#include <SingleResidueDunbrackLibrary.hh>

Public Types
typedef chemical::AA	AA

Public Member Functions
	SingleResidueDunbrackLibrary (AA const aa, Size const n_rotameric_chi, bool dun02)
	c-tor More...

virtual	~SingleResidueDunbrackLibrary ()

void	read_options ()

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

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

virtual utility::vector1 < DunbrackRotamerSampleData >	get_all_rotamer_samples (Real phi, Real psi) const =0
	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 =0
	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 =0

virtual Real	get_phi_from_rsd (conformation::Residue const &rsd) const =0

virtual Real	get_psi_from_rsd (conformation::Residue const &rsd) const =0

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

virtual Size	nchi () const =0
	The number of chi represented by the library. More...

virtual Size	n_rotamer_bins () const =0

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

virtual void	get_rotamer_from_chi (ChiVector const &chi, RotVector &rot) const =0
	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...

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 ()

virtual Real	rotamer_energy_deriv (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const =0

virtual Real	rotamer_energy (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const =0

virtual Real	best_rotamer_energy (conformation::Residue const &rsd, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const =0
	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 =0
	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 =0

virtual void	write_to_file (utility::io::ozstream &out) const =0

Static Public Member Functions
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
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...

Protected Member Functions
bool	dun02 () const
	Read access for the derived class. More...

virtual Size	memory_usage_static () const =0
	Worker functions available to the derived classes. More...

virtual Size	memory_usage_dynamic () const

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	hokey_template_workaround ()
	This function forces the instantiation of virtual templated methods in the derived classes. Functions like this one are necessary when combining polymorphism and templates. Though these functions must be compiled, they need never be called. Do not call this function. More...

Private Attributes
bool const	dun02_
	data More...

AA const	aa_

Size const	n_rotameric_chi_

utility::vector1< Size >	n_chi_bins_

utility::vector1< Size >	n_chi_products_

Size	n_packed_rots_

Size	n_possible_rots_

Real	prob_to_accumulate_buried_

Real	prob_to_accumulate_nonburied_

utility::vector1< bool >	rotwell_exists_

bool	packed_rotno_conversion_data_current_

utility::vector1< Size >	rotno_2_packed_rotno_

utility::vector1< Size >	packed_rotno_2_rotno_

utility::vector1 < utility::vector1< Size > >	packed_rotno_2_rotwell_

Member Typedef Documentation

typedef chemical::AA core::pack::dunbrack::SingleResidueDunbrackLibrary::AA

Constructor & Destructor Documentation

core::pack::dunbrack::SingleResidueDunbrackLibrary::SingleResidueDunbrackLibrary	(	AA const	aa,
		Size const	n_rotameric_chi,
		bool	dun02
	)

c-tor

References aa_, core::chemical::aa_unk, n_chi_bins_, n_chi_products_, n_possible_rots_, n_rotameric_bins_for_aa(), n_rotameric_chi_, read_options(), rotno_2_packed_rotno_, and rotwell_exists_.

core::pack::dunbrack::SingleResidueDunbrackLibrary::~SingleResidueDunbrackLibrary ( )

virtual

Member Function Documentation

AA core::pack::dunbrack::SingleResidueDunbrackLibrary::aa ( ) const

inline

The amino acid this library is representing.

References aa_.

void core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle	(	Real const	angle_start,
		Real const	angle_step,
		Real const	ASSERT_ONLYangle_range,
		Size const	nbins,
		Real const	ang,
		Size &	bin_lower,
		Size &	bin_upper,
		Real &	angle_alpha
	)		const

inline

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...

References ASSERT_ONLY, and numeric::mod().

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi	(	Real	chi,
		Size	which_chi
	)		const

inline

, 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.

References aa_, core::chemical::aa_dpr, core::chemical::aa_pro, and dun02_.

void core::pack::dunbrack::SingleResidueDunbrackLibrary::declare_all_existing_rotwells_encountered ( )

protected

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

References n_packed_rots_, n_possible_rots_, packed_rotno_2_rotno_, packed_rotno_2_rotwell_, packed_rotno_conversion_data_current_, rotno_2_packed_rotno_, rotno_2_rotwell(), and rotwell_exists_.

bool core::pack::dunbrack::SingleResidueDunbrackLibrary::dun02 ( ) const

inlineprotected

Read access for the derived class.

References dun02_.

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

pure 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.

Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

virtual Real core::pack::dunbrack::SingleResidueDunbrackLibrary::get_phi_from_rsd ( conformation::Residue const & rsd ) const

pure virtual

Implemented in core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

virtual Real core::pack::dunbrack::SingleResidueDunbrackLibrary::get_probability_for_rotamer	(	Real	phi,
		Real	psi,
		Size	rot_ind
	)		const

pure virtual

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

Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

virtual Real core::pack::dunbrack::SingleResidueDunbrackLibrary::get_psi_from_rsd ( conformation::Residue const & rsd ) const

pure virtual

Implemented in core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

virtual DunbrackRotamerSampleData core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer	(	Real	phi,
		Real	psi,
		Size	rot_ind
	)		const

pure virtual

Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

virtual void core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer_from_chi	(	ChiVector const &	chi,
		RotVector &	rot
	)		const

pure 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.

Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

void core::pack::dunbrack::SingleResidueDunbrackLibrary::hokey_template_workaround ( )

private

This function forces the instantiation of virtual templated methods in the derived classes. Functions like this one are necessary when combining polymorphism and templates. Though these functions must be compiled, they need never be called. Do not call this function.

forces instantiation of virtual functions for templated derived classes... part of the uglyness of mixing templates and polymorphism. Never invoke this function.

void core::pack::dunbrack::SingleResidueDunbrackLibrary::mark_rotwell_exists ( utility::vector1< Size > const & rotwell )

protected

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.

References packed_rotno_conversion_data_current_, rotwell_2_rotno(), and rotwell_exists_.

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_dynamic ( ) const

protectedvirtual

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

References n_chi_bins_, n_chi_products_, packed_rotno_2_rotno_, packed_rotno_2_rotwell_, rotno_2_packed_rotno_, and rotwell_exists_.

Referenced by memory_usage_in_bytes().

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_in_bytes ( ) const

virtual

Virtual functions the derived classes must implement.

Derived classes should invoke base class function as well.

References memory_usage_dynamic(), and memory_usage_static().

Referenced by hokey_template_workaround().

virtual Size core::pack::dunbrack::SingleResidueDunbrackLibrary::memory_usage_static ( ) const

protectedpure virtual

Worker functions available to the derived classes.

Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

Referenced by memory_usage_in_bytes().

utility::vector1< Size > const& core::pack::dunbrack::SingleResidueDunbrackLibrary::n_chi_bins ( ) const

inlineprotected

Read access to the n_chi_bins_ vector.

References n_chi_bins_.

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::n_packed_rots ( ) const

inlineprotected

The number of existing rotamers.

References n_packed_rots_.

Referenced by read_from_binary(), and write_to_binary().

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::n_possible_rots ( ) const

inlineprotected

The number of possible rotamers – product of the chi_nbins_ array.

References n_possible_rots_.

virtual Size core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins ( ) const

pure virtual

Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

void core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa	(	chemical::AA const	aa,
		RotVector &	rot
	)

static

Hard coded specifics about the amino acids.

the number of wells defined for the 08 library; includes the number of wells for the semi-rotameric chi (arbitrarily chosen).

void core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02	(	chemical::AA const	aa,
		RotVector &	rot
	)

static

Hard coded rotamer well info for the 2002 library.

To continue supporting the 2002 Dunbrack library, we need to preserve the rotamer well definitions that it made.

Referenced by n_rotameric_bins_for_aa().

void core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa	(	chemical::AA const	aa,
		RotVector &	rot,
		bool	dun02
	)

static

Reports information about the rotameric chi only; no details about the non rotameric chi.

For the rotameric chi – not all chi are rotameric

Referenced by SingleResidueDunbrackLibrary().

virtual Size core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi ( ) const

pure virtual

The number of chi represented by the library.

Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

void core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell	(	Size const	packed_rotno,
		utility::vector1< Size > &	rotwell
	)		const

Convert from the packed rotamer number to the rotamer well.

References packed_rotno_2_rotwell_.

Referenced by read_from_binary(), and write_to_binary().

void core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell	(	Size const	packed_rotno,
		Size4 &	rotwell
	)		const

References begin, utility::fixedsizearray1< T, S >::begin(), core::sequence::end, packed_rotno_2_rotwell_, utility::fixedsizearray1< T, S >::size(), and core::io::serialization::size().

utility::vector1< Size > const & core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell ( Size const packed_rotno ) const

References packed_rotno_2_rotwell_.

void core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate	(	Real	buried,
		Real	nonburied
	)

setters for accumulation probability cutoff (to support externally-controlled option dependence)

References prob_to_accumulate_buried(), and prob_to_accumulate_nonburied().

void core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate_buried ( Real buried )

References prob_to_accumulate_buried_, and utility_exit_with_message.

Referenced by prob_to_accumulate(), and read_options().

void core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate_nonburied ( Real nonburied )

References prob_to_accumulate_nonburied_, and utility_exit_with_message.

Referenced by prob_to_accumulate(), and read_options().

Real core::pack::dunbrack::SingleResidueDunbrackLibrary::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.

References prob_to_accumulate_buried_, and prob_to_accumulate_nonburied_.

void core::pack::dunbrack::SingleResidueDunbrackLibrary::read_from_binary ( utility::io::izstream & in )

virtual

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

References n_packed_rots(), n_packed_rots_, n_possible_rots_, n_rotameric_chi_, packed_rotno_2_rotno_, packed_rotno_2_rotwell(), packed_rotno_2_rotwell_, packed_rotno_conversion_data_current_, utility::io::izstream::read(), rotno_2_packed_rotno(), and rotno_2_packed_rotno_.

void core::pack::dunbrack::SingleResidueDunbrackLibrary::read_options ( )

References option, prob_to_accumulate_buried(), prob_to_accumulate_nonburied(), and user.

Referenced by SingleResidueDunbrackLibrary().

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::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.

References packed_rotno_conversion_data_current_, and rotno_2_packed_rotno_.

Referenced by read_from_binary(), rotwell_2_packed_rotno(), and write_to_binary().

void core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell	(	Size const	rotno,
		utility::vector1< Size > &	rotwell
	)		const

Convert from the rotamer number to the rotamer well.

not as fast as going through the packed_rotno_2_rotwell_ lookup table, but does the modulo converstion from a 1-based index to a lexicographical index ordering.

if there are 3 chi, and 3 rotamer bins per chi, then 21 would represent (3-1) * 3**2 + (1-1) * 3**1 + (3-1) * 3**0 + 1 = [ 3, 1, 3 ];

References n_chi_products_, n_rotameric_chi_, and remainder().

Referenced by declare_all_existing_rotwells_encountered().

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::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.

References packed_rotno_conversion_data_current_, rotno_2_packed_rotno(), and rotwell_2_rotno().

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::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.

References packed_rotno_conversion_data_current_, rotno_2_packed_rotno(), and rotwell_2_rotno().

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno ( utility::vector1< Size > const & rotwell ) const

Conversion functions.

Convert from the rotamer bin indices for each chi to the (non-compact) "rotamer number"

References n_chi_products_.

Referenced by mark_rotwell_exists(), and rotwell_2_packed_rotno().

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno ( Size4 const & rotwell ) const

Convert from the rotamer bin indices for each chi to the (non-compact) "rotamer number".

References n_chi_products_, and utility::fixedsizearray1< T, S >::size().

void core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins ( utility::vector1< Size > const & n_chi_bins )

Tell the base class the number of chi bins for each rotameric chi dimension.

Sets the number of bins for a particular chi angle, used for the NCAAs, info for CAAs is hardcoded bellow

References n_chi_bins_, n_chi_products_, n_possible_rots_, n_rotameric_chi_, rotno_2_packed_rotno_, and rotwell_exists_.

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

void core::pack::dunbrack::SingleResidueDunbrackLibrary::write_to_binary ( utility::io::ozstream & out ) const

virtual

Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.

References n_packed_rots(), n_packed_rots_, n_possible_rots_, n_rotameric_chi_, packed_rotno_2_rotno_, packed_rotno_2_rotwell(), packed_rotno_2_rotwell_, rotno_2_packed_rotno(), rotno_2_packed_rotno_, and utility::io::ozstream::write().

Member Data Documentation

AA const core::pack::dunbrack::SingleResidueDunbrackLibrary::aa_

private

Referenced by aa(), bin_rotameric_chi(), and SingleResidueDunbrackLibrary().

bool const core::pack::dunbrack::SingleResidueDunbrackLibrary::dun02_

private

data

Referenced by bin_rotameric_chi(), and dun02().

utility::vector1< Size > core::pack::dunbrack::SingleResidueDunbrackLibrary::n_chi_bins_

private

Referenced by memory_usage_dynamic(), n_chi_bins(), set_n_chi_bins(), and SingleResidueDunbrackLibrary().

utility::vector1< Size > core::pack::dunbrack::SingleResidueDunbrackLibrary::n_chi_products_

private

Referenced by memory_usage_dynamic(), rotno_2_rotwell(), rotwell_2_rotno(), set_n_chi_bins(), and SingleResidueDunbrackLibrary().

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::n_packed_rots_

private

Referenced by declare_all_existing_rotwells_encountered(), n_packed_rots(), read_from_binary(), and write_to_binary().

Size core::pack::dunbrack::SingleResidueDunbrackLibrary::n_possible_rots_

private

Referenced by declare_all_existing_rotwells_encountered(), n_possible_rots(), read_from_binary(), set_n_chi_bins(), SingleResidueDunbrackLibrary(), and write_to_binary().

Size const core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_chi_

private

Referenced by read_from_binary(), rotno_2_rotwell(), set_n_chi_bins(), SingleResidueDunbrackLibrary(), and write_to_binary().

Real const core::pack::dunbrack::SingleResidueDunbrackLibrary::NEUTRAL_PHI = -90

static

constants

A good "phi" value to use for N-term residues

Real const core::pack::dunbrack::SingleResidueDunbrackLibrary::NEUTRAL_PSI = 130

static

A good "psi" value to use for C-term residues.

utility::vector1< Size > core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotno_

private

Referenced by declare_all_existing_rotwells_encountered(), memory_usage_dynamic(), read_from_binary(), and write_to_binary().

utility::vector1< utility::vector1< Size > > core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell_

private

Referenced by declare_all_existing_rotwells_encountered(), memory_usage_dynamic(), packed_rotno_2_rotwell(), read_from_binary(), and write_to_binary().

bool core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_conversion_data_current_

private

Referenced by declare_all_existing_rotwells_encountered(), mark_rotwell_exists(), read_from_binary(), rotno_2_packed_rotno(), and rotwell_2_packed_rotno().

Real core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate_buried_

private

Referenced by prob_to_accumulate_buried(), and probability_to_accumulate_while_building_rotamers().

Real core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate_nonburied_

private

Referenced by prob_to_accumulate_nonburied(), and probability_to_accumulate_while_building_rotamers().

utility::vector1< Size > core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno_

private

Referenced by declare_all_existing_rotwells_encountered(), memory_usage_dynamic(), read_from_binary(), rotno_2_packed_rotno(), set_n_chi_bins(), SingleResidueDunbrackLibrary(), and write_to_binary().

utility::vector1< bool > core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_exists_

private

Referenced by declare_all_existing_rotwells_encountered(), mark_rotwell_exists(), memory_usage_dynamic(), set_n_chi_bins(), and SingleResidueDunbrackLibrary().

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

src/core/pack/dunbrack/SingleResidueDunbrackLibrary.hh
src/core/pack/dunbrack/SingleResidueDunbrackLibrary.cc

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