DOUG DOUG DOUG. More...

#include <RotamericSingleResidueDunbrackLibrary.hh>

Public Types
typedef SingleResidueDunbrackLibrary	parent

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

Public Member Functions
	RotamericSingleResidueDunbrackLibrary (AA const aa_in, bool dun02)

virtual	~RotamericSingleResidueDunbrackLibrary ()

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

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...

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
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 ()

virtual Size	memory_usage_static () const
	Worker functions. More...

virtual Size	memory_usage_dynamic () const

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...

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
	Used in tandem with enumerate_chi_sets, this function pushes back chi sample data into the four input vectors: the 1. chi value sample,. 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...

Static Protected Attributes
static Size const	N_PHIPSI_BINS = 36

static Real const	PHIPSI_BINRANGE = 10.0

Private Member Functions
void	build_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, RotamerVector &rotamers, PackedDunbrackRotamer< T, Real > const &interpolated_rotamer) const
	After an interpolated rotamer has been created, this method appends new rotamers to the vector of rotamers, taking extra samples at designated chi intervals if instructed to do so in the extra_chi_steps argument. More...

void	verify_phipsi_bins (Real phi, Real psi, Size const phibin, Size const psibin, Size const phibin_next, Size const psibin_next) const

Private Attributes
ObjexxFCL::FArray3D < PackedDunbrackRotamer< T > >	rotamers_

ObjexxFCL::FArray3D< Size >	packed_rotno_2_sorted_rotno_

ObjexxFCL::FArray2D< Real >	ShanonEntropy_

ObjexxFCL::FArray2D< Real >	S_dsecophi_

ObjexxFCL::FArray2D< Real >	S_dsecopsi_

ObjexxFCL::FArray2D< Real >	S_dsecophipsi_

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...

Detailed Description

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

DOUG DOUG DOUG.

Member Typedef Documentation

template<Size T>

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

Constructor & Destructor Documentation

template<Size T>

core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::RotamericSingleResidueDunbrackLibrary	(	AA const	aa_in,
		bool	dun02
	)

No default ctor RotamericSingleResidueDunbrackLibrary();

template<Size T>

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

virtual

Member Function Documentation

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::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

protected

References core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::chi_mean(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::chi_sd(), numeric::random::RandomGenerator::gaussian(), core::conformation::Residue::nchi(), and numeric::random::RandomGenerator::uniform().

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::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

protected

Assigns random chi angles and returns the packed_rotno for the chosen random rotamer.

References core::pack::dunbrack::interpolate_rotamers(), core::pack::dunbrack::PackedDunbrackRotamer< S, P >::packed_rotno(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotamer_probability(), and numeric::random::RandomGenerator::uniform().

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< 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.

Implements core::pack::dunbrack::SingleResidueRotamerLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< 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).

Implements core::pack::dunbrack::SingleResidueRotamerLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

References core::conformation::Residue::chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi_static(), core::pack::dunbrack::interpolate_rotamers(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotamer_probability(), and core::pack::dunbrack::RotamerLibraryScratchSpace::rotwell().

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

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::build_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,
		RotamerVector &	rotamers,
		PackedDunbrackRotamer< T, Real > const &	interpolated_rotamer
	)		const

private

After an interpolated rotamer has been created, this method appends new rotamers to the vector of rotamers, taking extra samples at designated chi intervals if instructed to do so in the extra_chi_steps argument.

Load interpolated rotamer data into a RotamericData object on the stack so that it can be handed into the enumerate_chi_sets method, which itself relies on the "template method" chisamples_for_rotamer_and_chi. Enumerate the chi samples, and build rotamers from these chi samples.

"template method" is a design pattern where a base class calls a polymorphic method that can be overloaded by a derived class, usually in the middle of a function that does a lot of work. See "Design Patterns," Gamma et al.

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

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< 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

Used in tandem with enumerate_chi_sets, this function pushes back chi sample data into the four input vectors: the 1. chi value sample,.

the rotamer well #, 3. a discription of the kind of sample (how far off the ideal rotamer) and 4. the probability of observing this chi at that sample. The rotamer_data that's input is the same data that was handed to the enumerate_chi_sets call (may be downcast as needed).

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

References core::chemical::ResidueType::atom(), core::chemical::ResidueType::chi_2_proton_chi(), core::chemical::ResidueType::chi_atoms(), core::chemical::ResidueType::chi_rotamers(), numeric::dihedral(), core::pack::task::ResidueLevelTask::extrachi_sample_level(), core::chemical::ResidueType::is_proton_chi(), core::pack::task::NO_EXTRA_CHI_SAMPLES, core::chemical::ResidueType::proton_chi_extra_samples(), core::chemical::ResidueType::proton_chi_samples(), and core::pack::dunbrack::RotamericData< T >::rotamer().

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::correct_termini_derivatives	(	conformation::Residue const &	rsd,
		RotamerLibraryScratchSpace &	scratch
	)		const

protected

References core::pack::dunbrack::RotamerLibraryScratchSpace::AA_PHI_INDEX, core::pack::dunbrack::RotamerLibraryScratchSpace::AA_PSI_INDEX, core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb(), core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_dev(), core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_rot(), core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb_semi(), core::conformation::Residue::is_lower_terminus(), and core::conformation::Residue::is_upper_terminus().

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::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

protected

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.

once a list of chi samples has been enumerated, this function instantiates Residue objectes and give them the correct geometry.

References core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::pack::task::ResidueLevelTask::preserve_c_beta(), core::pack::task::PackerTask::residue_task(), core::pack::task::ResidueLevelTask::rotamer_operations(), core::conformation::Residue::seqpos(), and core::conformation::Residue::set_chi().

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::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

protected

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.

References utility::LexicographicalIterator::at_end(), core::chemical::ResidueType::nchi(), core::pack::task::PackerTask::residue_task(), core::pack::dunbrack::RotamericData< T >::rotamer(), runtime_assert, and core::io::serialization::size().

template<Size T>

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

protected

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.

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< 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

Implements core::pack::dunbrack::SingleResidueRotamerLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

References core::conformation::Residue::aa(), core::pack::dunbrack::interpolate_rotamers(), core::chemical::is_canonical_D_aa(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotamer_probability(), and scratch.

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

template<Size T>

Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::find_another_representative_for_unlikely_rotamer	(	conformation::Residue const &	rsd,
		Size4 &	rotwell
	)		const

The new rotamer library represents only 75 of 81 possible arginine rotamers, and 75 of 81 lysine rotamers. In the unlikely event that a rotamer is encountered that's not represented in the library, find another rotamer to represent it. Ideally, this stand-in rotamer would be closest to the input rotamer in physical geometry. (sidechain atom rms, e.g.) The following code instead first looks through all possible rotamers with a Hamming distance of one from input rotamer trying to find one that works, looking first for rotamers from the furthest chi toward the closest chi. If no such rotamer may be found, it gives up and returns the most-probable rotamer for a phi-psi bin.

This function modifies the "rotwell" assigned to this rotamer so that later code that relies on the consistency of the rotwell and packed_rotno information will behave correctly.

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

template<Size T>

utility::vector1< DunbrackRotamerSampleData > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< 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.

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_phi_from_rsd ( conformation::Residue const & rsd ) const

protectedvirtual

Handle lower-term residues by returning a "neutral" phi value

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

References core::conformation::Residue::aa(), core::chemical::is_canonical_D_aa(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_peptoid(), core::conformation::Residue::is_protein(), and core::conformation::Residue::mainchain_torsion().

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_phipsi_bins	(	Real	phi,
		Real	psi,
		Size &	phibin,
		Size &	psibin,
		Size &	phibin_next,
		Size &	psibin_next,
		Real &	phi_alpha,
		Real &	psi_alpha
	)		const

protected

The Dunbrack library's phi/psi data for a grid point (x,y) collects data in the neighborhood of (x,y). As an interpolation point p moves toward a grid point (x,y), the (x,y) share in the interpolated value goes to 1. This is distinct from having interpolation wells where an interpolation in the center of a well produces the maximum contribution from that well. Most of the basic::interpolation code is designed for the second interpretation of interpolation, and so CTSA's Dunbrack library code did funky thinks like shift by 5 degrees so that the basic::interpolation code could shift it back by 5 degrees again. The code below makes no such shift.

The alpha fraction is the distance along each axis that the interpolation point has progressed from the lower grid point toward the upper grid point; it ranges from 0 to 1.

References basic::periodic_range().

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_phipsi_bins	(	Real	phi,
		Real	psi,
		Size &	phibin,
		Size &	psibin
	)		const

protected

template<Size T>

Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< 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).

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

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

template<Size T>

Real core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_psi_from_rsd ( conformation::Residue const & rsd ) const

protectedvirtual

Handle upper-term residues by returning a "neutral" psi value

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

References core::conformation::Residue::aa(), core::chemical::is_canonical_D_aa(), core::conformation::Residue::is_peptoid(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), and core::conformation::Residue::mainchain_torsion().

template<Size T>

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

virtual

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< 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.

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi_static	(	ChiVector const &	chi,
		Size4 &	rot
	)		const

protected

When given a statically sized fixedsizearray, use this method.

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

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi_static	(	Real4 const &	chi,
		Size4 &	rot
	)		const

protected

When given a statically sized fixedsizearray, use this method.

References aa2, core::chemical::get_L_equivalent(), core::chemical::is_canonical_D_aa(), basic::periodic_range(), core::pack::dunbrack::rotamer_from_chi_02(), and utility::fixedsizearray1< T, S >::size().

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::initialize_bicubic_splines ( )

protected

References e_Periodic, core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotamer_probability(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotE(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotE_dsecophi(), core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotE_dsecophipsi(), and core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >::rotE_dsecopsi().

template<Size T>

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

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

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

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::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

protected

template<Size T>

Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< 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::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

Size core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< 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.

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

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

virtual

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

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

virtual

The number of chi represented by the library.

Implements core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

template<class P >

DunbrackRotamer< T, P > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::packed_rotamer_2_regular_rotamer ( PackedDunbrackRotamer< T, P > const & packedrot ) const

protected

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

template<Size T>

ObjexxFCL::FArray3D< Size > const& core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::packed_rotno_2_sorted_rotno ( ) const

inlineprotected

References core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::packed_rotno_2_sorted_rotno_.

template<Size T>

ObjexxFCL::FArray3D< Size >& core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::packed_rotno_2_sorted_rotno ( )

inlineprotected

References core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::packed_rotno_2_sorted_rotno_.

template<Size T>

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

virtual

Reimplemented from core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

References basic::options::OptionKeys::corrections::score::dun_entropy_correction, basic::options::option, and utility::io::izstream::read().

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

template<Size T>

std::string core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file	(	utility::io::izstream &	infile,
		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.

Returns the three letter string of the next amino acid specified in the input library.

References basic::options::OptionKeys::corrections::score::dun_entropy_correction, core::pack::dunbrack::DUNBRACK_MAX_SCTOR, utility::io::izstream::getline(), core::chemical::name_from_aa(), basic::options::option, utility::io::izstream::peek(), and utility_exit.

Referenced by core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib(), and core::pack::dunbrack::RotamerLibrary::get_NCAA_rotamer_library().

template<Size T>

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

virtual

Virtual functions required by the base classes.

Implements core::pack::dunbrack::SingleResidueRotamerLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

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

virtual

Implements core::pack::dunbrack::SingleResidueRotamerLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

template<Size T>

ObjexxFCL::FArray3D< PackedDunbrackRotamer< T > > const& core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamers ( ) const

inlineprotected

Read and write access for derived classes.

References core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamers_.

template<Size T>

ObjexxFCL::FArray3D< PackedDunbrackRotamer< T > >& core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamers ( )

inlineprotected

References core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamers_.

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::setup_entropy_correction ( )

protected

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::setup_entropy_correction ( ) const

protected

template<Size T>

void core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::verify_phipsi_bins	(	Real	phi,
		Real	psi,
		Size const	phibin,
		Size const	psibin,
		Size const	phibin_next,
		Size const	psibin_next
	)		const

private

References utility_exit.

template<Size T>

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

virtual

Reimplemented from core::pack::dunbrack::SingleResidueDunbrackLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >.

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

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

template<Size T>

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

virtual

Implements core::pack::dunbrack::SingleResidueRotamerLibrary.

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< 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>

Size const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::N_PHIPSI_BINS = 36

staticprotected

template<Size T>

ObjexxFCL::FArray3D< Size > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::packed_rotno_2_sorted_rotno_

private

Quick lookup that lists the sorted position for the packed rotamer number given a phi/psi. Indexed by (phi, psi, packed_rotno ).

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::packed_rotno_2_sorted_rotno().

template<Size T>

Real const core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::PHIPSI_BINRANGE = 10.0

staticprotected

template<Size T>

ObjexxFCL::FArray3D< PackedDunbrackRotamer< T > > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamers_

private

The (chi_mean, chi_sd, packed_rotno, and prob) data for the chi dihedrals The FArray3D is indexed into by (phi, psi, sorted_index ), where sorted index simply means the order for a particular packed_rotno in the list of rotamers sorted by probability.

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

template<Size T>

ObjexxFCL::FArray2D< Real > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::S_dsecophi_

private

template<Size T>

ObjexxFCL::FArray2D< Real > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::S_dsecophipsi_

private

template<Size T>

ObjexxFCL::FArray2D< Real > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::S_dsecopsi_

private

template<Size T>

ObjexxFCL::FArray2D< Real > core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::ShanonEntropy_