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...

#include <SemiRotamericSingleResidueDunbrackLibrary.hh>

Public Types
typedef RotamericSingleResidueDunbrackLibrary < T >	parent

typedef SingleResidueDunbrackLibrary	grandparent

Public Types inherited from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
typedef SingleResidueDunbrackLibrary	parent

Public Types inherited from core::pack::dunbrack::SingleResidueDunbrackLibrary
typedef chemical::AA	AA

Public Member Functions
	SemiRotamericSingleResidueDunbrackLibrary (chemical::AA const aa_in, bool const backbone_independent_scoring, bool const backbone_independent_rotamer_sampling)
	The constructor determines the path the library takes: whether it uses a backbone dependent or independent score function for the non-rotameric chi (the rotameric chi score function is always backbone dependent) and whether it uses a backbone dependent or independent rotamer sampling scheme. All four combinations are possible, though backbone independent scoring and backbone dependent rotamer sampling seems a poor combination. More...

virtual	~SemiRotamericSingleResidueDunbrackLibrary ()

virtual Real	rotamer_energy (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const
	Virtual functions required by the base classes. More...

virtual Real	rotamer_energy_deriv (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const

virtual Real	best_rotamer_energy (conformation::Residue const &rsd, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const
	Returns the energy of the lowest-energy rotamer accessible to the given residue (based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue's current rotamer (local optimum); otherwise, consider all rotamers (global optimum). More...

virtual void	assign_random_rotamer_with_bias (conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const
	Pick a rotamer for the input residue according to the rotamer probability distribution and assign chi angles to the input rsd. If perturb_from_rotamer_center is true, then push the rotamer off from the center; for chi angles with a normal distribution, the perturbation is taken from a Gaussian random number with a standard deviation matching the chi angle's standard deviation. For chi angles that are not normally distributed, the behavior is open to the derived classe's interpretation. More...

virtual void	fill_rotamer_vector (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, RotamerVector &rotamers) const

virtual utility::vector1 < DunbrackRotamerSampleData >	get_all_rotamer_samples (Real phi, Real psi) const
	Return all of the rotamer sample data given a particular phi/psi. For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes. More...

virtual Real	get_probability_for_rotamer (Real phi, Real psi, Size rot_ind) const
	Return the probability for a particular rotamer where rotamers are indexed in order of decreasing probability (or something very close to decreasing probability). More...

virtual DunbrackRotamerSampleData	get_rotamer (Real phi, Real psi, Size rot_ind) const

virtual Size	nchi () const
	The number of chi represented by the library. More...

virtual Size	n_rotamer_bins () const

virtual void	write_to_file (utility::io::ozstream &out) const

virtual void	write_to_binary (utility::io::ozstream &out) const

void	read_from_files (utility::io::izstream &in_rotdef, utility::io::izstream &in_rotameric, utility::io::izstream &in_continmin_bbdep, utility::io::izstream &in_continmin_bbind)
	Initialize either a backbone-independent or a backbone-dependent SRSRDL from the set of four files which describe both (not all files are read). More...

void	read_from_files (utility::io::izstream &in_rotdef, utility::io::izstream &in_rotameric, utility::io::izstream &in_continmin_bbdep)
	Initialize a backbone-dependent SRSRDL from the set of three files which describe it. More...

virtual void	read_from_binary (utility::io::izstream &in)

virtual void	get_rotamer_from_chi (ChiVector const &chi, RotVector &rot) const
	Convert a vector of chi angles (degrees) into a integer vector of rotamer wells. Derived class should be consistent, but may be arbitrary in how wells divide angle space. More...

void	set_nrchi_periodicity (Real angle_in_degrees)
	Initialization functions that must be called before reading the input libraries. More...

void	set_nonrotameric_chi_start_angle (Real angle_in_degrees)
	What angle do the interpolation data start from? More...

void	set_nonrotameric_chi_bbdep_scoring_step_size (Real step_size_in_degrees)
	What is the angular step size of the bbdep score? More...

void	set_nonrotameric_chi_bbind_scoring_step_size (Real step_size_in_degrees)
	What is the angular step size of the bbind score? More...

Public Member Functions inherited from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
	RotamericSingleResidueDunbrackLibrary (AA const aa_in, bool dun02)

virtual	~RotamericSingleResidueDunbrackLibrary ()

std::string	read_from_file (utility::io::izstream &in, bool first_line_three_letter_code_already_read)
	Read from input stream; stream may contain data for other amino acids. Quit once another amino acid is specified in the input file, returning the name of the next amino acid specifed (since it's already been extracted from the input stream). Return the empty string if no other amino acid is specified. More...

Size	find_another_representative_for_unlikely_rotamer (conformation::Residue const &rsd, Size4 &rotwell) const

void	interpolate_rotamers (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, Size const packed_rotno, PackedDunbrackRotamer< T, Real > &interpolated_rotamer) const

Public Member Functions inherited from core::pack::dunbrack::SingleResidueDunbrackLibrary
	SingleResidueDunbrackLibrary (AA const aa, Size const n_rotameric_chi, bool dun02)
	c-tor More...

virtual	~SingleResidueDunbrackLibrary ()

void	read_options ()

virtual Size	memory_usage_in_bytes () const
	Virtual functions the derived classes must implement. More...

void	set_n_chi_bins (utility::vector1< Size > const &)
	Tell the base class the number of chi bins for each rotameric chi dimension. More...

Size	rotwell_2_rotno (utility::vector1< Size > const &rotwell) const
	Conversion functions. More...

Size	rotwell_2_rotno (Size4 const &rotwell) const
	Convert from the rotamer bin indices for each chi to the (non-compact) "rotamer number". More...

Size	rotno_2_packed_rotno (Size const rotno) const
	Convert from the rotamer number to the compacted "packed rotamer number". Returns 0 if rotno has no corresponding packed rotno. More...

Size	rotwell_2_packed_rotno (utility::vector1< Size > const &rotwell) const
	Convert from the rotamer bin indices for each chi to the compacted "packed rotamer number." Returns 0 if rotwell has no corresponding packed rotno. More...

Size	rotwell_2_packed_rotno (Size4 const &rotwell) const
	Convert from the rotamer bin indices for each chi to the compacted "packed rotamer number." Returns 0 if rotwell has no corresponding packed rotno. More...

void	packed_rotno_2_rotwell (Size const packed_rotno, utility::vector1< Size > &rotwell) const
	Convert from the packed rotamer number to the rotamer well. More...

void	packed_rotno_2_rotwell (Size const packed_rotno, Size4 &rotwell) const

utility::vector1< Size > const &	packed_rotno_2_rotwell (Size const packed_rotno) const

void	rotno_2_rotwell (Size const rotno, utility::vector1< Size > &rotwell) const
	Convert from the rotamer number to the rotamer well. More...

Size	bin_rotameric_chi (Real chi, Size which_chi) const
	, Turns out, when non-rotameric chi are taken out of the picture, all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. For D-amino acids, chi must be inverted before passing to this function. More...

void	bin_angle (Real const angle_start, Real const angle_step, Real const ASSERT_ONLY(angle_range), Size const nbins, Real const ang, Size &bin_lower, Size &bin_upper, Real &angle_alpha) const
	This is not the right place for this code, but the numeric interpolation library uselessly indexes by 0 and the basic functions aren't inlined... More...

AA	aa () const
	The amino acid this library is representing. More...

Real	probability_to_accumulate_while_building_rotamers (bool buried) const
	When creating rotamer, what position in the CDF should one build until? Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful. More...

void	prob_to_accumulate (Real, Real)
	setters for accumulation probability cutoff (to support externally-controlled option dependence) More...

void	prob_to_accumulate_buried (Real)

void	prob_to_accumulate_nonburied (Real)

Public Member Functions inherited from core::pack::dunbrack::SingleResidueRotamerLibrary
virtual	~SingleResidueRotamerLibrary ()

Protected Member Functions
virtual Size	memory_usage_static () const
	Worker functions. More...

virtual Size	memory_usage_dynamic () const

Real	rotamer_energy_deriv_bbdep (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, bool eval_deriv) const

Real	rotamer_energy_deriv_bbind (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, bool eval_deriv) const

void	assign_random_rotamer_with_bias_bbind (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const

void	assign_random_rotamer_with_bias_bbdep (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const

Real	bbind_nrchi_score (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, Real &dnrchi_score_dnrchi) const

Real	bbdep_nrchi_score (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, Real &dnrchi_score_dnrchi, Real &dnrchi_score_dphi, Real &dnrchi_score_dpsi) const
	Trilinear interpolation. Derivatives discontinuous at edge planes. Correction: it seems that this was updated at some point to use tricubic interpolation. Note: This function has been updated to handle D-amino acids properly. More...

void	fill_rotamer_vector_bbind (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, RotamerVector &rotamers) const

void	fill_rotamer_vector_bbdep (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, RotamerVector &rotamers) const

utility::vector1 < DunbrackRotamerSampleData >	get_all_rotamer_samples_bbind (Real phi, Real psi) const

utility::vector1 < DunbrackRotamerSampleData >	get_all_rotamer_samples_bbdep (Real phi, Real psi) const

Real	get_probability_for_rotamer_bbind (Real phi, Real psi, Size rot_ind) const

Real	get_probability_for_rotamer_bbdep (Real phi, Real psi, Size rot_ind) const

DunbrackRotamerSampleData	get_rotamer_bbind (Real phi, Real psi, Size rot_ind) const

DunbrackRotamerSampleData	get_rotamer_bbdep (Real phi, Real psi, Size rot_ind) const

virtual void	chisamples_for_rotamer_and_chi (chemical::ResidueType const &rsd_type, pack::task::ResidueLevelTask const &rtask, bool buried, Size const chi_index, RotamericData< T > const &rotamer_data, utility::vector1< Real > const &extra_steps, utility::vector1< Real > &total_chi, utility::vector1< int > &total_rot, utility::vector1< Real > &total_ex_steps, utility::vector1< Real > &chisample_prob) const
	overrides parent class for the non-rotameric chi, but falls back on the parent class functionality for all other chi. More...

Protected Member Functions inherited from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
void	initialize_bicubic_splines ()

void	get_rotamer_from_chi_static (ChiVector const &chi, Size4 &rot) const
	When given a statically sized fixedsizearray, use this method. More...

void	get_rotamer_from_chi_static (Real4 const &chi, Size4 &rot) const
	When given a statically sized fixedsizearray, use this method. More...

ObjexxFCL::FArray3D < PackedDunbrackRotamer< T > > const &	rotamers () const
	Read and write access for derived classes. More...

ObjexxFCL::FArray3D < PackedDunbrackRotamer< T > > &	rotamers ()

ObjexxFCL::FArray3D< Size > const &	packed_rotno_2_sorted_rotno () const

ObjexxFCL::FArray3D< Size > &	packed_rotno_2_sorted_rotno ()

Real	eval_rotameric_energy_deriv (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, bool eval_deriv) const
	Evaluates the score and chi-deviation penalty for the rotameric chi (in this class, that means all the chi) and stores the answers in the scratch object. If eval_deriv is true, then at the end of this function, scratch contains up-to-date dchidevpen_dbb, dchidevpen_dchi, chimean, chisd, chidev, chidevpen, dchimean_d(phi/psi), dchisd_d(phi/psi) rotwell and rotprob data. More...

void	interpolate_rotamers (RotamerLibraryScratchSpace &scratch, Size const packed_rotno, Size const phibin, Size const psibin, Size const phibin_next, Size const psibin_next, Real const phi_alpha, Real const psi_alpha, PackedDunbrackRotamer< T, Real > &interpolated_rotamer) const

void	assign_random_rotamer (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center, Size &packed_rotno) const
	Assigns random chi angles and returns the packed_rotno for the chosen random rotamer. More...

void	assign_chi_for_interpolated_rotamer (PackedDunbrackRotamer< T, Real > const &interpolated_rotamer, conformation::Residue const &rsd, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const

void	correct_termini_derivatives (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const

void	get_phipsi_bins (Real phi, Real psi, Size &phibin, Size &psibin, Size &phibin_next, Size &psibin_next, Real &phi_alpha, Real &psi_alpha) const

void	get_phipsi_bins (Real phi, Real psi, Size &phibin, Size &psibin) const

Real	get_phi_from_rsd (conformation::Residue const &rsd) const

Real	get_psi_from_rsd (conformation::Residue const &rsd) const

template<class P >
DunbrackRotamer< T, P >	packed_rotamer_2_regular_rotamer (PackedDunbrackRotamer< T, P > const &packedrot) const

void	enumerate_chi_sets (chemical::ResidueType const &rsd_type, pack::task::PackerTask const &task, Size const seqpos, bool buried, RotamericData< T > const &rotamer_data, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, utility::vector1< ChiSetOP > &chi_set_vector) const
	This member function constructs a list of all combinations of chi angles for a rotamer sample. It relies on a virtual function chisamples_for_rotamer_chi that may be overridden by derived classes. With a list of samples for each chi, this function then enumerates all combinations. More...

void	create_rotamers_from_chisets (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< ChiSetOP > const &chi_set_vector, RotamerVector &rotamers) const
	Once all the chi have been enumerated, building the rotamers is a trivial task. This function is protected so that derived classes may simply enumerate their chi and then invoke this function. This arguably should be moved into the SingleResidueRotamerLibrary base class. More...

void	setup_entropy_correction ()

void	setup_entropy_correction () const

Protected Member Functions inherited from core::pack::dunbrack::SingleResidueDunbrackLibrary
bool	dun02 () const
	Read access for the derived class. More...

utility::vector1< Size > const &	n_chi_bins () const
	Read access to the n_chi_bins_ vector. More...

void	mark_rotwell_exists (utility::vector1< Size > const &rotwell)
	The base class needs to be informed about which rotamer wells exist in order to create the rotwell to packed rot conversion data. set_chi_nbins must be called first. More...

void	declare_all_existing_rotwells_encountered ()
	After the derived class has marked all the rotwells that do exist, the base class will create the rotwell to packerot conversion data. More...

Size	n_packed_rots () const
	The number of existing rotamers. More...

Size	n_possible_rots () const
	The number of possible rotamers – product of the chi_nbins_ array. More...

Private Member Functions
void	read_rotamer_definitions (utility::io::izstream &in_rotdef)

void	read_bbdep_continuous_minimization_data (utility::io::izstream &in_contmin)

void	read_bbind_continuous_minimization_data (utility::io::izstream &in_contmin)

void	read_rotameric_data (utility::io::izstream &in_rotameric)

void	build_bbdep_rotamers (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, PackedDunbrackRotamer< T, Real > const &interpolated_rotamer, BBDepNRChiSample< Real > const interpolated_sample, RotamerVector &rotamers) const

void	build_bbind_rotamers (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, PackedDunbrackRotamer< T, Real > const &interpolated_rotamer, Size const nrchi_rotno, BBIndNRChiSample<> const &interpolated_sample, RotamerVector &rotamers) const

void	bbind_chisamples_for_rotamer_chi (chemical::ResidueType const &rsd_type, pack::task::ResidueLevelTask const &rtask, bool buried, Size const chi_index, RotamericData< T > const &rotamer_data, utility::vector1< Real > const &extra_steps, utility::vector1< Real > &total_chi, utility::vector1< int > &total_rot, utility::vector1< Real > &total_ex_steps, utility::vector1< Real > &chisample_prob) const

void	bbdep_chisamples_for_rotamer_chi (chemical::ResidueType const &rsd_type, pack::task::ResidueLevelTask const &rtask, bool buried, Size const chi_index, RotamericData< T > const &rotamer_data, utility::vector1< Real > const &extra_steps, utility::vector1< Real > &total_chi, utility::vector1< int > &total_rot, utility::vector1< Real > &total_ex_steps, utility::vector1< Real > &chisample_prob) const

Real	clip_to_nrchi_range (Real chi) const

void	get_bbdep_nrchi_bin (Real nrchi, Size &bin_lower, Size &bin_upper, Real &nrchi_alpha) const

void	get_bbind_nrchi_bin (Real nrchi, Size &bin_lower, Size &bin_upper, Real &nrchi_alpha) const

BBDepNRChiSample< Real >	interpolate_bbdep_nrchi_sample (Size const packed_rotno, Size const nrchi_bin, Size const phibin, Size const psibin, Size const phibin_next, Size const psibin_next, Real const phi_alpha, Real const psi_alpha) const

BBDepNRChiSample< Real >	interpolate_bbdep_nrchi_sample (BBDepNRChiSample<> const &nrchi_sample_00, BBDepNRChiSample<> const &nrchi_sample_01, BBDepNRChiSample<> const &nrchi_sample_10, BBDepNRChiSample<> const &nrchi_sample_11, Real const phi_alpha, Real const psi_alpha) const

Private Attributes
bool const	bbind_nrchi_scoring_
	no default ctor SemiRotamericSingleResidueDunbrackLibrary(); More...

bool const	bbind_nrchi_sampling_

Real	nrchi_periodicity_

Real	nrchi_lower_angle_

utility::vector1 < ObjexxFCL::FArray3D < BBDepScoreInterpData > >	bbdep_nrc_interpdata_

Size	bbdep_nrchi_nbins_

Real	bbdep_nrchi_binsize_

ObjexxFCL::FArray2D< Real >	bbind_non_rotameric_chi_scores_

Size	bbind_nrchi_nbins_

Real	bbind_nrchi_binsize_

Size	n_nrchi_sample_bins_

ObjexxFCL::FArray2D < BBIndNRChiSample<> >	bbind_rotamers_to_sample_

ObjexxFCL::FArray2D< Size >	bbind_rotamers_sorted_by_probability_

ObjexxFCL::FArray3D < BBDepNRChiSample<> >	bbdep_rotamers_to_sample_

ObjexxFCL::FArray4D< Size >	bbdep_rotsample_sorted_order_

Friends
class	SingleResidueDunbrackLibrary

Additional Inherited Members
Static Public Member Functions inherited from core::pack::dunbrack::SingleResidueDunbrackLibrary
static void	n_rotamer_bins_for_aa (chemical::AA const aa, RotVector &rot)
	Hard coded specifics about the amino acids. More...

static void	n_rotameric_bins_for_aa (chemical::AA const aa, RotVector &rot, bool dun02)
	Reports information about the rotameric chi only; no details about the non rotameric chi. More...

static void	n_rotamer_bins_for_aa_02 (chemical::AA const aa, RotVector &rot)
	Hard coded rotamer well info for the 2002 library. More...

Static Public Attributes inherited from core::pack::dunbrack::SingleResidueDunbrackLibrary
static Real const	NEUTRAL_PHI = -90
	constants More...

static Real const	NEUTRAL_PSI = 130
	A good "psi" value to use for C-term residues. More...

Static Protected Attributes inherited from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
static Size const	N_PHIPSI_BINS = 36

static Real const	PHIPSI_BINRANGE = 10.0

Detailed Description

template<Size T>
class core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >

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.

Member Typedef Documentation

template<Size T>

typedef SingleResidueDunbrackLibrary core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::grandparent

template<Size T>

typedef RotamericSingleResidueDunbrackLibrary< T > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::parent

Constructor & Destructor Documentation

template<Size T>

core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::SemiRotamericSingleResidueDunbrackLibrary	(	chemical::AA const	aa_in,
		bool const	backbone_independent_scoring,
		bool const	backbone_independent_rotamer_sampling
	)

The constructor determines the path the library takes: whether it uses a backbone dependent or independent score function for the non-rotameric chi (the rotameric chi score function is always backbone dependent) and whether it uses a backbone dependent or independent rotamer sampling scheme. All four combinations are possible, though backbone independent scoring and backbone dependent rotamer sampling seems a poor combination.

template<Size T>

core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::~SemiRotamericSingleResidueDunbrackLibrary ( )

virtual

Member Function Documentation

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		RotamerLibraryScratchSpace &	scratch,
		numeric::random::RandomGenerator &	RG,
		ChiVector &	new_chi_angles,
		bool	perturb_from_rotamer_center
	)		const

virtual

Pick a rotamer for the input residue according to the rotamer probability distribution and assign chi angles to the input rsd. If perturb_from_rotamer_center is true, then push the rotamer off from the center; for chi angles with a normal distribution, the perturbation is taken from a Gaussian random number with a standard deviation matching the chi angle's standard deviation. For chi angles that are not normally distributed, the behavior is open to the derived classe's interpretation.

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias_bbdep	(	conformation::Residue const &	rsd,
		RotamerLibraryScratchSpace &	scratch,
		numeric::random::RandomGenerator &	RG,
		ChiVector &	new_chi_angles,
		bool	perturb_from_rotamer_center
	)		const

protected

References numeric::random::RandomGenerator::gaussian(), core::pack::dunbrack::interpolate_rotamers(), core::pack::dunbrack::BBDepNRChiSample::nrchi_bin_, core::pack::dunbrack::BBDepNRChiSample::nrchi_mean_, core::pack::dunbrack::BBDepNRChiSample::nrchi_sd_, core::pack::dunbrack::BBDepNRChiSample::packed_rotno_, core::pack::dunbrack::BBDepNRChiSample::prob_, and numeric::random::RandomGenerator::uniform().

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias_bbind	(	conformation::Residue const &	rsd,
		RotamerLibraryScratchSpace &	scratch,
		numeric::random::RandomGenerator &	RG,
		ChiVector &	new_chi_angles,
		bool	perturb_from_rotamer_center
	)		const

protected

References core::sequence::left, right, and numeric::random::RandomGenerator::uniform().

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_chisamples_for_rotamer_chi	(	chemical::ResidueType const &	rsd_type,
		pack::task::ResidueLevelTask const &	rtask,
		bool	buried,
		Size const	chi_index,
		RotamericData< T > const &	rotamer_data,
		utility::vector1< Real > const &	extra_steps,
		utility::vector1< Real > &	total_chi,
		utility::vector1< int > &	total_rot,
		utility::vector1< Real > &	total_ex_steps,
		utility::vector1< Real > &	chisample_prob
	)		const

private

References core::pack::dunbrack::BBDepSemiRotamericData< T >::bbdep_nrchi_sample(), core::pack::task::ResidueLevelTask::extrachi_sample_level(), and core::pack::task::NO_EXTRA_CHI_SAMPLES.

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_score	(	conformation::Residue const &	rsd,
		RotamerLibraryScratchSpace &	scratch,
		Real &	dnrchi_score_dnrchi,
		Real &	dnrchi_score_dphi,
		Real &	dnrchi_score_dpsi
	)		const

protected

Trilinear interpolation. Derivatives discontinuous at edge planes. Correction: it seems that this was updated at some point to use tricubic interpolation. Note: This function has been updated to handle D-amino acids properly.

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_chisamples_for_rotamer_chi	(	chemical::ResidueType const &	rsd_type,
		pack::task::ResidueLevelTask const &	rtask,
		bool	buried,
		Size const	chi_index,
		RotamericData< T > const &	rotamer_data,
		utility::vector1< Real > const &	extra_steps,
		utility::vector1< Real > &	total_chi,
		utility::vector1< int > &	total_rot,
		utility::vector1< Real > &	total_ex_steps,
		utility::vector1< Real > &	chisample_prob
	)		const

private

References core::pack::dunbrack::BBIndSemiRotamericData< T >::bbind_nrchi_sample(), core::pack::task::ResidueLevelTask::extrachi_sample_level(), core::pack::task::NO_EXTRA_CHI_SAMPLES, core::pack::dunbrack::BBIndSemiRotamericData< T >::nrchi_bin_id(), and basic::periodic_range().

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_nrchi_score	(	conformation::Residue const &	rsd,
		RotamerLibraryScratchSpace &	scratch,
		Real &	dnrchi_score_dnrchi
	)		const

protected

simple interpolation; derivatives discontinuous at grid points

References core::conformation::Residue::chi(), and core::pack::dunbrack::RotamerLibraryScratchSpace::rotwell().

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy	(	conformation::Residue const &	rsd,
		bool	curr_rotamer_only,
		RotamerLibraryScratchSpace &	scratch
	)		const

virtual

Returns the energy of the lowest-energy rotamer accessible to the given residue (based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue's current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

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

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::build_bbdep_rotamers	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		pack::task::PackerTask const &	task,
		graph::GraphCOP	packer_neighbor_graph,
		chemical::ResidueTypeCOP	concrete_residue,
		conformation::Residue const &	existing_residue,
		utility::vector1< utility::vector1< Real > > const &	extra_chi_steps,
		bool	buried,
		PackedDunbrackRotamer< T, Real > const &	interpolated_rotamer,
		BBDepNRChiSample< Real > const	interpolated_sample,
		RotamerVector &	rotamers
	)		const

private

References core::conformation::Residue::seqpos().

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::build_bbind_rotamers	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		pack::task::PackerTask const &	task,
		graph::GraphCOP	packer_neighbor_graph,
		chemical::ResidueTypeCOP	concrete_residue,
		conformation::Residue const &	existing_residue,
		utility::vector1< utility::vector1< Real > > const &	extra_chi_steps,
		bool	buried,
		PackedDunbrackRotamer< T, Real > const &	interpolated_rotamer,
		Size const	nrchi_rotno,
		BBIndNRChiSample<> const &	interpolated_sample,
		RotamerVector &	rotamers
	)		const

private

References core::conformation::Residue::seqpos().

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi	(	chemical::ResidueType const &	rsd_type,
		pack::task::ResidueLevelTask const &	rtask,
		bool	buried,
		Size const	chi_index,
		RotamericData< T > const &	rotamer_data,
		utility::vector1< Real > const &	extra_steps,
		utility::vector1< Real > &	total_chi,
		utility::vector1< int > &	total_rot,
		utility::vector1< Real > &	total_ex_steps,
		utility::vector1< Real > &	chisample_prob
	)		const

protectedvirtual

overrides parent class for the non-rotameric chi, but falls back on the parent class functionality for all other chi.

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::clip_to_nrchi_range ( Real chi ) const

private

Clips to range [ nrchi_lower_angle_, nrchi_lower_angle_ + nrchi_periodicity ) Note: this isn't really "clipping" (i.e. values outside of this range are not set to the minimum or maximum of the range). Instead, it is properly returning the value within the range corresponding to a value outside of the range.

References basic::periodic_range().

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		pack::task::PackerTask const &	task,
		graph::GraphCOP	packer_neighbor_graph,
		chemical::ResidueTypeCOP	concrete_residue,
		conformation::Residue const &	existing_residue,
		utility::vector1< utility::vector1< Real > > const &	extra_chi_steps,
		bool	buried,
		RotamerVector &	rotamers
	)		const

virtual

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbdep	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		pack::task::PackerTask const &	task,
		graph::GraphCOP	packer_neighbor_graph,
		chemical::ResidueTypeCOP	concrete_residue,
		conformation::Residue const &	existing_residue,
		utility::vector1< utility::vector1< Real > > const &	extra_chi_steps,
		bool	buried,
		RotamerVector &	rotamers
	)		const

protected

References core::conformation::Residue::aa(), core::pack::dunbrack::interpolate_rotamers(), core::chemical::is_canonical_D_aa(), core::pack::dunbrack::BBDepNRChiSample::nrchi_bin_, core::pack::dunbrack::BBDepNRChiSample::packed_rotno_, core::pack::dunbrack::BBDepNRChiSample::prob_, and scratch.

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbind	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		pack::task::PackerTask const &	task,
		graph::GraphCOP	packer_neighbor_graph,
		chemical::ResidueTypeCOP	concrete_residue,
		conformation::Residue const &	existing_residue,
		utility::vector1< utility::vector1< Real > > const &	extra_chi_steps,
		bool	buried,
		RotamerVector &	rotamers
	)		const

protected

References core::conformation::Residue::aa(), utility::arg_max(), core::pack::dunbrack::interpolate_rotamers(), core::chemical::is_canonical_D_aa(), and scratch.

template<Size T>

utility::vector1< DunbrackRotamerSampleData > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples	(	Real	phi,
		Real	psi
	)		const

virtual

Return all of the rotamer sample data given a particular phi/psi. For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

utility::vector1< DunbrackRotamerSampleData > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples_bbdep	(	Real	phi,
		Real	psi
	)		const

protected

template<Size T>

utility::vector1< DunbrackRotamerSampleData > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples_bbind	(	Real	phi,
		Real	psi
	)		const

protected

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_bbdep_nrchi_bin	(	Real	nrchi,
		Size &	bin_lower,
		Size &	bin_upper,
		Real &	nrchi_alpha
	)		const

private

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_bbind_nrchi_bin	(	Real	nrchi,
		Size &	bin_lower,
		Size &	bin_upper,
		Real &	nrchi_alpha
	)		const

private

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_probability_for_rotamer	(	Real	phi,
		Real	psi,
		Size	rot_ind
	)		const

virtual

Return the probability for a particular rotamer where rotamers are indexed in order of decreasing probability (or something very close to decreasing probability).

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_probability_for_rotamer_bbdep	(	Real	phi,
		Real	psi,
		Size	rot_ind
	)		const

protected

References basic::interpolate_bilinear_by_value(), core::pack::dunbrack::BBDepNRChiSample::nrchi_bin_, core::pack::dunbrack::BBDepNRChiSample::packed_rotno_, and core::pack::dunbrack::BBDepNRChiSample::prob_.

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_probability_for_rotamer_bbind	(	Real	phi,
		Real	psi,
		Size	rot_ind
	)		const

protected

Lookup for bbind is significantly slower than for bbdep

References utility::arg_max(), basic::interpolate_bilinear_by_value(), core::pack::dunbrack::PackedDunbrackRotamer< S, P >::packed_rotno(), and core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotamer_probability().

template<Size T>

DunbrackRotamerSampleData core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer	(	Real	phi,
		Real	psi,
		Size	rot_ind
	)		const

virtual

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

DunbrackRotamerSampleData core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_bbdep	(	Real	phi,
		Real	psi,
		Size	rot_ind
	)		const

protected

template<Size T>

DunbrackRotamerSampleData core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_bbind	(	Real	phi,
		Real	psi,
		Size	rot_ind
	)		const

protected

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi	(	ChiVector const &	chi,
		RotVector &	rot
	)		const

virtual

Convert a vector of chi angles (degrees) into a integer vector of rotamer wells. Derived class should be consistent, but may be arbitrary in how wells divide angle space.

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

References core::sequence::left, right, and utility_exit.

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

template<Size T>

BBDepNRChiSample< Real > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::interpolate_bbdep_nrchi_sample	(	Size const	packed_rotno,
		Size const	nrchi_bin,
		Size const	phibin,
		Size const	psibin,
		Size const	phibin_next,
		Size const	psibin_next,
		Real const	phi_alpha,
		Real const	psi_alpha
	)		const

private

template<Size T>

BBDepNRChiSample< Real > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::interpolate_bbdep_nrchi_sample	(	BBDepNRChiSample<> const &	nrchi_sample_00,
		BBDepNRChiSample<> const &	nrchi_sample_01,
		BBDepNRChiSample<> const &	nrchi_sample_10,
		BBDepNRChiSample<> const &	nrchi_sample_11,
		Real const	phi_alpha,
		Real const	psi_alpha
	)		const

private

References basic::interpolate_bilinear_by_value(), core::pack::dunbrack::BBDepNRChiSample::nrchi_bin_, core::pack::dunbrack::BBDepNRChiSample::nrchi_mean_, core::pack::dunbrack::BBDepNRChiSample::nrchi_sd_, core::pack::dunbrack::BBDepNRChiSample::packed_rotno_, and core::pack::dunbrack::BBDepNRChiSample::prob_.

template<Size T>

Size core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::memory_usage_dynamic ( ) const

protectedvirtual

Measures the amount of dynamically allocated data in this class. Must recurse to parent to count parent's dynamically allocated data.

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

Size core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::memory_usage_static ( ) const

protectedvirtual

Worker functions.

called only if the library is actually an RSRDL<T> object. Derived classes should not call this function or recurse. Accounts for the statically allocated data that's part of this class.

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

Size core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::n_rotamer_bins ( ) const

virtual

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

Size core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::nchi ( ) const

virtual

The number of chi represented by the library.

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_bbdep_continuous_minimization_data ( utility::io::izstream & in_contmin )

private

References e_Periodic, numeric::interpolation::spline::TricubicSpline::get_dsecox(), numeric::interpolation::spline::TricubicSpline::get_dsecoxy(), numeric::interpolation::spline::TricubicSpline::get_dsecoxyz(), numeric::interpolation::spline::TricubicSpline::get_dsecoxz(), numeric::interpolation::spline::TricubicSpline::get_dsecoy(), numeric::interpolation::spline::TricubicSpline::get_dsecoyz(), numeric::interpolation::spline::TricubicSpline::get_dsecoz(), utility::io::izstream::getline(), utility::io::izstream::peek(), start, and numeric::interpolation::spline::TricubicSpline::train().

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_bbind_continuous_minimization_data ( utility::io::izstream & in_contmin )

private

References utility::io::izstream::getline(), and utility::io::izstream::peek().

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_from_binary ( utility::io::izstream & in )

virtual

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

References utility::io::izstream::read(), and utility_exit.

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

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_from_files	(	utility::io::izstream &	in_rotdef,
		utility::io::izstream &	in_rotameric,
		utility::io::izstream &	in_continmin_bbdep,
		utility::io::izstream &	in_continmin_bbind
	)

Initialize either a backbone-independent or a backbone-dependent SRSRDL from the set of four files which describe both (not all files are read).

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

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_from_files	(	utility::io::izstream &	in_rotdef,
		utility::io::izstream &	in_rotameric,
		utility::io::izstream &	in_continmin_bbdep
	)

Initialize a backbone-dependent SRSRDL from the set of three files which describe it.

read-from-files that does not require the in_continmin_bbind file

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotamer_definitions ( utility::io::izstream & in_rotdef )

private

the rotamer definition file must be the first file read. Reading this file gives the number of pseudorotamers used for both the bbdep and bbind rotamer building. The bbind rotamer data is saved iff the bbind_rotamer_building_ flag is true.

References utility::io::izstream::getline(), core::sequence::left, median(), utility::io::izstream::peek(), core::pack::dunbrack::psc_compare(), right, core::io::serialization::size(), and utility_exit.

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotameric_data ( utility::io::izstream & in_rotameric )

private

The rotamer definition file has already been read before this function is called, so all of the rotameric rotamer wells have been encountered and the packed_rotno enumeration may be used instead of the regular rotno.

References core::pack::dunbrack::DUNBRACK_MAX_SCTOR, utility::io::izstream::getline(), mean, core::pack::dunbrack::BBDepNRChiSample::nrchi_bin_, core::pack::dunbrack::BBDepNRChiSample::nrchi_mean_, core::pack::dunbrack::BBDepNRChiSample::nrchi_sd_, core::pack::dunbrack::BBDepNRChiSample::packed_rotno_, utility::io::izstream::peek(), basic::periodic_range(), core::pack::dunbrack::BBDepNRChiSample::prob_, and utility_exit.

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy	(	conformation::Residue const &	rsd,
		RotamerLibraryScratchSpace &	scratch
	)		const

virtual

Virtual functions required by the base classes.

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv	(	conformation::Residue const &	rsd,
		RotamerLibraryScratchSpace &	scratch
	)		const

virtual

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv_bbdep	(	conformation::Residue const &	rsd,
		RotamerLibraryScratchSpace &	scratch,
		bool	eval_deriv
	)		const

protected

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv_bbind	(	conformation::Residue const &	rsd,
		RotamerLibraryScratchSpace &	scratch,
		bool	eval_deriv
	)		const

protected

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::set_nonrotameric_chi_bbdep_scoring_step_size ( Real step_size_in_degrees )

What is the angular step size of the bbdep score?

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

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::set_nonrotameric_chi_bbind_scoring_step_size ( Real step_size_in_degrees )

What is the angular step size of the bbind score?

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

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::set_nonrotameric_chi_start_angle ( Real angle_in_degrees )

What angle do the interpolation data start from?

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

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::set_nrchi_periodicity ( Real angle_in_degrees )

Initialization functions that must be called before reading the input libraries.

For the non rotameric chi, how many asymmetric degrees are there? (e.g. 360 for asn, 180 for asp)

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

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::write_to_binary ( utility::io::ozstream & out ) const

virtual

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

References utility::io::ozstream::write().

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

template<Size T>

void core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::write_to_file ( utility::io::ozstream & out ) const

virtual

Reimplemented from core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

References utility_exit_with_message.

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

Friends And Related Function Documentation

template<Size T>

friend class SingleResidueDunbrackLibrary

friend

Member Data Documentation

template<Size T>

utility::vector1< ObjexxFCL::FArray3D< BBDepScoreInterpData > > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrc_interpdata_

private

The non rotameric chi is n_rotameric_chi + 1; The FArray3D is indexed as (phi, psi, nrchi). Probabilities are input; the parameters for tricubic interpolation are stored. The supporting information is used to snap chi values stored in a residue to a meaningful periodic range and to make tricubic interpolation possible. This data is used only if bbind_nrchi_scoring is false.

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_binsize_

private

template<Size T>

Size core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_nbins_

private

template<Size T>

ObjexxFCL::FArray3D< BBDepNRChiSample<> > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_rotamers_to_sample_

private

This variable is used iff bbind_nrchi_sampling_ is false; Space is not allocated if it is true.

template<Size T>

ObjexxFCL::FArray4D< Size > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_rotsample_sorted_order_

private

template<Size T>

ObjexxFCL::FArray2D< Real > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_non_rotameric_chi_scores_

private

If bbind_nrchi_scoring_ is true, then this array holds the continuous minimization data for each of the packed rotamers.

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_nrchi_binsize_

private

template<Size T>

Size core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_nrchi_nbins_

private

template<Size T>

bool const core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_nrchi_sampling_

private

template<Size T>

bool const core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_nrchi_scoring_

private

no default ctor SemiRotamericSingleResidueDunbrackLibrary();

template<Size T>

ObjexxFCL::FArray2D< Size > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_rotamers_sorted_by_probability_

private

template<Size T>

ObjexxFCL::FArray2D< BBIndNRChiSample<> > core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_rotamers_to_sample_

private

This variable is used iff bbind_nrchi_sampling_ is true; Space is not allocated if it is false. The algorithm for creating the top 95% most probable rotamers relies on a sorted order for these rotamers, which is why we need bbind_rotamers_sorted_by_probability_.

template<Size T>

Size core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::n_nrchi_sample_bins_

private

For rotamer sampling, "pseudo rotamers" are defined for the non rotameric chi. These rotamers are arbitrary bins in chi space, and each bin gives a left and right edge as well as a median (mode?) angle which is used for rotamer sampling iff bbind_nrchi_sampling_ is true. The bins do not have a uniform width.

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::nrchi_lower_angle_

private

template<Size T>

Real core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::nrchi_periodicity_

private

The documentation for this class was generated from the following files: