core::pack::dunbrack Namespace Reference

Namespaces
	cenrot

Classes
class	ChiSet
class	DunbrackConstraint
class	DunbrackConstraintCreator
	Mover creator for the DunbrackConstraint constraint. More...
class	DunbrackEnergy
class	DunbrackEnergyCreator
class	DunbrackRotamerMeanSD
	forward declaration; default precision is DunbrackReal More...
class	PackedDunbrackRotamer
	forward declaration; default precision is DunbrackReal; More...
class	DunbrackRotamer
	forward declaration; default precision is DunbrackReal More...
class	RotamericData
	DOUG DOUG DOUG. More...
class	DunbrackRotamerSampleData
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	PeptoidOmegaReporter
class	PeptoidGeneralDOFReporter
class	ResidueDOFReporter
class	RotamerConstraint
	This class favors a particular rotamer at a particular position by reducing its Dunbrack energy. More...
class	RotamericSingleResidueDunbrackLibrary
class	RotamericSingleResidueDunbrackLibraryParser
	A helper class to assist in parsing rotamer libraries. More...
struct	DunbrackAAParameterSet
	A small structure to hold overview parameters about the Dunbrack Libraries. More...
class	RotamerLibrary
	A class to manage the Dunbrack Rotamer Libraries. More...
class	RotamerLibraryInterpolationScratch
	A scratch-space class to store the information needed for Dunbrack Rotamer interpolation. More...
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	BBDepNRChiSample
	P for precision. More...
class	BBIndNRChiSample
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...
struct	BBDepScoreInterpData
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	ProbSortClass
class	SingleResidueDunbrackLibraryConcrete
class	SingleResidueDunbrackLibrary
class	SingleResidueDunbrackLibraryCreator
class	MainchainTorsionReporter
class	PeptideTorsionReporter

Typedefs
typedef utility::pointer::shared_ptr< ChiSet >	ChiSetOP
typedef utility::pointer::shared_ptr< ChiSet const >	ChiSetCOP
typedef utility::pointer::shared_ptr< DunbrackConstraint >	DunbrackConstraintOP
typedef utility::pointer::shared_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::shared_ptr< ResidueDOFReporter >	ResidueDOFReporterOP
typedef utility::pointer::shared_ptr< ResidueDOFReporter const >	ResidueDOFReporterCOP
typedef utility::pointer::shared_ptr< RotamerConstraint >	RotamerConstraintOP
typedef utility::pointer::shared_ptr< RotamerConstraint const >	RotamerConstraintCOP
typedef utility::pointer::shared_ptr< RotamericSingleResidueDunbrackLibraryParser >	RotamericSingleResidueDunbrackLibraryParserOP
typedef utility::pointer::shared_ptr< RotamericSingleResidueDunbrackLibraryParser const >	RotamericSingleResidueDunbrackLibraryParserCOP
typedef utility::pointer::shared_ptr< RotamerLibrary >	RotamerLibraryOP
typedef utility::pointer::shared_ptr< RotamerLibrary const >	RotamerLibraryCOP
typedef utility::fixedsizearray1< utility::fixedsizearray1< Real, DUNBRACK_MAX_SCTOR >, DUNBRACK_MAX_BBTOR >	FiveReal4
typedef utility::fixedsizearray1< Real, DUNBRACK_MAX_SCTOR >	Real4
typedef utility::fixedsizearray1< Size, DUNBRACK_MAX_SCTOR >	Size4
typedef utility::fixedsizearray1< Real, DUNBRACK_MAX_BBTOR >	Real5
typedef utility::fixedsizearray1< Size, DUNBRACK_MAX_BBTOR >	Size5
typedef utility::pointer::shared_ptr< RotamerLibraryScratchSpace >	RotamerLibraryScratchSpaceOP
typedef utility::pointer::shared_ptr< RotamerLibraryScratchSpace const >	RotamerLibraryScratchSpaceCOP
typedef utility::pointer::shared_ptr< SingleResidueDunbrackLibrary >	SingleResidueDunbrackLibraryOP
typedef utility::pointer::weak_ptr< SingleResidueDunbrackLibrary >	SingleResidueDunbrackLibraryAP
typedef utility::pointer::shared_ptr< SingleResidueDunbrackLibrary const >	SingleResidueDunbrackLibraryCOP
typedef utility::pointer::weak_ptr< SingleResidueDunbrackLibrary const >	SingleResidueDunbrackLibraryCAP
typedef utility::pointer::shared_ptr< SingleResidueDunbrackLibraryCreator >	SingleResidueDunbrackLibraryCreatorOP
typedef utility::pointer::shared_ptr< SingleResidueDunbrackLibraryCreator const >	SingleResidueDunbrackLibraryCreatorCOP

Functions
static basic::Tracer	TR ("core.pack.dunbrack.DunbrackConstraint")
Size	positive_pow (Size mantissa, Size exponent)
template<Size N>
void	interpolate_rotamers (utility::fixedsizearray1< DunbrackRotamer< FOUR, N >,(1<< N) > const &rot, utility::fixedsizearray1< Real, N > bb_err, Real binrange, Size nchi_aa, DunbrackRotamer< FOUR, N, Real > &interpolated_rotamer)
template<Size N>
Size	product (utility::fixedsizearray1< Size, N > factors)
bool	bit_is_set (Size num, Size num_len, Size pos)
template<Size N>
Size	make_index (utility::fixedsizearray1< Size, N > const &num_bins, utility::fixedsizearray1< Size, N > const &bb_bin)
template<Size N>
Size	make_index (utility::fixedsizearray1< Size, N > const &num_bins, utility::fixedsizearray1< Size, N+1 > const &bb_bin)
template<Size N>
Size	make_index (utility::fixedsizearray1< Size, N > const &num_bins, utility::vector1< Size > const &bb_bin)
	Variant of above make_index function for bb_bin as a vector. More...
template<Size N>
Size	make_conditional_index (utility::fixedsizearray1< Size, N > num_bins, Size cond_i, utility::fixedsizearray1< Size, N > bin_true, utility::fixedsizearray1< Size, N > bin_false)
template<Size N>
Size	make_conditional_index (utility::fixedsizearray1< Size, N > num_bins, Size cond_i, utility::fixedsizearray1< Size, N+1 > bin_true, utility::fixedsizearray1< Size, N+1 > bin_false)
	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA. More...
template<Size N>
void	polycubic_interpolation (utility::fixedsizearray1< utility::fixedsizearray1< Real,(1<< N) >,(1<< N) > n_derivs, utility::fixedsizearray1< Real, N > dbbp, utility::fixedsizearray1< Real, N > binwbb, Real &val, utility::fixedsizearray1< Real, N > &dvaldbb)
	Perform cubic interpolation over each of N axes, using the 2^N derivatives at 2^N gridpoints. More...
template<Size N>
void	interpolate_polylinear_by_value_noangles (utility::fixedsizearray1< core::Real,(1<< N) > const &vals, utility::fixedsizearray1< core::Real, N > const &bbd, utility::fixedsizearray1< core::Real, N > const &binrange, core::Real &val, utility::fixedsizearray1< core::Real, N > &dval_dbb)
	Interpolate polylinearly in N dimensions for values that AREN'T angles. More...
template<core::Size N>
void	interpolate_polylinear_by_value_angles_degrees (utility::fixedsizearray1< core::Real,(1<< N) > const &vals, utility::fixedsizearray1< core::Real, N > const &bbd, utility::fixedsizearray1< core::Real, N > const &binrange, core::Real &val, utility::fixedsizearray1< core::Real, N > &dval_dbb)
	Interpolate polylinearly in N dimensions, for outputs that are angles (and have to handle wraparound properly). More...
template<>
void	interpolate_polylinear_by_value_angles_degrees< 1 > (utility::fixedsizearray1< core::Real, 2 > const &vals, utility::fixedsizearray1< core::Real, 1 > const &bbd, utility::fixedsizearray1< core::Real, 1 > const &binrange, core::Real &val, utility::fixedsizearray1< core::Real, 1 > &dval_dbb)
	Interpolate polylinearly in N dimensions, for outputs that are angles (and have to handle wraparound properly). More...
template<Size N>
void	interpolate_polylinear_by_value (utility::fixedsizearray1< core::Real,(1<< N) > const &vals, utility::fixedsizearray1< core::Real, N > const &bbd, utility::fixedsizearray1< core::Real, N > const &binrange, bool angles, core::Real &val, utility::fixedsizearray1< core::Real, N > &dval_dbb)
	Interpolate polylinearly in N dimensions. More...
template<Size S, Size N>
DunbrackRotamer< S, N, Real >	increase_rotamer_precision (DunbrackRotamer< S, N, DunbrackReal > const &original_rotamer)
static basic::Tracer	TR ("core.pack.dunbrack.RotamerConstraint")
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...
static basic::Tracer	TR ("core.pack.dunbrack.RotamerLibrary")
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)
	DEPRECATED convert between the real-valued chi dihedrals and the rotamer well indices. More...
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)
template<Size T, Size N>
void	initialize_and_read_srsrdl (SemiRotamericSingleResidueDunbrackLibrary< T, N > &srsrdl, bool const nrchi_is_symmetric, Real const nrchi_start_angle, utility::io::izstream &rotamer_definitions, utility::io::izstream &regular_library, utility::io::izstream &continuous_minimization_bbdep)
template<Size T, Size N>
void	initialize_srsrdl (SemiRotamericSingleResidueDunbrackLibrary< T, N > &srsrdl, bool const nrchi_is_symmetric, Real const nrchi_start_angle)
static basic::Tracer	TR ("core.pack.dunbrack")
static basic::Tracer	TR ("core.pack.dunbrack.SingleResidueDunbrackLibraryCreator")

Variables
Size const	ONE = 1
Size const	TWO = 2
Size const	THREE = 3
Size const	FOUR = 4
Size const	FIVE = 5
Size const	DUNBRACK_MAX_BBTOR = 5
Size const	DUNBRACK_MAX_SCTOR = 5
Size const	DUNBRACK_FILE_DEFAULT_SCTOR = 4

Typedef Documentation

AngleVector

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

ChiSetCOP

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

ChiSetOP

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

ChiVector

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

DunbrackConstraintCOP

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

DunbrackConstraintOP

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

DunbrackReal

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.

FiveReal4

typedef utility::fixedsizearray1< utility::fixedsizearray1< Real, DUNBRACK_MAX_SCTOR >, DUNBRACK_MAX_BBTOR > core::pack::dunbrack::FiveReal4

Real4

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

Real5

typedef utility::fixedsizearray1< Real, DUNBRACK_MAX_BBTOR > core::pack::dunbrack::Real5

ResidueDOFReporterCOP

typedef utility::pointer::shared_ptr< ResidueDOFReporter const > core::pack::dunbrack::ResidueDOFReporterCOP

ResidueDOFReporterOP

typedef utility::pointer::shared_ptr< ResidueDOFReporter > core::pack::dunbrack::ResidueDOFReporterOP

RotamerConstraintCOP

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

RotamerConstraintOP

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

RotamericSingleResidueDunbrackLibraryParserCOP

typedef utility::pointer::shared_ptr< RotamericSingleResidueDunbrackLibraryParser const > core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParserCOP

RotamericSingleResidueDunbrackLibraryParserOP

typedef utility::pointer::shared_ptr< RotamericSingleResidueDunbrackLibraryParser > core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParserOP

RotamerLibraryCOP

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

RotamerLibraryOP

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

RotamerLibraryScratchSpaceCOP

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

RotamerLibraryScratchSpaceOP

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

RotVector

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

SingleResidueDunbrackLibraryAP

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

SingleResidueDunbrackLibraryCAP

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

SingleResidueDunbrackLibraryCOP

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

SingleResidueDunbrackLibraryCreatorCOP

typedef utility::pointer::shared_ptr< SingleResidueDunbrackLibraryCreator const > core::pack::dunbrack::SingleResidueDunbrackLibraryCreatorCOP

SingleResidueDunbrackLibraryCreatorOP

typedef utility::pointer::shared_ptr< SingleResidueDunbrackLibraryCreator > core::pack::dunbrack::SingleResidueDunbrackLibraryCreatorOP

SingleResidueDunbrackLibraryOP

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

Size4

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

Size5

typedef utility::fixedsizearray1< Size, DUNBRACK_MAX_BBTOR > core::pack::dunbrack::Size5

Function Documentation

bit_is_set()

bool core::pack::dunbrack::bit_is_set ( Size  num, Size  num_len, Size  pos  )

inline

Referenced by interpolate_polylinear_by_value_noangles().

increase_rotamer_precision()

template<Size S, Size N>

DunbrackRotamer< S, N, Real > core::pack::dunbrack::increase_rotamer_precision

(

DunbrackRotamer< S, N, DunbrackReal > const &

original_rotamer

)

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

initialize_and_read_srsrdl()

template<Size T, Size N>

void core::pack::dunbrack::initialize_and_read_srsrdl	(	SemiRotamericSingleResidueDunbrackLibrary< T, N > &	srsrdl,
		bool const	nrchi_is_symmetric,
		Real const	nrchi_start_angle,
		utility::io::izstream &	rotamer_definitions,
		utility::io::izstream &	regular_library,
		utility::io::izstream &	continuous_minimization_bbdep
	)

References initialize_srsrdl(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::read_from_files().

Referenced by core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), and core::pack::dunbrack::RotamerLibrary::create_semi_rotameric_dunlib().

initialize_srsrdl()

template<Size T, Size N>

void core::pack::dunbrack::initialize_srsrdl	(	SemiRotamericSingleResidueDunbrackLibrary< T, N > &	srsrdl,
		bool const	nrchi_is_symmetric,
		Real const	nrchi_start_angle
	)

References core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::set_nonrotameric_chi_bbdep_scoring_step_size(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::set_nonrotameric_chi_bbind_scoring_step_size(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::set_nonrotameric_chi_start_angle(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::set_nrchi_periodicity().

Referenced by core::pack::dunbrack::RotamerLibrary::create_semi_rotameric_dunlib(), and initialize_and_read_srsrdl().

interpolate_polylinear_by_value()

template<Size N>

void core::pack::dunbrack::interpolate_polylinear_by_value	(	utility::fixedsizearray1< core::Real,(1<< N) > const &	vals,
		utility::fixedsizearray1< core::Real, N > const &	bbd,
		utility::fixedsizearray1< core::Real, N > const &	binrange,
		bool	angles,
		core::Real &	val,
		utility::fixedsizearray1< core::Real, N > &	dval_dbb
	)

Interpolate polylinearly in N dimensions.

Author

Original author unknown.

Angle interpolation rewritten by Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org) and Andy Watkins, 12 Sept. 2018.

Parameters

[in]	vals	The values at the corners of the gridpoints. This vector should have N^2 points.
[in]	bbd	Coordinate within the grid square/cube/hypercube, with each dimension ranging from 0 to 1.
[in]	binrange	Size of each bin. For example, 10 degrees by 10 degrees by 10 degrees...
[in]	angles	Are we interpolating angles, or just some value? Note that, if angles, we assume angles are in DEGREES.
[out]	val	The interpolated value.
[out]	dval_dbb	The derivatives of the interpolated value, with respect to the degrees of freedom over which the grid is defined.

References core::scoring::packstat::old::angles, interpolate_polylinear_by_value_angles_degrees(), interpolate_polylinear_by_value_noangles(), core::chemical::element::N, and protocols::hybridization::val.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_probability_for_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_probability_for_rotamer_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::interpolate_bbdep_nrchi_sample(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::interpolate_nrchi_values(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers(), and interpolate_rotamers().

interpolate_polylinear_by_value_angles_degrees()

template<core::Size N>

void core::pack::dunbrack::interpolate_polylinear_by_value_angles_degrees ( utility::fixedsizearray1< core::Real,(1<< N) > const &  vals, utility::fixedsizearray1< core::Real, N > const &  bbd, utility::fixedsizearray1< core::Real, N > const &  binrange, core::Real &  val, utility::fixedsizearray1< core::Real, N > &  dval_dbb  )

inline

Interpolate polylinearly in N dimensions, for outputs that are angles (and have to handle wraparound properly).

Author

Original author unknown.

Angle interpolation rewritten by Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org) and Andy Watkins, 12 Sept. 2018.

Note

We assume that angles are in DEGREES.

Parameters

[in]	vals	The values at the corners of the gridpoints. This vector should have N^2 points.
[in]	bbd	Coordinate within the grid square/cube/hypercube, with each dimension ranging from 0 to 1.
[in]	binrange	Size of each bin. For example, 10 degrees by 10 degrees by 10 degrees...
[out]	val	The interpolated value.
[out]	dval_dbb	The derivatives of the interpolated value, with respect to the degrees of freedom over which the grid is defined.

References interpolate_polylinear_by_value_noangles(), core::chemical::element::N, and protocols::hybridization::val.

Referenced by interpolate_polylinear_by_value().

interpolate_polylinear_by_value_angles_degrees< 1 >()

template<>

void core::pack::dunbrack::interpolate_polylinear_by_value_angles_degrees< 1 > ( utility::fixedsizearray1< core::Real, 2 > const &  vals, utility::fixedsizearray1< core::Real, 1 > const &  bbd, utility::fixedsizearray1< core::Real, 1 > const &  binrange, core::Real &  val, utility::fixedsizearray1< core::Real, 1 > &  dval_dbb  )

inline

Interpolate polylinearly in N dimensions, for outputs that are angles (and have to handle wraparound properly).

This version is for the special N=1 case. It is ultimately the end of the recusive call chain for the version below.

Author

Original author unknown.

Angle interpolation rewritten by Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org) and Andy Watkins, 12 Sept. 2018.

Note

We assume that angles are in DEGREES.

Parameters

[in]	vals	The values at the corners of the gridpoints. This vector should have N^2 points.
[in]	bbd	Coordinate within the grid square/cube/hypercube, with each dimension ranging from 0 to 1.
[in]	binrange	Size of each bin. For example, 10 degrees by 10 degrees by 10 degrees...
[out]	val	The interpolated value.
[out]	dval_dbb	The derivatives of the interpolated value, with respect to the degrees of freedom over which the grid is defined.

References protocols::hybridization::val.

interpolate_polylinear_by_value_noangles()

template<Size N>

void core::pack::dunbrack::interpolate_polylinear_by_value_noangles	(	utility::fixedsizearray1< core::Real,(1<< N) > const &	vals,
		utility::fixedsizearray1< core::Real, N > const &	bbd,
		utility::fixedsizearray1< core::Real, N > const &	binrange,
		core::Real &	val,
		utility::fixedsizearray1< core::Real, N > &	dval_dbb
	)

Interpolate polylinearly in N dimensions for values that AREN'T angles.

This doesn't handle wraparound.

Author

Original author unknown.

Pulled into a new function by Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org), 12 Sept. 2018.

Parameters

[in]	vals	The values at the corners of the gridpoints. This vector should have N^2 points.
[in]	bbd	Coordinate within the grid square/cube/hypercube, with each dimension ranging from 0 to 1.
[in]	binrange	Size of each bin. For example, 10 degrees by 10 degrees by 10 degrees...
[out]	val	The interpolated value.
[out]	dval_dbb	The derivatives of the interpolated value, with respect to the degrees of freedom over which the grid is defined.

References bit_is_set(), core::chemical::element::N, and protocols::hybridization::val.

Referenced by interpolate_polylinear_by_value(), and interpolate_polylinear_by_value_angles_degrees().

interpolate_rotamers()

template<Size N>

void core::pack::dunbrack::interpolate_rotamers	(	utility::fixedsizearray1< DunbrackRotamer< FOUR, N >,(1<< N) > const &	rot,
		utility::fixedsizearray1< Real, N >	bb_err,
		Real	binrange,
		Size	nchi_aa,
		DunbrackRotamer< FOUR, N, Real > &	interpolated_rotamer
	)

alternative interpolate_rotamers that uses polylinear interpolation

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

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::assign_random_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::assign_random_rotamer_with_bias_bbdep(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::fill_rotamer_vector_bbdep(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_all_rotamer_samples_bbdep(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_bbdep(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers().

load_unboundrot() [1/2]

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(), protocols::abinitio::filename(), and TR().

Referenced by protocols::ligand_docking::LigandDockProtocol::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::simple_moves::LoadUnboundRotMover::apply(), protocols::antibody::setup_packer_task(), protocols::antibody_legacy::AntibodyModeler::setup_packer_task(), protocols::antibody_legacy::CDRH3Modeler::setup_packer_task(), protocols::antibody_legacy::LoopRlxMover::setup_packer_task(), protocols::ub_e2c::ubi_e2c_modeler::setup_packer_task(), protocols::docking::DockingHighResLegacy::setup_packing(), and protocols::symmetric_docking::SymDockingHiRes::setup_packing().

load_unboundrot() [2/2]

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::conformation::Residue::is_protein(), core::chemical::ResidueTypeBase::name(), core::pose::Pose::size(), TR(), and core::conformation::Residue::type().

make_conditional_index() [1/2]

template<Size N>

Size core::pack::dunbrack::make_conditional_index ( utility::fixedsizearray1< Size, N >  num_bins, Size  cond_i, utility::fixedsizearray1< Size, N >  bin_true, utility::fixedsizearray1< Size, N >  bin_false  )

inline

References core::chemical::element::N.

make_conditional_index() [2/2]

template<Size N>

Size core::pack::dunbrack::make_conditional_index ( utility::fixedsizearray1< Size, N >  num_bins, Size  cond_i, utility::fixedsizearray1< Size, N+1 >  bin_true, utility::fixedsizearray1< Size, N+1 >  bin_false  )

inline

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA.

References core::chemical::element::N, and positive_pow().

make_index() [1/3]

template<Size N>

Size core::pack::dunbrack::make_index ( utility::fixedsizearray1< Size, N > const &  num_bins, utility::fixedsizearray1< Size, N > const &  bb_bin  )

inline

References core::chemical::element::N.

make_index() [2/3]

template<Size N>

Size core::pack::dunbrack::make_index ( utility::fixedsizearray1< Size, N > const &  num_bins, utility::fixedsizearray1< Size, N+1 > const &  bb_bin  )

inline

References core::chemical::element::N, and positive_pow().

make_index() [3/3]

template<Size N>

Size core::pack::dunbrack::make_index ( utility::fixedsizearray1< Size, N > const &  num_bins, utility::vector1< Size > const &  bb_bin  )

inline

Variant of above make_index function for bb_bin as a vector.

References core::chemical::element::N.

polycubic_interpolation()

template<Size N>

void core::pack::dunbrack::polycubic_interpolation	(	utility::fixedsizearray1< utility::fixedsizearray1< Real,(1<< N) >,(1<< N) >	n_derivs,
		utility::fixedsizearray1< Real, N >	dbbp,
		utility::fixedsizearray1< Real, N >	binwbb,
		Real &	val,
		utility::fixedsizearray1< Real, N > &	dvaldbb
	)

Perform cubic interpolation over each of N axes, using the 2^N derivatives at 2^N gridpoints.

The way encoding gridpoints and derivatives into a linear structure like this is actually pretty simple. Imagine the "right or left" part of a cube, or the "derivative taken or not" on a particular variable, as zero or one. Then "just the actual function value" maps to 000, the z derivative (for example) maps to 001, d2/dydz maps to 011, etc.

Parameters

[in]	n_derivs	is a 2^N x 2^N matrix: 2^N derivatives at 2^N gridpoints
[in]	dbbp	is how far along the bin our target point is, in each direction
[in]	binwbb	is the bin width in each direction
[out]	val	is the interpolated value
[out]	dvaldbb	are the interpolated derivatives

References core::chemical::element::N, and protocols::hybridization::val.

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::bbdep_nrchi_score(), core::scoring::rna::data::RNA_DMS_Potential::evaluate(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers().

positive_pow()

Size core::pack::dunbrack::positive_pow	(	Size	mantissa,
		Size	exponent
	)

Referenced by make_conditional_index(), and make_index().

product()

template<Size N>

Size core::pack::dunbrack::product ( utility::fixedsizearray1< Size, N >  factors )

inline

References core::chemical::element::N.

Referenced by core::scoring::ChemicalShiftAnisotropy::compute_csascore(), protocols::medal::MedalMover::compute_per_residue_probabilities(), protocols::pockets::NonPlaidFingerprint::place_origin_point(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::read_bbdep_continuous_minimization_data(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::read_from_binary(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::read_from_binary(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::read_rotamer_definitions(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::read_rotameric_data(), protocols::pockets::NonPlaidFingerprint::set_multiple_origin(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::setup_entropy_correction(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::write_to_binary(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::write_to_binary().

psc_compare()

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

References core::sequence::left, and core::pack::dunbrack::ProbSortClass::probability_.

rotamer_from_chi() [1/2]

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 rot().

rotamer_from_chi() [2/2]

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::chemical::num_canonical_aas, rot(), and core::conformation::Residue::type().

Referenced by core::pack::dunbrack::RotamerConstraint::add_residue(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::comparative_modeling::Align_RotamerEvaluator::apply(), core::pack::dunbrack::DunbrackConstraint::bin_matches(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::optimize_weights::IterativeOptEDriver::measure_rotamer_recovery(), protocols::comparative_modeling::rots_from_pose(), protocols::pose_metric_calculators::RotamerRecovery::rots_from_pose(), core::pack::dunbrack::RotamerConstraint::score(), and protocols::rotamer_recovery::PerNativeRRReporterHuman::set_native().

rotamer_from_chi_02() [1/2]

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, and rot().

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

rotamer_from_chi_02() [2/2]

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

DEPRECATED 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)*‍/ c;

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, core::chemical::num_canonical_aas, and rot().

subtract_chi_angles()

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::pack::dunbrack::SingleResidueDunbrackLibrary::aa(), core::chemical::aa_asp, core::chemical::aa_glu, core::chemical::aa_phe, and core::chemical::aa_tyr.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), and protocols::features::RotamerFeatures::report_features().

TR() [1/5]

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

static

TR() [2/5]

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

static

Referenced by core::pack::dunbrack::RotamerLibrary::add_residue_library(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_ASCII(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_binary(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_binary(), core::pack::dunbrack::RotamerLibrary::decide_read_from_binary(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::determine_rotamer_well_order(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::do_all_checks_and_corrections(), core::pack::dunbrack::RotamerLibrary::get_library_by_aa(), core::pack::dunbrack::RotamerLibrary::get_library_name_10(), load_unboundrot(), core::pack::dunbrack::BBDepNRChiSample< P >::operator==(), core::pack::dunbrack::BBDepScoreInterpData< N >::operator==(), core::pack::dunbrack::BBIndNRChiSample< P >::operator==(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::operator==(), core::pack::dunbrack::SingleResidueDunbrackLibrary::operator==(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::operator==(), core::pack::dunbrack::RotamerLibrary::random_tempname(), core::pack::dunbrack::RotamerConstraint::score(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::symmetrize_library(), core::pack::dunbrack::RotamerLibrary::validate_dunbrack_binary(), core::pack::dunbrack::RotamerLibrary::write_binary_fa_dunbrack_libraries_02(), and core::pack::dunbrack::RotamerLibrary::write_binary_fa_dunbrack_libraries_10().

TR() [3/5]

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

static

TR() [4/5]

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

static

TR() [5/5]

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

static

Variable Documentation

DUNBRACK_FILE_DEFAULT_SCTOR

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

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::read_from_file().

DUNBRACK_MAX_BBTOR

Size const core::pack::dunbrack::DUNBRACK_MAX_BBTOR = 5

Referenced by core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_bb_dof_deriv(), and core::pack::dunbrack::RotamerLibraryScratchSpace::extract_torsion_deriv().

DUNBRACK_MAX_SCTOR

Size const core::pack::dunbrack::DUNBRACK_MAX_SCTOR = 5

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(), core::pack::dunbrack::RotamerLibraryScratchSpace::extract_torsion_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::read_rotameric_data(), rotamer_from_chi_02(), and core::pack::dunbrack::DunbrackRotamerSampleData::set_nchi().

FIVE

Size const core::pack::dunbrack::FIVE = 5

Referenced by core::pack::dunbrack::SingleResidueDunbrackLibrary::hokey_template_workaround().

FOUR

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

Referenced by protocols::features::RotamerFeatures::report_features().

ONE

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

Referenced by protocols::features::RotamerFeatures::report_features().

THREE

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

Referenced by protocols::features::RotamerFeatures::report_features().

TWO

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

Referenced by protocols::features::RotamerFeatures::report_features().