Namespaces
	cenrot

	peptoid

Classes
class	BBDepNRChiSample
	P for precision. More...

struct	BBDepScoreInterpData

class	BBDepSemiRotamericData
	A class to hold rotamer building data on the stack and yet have it accessible to derived classes when invoking base class functions. An alternative would have been to store mutable member data in the Library class itself. This option, however, is not thread safe. This data is used by the SemiRotamericSRDL class for when building backbone dependent rotamers. More...

class	BBIndNRChiSample

class	BBIndSemiRotamericData
	A class to hold rotamer building data on the stack and yet have it accessible to derived classes when invoking base class functions. An alternative would have been to store mutable member data in the Library class itself. This option, however, is not thread safe. This data is used by the SemiRotamericSRDL class for when building backbone independent rotamers. More...

class	ChiSet

class	CoarseRotamer

class	CoarseRotamerSet

class	CoarseSingleResidueLibrary

class	DunbrackConstraint

class	DunbrackConstraintCreator
	Mover creator for the DunbrackConstraint constraint. More...

class	DunbrackEnergy

class	DunbrackEnergyCreator

class	DunbrackRotamer
	forward declaration; default precision is DunbrackReal More...

class	DunbrackRotamerMeanSD
	forward declaration; default precision is DunbrackReal More...

class	DunbrackRotamerSampleData

class	PackedDunbrackRotamer
	forward declaration; default precision is DunbrackReal; More...

class	ProbSortClass

class	RotamerBuildingData
	a simple class for passing data around in virtual function calls of the rotamer creating process. Derived classes will be simple containers for interpolated rotameric data that 1) has to be available to the derived class when building rotamers and 2) cannot be stored as member data in the derived class in a thread-safe manner. Derived classes of the RotamerBuildingData can be declared on the stack, passed into the RotamericSingleResidueDunbrackLibrary::build_chi_sets function, and then in the (virtual) chisamples_for_rotamer function, the derived classes may be downcast. More...

class	RotamerConstraint
	This class favors a particular rotamer at a particular position by reducing its Dunbrack energy. More...

class	RotamericData
	DOUG DOUG DOUG. More...

class	RotamericSingleResidueDunbrackLibrary
	DOUG DOUG DOUG. More...

class	RotamericSingleResiduePeptoidLibrary

class	RotamerLibrary

class	RotamerLibraryScratchSpace

class	SemiRotamericSingleResidueDunbrackLibrary
	This class is meant to represent the non-rotameric chi observed in several amino acids (asn, asp, gln, glu, his, phe, trp, tyr ) which are rotameric for the chi closest to the backbone and non rotameric for exactly one chi angle. This non-rotameric chi (abv. nrchi) is the last chi for each of these 8 amino acids except tyrosine, where this chi is the last heavy-atom chi. The last chi on tyrosine governs a hydroxyl. Unlike in the fully rotameric residues, the last heavyatom chi in semi-rotameric residues do not "communicate" to the rotameric chi. That is, in the rotameric chi, the mean chi1 value is sensitive to the chi3 value. If the third diherdal switches from trans to g+, then chi1 would shift in response. Changes to the non-rotameric chi do not effect the rotameric chi. The data structure here is good for this model but no other. More...

class	SingleLigandRotamerLibrary
	A fixed library of conformations for some residue type (doesn't have to be a ligand). More...

class	SingleResidueDunbrackLibrary

class	SingleResidueDunbrackLibraryConcrete

class	SingleResiduePeptoidLibrary

class	SingleResidueRotamerLibrary
	SingleResidueRotamerLibrary pure virtual base class. More...

Typedefs
typedef utility::pointer::owning_ptr < ChiSet >	ChiSetOP

typedef utility::pointer::owning_ptr < ChiSet const >	ChiSetCOP

typedef utility::pointer::owning_ptr < CoarseRotamer >	CoarseRotamerOP

typedef utility::pointer::owning_ptr < CoarseRotamer const >	CoarseRotamerCOP

typedef utility::pointer::owning_ptr < CoarseRotamerSet >	CoarseRotamerSetOP

typedef utility::pointer::owning_ptr < CoarseRotamerSet const >	CoarseRotamerSetCOP

typedef utility::pointer::owning_ptr < CoarseSingleResidueLibrary >	CoarseSingleResidueLibraryOP

typedef utility::pointer::owning_ptr < CoarseSingleResidueLibrary const >	CoarseSingleResidueLibraryCOP

typedef utility::pointer::owning_ptr < DunbrackConstraint >	DunbrackConstraintOP

typedef utility::pointer::owning_ptr < DunbrackConstraint const >	DunbrackConstraintCOP

typedef float	DunbrackReal

typedef utility::vector1< Size >	RotVector

typedef utility::vector1< Real >	ChiVector

typedef utility::vector1< Real >	AngleVector

typedef utility::pointer::owning_ptr < RotamerConstraint >	RotamerConstraintOP

typedef utility::pointer::owning_ptr < RotamerConstraint const >	RotamerConstraintCOP

typedef utility::pointer::owning_ptr < RotamerLibrary >	RotamerLibraryOP

typedef utility::pointer::owning_ptr < RotamerLibrary const >	RotamerLibraryCOP

typedef utility::fixedsizearray1< Real, DUNBRACK_MAX_SCTOR >	Real4

typedef utility::fixedsizearray1< Size, DUNBRACK_MAX_SCTOR >	Size4

typedef utility::fixedsizearray1< Real, DUNBRACK_MAX_BBTOR >	Real3

typedef utility::fixedsizearray1< Size, DUNBRACK_MAX_BBTOR >	Size3

typedef utility::pointer::owning_ptr < RotamerLibraryScratchSpace >	RotamerLibraryScratchSpaceOP

typedef utility::pointer::owning_ptr < RotamerLibraryScratchSpace const >	RotamerLibraryScratchSpaceCOP

typedef utility::pointer::owning_ptr < SingleLigandRotamerLibrary >	SingleLigandRotamerLibraryOP

typedef utility::pointer::owning_ptr < SingleLigandRotamerLibrary const >	SingleLigandRotamerLibraryCOP

typedef utility::pointer::access_ptr < SingleLigandRotamerLibrary >	SingleLigandRotamerLibraryAP

typedef utility::pointer::access_ptr < SingleLigandRotamerLibrary const >	SingleLigandRotamerLibraryCAP

typedef utility::pointer::owning_ptr < SingleResidueDunbrackLibrary >	SingleResidueDunbrackLibraryOP

typedef utility::pointer::access_ptr < SingleResidueDunbrackLibrary >	SingleResidueDunbrackLibraryAP

typedef utility::pointer::owning_ptr < SingleResidueDunbrackLibrary const >	SingleResidueDunbrackLibraryCOP

typedef utility::pointer::access_ptr < SingleResidueDunbrackLibrary const >	SingleResidueDunbrackLibraryCAP

typedef utility::pointer::owning_ptr < SingleResiduePeptoidLibrary >	SingleResiduePeptoidLibraryOP

typedef utility::pointer::access_ptr < SingleResiduePeptoidLibrary >	SingleResiduePeptoidLibraryAP

typedef utility::pointer::owning_ptr < SingleResiduePeptoidLibrary const >	SingleResiduePeptoidLibraryCOP

typedef utility::pointer::access_ptr < SingleResiduePeptoidLibrary const >	SingleResiduePeptoidLibraryCAP

typedef utility::pointer::owning_ptr < SingleResidueRotamerLibrary >	SingleResidueRotamerLibraryOP

typedef utility::pointer::owning_ptr < SingleResidueRotamerLibrary const >	SingleResidueRotamerLibraryCOP

typedef utility::pointer::access_ptr < SingleResidueRotamerLibrary >	SingleResidueRotamerLibraryAP

typedef utility::pointer::access_ptr < SingleResidueRotamerLibrary const >	SingleResidueRotamerLibraryCAP

typedef utility::vector1 < conformation::ResidueOP >	RotamerVector

Functions
void	bicubic_interpolation (Real v00, Real d2dx200, Real d2dy200, Real d4dx2y200, Real v01, Real d2dx201, Real d2dy201, Real d4dx2y201, Real v10, Real d2dx210, Real d2dy210, Real d4dx2y210, Real v11, Real d2dx211, Real d2dy211, Real d4dx2y211, Real dxp, Real dyp, Real binwx, Real binwy, Real &val, Real &dvaldx, Real &dvaldy)
	Interpolate in a grid with the values, and second derivatives given, and simultaneously evaluate the derivative. No option for working with periodic ranges. Instead, make sure that interpolation doesn't need to span > 180 degrees. More...

void	tricubic_interpolation (Real v000, Real dvdx000, Real dvdy000, Real dvdz000, Real dvdxy000, Real dvdxz000, Real dvdyz000, Real dvdxyz000, Real v001, Real dvdx001, Real dvdy001, Real dvdz001, Real dvdxy001, Real dvdxz001, Real dvdyz001, Real dvdxyz001, Real v010, Real dvdx010, Real dvdy010, Real dvdz010, Real dvdxy010, Real dvdxz010, Real dvdyz010, Real dvdxyz010, Real v011, Real dvdx011, Real dvdy011, Real dvdz011, Real dvdxy011, Real dvdxz011, Real dvdyz011, Real dvdxyz011, Real v100, Real dvdx100, Real dvdy100, Real dvdz100, Real dvdxy100, Real dvdxz100, Real dvdyz100, Real dvdxyz100, Real v101, Real dvdx101, Real dvdy101, Real dvdz101, Real dvdxy101, Real dvdxz101, Real dvdyz101, Real dvdxyz101, Real v110, Real dvdx110, Real dvdy110, Real dvdz110, Real dvdxy110, Real dvdxz110, Real dvdyz110, Real dvdxyz110, Real v111, Real dvdx111, Real dvdy111, Real dvdz111, Real dvdxy111, Real dvdxz111, Real dvdyz111, Real dvdxyz111, Real dxp, Real dyp, Real dzp, Real binwx, Real binwy, Real binwz, Real &val, Real &dvaldx, Real &dvaldy, Real &dvaldz)

void	interpolate_rotamers (DunbrackRotamer< FOUR > const &rot00, DunbrackRotamer< FOUR > const &rot10, DunbrackRotamer< FOUR > const &rot01, DunbrackRotamer< FOUR > const &rot11, Real phi_err, Real psi_err, Real binrange, Size nchi_aa, DunbrackRotamer< FOUR, Real > &interpolated_rotamer)

void	expand_proton_chi_oldversion (pack::task::ExtraRotSample ex_samp_level, chemical::ResidueTypeCOP concrete_residue, Size proton_chi, utility::vector1< ChiSetOP > &chi_set_vector)

void	expand_proton_chi (pack::task::ExtraRotSample ex_samp_level, chemical::ResidueTypeCOP concrete_residue, Size proton_chi, utility::vector1< ChiSetOP > &chi_set_vector)
	Should this be here? More...

template<Size S>
DunbrackRotamer< S, Real >	increase_rotamer_precision (DunbrackRotamer< S, DunbrackReal > const &original_rotamer)

void	load_unboundrot (pose::Pose &pose)
	Convenience function adds constraints to the supplied pose based on the -unboundrot command line flag. More...

void	load_unboundrot (pose::Pose &pose, core::pose::PoseCOPs const &unboundrot_poses)
	Convenience function adds constraints to the supplied pose based on the list of provided poses. More...

void	rotamer_from_chi (conformation::Residue const &rsd, RotVector &rot)
	helper that'll determine the rotamer bins for a residue by asking its associated rotamer library for that information. More...

void	rotamer_from_chi (chemical::ResidueType const &rsd_type, ChiVector const &chi, RotVector &rot)
	helper that'll determine the rotamer bins for a residue_type by asking its associated rotamer library for that information. Takes chi vector as input parameter. More...

void	rotamer_from_chi_02 (ChiVector const &chi,chemical::AA const res,RotVector &rot)
	Do not bother calling this function if you're interested in staying up to date with changes in the rotamer library. Call rotamer_from_chi instead. It will eventually call this function iff dun10 is not set to true. More...

*void	rotamer_from_chi_02 (Real4 const &chi, chemical::AA const res, Size nchi, Size4 &rot)

void	read_dunbrack_library (RotamerLibrary &rotamer_library)

Real	subtract_chi_angles (Real chi1, Real chi2, chemical::AA const &aa, int chino)
	Find the difference in angles between two chi values using hard-coded symmetry information for the symmetric amino acids. Disappears for 2010 library. More...

bool	psc_compare (ProbSortClass left, ProbSortClass right)

void	dump_library (std::string filename, RotamerVector const &rotamers)

conformation::ResidueOP	dup_residue (conformation::Residue const &existing, conformation::Residue const &conformer)
	Helper function for superposition. More...

Variables
static basic::Tracer	TR ("core.pack.dunbrack.DunbrackConstraint")

Size const	ONE = 1

Size const	TWO = 2

Size const	THREE = 3

Size const	FOUR = 4

static basic::Tracer	TR ("core.pack.dunbrack.RotamerConstraint")

	c
	DEPRICATED convert between the real-valued chi dihedrals and the rotamer well indices. More...

Size const	DUNBRACK_MAX_BBTOR = 3

Size const	DUNBRACK_MAX_SCTOR = 4

static basic::Tracer	TR ("core.pack.dunbrack.SingleLigandRotamerLibrary")

static basic::Tracer	SRDL_TR ("core.pack.dunbrack")

static basic::Tracer	SRPL_TR ("core.pack.dunbrack")

static const Real	MIN_ROT_PROB = 1.e-8

Typedef Documentation

typedef utility::vector1< Real > core::pack::dunbrack::AngleVector

typedef utility::pointer::owning_ptr< ChiSet const > core::pack::dunbrack::ChiSetCOP

typedef utility::pointer::owning_ptr< ChiSet > core::pack::dunbrack::ChiSetOP

typedef utility::vector1< Real > core::pack::dunbrack::ChiVector

typedef utility::pointer::owning_ptr< CoarseRotamer const > core::pack::dunbrack::CoarseRotamerCOP

typedef utility::pointer::owning_ptr< CoarseRotamer > core::pack::dunbrack::CoarseRotamerOP

typedef utility::pointer::owning_ptr< CoarseRotamerSet const > core::pack::dunbrack::CoarseRotamerSetCOP

typedef utility::pointer::owning_ptr< CoarseRotamerSet > core::pack::dunbrack::CoarseRotamerSetOP

typedef utility::pointer::owning_ptr< CoarseSingleResidueLibrary const > core::pack::dunbrack::CoarseSingleResidueLibraryCOP

typedef utility::pointer::owning_ptr< CoarseSingleResidueLibrary > core::pack::dunbrack::CoarseSingleResidueLibraryOP

typedef utility::pointer::owning_ptr< DunbrackConstraint const > core::pack::dunbrack::DunbrackConstraintCOP

typedef utility::pointer::owning_ptr< DunbrackConstraint > core::pack::dunbrack::DunbrackConstraintOP

typedef float core::pack::dunbrack::DunbrackReal

Low precision in Dunbrack rotamer library suggests no need to store chi dihedrals and standard deviations with 64 bits.

typedef utility::fixedsizearray1< Real, DUNBRACK_MAX_BBTOR > core::pack::dunbrack::Real3

typedef utility::fixedsizearray1< Real, DUNBRACK_MAX_SCTOR > core::pack::dunbrack::Real4

typedef utility::pointer::owning_ptr< RotamerConstraint const > core::pack::dunbrack::RotamerConstraintCOP

typedef utility::pointer::owning_ptr< RotamerConstraint > core::pack::dunbrack::RotamerConstraintOP

typedef utility::pointer::owning_ptr< RotamerLibrary const > core::pack::dunbrack::RotamerLibraryCOP

typedef utility::pointer::owning_ptr< RotamerLibrary > core::pack::dunbrack::RotamerLibraryOP

typedef utility::pointer::owning_ptr< RotamerLibraryScratchSpace const > core::pack::dunbrack::RotamerLibraryScratchSpaceCOP

typedef utility::pointer::owning_ptr< RotamerLibraryScratchSpace > core::pack::dunbrack::RotamerLibraryScratchSpaceOP

typedef utility::vector1< conformation::ResidueOP > core::pack::dunbrack::RotamerVector

typedef utility::vector1< Size > core::pack::dunbrack::RotVector

typedef utility::pointer::access_ptr< SingleLigandRotamerLibrary > core::pack::dunbrack::SingleLigandRotamerLibraryAP

typedef utility::pointer::access_ptr< SingleLigandRotamerLibrary const > core::pack::dunbrack::SingleLigandRotamerLibraryCAP

typedef utility::pointer::owning_ptr< SingleLigandRotamerLibrary const > core::pack::dunbrack::SingleLigandRotamerLibraryCOP

typedef utility::pointer::owning_ptr< SingleLigandRotamerLibrary > core::pack::dunbrack::SingleLigandRotamerLibraryOP

typedef utility::pointer::access_ptr< SingleResidueDunbrackLibrary > core::pack::dunbrack::SingleResidueDunbrackLibraryAP

typedef utility::pointer::access_ptr< SingleResidueDunbrackLibrary const > core::pack::dunbrack::SingleResidueDunbrackLibraryCAP

typedef utility::pointer::owning_ptr< SingleResidueDunbrackLibrary const > core::pack::dunbrack::SingleResidueDunbrackLibraryCOP

typedef utility::pointer::owning_ptr< SingleResidueDunbrackLibrary > core::pack::dunbrack::SingleResidueDunbrackLibraryOP

typedef utility::pointer::access_ptr< SingleResiduePeptoidLibrary > core::pack::dunbrack::SingleResiduePeptoidLibraryAP

typedef utility::pointer::access_ptr< SingleResiduePeptoidLibrary const > core::pack::dunbrack::SingleResiduePeptoidLibraryCAP

typedef utility::pointer::owning_ptr< SingleResiduePeptoidLibrary const > core::pack::dunbrack::SingleResiduePeptoidLibraryCOP

typedef utility::pointer::owning_ptr< SingleResiduePeptoidLibrary > core::pack::dunbrack::SingleResiduePeptoidLibraryOP

typedef utility::pointer::access_ptr< SingleResidueRotamerLibrary > core::pack::dunbrack::SingleResidueRotamerLibraryAP

typedef utility::pointer::access_ptr< SingleResidueRotamerLibrary const > core::pack::dunbrack::SingleResidueRotamerLibraryCAP

typedef utility::pointer::owning_ptr< SingleResidueRotamerLibrary const > core::pack::dunbrack::SingleResidueRotamerLibraryCOP

typedef utility::pointer::owning_ptr< SingleResidueRotamerLibrary > core::pack::dunbrack::SingleResidueRotamerLibraryOP

typedef utility::fixedsizearray1< Size, DUNBRACK_MAX_BBTOR > core::pack::dunbrack::Size3

typedef utility::fixedsizearray1< Size, DUNBRACK_MAX_SCTOR > core::pack::dunbrack::Size4

Function Documentation

void core::pack::dunbrack::bicubic_interpolation	(	Real	v00,
		Real	d2dx200,
		Real	d2dy200,
		Real	d4dx2y200,
		Real	v01,
		Real	d2dx201,
		Real	d2dy201,
		Real	d4dx2y201,
		Real	v10,
		Real	d2dx210,
		Real	d2dy210,
		Real	d4dx2y210,
		Real	v11,
		Real	d2dx211,
		Real	d2dy211,
		Real	d4dx2y211,
		Real	dxp,
		Real	dyp,
		Real	binwx,
		Real	binwy,
		Real &	val,
		Real &	dvaldx,
		Real &	dvaldy
	)

Interpolate in a grid with the values, and second derivatives given, and simultaneously evaluate the derivative. No option for working with periodic ranges. Instead, make sure that interpolation doesn't need to span > 180 degrees.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers().

void core::pack::dunbrack::dump_library	(	std::string	filename,
		RotamerVector const &	rotamers
	)

References core::io::pdb::dump_pdb_residue(), and out.

conformation::ResidueOP core::pack::dunbrack::dup_residue	(	conformation::Residue const &	existing,
		conformation::Residue const &	conformer
	)

Helper function for superposition.

Helper function, combines existing's metadata with conformer's conformation.

References core::conformation::Residue::chain(), core::conformation::Residue::clone(), and core::conformation::Residue::seqpos().

Referenced by core::pack::dunbrack::SingleLigandRotamerLibrary::fill_rotamer_vector().

void core::pack::dunbrack::expand_proton_chi	(	pack::task::ExtraRotSample	ex_samp_level,
		chemical::ResidueTypeCOP	concrete_residue,
		Size	proton_chi,
		utility::vector1< ChiSetOP > &	chi_set_vector
	)

Should this be here?

olli – I think this is slightly simpler to read than the original version apl – needs to find a new residence

References core::pack::task::NO_EXTRA_CHI_SAMPLES.

Referenced by core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::build_proton_chi_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), and core::pack::dunbrack::SingleLigandRotamerLibrary::fill_rotamer_vector().

void core::pack::dunbrack::expand_proton_chi_oldversion	(	pack::task::ExtraRotSample	ex_samp_level,
		chemical::ResidueTypeCOP	concrete_residue,
		Size	proton_chi,
		utility::vector1< ChiSetOP > &	chi_set_vector
	)

References core::pack::task::NO_EXTRA_CHI_SAMPLES.

template<Size S>

DunbrackRotamer< S, Real > core::pack::dunbrack::increase_rotamer_precision ( DunbrackRotamer< S, DunbrackReal > const & original_rotamer )

References core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::chi_mean(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::chi_sd(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotamer_probability(), core::pack::dunbrack::DunbrackRotamer< S, P >::rotwell(), and core::chemical::element::S.

Referenced by average_rotamers(), and find_most_frequent_rotamer().

void core::pack::dunbrack::interpolate_rotamers	(	DunbrackRotamer< FOUR > const &	rot00,
		DunbrackRotamer< FOUR > const &	rot10,
		DunbrackRotamer< FOUR > const &	rot01,
		DunbrackRotamer< FOUR > const &	rot11,
		Real	phi_err,
		Real	psi_err,
		Real	binrange,
		Size	nchi_aa,
		DunbrackRotamer< FOUR, Real > &	interpolated_rotamer
	)

interpolates the angles and the sdevs as Reals (doubles)

References core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::chi_mean(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::chi_sd(), interpolate_bilinear_by_value(), basic::interpolate_bilinear_by_value(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotamer_probability(), core::pack::dunbrack::DunbrackRotamer< S, P >::rotwell(), and utility_exit_with_message.

void core::pack::dunbrack::load_unboundrot ( pose::Pose & pose )

Convenience function adds constraints to the supplied pose based on the -unboundrot command line flag.

References core::io::pdb::build_pose_from_pdb_as_is(), filename(), option, core::io::serialization::size(), and TR.

void core::pack::dunbrack::load_unboundrot	(	pose::Pose &	pose,
		core::pose::PoseCOPs const &	unboundrot_poses
	)

Convenience function adds constraints to the supplied pose based on the list of provided poses.

References core::pose::Pose::add_constraint(), core::pack::dunbrack::RotamerLibrary::get_instance(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::name(), residue, core::pose::Pose::total_residue(), TR, and core::conformation::Residue::type().

bool core::pack::dunbrack::psc_compare	(	ProbSortClass	left,
		ProbSortClass	right
	)

References core::pack::dunbrack::ProbSortClass::probability_.

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotamer_definitions().

void core::pack::dunbrack::read_dunbrack_library ( RotamerLibrary & rotamer_library )

References core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries().

Referenced by core::pack::dunbrack::RotamerLibrary::create_singleton_instance().

void core::pack::dunbrack::rotamer_from_chi	(	conformation::Residue const &	rsd,
		RotVector &	rot
	)

helper that'll determine the rotamer bins for a residue by asking its associated rotamer library for that information.

References core::conformation::Residue::aa(), core::conformation::Residue::chi(), core::pack::dunbrack::RotamerLibrary::get_instance(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::chemical::num_canonical_aas, and core::conformation::Residue::type().

Referenced by core::pack::dunbrack::RotamerConstraint::add_residue(), core::pack::dunbrack::DunbrackConstraint::score(), and core::pack::dunbrack::RotamerConstraint::score().

void core::pack::dunbrack::rotamer_from_chi	(	chemical::ResidueType const &	rsd_type,
		ChiVector const &	chi,
		RotVector &	rot
	)

helper that'll determine the rotamer bins for a residue_type by asking its associated rotamer library for that information. Takes chi vector as input parameter.

References core::pack::dunbrack::RotamerLibrary::get_instance(), and core::pack::dunbrack::RotamerLibrary::get_rsd_library().

void core::pack::dunbrack::rotamer_from_chi_02	(	ChiVector const &	chi,
		chemical::AA const	res,
		RotVector &	rot
	)

Do not bother calling this function if you're interested in staying up to date with changes in the rotamer library. Call rotamer_from_chi instead. It will eventually call this function iff dun10 is not set to true.

References DUNBRACK_MAX_SCTOR.

Referenced by core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >::get_rotamer_from_chi_static(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi_static().

void core::pack::dunbrack::rotamer_from_chi_02	(	Real4 const &	chi,
		chemical::AA const	res,
		Size	nchi,
		Size4 &	rot
	)

References core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_trp, core::chemical::aa_tyr, chemical, core::chemical::num_canonical_aas, and basic::periodic_range().

Real core::pack::dunbrack::subtract_chi_angles	(	Real	chi1,
		Real	chi2,
		chemical::AA const &	aa,
		int	chino
	)

Find the difference in angles between two chi values using hard-coded symmetry information for the symmetric amino acids. Disappears for 2010 library.

2002 Library hard code symmetry information.

References core::chemical::aa_asp, core::chemical::aa_glu, core::chemical::aa_phe, core::chemical::aa_tyr, chemical, basic::periodic_range(), and periodic_range().

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv().

void core::pack::dunbrack::tricubic_interpolation	(	Real	v000,
		Real	dvdx000,
		Real	dvdy000,
		Real	dvdz000,
		Real	dvdxy000,
		Real	dvdxz000,
		Real	dvdyz000,
		Real	dvdxyz000,
		Real	v001,
		Real	dvdx001,
		Real	dvdy001,
		Real	dvdz001,
		Real	dvdxy001,
		Real	dvdxz001,
		Real	dvdyz001,
		Real	dvdxyz001,
		Real	v010,
		Real	dvdx010,
		Real	dvdy010,
		Real	dvdz010,
		Real	dvdxy010,
		Real	dvdxz010,
		Real	dvdyz010,
		Real	dvdxyz010,
		Real	v011,
		Real	dvdx011,
		Real	dvdy011,
		Real	dvdz011,
		Real	dvdxy011,
		Real	dvdxz011,
		Real	dvdyz011,
		Real	dvdxyz011,
		Real	v100,
		Real	dvdx100,
		Real	dvdy100,
		Real	dvdz100,
		Real	dvdxy100,
		Real	dvdxz100,
		Real	dvdyz100,
		Real	dvdxyz100,
		Real	v101,
		Real	dvdx101,
		Real	dvdy101,
		Real	dvdz101,
		Real	dvdxy101,
		Real	dvdxz101,
		Real	dvdyz101,
		Real	dvdxyz101,
		Real	v110,
		Real	dvdx110,
		Real	dvdy110,
		Real	dvdz110,
		Real	dvdxy110,
		Real	dvdxz110,
		Real	dvdyz110,
		Real	dvdxyz110,
		Real	v111,
		Real	dvdx111,
		Real	dvdy111,
		Real	dvdz111,
		Real	dvdxy111,
		Real	dvdxz111,
		Real	dvdyz111,
		Real	dvdxyz111,
		Real	dxp,
		Real	dyp,
		Real	dzp,
		Real	binwx,
		Real	binwy,
		Real	binwz,
		Real &	val,
		Real &	dvaldx,
		Real &	dvaldy,
		Real &	dvaldz
	)

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_score().

Variable Documentation

core::pack::dunbrack::c

DEPRICATED convert between the real-valued chi dihedrals and the rotamer well indices.

This code comes directly from Roland Dunbrack. In certain rare edge cases, floating point comparison breaks down (e.g. ! x >= 120.0 && ! x < 120.0 ) and Dunbrack's code leaves the rotamer well unassigned – a value of zero. I'm modifying the code to guarantee that the rotamer well is assigned, but so that Dunbrack's original form is still recognizable. e.g. if (x) a; if (y) b; if (z) c; now reads as: if (x) a; else if ( y ) b; else /*if (z)

Referenced by core::fragment::picking_old::vall::VallResidue::aa(), core::pose::Pose::annotated_sequence(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared(), core::scoring::sc::ShapeComplementarityCalculator::CalcNeighborDistance(), core::sequence::AnnotatedSequence::calculate_map(), core::pack::task::operation::RotamerExplosion::chi(), core::scoring::packstat::compute_cav_ball_clusters(), core::scoring::packstat::compute_cav_ball_neighbor_count(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR(), core::chemical::orbitals::AssignOrbitals::Coordinates_TriganolPlanar_bondedto1atom_helper(), core::scoring::orbitals::OrbitalsAssigned::CoordinatesDihedral(), core::scoring::etable::Etable::cubic_polynomial_from_spline(), core::sequence::DP_Matrix::DP_Matrix(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), core::scoring::methods::MetalloPlacementEnergy::finalize_total_energy(), core::chemical::find_chi_bonds(), core::scoring::frdc(), core::scoring::frdcDa(), core::scoring::frdcDaR(), core::scoring::frdcR(), core::kinematics::TreeVizBuilder::get_ft_node_bounds(), core::pose::symmetry::get_full_intracomponent_subs(), core::scoring::disulfides::RT_helper::get_ncac(), core::scoring::dna::DirectReadoutPotential::get_xy_bin(), core::scoring::dna::DirectReadoutPotential::get_z_bin(), core::scoring::SecondaryStructurePotential::identify_ss(), core::scoring::hbonds::HBondDatabase::initialize_HBPoly1D(), core::scoring::jacobi(), core::scoring::jacobi3(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), core::scoring::electron_density::KromerMann::KromerMann(), core::scoring::saxs::FormFactorManager::load_ff(), core::scoring::saxs::FormFactorManager::load_ff_from_db(), core::scoring::etable::MembEtable::modify_pot(), core::scoring::etable::Etable::modify_pot_one_pair(), core::chemical::gasteiger::parse_enum_set(), core::fragment::SecstructSRFD::read_data(), core::scoring::constraints::ConstraintIO::read_individual_constraint_new(), core::scoring::dssp::read_pairing_list(), core::fragment::picking_old::vall::VallResidue::ss(), core::scoring::methods::ProQ_Energy::stride_feature(), core::scoring::sc::MolecularSurfaceCalculator::SubDiv(), and core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::svdcmp().

Size const core::pack::dunbrack::DUNBRACK_MAX_BBTOR = 3

Size const core::pack::dunbrack::DUNBRACK_MAX_SCTOR = 4

Referenced by core::pack::dunbrack::DunbrackEnergy::eval_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >::read_from_file(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotameric_data(), rotamer_from_chi_02(), and core::pack::dunbrack::DunbrackRotamerSampleData::set_nchi().

Size const core::pack::dunbrack::FOUR = 4

const Real core::pack::dunbrack::MIN_ROT_PROB = 1.e-8

static

Size const core::pack::dunbrack::ONE = 1

basic::Tracer core::pack::dunbrack::SRDL_TR("core.pack.dunbrack")

static

basic::Tracer core::pack::dunbrack::SRPL_TR("core.pack.dunbrack")

static

Size const core::pack::dunbrack::THREE = 3

basic::Tracer core::pack::dunbrack::TR("core.pack.dunbrack.DunbrackConstraint")

static

basic::Tracer core::pack::dunbrack::TR("core.pack.dunbrack.RotamerConstraint")

static

basic::Tracer core::pack::dunbrack::TR("core.pack.dunbrack.SingleLigandRotamerLibrary")

static

Size const core::pack::dunbrack::TWO = 2

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