols::indexed_structure_store::movers::DirectSegmentLookupMover::structure_store_path(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::structure_store_path(), core::scoring::rna::TNA_SuitePotential::TNA_SuitePotential(), protocols::docking::DockingEnsemble::update_pdblist_file(), and protocols::jd2::wwPDBJobOutputter::wwPDBJobOutputter().

r1

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

Referenced by protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_symmetric(), protocols::fldsgn::topology::StrandPairing::add_pair(), protocols::denovo_design::add_to_list(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::add_to_twobody(), core::select::residue_selector::NeighborhoodResidueSelector::apply(), protocols::protein_interface_design::filters::atom_distance(), protocols::simple_filters::atom_distance(), protocols::motifs::backbone_stub_match(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), core::scoring::sc::ElectrostaticSimilarityCalculator::Calc(), protocols::fldsgn::topology::HelixPairing::calc_geometry(), protocols::sparta::PDB::calc_HN_S2(), core::scoring::sc::ShapeSimilarityCalculator::CalcSs(), protocols::sparta::PDB::calcSurface(), protocols::simple_moves::BBConRotMover::closure(), protocols::sparta::PDB::collect_HN_S2_and_EF(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::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::electron_density::dump_and_raise_bad_pose_alignment(), protocols::electron_density::dump_and_raise_no_pose_alignment(), protocols::fldsgn::topology::StrandPairing::elongate(), core::scoring::GenBornPotential::eval_atom_derivative(), core::scoring::eval_bbbb_sr2b_energies(), core::scoring::eval_bbsc_sr2b_energies(), core::scoring::eval_scsc_sr2b_energies(), core::scoring::frdc(), core::scoring::frdcDa(), core::scoring::frdcDaR(), core::scoring::frdcR(), protocols::helical_bundle::generate_atom_positions(), protocols::sparta::Sparta::SpartaLib::get_ANN_data(), core::pack::interaction_graph::SimpleEdge::get_bb_E(), protocols::simple_moves::BBGaussianMover::get_dRdPhi(), protocols::simple_moves::BBGaussianMover::get_dRdTheta(), protocols::electron_density::get_gdt(), protocols::hbnet::HBNetStapleInterface::get_helix_id(), protocols::kinematic_closure::ClosureSolution::get_jacobian(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_jacobian(), core::scoring::GenBornPotential::get_res_res_elecE(), protocols::rna::denovo::get_residues_within_dist_of_RNA(), protocols::electron_density::get_rms(), protocols::sparta::PDB::getOrbitalShift(), protocols::sparta::Sparta::SpartaLib::getResInfo(), protocols::neighbor::in_ngbat_sphere(), protocols::neighbor::in_nrg_graph(), protocols::simple_moves::DEEROptimizeCoordsMover::init_data(), protocols::helical_bundle::BundleParametrizationCalculator::init_from_file(), core::scoring::ResiduePairNeighborList::initialize_from_residues(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_backbone_backbone(), protocols::hbnet::HBNetStapleInterface::interhelical_contact(), protocols::sparta::PDB::loadPDB(), protocols::simple_moves::BBConRotMover::make_move(), protocols::fold_from_loops::utils::map_by_residue_subsets(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::NC_distance_filter(), protocols::helical_bundle::FitSimpleHelixMultiFunc::operator()(), core::scoring::packstat::overlap(), core::scoring::packstat::Circle::overlap(), protocols::motifs::LigandMotifSearch::override_option_input(), protocols::motifs::MotifSearch::override_option_input(), protocols::sparta::PDB::PDB(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::prestore_sc_oversat(), protocols::frag_picker::FragmentCandidate::print_fragment_seq(), protocols::helical_bundle::read_minor_helix_params(), protocols::simple_filters::res_res_min_distance(), protocols::protein_interface_design::filters::res_rmsd(), protocols::simple_filters::res_rmsd(), protocols::motifs::LigandMotifSearch::reset_option_input(), protocols::motifs::MotifSearch::reset_option_input(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::chemical::residue_type_bases_identical(), core::chemical::residue_types_identical(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), core::pack::RTMin::rtmin(), protocols::hbnet::HBNetStapleInterface::same_helix(), protocols::simple_moves::DEEROptimizeCoordsMover::score(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), core::scoring::SecondaryStructurePotential::spherical(), protocols::fldsgn::potentials::sspot::spherical(), protocols::rbsegment_relax::ConfChangeMover::stage2(), protocols::canonical_sampling::SimulatedTempering::temperature_move(), protocols::helical_bundle::FitSimpleHelixMultiFunc::vars_to_params(), protocols::helical_bundle::write_crick_params_file_data(), and protocols::helical_bundle::write_minor_helix_params().

r2

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

Referenced by protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_symmetric(), protocols::fldsgn::topology::StrandPairing::add_pair(), protocols::denovo_design::add_to_list(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::add_to_twobody(), core::select::residue_selector::NeighborhoodResidueSelector::apply(), protocols::constraint_generator::DistanceConstraintGenerator::apply(), protocols::protein_interface_design::filters::atom_distance(), protocols::simple_filters::atom_distance(), protocols::motifs::backbone_stub_match(), core::scoring::nmr::pcs::PCSSingleSet::basic_pcs_equation(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), core::scoring::sc::ElectrostaticSimilarityCalculator::Calc(), protocols::fldsgn::topology::HelixPairing::calc_geometry(), protocols::normalmode::NormalMode::calc_inertia_tensor(), core::scoring::sc::ShapeSimilarityCalculator::CalcSs(), 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::create_minimization_graph(), core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib(), protocols::denovo_design::components::StructureData::delete_segment(), protocols::scoring::methods::pcs::TensorsOptimizer::dfunc(), protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1::dfunc(), protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2::dfunc(), protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3::dfunc(), protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4::dfunc(), protocols::nmr::pcs::PCSTensorOptimizer::dfunc(), protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc_exact(), protocols::scoring::methods::pcs2::TensorsOptimizerSvd::dfunc_exact(), core::scoring::ResidualDipolarCoupling::do_correct_NH(), protocols::electron_density::dump_and_raise_bad_pose_alignment(), protocols::electron_density::dump_and_raise_no_pose_alignment(), protocols::fldsgn::topology::StrandPairing::elongate(), core::scoring::GenBornPotential::eval_atom_derivative(), core::scoring::eval_bbbb_sr2b_energies(), core::scoring::eval_bbsc_sr2b_energies(), core::scoring::eval_scsc_sr2b_energies(), protocols::scoring::methods::pcs::fill_A_line(), protocols::scoring::methods::pcsTs1::fill_A_line(), protocols::scoring::methods::pcsTs2::fill_A_line(), protocols::scoring::methods::pcsTs3::fill_A_line(), protocols::scoring::methods::pcsTs4::fill_A_line(), protocols::scoring::methods::pcs2::fill_A_line_fast(), protocols::scoring::methods::pcs2::fill_A_line_slow(), core::scoring::nmr::pcs::PCSSingleSet::fill_matrix_A_row(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::frdc(), core::scoring::frdcDa(), core::scoring::frdcDaR(), core::scoring::frdcR(), core::pack::interaction_graph::SimpleEdge::get_bb_E(), protocols::simple_moves::BBGaussianMover::get_dRdPhi(), protocols::simple_moves::BBGaussianMover::get_dRdTheta(), protocols::electron_density::get_gdt(), protocols::kinematic_closure::ClosureSolution::get_jacobian(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_jacobian(), core::scoring::GenBornPotential::get_res_res_elecE(), protocols::rna::denovo::get_residues_within_dist_of_RNA(), protocols::electron_density::get_rms(), core::energy_methods::StackElecEnergy::get_stack_elec_deriv(), protocols::sparta::PDB::getOrbitalShift(), protocols::neighbor::in_ngbat_sphere(), protocols::neighbor::in_nrg_graph(), protocols::simple_moves::DEEROptimizeCoordsMover::init_data(), core::scoring::ResiduePairNeighborList::initialize_from_residues(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_backbone_backbone(), protocols::hbnet::HBNetStapleInterface::interhelical_contact(), protocols::simple_moves::BBConRotMover::make_move(), protocols::fold_from_loops::utils::map_by_residue_subsets(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::NC_distance_filter(), protocols::scoring::methods::pcs::GridSearchIterator::next_center(), protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1::next_center(), protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2::next_center(), protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3::next_center(), protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4::next_center(), core::scoring::packstat::overlap(), protocols::motifs::LigandMotifSearch::override_option_input(), protocols::motifs::MotifSearch::override_option_input(), core::scoring::nmr::pcs_func(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::prestore_sc_oversat(), protocols::simple_filters::res_res_min_distance(), protocols::protein_interface_design::filters::res_rmsd(), protocols::simple_filters::res_rmsd(), protocols::motifs::LigandMotifSearch::reset_option_input(), protocols::motifs::MotifSearch::reset_option_input(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::chemical::residue_type_bases_identical(), core::chemical::residue_types_identical(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), core::pack::RTMin::rtmin(), protocols::hbnet::HBNetStapleInterface::same_helix(), protocols::simple_moves::DEEROptimizeCoordsMover::score(), core::scoring::nmr::pcs::PCSSingleSet::set_atom_derivatives(), core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), protocols::nmr::pcs::PCSEnergy::show_additional_info(), core::scoring::sc::ShapeComplementarityCalculator::TrimPeripheralBandCheckDot(), and core::scoring::sc::ShapeSimilarityCalculator::TrimPeripheralBandCheckDot().

score

std::vector< std::vector < core::Real > > protocols::hybridization::score

Referenced by protocols::abinitio::Templates::_get_scored_list(), protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::accumulate_bur_rotamer_oversats(), protocols::constraint_movers::CstInfoMover::add_info_for_csts(), protocols::mpi_refinement::add_init_dev_penalty(), protocols::match::output::BestMatchesCollection::add_match(), protocols::match::output::MatchScoreWriter::add_match(), protocols::match::output::BestMatchesCollection::add_match_dspos1(), protocols::loops::addScoresForLoopParts(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::simple_moves::WriteFiltersToPose::apply(), protocols::constraints_additional::ConstraintEvaluator::apply(), protocols::topology_broker::ConstraintEvaluatorWrapper::apply(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::cluster::GatherPosesMover::apply(), protocols::cluster::AssignToClustersMover::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), protocols::cryst::CrystRMS::apply(), protocols::cryst::DockLatticeMover::apply(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::medal::MedalMover::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::normalmode::NormalModeRelaxMover::apply(), protocols::membrane::HelixFromSequence::apply(), protocols::pose_sewing::movers::SewAnythingAddMover::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::relax::AcceptToBestMover::apply(), protocols::star::StarAbinitio::apply(), protocols::simple_filters::JScoreEvaluator::apply(), protocols::simple_filters::PredictedBurialEvaluator::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::task_operations::SelectByDensityFitOperation::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), core::select::residue_selector::ScoreTermValueBasedSelector::apply(), protocols::simple_filters::MotifScoreFilter::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::protein_interface_design::movers::SecretionOptimizationMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::forge::remodel::RemodelAccumulator::apply(), protocols::canonical_sampling::PatchOperation::apply(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply_solutions(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::apply_solutions(), protocols::multistage_rosetta_scripts::cluster::assign_non_medoids_to_clusters(), protocols::multistage_rosetta_scripts::cluster::assign_non_medoids_to_clusters_on_the_fly(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), protocols::hybridization::FragmentBiasAssigner::automode(), protocols::hybridization::FragmentBiasAssigner::automode_scores(), protocols::qsar::scoring_grid::GridSet::average_score(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::energy_methods::RNA_CoarseDistEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::energy_methods::RNA_CoarseDistEnergy::backbone_sidechain_energy(), core::scoring::dna::DNA_BasePotential::base_score(), protocols::relax::FastRelax::batch_apply(), protocols::protein_interface_design::best_bbcst_residues(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), protocols::boinc::boincOutputFilter(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), protocols::moves::MixedMonteCarlo::boltzmann(), protocols::moves::MonteCarlo::boltzmann(), protocols::canonical_sampling::BiasedMonteCarlo::boltzmann(), protocols::monte_carlo::MonteCarloInterface::boltzmann(), protocols::forge::remodel::build_and_score_disulfide(), protocols::denovo_design::DisulfidizeMover::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::energy_methods::ResidualDipolarCouplingEnergy_Rohl::calc_dipscore(), core::energy_methods::MPHelicalityEnergy::calc_energy(), core::energy_methods::MPResidueLipophilicityEnergy::calc_energy(), core::energy_methods::MembraneEnvSmoothEnergy::calc_energy(), core::energy_methods::FaMPEnvSmoothEnergy::calc_energy(), core::energy_methods::EnvSmoothEnergy::calc_energy(), protocols::sparta::calc_per_residue_scores(), core::simple_metrics::metrics::TotalEnergyMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::calculate(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), protocols::pose_sewing::calculate_bw_pose_compat_motifs(), protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_cost_only_with_svd(), core::energy_methods::RNA_ChemicalMappingEnergy::calculate_energy(), core::pack::guidance_scoreterms::sap::SapConstraintEnergy::calculate_energy(), core::energy_methods::RNA_PartitionEnergy::calculate_energy(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_receptor_score(), core::pack::guidance_scoreterms::sap::calculate_sap(), protocols::scoring::methods::pcs::PCS_Energy::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::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(), core::pack::guidance_scoreterms::sap::calculate_slow_approx_sap(), protocols::dna::DnaInterfacePacker::calculate_specificity(), protocols::scoring::methods::pcs::PCS_data_per_lanthanides::calculate_tensor_and_cost_with_svd(), 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::pcs2::PcsDataLanthanide::calculate_tensor_and_cost_with_svd(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), protocols::relax::CentroidRelax::CentroidRelax(), protocols::loop_grower::LoopGrower::check_auto_stop(), 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::loop_grower::LoopPartialSolutionStore::cluster_check(), protocols::relax::FastRelax::cmd_accept_to_best(), protocols::simple_filters::MotifScoreFilter::compute(), core::scoring::dna::TorsionFourierComponent::compute(), protocols::pose_metric_calculators::RotamerBoltzCalculator::compute_boltz_weight_packrotamers(), 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::scoring::nmr::pcs::PCSSingleSet::compute_pcs_values_and_score_from_tensor(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::scoring::ResidualDipolarCouplingRigidSegments::compute_total_score(), protocols::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzSum(), protocols::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzWeight_lazy(), protocols::star::configure_rmc(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::convert_silent_file_to_pose_data_list(), protocols::medal::MedalMover::create_fragment_and_rigid_mover(), protocols::medal::MedalMover::create_fragment_mover(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), core::scoring::ScoringManager::create_mhc_map_from_db(), core::scoring::ScoringManager::create_mm_bondangle_library_instance(), core::scoring::ScoringManager::create_mm_bondlength_library_instance(), core::scoring::ScoringManager::create_mm_torsion_library_instance(), core::scoring::ScoringManager::create_nmer_pssm(), core::scoring::ScoringManager::create_nmer_svm_rank(), protocols::medal::MedalMover::create_small_mover(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_all_ligand_phores(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_receptor_phores(), protocols::relax::RelaxScriptManager::determine_closest_scorefunction(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::dfs_cycle_finder(), core::scoring::func::USOGFunc::dfunc(), protocols::electron_density::BfactorMultifunc::dfunc(), protocols::optimize_weights::OptEMultifunc::dfunc(), protocols::frag_picker::scores::FragmentScoreManager::do_caching(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::do_some_clustering(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::do_some_clustering(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::do_some_clustering(), protocols::toolbox::sample_around::do_xy_scan(), protocols::electron_density::BfactorMultifunc::dump(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), core::energy_methods::ChemicalShiftAnisotropyEnergy::eval_csa(), core::energy_methods::DipolarCouplingEnergy::eval_dc(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments::eval_dipolar(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::eval_dipolar(), core::energy_methods::ResidualDipolarCouplingEnergy::eval_dipolar(), core::scoring::dna::DNABFormPotential::eval_dna_bform_bb_torsion_score_residue(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::energy_methods::FaMPEnvEnergy::eval_fa_mbenv(), protocols::membrane::scoring::FaWaterToBilayerEnergy::eval_fa_wtbe(), protocols::membrane::scoring::ElectricfieldLipidlayer::eval_felec_lipidlayer(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_derivatives(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_energy(), core::energy_methods::FA_GrpElecEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::energy_methods::DNA_DihedralEnergy::eval_intraresidue_dof_derivative(), core::scoring::rna::RNA_SuitePotential::eval_likelihood_potential(), core::energy_methods::FaMPSolvEnergy::eval_lk(), protocols::moves::MonteCarlo::eval_lowest_score_pose(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::energy_methods::DNA_DihedralEnergy::eval_residue_pair_derivatives(), core::energy_methods::RNA_SuiteEnergy::eval_residue_pair_derivatives(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::rna::RNA_SuitePotential::eval_score(), core::scoring::dna::DNA_DihedralPotential::eval_sugar_torsion_score_and_deriv(), core::scoring::rna::RNA_SuitePotential::eval_suiteness_bonus(), core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator::evaluate(), 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::ub_e2c::ubi_e2c_modeler::evaluate_native(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::scoring::TMscore::extend(), core::fragment::picking_old::vall::extent_to_fragdata(), protocols::jd3::pose_outputters::ScoreFileOutputter::filename_for_job(), protocols::hotspot_hashing::HotspotStubSet::fill(), protocols::jd2::AtomTreeDiffJobInputter::fill_jobs(), core::scoring::motif::ResPairMotif::filter(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::filter_score(), protocols::loop_grower::LoopPartialSolutionStore::filterprevious(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), core::energy_methods::StackElecEnergy::finalize_total_energy(), core::energy_methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::energy_methods::CenPairMotifEnergy::finalize_total_energy(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), core::energy_methods::RNA_PartitionEnergy::finalize_total_energy(), core::energy_methods::SSElementMotifContactEnergy::finalize_total_energy(), core::energy_methods::RNA_CoarseDistEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::find_type_matches(), protocols::denovo_design::movers::FoldArchitectMover::folding_score(), core::energy_methods::MHCEpitopeEnergy::full_rescore(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation(), core::scoring::func::USOGFunc::func(), protocols::scoring::methods::pcs2::TensorsOptimizer::func(), protocols::scoring::methods::pcs2::TensorsOptimizerFix::func(), protocols::scoring::methods::pcs2::TensorsOptimizerSvd::func(), core::scoring::disulfides::Cb_Distance_Func::func(), core::scoring::func::SOGFunc_Impl::func(), core::scoring::func::MixtureFunc::func(), core::scoring::func::SoedingFunc::func(), core::scoring::func::TopOutFunc::func(), core::scoring::func::MixtureFunc::func_(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::generate_assembly(), core::energy_methods::GoapEnergy::get_angle_score(), protocols::frags::VallData::get_cheating_frags(), core::scoring::Ramachandran::get_custom_rama_table_filename(), core::energy_methods::RNA_FullAtomStackingEnergy::get_fa_stack_score(), protocols::frags::VallData::get_frags(), protocols::frags::RMSVallData::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::nv::NVlookup::get_potentials(), core::energy_methods::FaMPSolvEnergy::get_residue_pair_energy(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), core::scoring::rna::get_rna_motif_score(), protocols::magnesium::MgScanner::get_score(), core::energy_methods::RNA_PartitionEnergy::get_score_from_sequences(), core::energy_methods::StackElecEnergy::get_stack_elec_score(), protocols::hotspot_hashing::HotspotStubSet::get_stub(), core::energy_methods::RNA_DataBackboneEnergy::get_sugar_env_score(), core::scoring::cryst::PhenixInterface::getScore(), core::scoring::cryst::PhenixInterface::getScoreAndDerivs(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(), protocols::ligand_docking::grid_score(), core::scoring::elec::electrie::ElecTrieEvaluator::heavyatom_heavyatom_energy(), core::scoring::lkball::lkbtrie::LKBTrieEvaluator::heavyatom_heavyatom_energy(), core::scoring::elec::electrie::ElecTrieEvaluator::heavyatom_hydrogenatom_energy(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), core::scoring::elec::electrie::ElecTrieEvaluator::hydrogenatom_heavyatom_energy(), core::scoring::elec::electrie::ElecTrieEvaluator::hydrogenatom_hydrogenatom_energy(), protocols::electron_density::DockPDBIntoDensityMover::import_refinement_silent_files(), protocols::match::output::BestMatchesCollection::index_for_new_match(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::initial_search(), protocols::canonical_sampling::HamiltonianExchange::initialize_from_file(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::relax::FastRelax::inner_loop_accept_to_best_command(), protocols::frag_picker::scores::AdaptiveScoreHistogram::insert(), core::scoring::ResidualDipolarCoupling::iterate_tensor_weights(), protocols::monte_carlo::GenericMonteCarloMover::last_accepted_score(), protocols::jd3::pose_outputters::ScoreFileOutputter::list_options_read(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::load_csv(), protocols::loop_grower::LoopPartialSolution::LoopPartialSolution(), protocols::monte_carlo::GenericMonteCarloMover::lowest_score(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::match(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRProtocol::measure_rotamer_recovery(), protocols::simple_moves::DEEROptimizeCoordsMover::minimize(), core::scoring::mm::MMTorsionLibrary::MMTorsionLibrary(), protocols::loop_grower::LoopGrower::modifiedscore(), 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::energy_methods::DirectReadoutEnergy::my_residue_pair_energy(), protocols::qsar::scoring_grid::GridSet::normalize(), protocols::canonical_sampling::TemperatureController::observe_after_metropolis(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::operator()(), protocols::normalmode::NormalModeMultifunc::operator()(), protocols::pockets::FingerprintMultifunc::operator()(), protocols::pockets::PocketExemplarMultifunc::operator()(), protocols::scoring::methods::pcs::TensorsOptimizer::operator()(), protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1::operator()(), protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2::operator()(), protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3::operator()(), protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4::operator()(), core::optimization::AtomTreeMultifunc::operator()(), core::optimization::CartesianMultifunc::operator()(), core::optimization::SingleResidueMultifunc::operator()(), core::optimization::symmetry::SymAtomTreeMultifunc::operator()(), protocols::optimize_weights::OptEMultifunc::operator()(), protocols::optimize_weights::WrapperOptEMultifunc::operator()(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::optimize_generation(), protocols::frag_picker::scores::AdaptiveScoreHistogram::p_value(), protocols::pose_creation::MergePDBMover::pack_and_minimize(), protocols::magnesium::MgWaterHydrogenPacker::pack_mg_water_hydrogens_in_pose(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::parse_alternative_score_file(), protocols::mpi_refinement::Scheduler::pick_enrich_methods(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::prestore_sc_oversat(), protocols::simple_moves::Hit::print(), protocols::simple_moves::DEEROptimizeCoordsMover::print_coords(), core::scoring::motif::XformScore::print_quantiles(), core::scoring::motif::XformScore::print_scores(), core::scoring::motif::XformScore::print_scores_norm(), protocols::cluster::ClusterBase::print_summary(), core::scoring::func::SOGFunc_Impl::prob_sum_of_gaussians(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), protocols::match::output::MatchConsolidator::process_match(), protocols::denovo_design::DisulfidizeMover::process_pose(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_line(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_VECTOR_line(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::rna::denovo::RNA_FragmentMonteCarlo::randomize_and_close_all_chains(), protocols::simple_moves::rational_mc::RationalMonteCarlo::RationalMonteCarlo(), protocols::electron_density::RBfitResult::RBfitResult(), core::scoring::motif::XformScore::read_binary(), protocols::monte_carlo::GenericSimulatedAnnealer::read_checkpoint_line(), protocols::hotspot_hashing::HotspotStubSet::read_data(), protocols::denovo_design::task_operations::ConsensusLoopDatabase::read_db(), core::fragment::ConstantLengthFragSet::read_fragment_stream(), protocols::loop_grower::LoopGrower::read_from_disk(), protocols::loop_grower::LoopComparator::read_from_file(), core::sequence::SequenceProfile::read_from_file(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::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(), protocols::electron_density::DockPDBIntoDensityMover::read_in_partial_search_results(), 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::mean_field::EnergiesByTaskCalculator::recompute(), protocols::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::loop_modeling::utilities::TrajectoryLogger::record_endpoint(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::electron_density::RefinementResult::RefinementResult(), core::scoring::hbonds::graph::HBondGraph::register_hbond(), protocols::jd3::dag_node_managers::SimpleNodeManager::register_result(), protocols::jd3::dag_node_managers::NodeManager::register_result(), protocols::jd3::dag_node_managers::SimpleNodeManager::register_result_with_token(), protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group(), protocols::simple_filters::MotifScoreFilter::report(), protocols::md::CartesianMD::report_MD(), core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv(), protocols::rotamer_recovery::PerNativeRRReporterHuman::report_rotamer_recovery(), protocols::rotamer_recovery::RRReporterHuman::report_rotamer_recovery(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_features(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::simple_filters::MotifScoreFilter::report_sm(), protocols::hotspot_hashing::HotspotStubSet::rescore(), protocols::loop_grower::LoopGrower::rescoresolutionset(), protocols::moves::MixedMonteCarlo::reset(), protocols::monte_carlo::GenericMonteCarloMover::reset(), protocols::moves::MonteCarlo::reset(), protocols::canonical_sampling::BiasedMonteCarlo::reset(), protocols::monte_carlo::MonteCarloInterface::reset(), core::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::MembraneEnvSmoothEnergy::residue_energy(), core::energy_methods::MPHelicalityEnergy::residue_energy(), core::energy_methods::MPResidueLipophilicityEnergy::residue_energy(), core::energy_methods::HydroxylTorsionEnergy::residue_energy(), core::energy_methods::BurialEnergy::residue_energy(), core::energy_methods::SugarBackboneEnergy::residue_energy(), core::energy_methods::SymmetricLigandEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCGEnergy::residue_energy(), core::energy_methods::FaMPEnvSmoothEnergy::residue_energy(), core::energy_methods::CenHBEnergy::residue_pair_energy(), core::energy_methods::FA_GrpElecEnergy::residue_pair_energy(), core::energy_methods::HybridVDW_Energy::residue_pair_energy(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::MotifDockEnergy::residue_pair_energy(), core::energy_methods::PointWaterEnergy::residue_pair_energy(), core::energy_methods::RNA_SuiteEnergy::residue_pair_energy(), core::energy_methods::RNA_VDW_Energy::residue_pair_energy(), core::energy_methods::StackElecEnergy::residue_pair_energy(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), core::energy_methods::ArgCationPiEnergy::residue_pair_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::energy_methods::RNA_CoarseDistEnergy::residue_pair_energy(), core::energy_methods::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::energy_methods::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::energy_methods::FA_GrpElecEnergy::residue_pair_energy_ext(), core::energy_methods::StackElecEnergy::residue_pair_energy_ext(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy_ext(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_CoarseDistEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::fragment::CacheWrapper< T, XCacheUnit >::retrieve(), protocols::dna::DnaInterfacePacker::reversion_scan(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_axis_pairwise_pair_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_pair_pairwise_pair_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_stagger_pairwise_pair_energy(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::sparta::Sparta::run_A_ANN_Prediction(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), protocols::multistage_rosetta_scripts::MRSJob::run_inner(), protocols::toolbox::sample_around::sample_all_rotations_at_jump(), protocols::farnesyl::SampleFarnesylMover::sample_farnesyl(), protocols::farnesyl::InstallFarnesylMover::sample_first(), protocols::magnesium::MgOrbitalFrameFinder::sample_orbital_frame(), protocols::farnesyl::InstallFarnesylMover::sample_second(), protocols::farnesyl::InstallFarnesylMover::sample_third(), protocols::magnesium::MgScanner::scan_magnesiums(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::score(), protocols::electron_density::DockPDBIntoDensityMover::score_and_dump_natives(), protocols::frag_picker::scores::FragmentScoreManager::score_fragment(), protocols::frag_picker::scores::FragmentScoreManager::score_fragment_from_cache(), core::scoring::TMscore::score_fun(), protocols::medal::MedalMover::score_function(), protocols::canonical_sampling::BiasedMonteCarlo::score_function(), protocols::monte_carlo::MonteCarloInterface::score_function(), protocols::ligand_docking::Transform::score_ligand(), protocols::ligand_docking::TransformEnsemble::score_ligands(), core::io::pose_from_sfr::score_mapping(), protocols::moves::MixedMonteCarlo::score_mixed_res(), core::scoring::MembranePotential::score_normal_center(), core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide(), core::fragment::CacheWrapper< T, XCacheUnit >::scored_frag_ids(), protocols::legacy_sewing::scores_to_alignments(), core::sequence::SequenceProfile::scores_to_probs_(), protocols::monte_carlo::GenericMonteCarloMover::scoring(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_five_prime_phosphate(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_three_prime_phosphate(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::set_accurate_sasa_and_recalc(), protocols::multistate_design::SingleState::set_best_score(), protocols::relax::CentroidRelax::set_cartesian(), protocols::grafting::AnchoredGraftMover::set_cen_scorefunction(), core::scoring::nmr::NMRDummySpinlabelConformer::set_clash_score(), protocols::jd2::FileJobOutputter::set_defaults(), protocols::relax::CentroidRelax::set_fa_score_function(), protocols::grafting::AnchoredGraftMover::set_fa_scorefunction(), protocols::moves::MonteCarlo::set_last_accepted(), protocols::moves::MonteCarlo::set_last_accepted_pose(), protocols::moves::MonteCarlo::set_last_accepted_score(), protocols::moves::MonteCarlo::set_lowest(), protocols::moves::MonteCarlo::set_lowest_score_pose(), protocols::loop_grower::LoopPartialSolution::set_score(), protocols::relax::CentroidRelax::set_score_function(), protocols::simple_moves::rational_mc::RationalMonteCarlo::set_score_function(), protocols::loop_grower::LoopComparator::set_scores(), protocols::moves::MonteCarlo::set_total_score_last_considered(), core::energy_methods::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::EnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), protocols::rna::denovo::RNA_FragmentMonteCarlo::setup_full_initial_structure(), protocols::star::setup_score(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), core::energy_methods::RNA_CoarseDistEnergy::sidechain_sidechain_energy(), protocols::multistate_design::MultiStatePacker::single_state_design(), protocols::symmetry::SymmetrySlider::slide(), protocols::sic_dock::slide_into_contact_and_score(), protocols::sic_dock::slide_into_contact_and_score_DEPRICATED(), core::scoring::nmr::pcs::PCSSingleSet::solve_tensor_and_compute_score_by_nls(), core::scoring::nmr::pcs::PCSSingleSet::solve_tensor_and_compute_score_by_svd(), protocols::cluster::ClusterBase::sort_each_group_by_energy(), protocols::toolbox::ClusterBase::sort_each_group_by_energy(), protocols::cluster::ClusterBase::sort_groups_by_energy(), core::scoring::motif::MotifHits::stat_motifs(), core::fragment::CacheWrapper< T, XCacheUnit >::store(), protocols::hbnet::HBNet::store_network(), protocols::canonical_sampling::ParallelTempering::temperature_move(), protocols::canonical_sampling::SimulatedTempering::temperature_move(), protocols::abinitio::Templates::Templates(), protocols::hybridization::TMalign::TMscore8_search(), protocols::electron_density::ResultDB< T, Tcomp >::to_add_element(), protocols::qsar::scoring_grid::GridSet::total_score(), core::pack::guidance_scoreterms::sap::SapConstraintOptions::transform_sap_to_score(), protocols::ligand_docking::Translate::translate_ligand(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::trilinear_gradient(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::trilinear_interpolation(), protocols::rna::setup::RNA_CSA_JobDistributor::update_bank(), core::io::silent::SilentStruct::update_score(), core::energy_methods::Burial_v2Energy::using_atom_distance(), core::energy_methods::Burial_v2Energy::using_totalSasa(), core::energy_methods::WaterSpecificEnergy::WaterSpecificEnergy(), protocols::mpi_refinement::StructAvrgMover::weighted_average(), core::scoring::motif::XformScore::write_binary(), protocols::canonical_sampling::DbTrajectoryRecorder::write_cache_to_db(), protocols::trajectory::DbTrajectoryWriter::write_cache_to_db(), protocols::legacy_sewing::write_hashing_scores_to_file(), protocols::rotamer_recovery::RRReporterSQLite::write_rotamer_recovery_full_table_schema(), protocols::canonical_sampling::DbTrajectoryRecorder::write_schema_to_db(), protocols::trajectory::DbTrajectoryWriter::write_schema_to_db(), protocols::features::ResidueGridScoresFeatures::write_schema_to_db(), protocols::features::TotalScoreFeatures::write_schema_to_db(), protocols::mpi_refinement::Zscore_to_library(), and protocols::loop_grower::LoopPartialSolutionStore::zscoretransform().

score_d8

core::Real protocols::hybridization::score_d8

secx

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

Referenced by protocols::hybridization::TMalign::NWDP_TM().

secy

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

Referenced by protocols::hybridization::TMalign::NWDP_TM().

seqx

std::string protocols::hybridization::seqx

seqy

std::string protocols::hybridization::seqy

t

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

Referenced by protocols::frag_picker::quota::ABEGO_SS_Config::ABEGO_SS_Config(), protocols::nmr::pre::PREDistanceRecord::add_and_average(), protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), core::scoring::constraints::ConstraintSet::add_dof_constraint(), core::scoring::ScoreFunction::add_to_weight(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::denovo_design::components::DivideAndConqueror::all_permutations(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::matdes::SymDofMover::apply(), protocols::protein_interface_design::movers::PatchdockTransform::apply(), protocols::loophash::LoopHashLibrary::apply_random(), core::scoring::apply_set_weights(), 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(), protocols::simple_filters::ChainBreak::chain_num(), protocols::moves::MonteCarlo::change_weight(), core::import_pose::libraries::RNA_JumpLibrary::check_forward_backward(), core::scoring::ScoreFunction::check_methods(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::compute_aas_after_disallowing(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::compute_best_allowed_aas(), protocols::denovo_design::components::FoldGraph::compute_best_solution(), core::scoring::packstat::Slice::compute_surface(), protocols::features::LoopAnchorFeatures::compute_transform_and_write_to_db(), protocols::electron_density::density_grid_search(), protocols::hybridization::TMalign::detailed_search(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), protocols::hybridization::TMalign::do_rotation(), core::id::DOF_type_is_rb(), protocols::hybridization::TMalign::DP_iter(), core::energy_methods::Fa_MbsolvEnergy::dsolvationE(), core::energy_methods::FaMPSolvEnergy::dsolvationE(), protocols::sic_dock::dump_points_pdb(), protocols::moves::PyMOLMover::energy_type(), core::scoring::loop_graph::evaluator::SixDTransRotPotential::evaluate(), core::scoring::loop_graph::evaluator::SixDTransRotPotential::evaluate_constraining_potential_derivative(), protocols::evolution::AlignmentAAFinder::exclude_AA_threshold(), core::io::rcsb::experimental_technique_to_string(), core::scoring::TMscore::extend(), protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::indexed_structure_store::extract_residue_entries(), core::conformation::membrane::MembraneGeometry::f_imm1(), core::conformation::membrane::MembraneGeometry::f_imm1_deriv(), core::io::HeaderInformation::fill_compound_records(), core::kinematics::MoveMap::find(), core::scoring::packstat::LeeRichards::find_first_slice(), core::kinematics::find_stub_transform(), protocols::simple_moves::rational_mc::RationalMonteCarlo::fire_all_triggers(), protocols::monte_carlo::GenericMonteCarloMover::fire_all_triggers(), protocols::sic_dock::flood_fill3D(), protocols::helical_bundle::generate_atom_positions(), core::kinematics::MoveMap::get(), protocols::loophash::LoopHashLibrary::get_all(), core::scoring::dna::DNA_BasePotential::get_array_indices(), core::scoring::loop_graph::evaluator::SixDTransRotPotential::get_derivative(), protocols::forge::remodel::RemodelGlobalFrame::get_helical_params(), protocols::hybridization::TMalign::get_initial_local(), core::scoring::packstat::old::get_orientation(), core::pose::rna::get_phosphate_atom_and_neighbor_list(), protocols::jumping::PairingLibrary::get_random_beta_sheet_jump(), protocols::jumping::PairingLibrary::get_random_tmh_jump(), core::id::get_rb_number(), protocols::cluster::calibur::Clustering::get_threshold(), core::scoring::TMscore::get_transrot_ref(), core::scoring::ScoreFunction::get_weight(), protocols::cluster::calibur::Clustering::getRandomDecoyNames(), protocols::frags::has_element(), core::scoring::ScoreFunction::has_nonzero_weight(), protocols::mean_field::jagged_array< T, A >::has_value(), core::scoring::ScoreFunction::has_zero_weight(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::HPool_RMSD(), protocols::mean_field::jagged_array< T, A >::index(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::initial_search(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::initialize_kernel(), core::kinematics::AtomTree::insert_single_fragment(), core::io::HeaderInformation::is_experimental_technique(), protocols::moves::PyMOLMover::is_it_time(), protocols::constel::NeighTeller::is_neigh_tree(), protocols::evaluation::PCA::jacobi(), protocols::toolbox::jacobi(), core::scoring::jacobi(), protocols::cluster::calibur::jacobi3(), core::scoring::jacobi3(), protocols::hybridization::TMalign::Kabsch(), 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::evolution::AlignmentAAFinder::loop_seqid_threshold(), protocols::kinmatch::lzs(), protocols::toolbox::KClusterData::mark_tags(), core::scoring::dna::DNA_BasePotential::mean(), protocols::simple_moves::DEEROptimizeCoordsMover::minimize(), protocols::evolution::AlignmentGapInserter::nbr_e_threshold(), protocols::denovo_design::components::SegmentCounts::new_segment_name(), protocols::hybridization::TMalign::NWDP_TM(), protocols::evolution::AlignmentGapInserter::only_clean_seq_num(), protocols::helical_bundle::FitSimpleHelixMultiFunc::operator()(), protocols::jumping::operator<<(), core::fragment::operator<<(), core::scoring::ScoreFunction::operator[](), protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::output_jump_information(), protocols::denovo_design::architects::CompoundArchitect::parse_architect_tags(), protocols::denovo_design::architects::CompoundArchitect::parse_connection_tags(), core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log(), protocols::qsar::scoring_grid::ScoringGridLoader::parse_gridset_tag(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::parse_my_tag(), protocols::denovo_design::architects::CompoundArchitect::parse_pairing_tags(), core::io::external::PsiPredInterface::parse_psipred_horiz_output(), protocols::denovo_design::components::StructureData::parse_tag(), protocols::denovo_design::architects::CompoundArchitect::parse_tag(), protocols::electron_density::pose_spherical_samples(), protocols::constel::ChainTerm::print(), protocols::constel::print_chains(), core::optimization::GA_Minimizer::randomize(), protocols::frag_picker::CSTalosIO::read(), protocols::frag_picker::PhiPsiTalosIO::read(), protocols::cluster::read1(), core::fragment::BBTorsionSRFD::read_data(), core::scoring::UnfoldedStatePotential::read_database_file(), protocols::loophash::LoopHashMap::read_db(), core::chemical::Metapatch::read_file(), core::chemical::Patch::read_file(), core::fragment::MinimalFragSet::read_fragment_stream(), 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(), 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::io::external::PsiPredInterface::run_psipred_prob(), core::scoring::ScoreFunction::score_by_scoretype(), protocols::hybridization::TMalign::score_matrix_rmsd(), protocols::hybridization::TMalign::score_matrix_rmsd_sec(), core::scoring::ScoreFunction::score_types_by_method_type(), core::kinematics::MoveMap::set(), core::scoring::ScoreFunction::set_method_weights(), protocols::pockets::SmallMol::set_size(), protocols::toolbox::KMedoid::set_threshold(), protocols::jumping::PairingLibrary::set_tmh_jump(), protocols::nmr::pre::PREDistanceRecord::set_tol(), core::kinematics::Jump::set_translation(), core::kinematics::RT::set_translation(), core::scoring::ScoreFunction::set_weight(), core::scoring::ScoreFunction::set_weight_if_zero(), protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_jump(), protocols::sic_dock::SICFast::slide_into_contact(), core::energy_methods::Fa_MbsolvEnergy::solvationE(), core::energy_methods::FaMPSolvEnergy::solvationE(), protocols::cartesian::sqr(), core::scoring::dna::DNA_BasePotential::stddev(), core::scoring::dna::DNA_BasePotential::stiffness(), protocols::kinmatch::str(), protocols::docking::DockingProtocol::sync_objects_with_flags(), protocols::minimization_packing::MinPackMover::task(), protocols::minimization_packing::PackRotamersMover::task(), protocols::minimization_packing::RotamerizeMover::task(), 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::calc_taskop_filters::RelativePoseFilter::thread(), protocols::calc_taskop_filters::MultipleSigmoids::threshold(), protocols::calc_taskop_filters::Operator::threshold(), protocols::calc_taskop_filters::Sigmoid::threshold(), protocols::matdes::OligomericAverageDegreeFilter::threshold(), protocols::protein_interface_design::filters::BindingStrainFilter::threshold(), protocols::simple_filters::TaskAwareSASAFilter::threshold(), protocols::protein_interface_design::filters::AverageDegreeFilter::threshold(), protocols::evolution::AASynthesisFitnessCost::threshold(), protocols::simple_filters::ChainBreak::threshold(), protocols::simple_filters::SequenceDistance::threshold(), protocols::matdes::ClashCheckFilter::threshold(), protocols::hybridization::TMalign::TMscore8_search(), protocols::protein_interface_design::PatchdockReader::to_entry(), protocols::splice::Splice::to_res(), protocols::simple_filters::ChainBreak::tolerance(), protocols::protein_interface_design::filters::Torsion::torsion(), protocols::hybridization::TMalign::transform(), protocols::protein_interface_design::PatchdockReader::transform_pose(), protocols::protein_interface_design::filters::BoltzmannFilter::triage_threshold(), protocols::protein_interface_design::movers::SetAtomTree::two_parts_chain1(), core::pack::task::PackerTask_::update_commutative(), core::pack::task::ResidueLevelTask_::update_commutative(), core::pack::task::ResidueLevelTask_::update_intersection(), protocols::moves::PyMOLMover::update_interval(), core::pack::task::PackerTask_::update_residue_commutative(), core::pack::task::PackerTask_::update_residue_intersection(), core::pack::task::PackerTask_::update_residue_union(), core::pack::task::ResidueLevelTask_::update_union(), protocols::frag_picker::VallProvider::vallChunksFromLibrary(), core::scoring::vector1_remove(), protocols::cluster::write1(), and protocols::features::HBondFeatures::write_hbond_chem_types_table_schema().

u

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::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::protein_interface_design::best_cutpoint(), protocols::toolbox::calc_fit_R(), protocols::evaluation::PCA::calc_fit_R(), protocols::sic_dock::Rose::clashes_naive(), protocols::sic_dock::Rose::contacts_naive(), protocols::fldsgn::BluePrintBDR::create_directed_dependency(), protocols::forge::build::BuildManager::create_directed_dependency(), protocols::forge::components::BDR::create_directed_dependency(), protocols::pockets::dD_dv1(), protocols::pockets::dD_dv2(), protocols::pockets::dD_dv3(), protocols::hybridization::TMalign::detailed_search(), protocols::hybridization::TMalign::do_rotation(), protocols::hybridization::TMalign::DP_iter(), core::scoring::TMscore::extend(), core::scoring::dna::find_basepairs(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_pnts(), protocols::forge::methods::find_connecting_jump(), protocols::forge::build::BuildManager::find_dependency(), protocols::forge::build::BuildManager::find_instruction(), protocols::pockets::SmallMol::findRoot(), protocols::hybridization::TMalign::get_initial_local(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz(), core::scoring::TMscore::get_transrot_ref(), core::chemical::RerootRestypeVisitor::initialize_vertex(), protocols::hybridization::TMalign::Kabsch(), protocols::frag_picker::scores::MakeDisulfideDistance::make(), protocols::moves::ResId::modifiable(), protocols::hybridization::TMalign::NWDP_TM(), core::io::raw_data::DisulfideFile::parse_disulf_file(), protocols::sic_dock::projperp(), core::io::raw_data::DisulfideFile::read_in_and_set_disulfides(), protocols::simple_filters::DeltaFilter::relax_unbound(), core::scoring::MembranePotential::rigid_perturb_vector(), core::scoring::MembranePotential::rot_perturb_vector(), protocols::hybridization::TMalign::score_matrix_rmsd(), protocols::hybridization::TMalign::score_matrix_rmsd_sec(), core::scoring::MembranePotential::search_memb_normal(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::set_unseen_score(), core::chemical::RerootRestypeVisitor::start_vertex(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::svbksb(), protocols::hybridization::TMalign::TMscore8_search(), protocols::hybridization::TMalign::transform(), core::chemical::RerootRestypeVisitor::tree_edge(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::unbound(), protocols::protein_interface_design::filters::FilterScanFilter::unbound(), protocols::simple_filters::DeltaFilter::unbound(), protocols::simple_filters::DeltaFilter::upper(), protocols::protein_interface_design::filters::Torsion::upper(), protocols::matdes::InterfacePackingFilter::upper_threshold(), and protocols::protein_interface_design::filters::DesignableResiduesFilter::upper_threshold().

val

std::vector< std::vector < core::Real > > protocols::hybridization::val

Referenced by core::optimization::SimpleDerivCheckResult::abs_deriv_dev(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::add(), core::pose::add_comment(), core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >::add_extent_eval(), protocols::denovo_design::architects::BetaSheetArchitect::add_register_shifts(), core::pose::add_score_line_string(), protocols::stepwise::modeler::add_these(), core::scoring::epr_deer::add_to_map(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::add_to_twobody(), protocols::generalized_kinematic_closure::GeneralizedKIC::add_value_to_perturber_value_list(), core::scoring::epr_deer::append_to_map(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::simple_filters::ScoreEvaluator::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::constraints_additional::CombinedConstraintEvaluator::apply(), protocols::calc_taskop_filters::MultipleSigmoids::apply(), protocols::calc_taskop_filters::Operator::apply(), protocols::calc_taskop_filters::Sigmoid::apply(), protocols::evolution::AASynthesisFitnessCost::apply(), protocols::simple_filters::ChainBreak::apply(), protocols::simple_filters::PoseComment::apply(), protocols::simple_filters::SequenceDistance::apply(), protocols::mean_field::AAMatrix::ave_abs_diff(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::bb(), protocols::minimization_packing::TaskAwareMinMover::bb(), core::scoring::epr_deer::metrics::DEERDecayData::bckg(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::bckg_type(), core::optimization::SimpleDerivCheckResult::best_abs_log_norm_ratio(), core::optimization::SimpleDerivCheckResult::best_cos_theta(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::best_fit(), core::optimization::SimpleDerivCheckResult::best_norm_analytic(), core::optimization::SimpleDerivCheckResult::best_norm_numeric(), protocols::frag_picker::VallResidue::bF(), core::scoring::motif::ResPairMotifMetaBinner::bin0_of_real(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::bins_per_a(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::blanket_set(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::bounds(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::calc_orderparam(), protocols::frag_picker::VallResidue::cbx(), protocols::frag_picker::VallResidue::cby(), protocols::frag_picker::VallResidue::cbz(), protocols::canonical_sampling::BiasEnergy::Histogram< T >::cell_index(), protocols::frag_picker::VallResidue::cenx(), protocols::frag_picker::VallResidue::ceny(), protocols::frag_picker::VallResidue::cenz(), core::scoring::func::SOGFunc::check_bounds(), core::scoring::func::SOGFunc_Impl::check_bounds(), protocols::canonical_sampling::BiasEnergy::Histogram< T >::check_range(), protocols::minimization_packing::TaskAwareMinMover::chi(), core::scoring::func::CircularGeneral1D_Func::CircularGeneral1D_Func(), core::membrane::clockwise(), protocols::dna::DnaNeighbor::close(), core::io::silent::SilentStruct::comment_from_line(), core::chemical::gasteiger::compact_enum_set(), protocols::calc_taskop_filters::MultipleSigmoids::compute(), protocols::calc_taskop_filters::Operator::compute(), protocols::calc_taskop_filters::Sigmoid::compute(), protocols::simple_ddg::DdgFilter::compute(), protocols::simple_filters::PoseComment::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(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::connect(), protocols::dna::DnaNeighbor::contact(), core::conformation::parametric::RealValuedParameter::convert_angle(), protocols::ligand_docking::count_buried_unsat_Hbonds(), core::scoring::ScoringManager::create_mhc_map_from_db(), core::scoring::ScoringManager::create_nmer_svm_aa_matrix(), protocols::toolbox::match_enzdes_util::GeomSampleInfo::create_sample_vector(), core::scoring::lkball::cubed_root(), core::scoring::epr_deer::Simulated4PDEERTrace::deer_trace(), core::scoring::epr_deer::Simulated4PDEERTrace::deer_trace_intra(), core::scoring::epr_deer::Simulated4PDEERTrace::depth(), core::scoring::constraints::DOF_Constraint::dfunc(), core::scoring::epr_deer::Simulated4PDEERTrace::dim(), protocols::stepwise::modeler::StepWiseMinimizer::do_clustering(), protocols::relax::FastRelax::dualspace(), core::import_pose::atom_tree_diffs::dump_score_line(), protocols::design_opt::PointMutationCalculator::eval_filters(), protocols::matdes::MatDesPointMutationCalculator::eval_filters(), core::energy_methods::CartesianBondedEnergy::eval_score(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_pair_energies(), protocols::denovo_design::extract_int(), core::scoring::epr_deer::metrics::DEERDecayData::factory(), core::scoring::rna::data::RNA_DMS_Potential::figure_out_potential(), core::pack::hbonds::HBondGraphInitializerIG::finalize_hbond_graph(), core::scoring::epr_deer::metrics::DEERDecayData::fit_stdev(), protocols::mean_field::AAMatrix::frob_distance(), core::scoring::constraints::DOF_Constraint::func(), core::pose::metrics::PoseMetricContainer::get(), core::pose::metrics::StructureDependentCalculator::get(), core::pose::metrics::EnergyDependentCalculator::get(), core::pose::get_comment(), core::scoring::dna::get_mean_median_and_sdev(), core::io::silent::SilentStruct::get_parent_remark_from_line(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::get_prs(), core::scoring::epr_deer::metrics::DEEROverlapMethod::get_score(), core::pose::get_score_line_string(), core::energy_methods::gnl_R_qfht(), protocols::ligand_docking::grid_score_atr_rep(), protocols::abinitio::hash_value(), protocols::frags::heap_extract(), protocols::frags::heap_insert(), protocols::frags::heap_replace(), core::scoring::bin_transitions::BinTransitionData::in_bin(), protocols::match::Matcher::increment_upstream_only_hit_combination(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::initial_search(), core::scoring::SigmoidWeightedCenList< T >::initialize(), protocols::helical_bundle_predict::HBPHelixAssignments::initialize_helices_from_file_contents(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::initialize_kernel(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::integral(), protocols::relax::loop::LoopRelaxMover::intermedrelax(), core::pack::dunbrack::interpolate_polylinear_by_value(), core::pack::dunbrack::interpolate_polylinear_by_value_angles_degrees(), core::pack::dunbrack::interpolate_polylinear_by_value_angles_degrees< 1 >(), core::pack::dunbrack::interpolate_polylinear_by_value_noangles(), core::scoring::EMapVector::is_finite(), core::scoring::bin_transitions::BinTransitionData::is_in_list(), protocols::generalized_kinematic_closure::is_in_list(), protocols::cyclic_peptide::TryDisulfPermutations::is_in_list(), protocols::helical_bundle::BackboneGridSampler::is_in_list(), protocols::helical_bundle::BundleGridSampler::is_in_list(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::is_in_list(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::is_in_list(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::kernel_mult(), core::optimization::MinimizerOptions::linmin_deriv_cutoff(), protocols::splice::Splice::load_pdb_segments_from_pose_comments(), protocols::splice::SpliceOut::load_pdb_segments_from_pose_comments(), protocols::splice::load_pdb_segments_from_pose_comments(), protocols::relax::loop::LoopRelaxMover::loops(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::lower_bound(), core::scoring::epr_deer::metrics::DEERDecayData::max_dist(), protocols::forge::remodel::RemodelLoopMover::max_linear_chainbreak(), core::pose::Pose::metric(), core::scoring::epr_deer::metrics::DEERMiscMethod::mode(), protocols::frag_picker::VallResidue::nali(), core::scoring::epr_deer::metrics::DEERDecayData::noise(), core::scoring::EMapVector::norm_squared(), protocols::frag_picker::VallResidue::omega(), core::fragment::picking_old::vall::VallResidue::omega(), protocols::pack_daemon::InSetExpression::operator()(), core::pack::guidance_scoreterms::sap::MyTemplatePointerHash1< Tval >::operator()(), core::chemical::gasteiger::parse_enum_set(), protocols::helical_bundle::BackboneGridSampler::parse_my_tag(), protocols::helical_bundle::BundleGridSampler::parse_my_tag(), core::conformation::parametric::RealVectorValuedParameter::parse_setting(), core::conformation::parametric::SizeVectorValuedParameter::parse_setting(), protocols::constraint_generator::MetalContactsConstraintGenerator::parse_tag(), protocols::simple_filters::ResidueDepthCalculator::pert_protein(), protocols::frag_picker::VallResidue::phi(), core::fragment::picking_old::vall::VallResidue::phi(), core::pack::dunbrack::polycubic_interpolation(), protocols::optimize_weights::IterativeOptEDriver::print_energies(), protocols::frag_picker::VallResidue::psi(), core::fragment::picking_old::vall::VallResidue::psi(), core::scoring::lDDT_Calculator::R0(), protocols::pose_metric_calculators::FragQualCalculator::ratio_cutoff(), protocols::frag_picker::JCouplingIO::read(), protocols::noesy_assign::PeakFileFormat::read_assignments(), core::scoring::UnfoldedStatePotential::read_database_file(), core::scoring::SplitUnfoldedTwoBodyPotential::read_database_file(), core::scoring::epr_deer::EPRSpinLabel::read_db_file(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), protocols::optimize_weights::PNatAAOptEPositionData::read_from_file(), protocols::simple_filters::ResidueDepthFilter::read_GUIP_matrix(), protocols::noesy_assign::PeakFileFormat::read_header(), protocols::noesy_assign::PeakFileFormat::read_resonances(), protocols::noesy_assign::PeakFileFormat::read_strength(), core::chemical::read_topology_file(), core::scoring::motif::real_to_uint16(), core::scoring::motif::real_to_uint8(), protocols::relax::loop::LoopRelaxMover::refine(), core::optimization::SimpleDerivCheckResult::rel_deriv_dev(), protocols::relax::loop::LoopRelaxMover::relax(), protocols::relax::loop::LoopRelaxMover::remodel(), protocols::calc_taskop_filters::MultipleSigmoids::report(), protocols::calc_taskop_filters::Operator::report(), protocols::calc_taskop_filters::Sigmoid::report(), protocols::evolution::AASynthesisFitnessCost::report(), protocols::simple_filters::ChainBreak::report(), protocols::simple_filters::PoseComment::report(), protocols::simple_filters::SequenceDistance::report(), protocols::calc_taskop_filters::Operator::report_sm(), core::fragment::CacheWrapper< T, XCacheUnit >::retrieve(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::reverse(), protocols::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(), core::scoring::epr_deer::metrics::DEERData::score(), protocols::sic_dock::XfoxmScore::score(), protocols::frag_picker::DiversifyCrmsdByClustering::select_fragments(), core::scoring::EMapVector::set(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::set(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_AHD_cutoff(), core::select::util::SelectResiduesByLayer::set_angle_exponent(), core::select::residue_selector::LayerSelector::set_angle_exponent(), core::select::util::SelectResiduesByLayer::set_angle_shift_factor(), core::select::residue_selector::LayerSelector::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::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::set_cis_peptide_bonds(), protocols::simple_moves::ExplicitWaterMover::set_clust_cutoff(), protocols::simple_moves::ExplicitWaterMover::set_clust_radius(), core::scoring::PolymerBondedEnergyContainer::set_computed(), 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_helix_length(), core::optimization::BrentLineMinimization::set_deriv_cutoff(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_dist_cutoff(), core::select::util::SelectResiduesByLayer::set_dist_exponent(), core::select::residue_selector::LayerSelector::set_dist_exponent(), core::select::util::SelectResiduesByLayer::set_dist_midpoint(), protocols::simple_moves::ExplicitWaterMover::set_dwell_cutoff(), 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::simple_moves::ExplicitWaterMover::set_gen_fixed(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_generous_hbonds(), protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::set_hbonds(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_hxl_dist_cutoff(), protocols::flxbb::LayerDesignOperation::set_ignore_pikaa_natro(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_iterations(), protocols::helical_bundle::MakeBundle::set_last_apply_failed(), protocols::helical_bundle::MakeBundleHelix::set_last_apply_failed(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_layered_sasa(), protocols::make_rot_lib::RotData::set_lib_chi_val(), protocols::simple_moves::ExplicitWaterMover::set_lkb_clust_rad(), protocols::simple_moves::ExplicitWaterMover::set_lkb_overlap_dist(), protocols::simple_moves::ExplicitWaterMover::set_lkb_rotset_radius(), 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::buns::BuriedUnsatisfiedPolarsCalculator2::set_metal_dist_cutoff(), protocols::cyclic_peptide::TryDisulfPermutations::set_mintolerance(), core::conformation::symmetry::SymmetryTransform::set_mirror_z(), core::conformation::symmetry::VirtualCoordinate::set_mirror_z(), protocols::simple_moves::ExplicitWaterMover::set_mode(), protocols::cryst::MakeLayerMover::set_moving_lattice(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_must_switch_bins(), protocols::simple_moves::bin_transitions::PerturbByBins::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::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::generalized_kinematic_closure::GeneralizedKIC::set_perturber_iterations(), protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_must_switch_bins(), protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::set_pose_energy(), protocols::simple_moves::MutateResidue::set_preserve_atom_coords(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_rama_cutoff_energy(), protocols::cryst::MakeLatticeMover::set_refinable_lattice(), protocols::denovo_design::filters::SSShapeComplementarityFilter::set_rejection_thresh(), protocols::helical_bundle::BundleReporterFilter::set_report_sequence(), protocols::helical_bundle::BundleGridSampler::set_reset_mode(), protocols::helical_bundle::BackboneGridSampler::set_residues_per_repeat(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_resnum(), protocols::protein_interface_design::filters::HbondsToResidueFilter::set_resnum(), protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary::set_rmsd(), core::select::util::SelectResiduesByLayer::set_rsd_neighbor_denominator(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange::set_sampler_values(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_sasa_burial_cutoff(), core::select::residue_selector::LayerSelector::set_sc_neighbor_denominator(), core::select::residue_selector::LayerSelector::set_sc_neighbor_dist_midpoint(), 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::energy_methods::ProClosureEnergy::set_skip_ring_closure(), protocols::jd2::MPIWorkPoolJobDistributor::set_starter_for_sequential_distribution(), core::scoring::dna::DNA_BasePotential::set_stiffness(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_sulph_dist_cutoff(), core::scoring::packing::PoseBalls::set_surf(), protocols::simple_moves::ExplicitWaterMover::set_taskop(), protocols::cryst::DockLatticeMover::set_temp(), core::io::ResidueInformation::set_temp(), protocols::canonical_sampling::BiasEnergy::set_temperature(), protocols::filters::CombinedFilter::set_threshold(), protocols::helical_bundle::MakeBundle::set_use_degrees(), core::select::residue_selector::LayerSelector::set_use_sc_neighbors(), protocols::flxbb::LayerDesignOperation::set_use_symmetry(), protocols::helical_bundle::BundleReporterFilter::set_use_threeletter(), core::energy_methods::GoapRsdType::set_using(), protocols::cryst::MakeLatticeMover::set_validate_lattice(), protocols::noesy_assign::CrossPeak::set_volume(), protocols::simple_moves::ExplicitWaterMover::set_watlim_scale(), protocols::electron_density::DockFragmentsIntoDensityMover::setCenterOnMiddleCA(), protocols::electron_density::DockPDBIntoDensityMover::setRotateOnSeqCenter(), core::scoring::EMapVector::show_if_nonzero_weight(), core::scoring::EMapVector::show_nonzero(), core::scoring::EMapVector::show_weighted(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::singleval(), protocols::symmetry::SetupForSymmetryMover::slide_into_contact(), core::scoring::epr_deer::Simulated4PDEERTrace::slope(), core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >::static_set(), core::scoring::epr_deer::metrics::DEERData::stdev(), core::chemical::mainchain_potential::MainchainScoreTable::symmetrize_tensor(), protocols::match::Matcher::test_upstream_only_hit_incompatibility(), protocols::optimize_weights::IterativeOptEDriver::test_weight_sensitivity(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), core::scoring::epr_deer::Simulated4PDEERTrace::time_pts(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::time_pts(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::trace(), protocols::loops::Loops::transfer_to_residue_vector(), core::scoring::motif::uint16_to_real(), core::scoring::motif::uint8_to_real(), protocols::symmetry::SetupForSequenceSymmetryMover::validate_residue_selectors(), core::scoring::hbonds::FadeInterval::value_deriv(), protocols::noesy_assign::PeakFileFormat::write_assignment(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), protocols::noesy_assign::PeakFileFormat_xpk::write_assignment(), protocols::noesy_assign::PeakFileFormat::write_assignment_stats(), protocols::noesy_assign::PeakFileFormat::write_assignments(), protocols::noesy_assign::PeakFileFormat::write_resonances(), protocols::frag_picker::VallResidue::x(), core::fragment::picking_old::vall::VallResidue::x(), protocols::frag_picker::VallResidue::y(), core::fragment::picking_old::vall::VallResidue::y(), protocols::frag_picker::VallResidue::z(), and core::fragment::picking_old::vall::VallResidue::z().

xa

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

Referenced by protocols::hybridization::TMalign::score_fun8(), protocols::sic_dock::SICFast::slide_into_contact(), protocols::sic_dock::slide_into_contact_and_score(), protocols::sic_dock::slide_into_contact_and_score_DEPRICATED(), and protocols::sic_dock::SICFast::slide_into_contact_DEPRICATED().

xlen

int protocols::hybridization::xlen

Referenced by protocols::hybridization::TMalign::parameter_set4search().

xresno

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

Referenced by protocols::hybridization::TMalign::get_initial_fgt().

xt

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

xtm

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

Referenced by protocols::hybridization::TMalign::TMscore8_search().

ya

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

Referenced by protocols::hybridization::TMalign::score_fun8().

ylen

int protocols::hybridization::ylen

Referenced by protocols::hybridization::TMalign::parameter_set4search().

yresno

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

Referenced by protocols::hybridization::TMalign::get_initial_fgt().

ytm

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

Referenced by protocols::hybridization::TMalign::TMscore8_search().