core::pack::dunbrack::SingleResidueDunbrackLibrary Class Reference

#include <SingleResidueDunbrackLibrary.hh>

Inheritance diagram for core::pack::dunbrack::SingleResidueDunbrackLibrary:

Public Types
typedef chemical::AA	AA

Public Member Functions
SingleResidueDunbrackLibrary &	operator= (SingleResidueDunbrackLibrary const &other)=delete
	SingleResidueDunbrackLibrary (SingleResidueDunbrackLibrary const &)=delete
	SingleResidueDunbrackLibrary (chemical::ResidueType const &rt, Size const n_rotameric_chi, bool dun02, bool use_bicubic, bool dun_entropy_correction, core::Real prob_buried, core::Real prob_nonburied)
	c-tor More...
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 (Real5 bbs) 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	nbb () const =0
	the number of backbone dihedrals 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
void	bin_angle (Real const angle_start, utility::vector1< core::Size > const &bin_equivs, 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
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)
bool	operator== (rotamers::SingleResidueRotamerLibrary const &) const override
	Comparison operator, mainly intended to use in ASCII/binary comparsion tests Values tested should parallel those used in the read_from_binary() function. More...
Public Member Functions inherited from core::pack::rotamers::SingleResidueRotamerLibrary
	SingleResidueRotamerLibrary ()
	~SingleResidueRotamerLibrary () override
virtual Real	rotamer_energy_deriv (conformation::Residue const &rsd, pose::Pose const &pose, dunbrack::RotamerLibraryScratchSpace &scratch) const =0
virtual Real	rotamer_energy (conformation::Residue const &rsd, pose::Pose const &pose, dunbrack::RotamerLibraryScratchSpace &scratch) const =0
virtual std::set < id::PartialAtomID >	atoms_w_dof_derivatives (conformation::Residue const &rsd, pose::Pose const &pose) const =0
	Return the set of atoms ids (or, if they come from another residue, PartialAtomIDs) for the set of atoms that are used in defining the DOF derivatives for a particular residue. More...
virtual Real	best_rotamer_energy (conformation::Residue const &rsd, pose::Pose const &pose, bool curr_rotamer_only, dunbrack::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, dunbrack::RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, dunbrack::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, utility::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 utility::vector1 < utility::vector1< core::Real > >	compute_proton_chi_samplings (chemical::ResidueType const &concrete_residue, pack::task::ResidueLevelTask const &rlt, bool buried) const
	Return a vector (indexed by proton_chi number) of vectors of dihedral values to use in proton chi sampling. More...
virtual utility::vector1 < dunbrack::ChiSetOP >	expand_proton_chis (utility::vector1< utility::vector1< core::Real > > const &sampling, chemical::ResidueType const &concrete_residue, core::Size max_rotamers=5000) const
	Given a vector of vectors of dihedrals to sample on proton chis, Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.) More...
virtual void	bump_filter (RotamerVector &rotamers, core::Size resid, scoring::ScoreFunction const &sf, pose::Pose const &pose, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph) const
	Filter a RotamerVector by "bump energy" of a rotamer: All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector "rotamers" will be modified "in-place". More...
virtual core::PackerEnergy	bump_check (core::conformation::ResidueCOP rotamer, core::Size resid, scoring::ScoreFunction const &sf, pose::Pose const &pose, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph) const
	Computes the "bump energy" of a rotamer: the bump energy is the sum of rotamer's interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization. More...
virtual core::Size	current_rotamer (RotamerVector &rotamers, core::Size resid, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue) const
	Adds the current rotamer to rotamer vector, if the Rotlib supports it. More...
virtual void	emergency_rotamer (RotamerVector &rotamers, core::Size resid, pose::Pose const &pose, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue) const
	Generate an "emergency rotamer" if we don't have any. More...
RotamerVector	virtual_sidechain (RotamerVector const &rotamers, core::Size resid, pose::Pose const &pose, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue) const
	Add a virtualized sidechain to the rotamer vector if settings call for it. More...
virtual void	write_to_file (utility::io::ozstream &out) const =0

Static Public Member Functions
static void	n_rotamer_bins_for_aa (chemical::ResidueType const &rt, RotVector &rot, bool const dun02=false)
	Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType and store it in rot. More...
static void	n_rotamer_bins_for_aa (chemical::AA const aa, RotVector &rot)
static void	n_rotameric_bins_for_aa (chemical::AA const aa, RotVector &rot, bool dun02)
static void	n_rotamer_bins_for_aa_02 (chemical::AA const aa, RotVector &rot)

Static Public Attributes
static Real const	PEPTIDE_NEUTRAL_PHI = -90
	constants More...
static Real const	PEPTIDE_NEUTRAL_PSI = 130
static Real const	PEPTOID_NEUTRAL_OMG = 180
	A good omega, phi, and psi values to use for terminal peptoid residues where they cannont be completely defined. More...
static Real const	PEPTOID_NEUTRAL_PHI = -90
static Real const	PEPTOID_NEUTRAL_PSI = 180
static Real const	ANGLE_DELTA
	Precision measures for comparsions. More...
static Real const	PROB_DELTA
static Real const	ENERGY_DELTA
static Real const	COEF_DELTA

Protected Member Functions
bool	dun02 () const
	Read access for the derived class. More...
bool	use_bicubic () const
	Read access for the derived class. More...
bool	dun_entropy_correction () 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_
bool	use_bicubic_
bool	dun_entropy_correction_
AA const	aa_
	data More...
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 ( SingleResidueDunbrackLibrary const &  )

delete

core::pack::dunbrack::SingleResidueDunbrackLibrary::SingleResidueDunbrackLibrary	(	chemical::ResidueType const &	rt,
		Size const	n_rotameric_chi,
		bool	dun02,
		bool	use_bicubic,
		bool	dun_entropy_correction,
		core::Real	prob_buried,
		core::Real	prob_nonburied
	)

c-tor

References core::chemical::ResidueType::is_canonical_aa(), n_chi_bins_, n_chi_products_, n_possible_rots_, n_rotamer_bins_for_aa(), n_rotameric_chi_, rotno_2_packed_rotno_, and rotwell_exists_.

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

void core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_angle ( Real const  angle_start, utility::vector1< core::Size > const &  bin_equivs, 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

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_b3p, core::chemical::aa_dpr, core::chemical::aa_pro, core::chemical::ou3_pro, and core::id::to_string().

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.

After the derived class has marked all the rotwells that do exist, the base class will create the rotwell to packedrot 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_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library().

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

inlineprotected

Read access for the derived class.

References dun02_.

Referenced by n_rotamer_bins_for_aa().

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

inlineprotected

Read access for the derived class.

References dun_entropy_correction_.

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv_bbdep().

virtual utility::vector1< DunbrackRotamerSampleData > core::pack::dunbrack::SingleResidueDunbrackLibrary::get_all_rotamer_samples ( Real5  bbs ) 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, N >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >.

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

pure virtual

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

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::RotamericSingleResidueDunbrackLibrary< T, N >.

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

pure virtual

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

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

pure virtual

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

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, N >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >.

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.

References core::pack::dunbrack::FIVE, FOREACH_Chi_BB, INIT, core::chemical::ResidueType::make(), and rot().

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_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library().

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

protectedvirtual

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

References n_chi_bins_, n_chi_products_, packed_rotno_2_rotno_, packed_rotno_2_rotwell_, rotno_2_packed_rotno_, rotwell_exists_, and protocols::analysis::total.

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().

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, N >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >.

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 core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::operator==(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::operator==(), 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_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library().

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

pure virtual

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

void core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa ( chemical::ResidueType const &  rt, RotVector &  rot, bool const  dun02 = false  )

static

Extract the number of rotamer bins (vector of bin counts for each chi) from the ResidueType and store it in rot.

Author

Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu) to make this general and to remove hard-coded information about canonical amino acids.

References core::chemical::ResidueTypeBase::aa(), core::chemical::ResidueType::chi_rotamers(), dun02(), core::chemical::ResidueType::is_canonical_aa(), n_rotameric_bins_for_aa(), core::chemical::ResidueType::nchi(), and rot().

Referenced by SingleResidueDunbrackLibrary().

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

static

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

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

References core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, and core::chemical::aa_val.

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

static

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

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

References core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, and core::chemical::aa_val.

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

For the rotameric chi – not all chi are rotameric

References core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_val, and n_rotamer_bins_for_aa_02().

Referenced by n_rotamer_bins_for_aa().

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

pure virtual

the number of backbone dihedrals represented by the library

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

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, N >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >.

SingleResidueDunbrackLibrary& core::pack::dunbrack::SingleResidueDunbrackLibrary::operator= ( SingleResidueDunbrackLibrary const &  other )

delete

bool core::pack::dunbrack::SingleResidueDunbrackLibrary::operator== ( rotamers::SingleResidueRotamerLibrary const &  rhs ) const

overridevirtual

Comparison operator, mainly intended to use in ASCII/binary comparsion tests Values tested should parallel those used in the read_from_binary() function.

Reimplemented from core::pack::rotamers::SingleResidueRotamerLibrary.

References aa_, dun02_, n_chi_bins_, n_chi_products_, n_packed_rots_, n_possible_rots_, n_rotameric_chi_, core::chemical::name_from_aa(), packed_rotno_2_rotno_, packed_rotno_2_rotwell_, packed_rotno_conversion_data_current_, PROB_DELTA, prob_to_accumulate_buried_, prob_to_accumulate_nonburied_, rotno_2_packed_rotno_, and core::pack::dunbrack::TR().

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 protocols::features::RotamerInitializer< T, N >::initialize_rotamer(), read_from_binary(), and write_to_binary().

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

References core::sequence::end, and packed_rotno_2_rotwell_.

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_.

Referenced by prob_to_accumulate().

void core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate_nonburied

(

Real

nonburied

)

References prob_to_accumulate_nonburied_.

Referenced by prob_to_accumulate().

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, N >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >.

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_, rotno_2_packed_rotno(), and rotno_2_packed_rotno_.

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_, and n_rotameric_chi_.

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().

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(), and protocols::features::RotamerInitializer< T, N >::initialize_rotamer().

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 protocols::features::RotamerInitializer< T, N >::initialize_rotamer(), 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_.

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_.

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

inlineprotected

Read access for the derived class.

References use_bicubic_.

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

virtual

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

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(), and rotno_2_packed_rotno_.

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

Member Data Documentation

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

private

data

Referenced by aa(), bin_rotameric_chi(), and operator==().

core::Real const core::pack::dunbrack::SingleResidueDunbrackLibrary::ANGLE_DELTA

static

Precision measures for comparsions.

Referenced by core::pack::dunbrack::BBDepNRChiSample< P >::operator==(), and core::pack::dunbrack::BBIndNRChiSample< P >::operator==().

core::Real const core::pack::dunbrack::SingleResidueDunbrackLibrary::COEF_DELTA

static

Referenced by core::pack::dunbrack::BBDepScoreInterpData< N >::operator==().

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

private

Referenced by dun02(), and operator==().

bool core::pack::dunbrack::SingleResidueDunbrackLibrary::dun_entropy_correction_

private

Referenced by dun_entropy_correction().

core::Real const core::pack::dunbrack::SingleResidueDunbrackLibrary::ENERGY_DELTA

static

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

private

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

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

private

Referenced by memory_usage_dynamic(), operator==(), 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(), operator==(), 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(), operator==(), read_from_binary(), set_n_chi_bins(), SingleResidueDunbrackLibrary(), and write_to_binary().

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

private

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

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

private

Referenced by declare_all_existing_rotwells_encountered(), memory_usage_dynamic(), operator==(), 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(), operator==(), 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(), operator==(), read_from_binary(), rotno_2_packed_rotno(), and rotwell_2_packed_rotno().

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

static

constants

A good phi and psi values to use for terminal peptide residues where they cannont be completely defined

Referenced by protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary().

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

static

Referenced by protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary().

Real const core::pack::dunbrack::SingleResidueDunbrackLibrary::PEPTOID_NEUTRAL_OMG = 180

static

A good omega, phi, and psi values to use for terminal peptoid residues where they cannont be completely defined.

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

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

static

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

Real const core::pack::dunbrack::SingleResidueDunbrackLibrary::PEPTOID_NEUTRAL_PSI = 180

static

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

core::Real const core::pack::dunbrack::SingleResidueDunbrackLibrary::PROB_DELTA

static

Referenced by core::pack::dunbrack::BBDepNRChiSample< P >::operator==(), core::pack::dunbrack::BBIndNRChiSample< P >::operator==(), and operator==().

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

private

Referenced by operator==(), prob_to_accumulate_buried(), and probability_to_accumulate_while_building_rotamers().

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

private

Referenced by operator==(), 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(), operator==(), 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().

bool core::pack::dunbrack::SingleResidueDunbrackLibrary::use_bicubic_

private

Referenced by use_bicubic().

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

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