Rosetta Core  2014.35
Public Types | Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
core::pack::dunbrack::SingleResidueDunbrackLibrary Class Referenceabstract

#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< Sizen_chi_bins_
 
utility::vector1< Sizen_chi_products_
 
Size n_packed_rots_
 
Size n_possible_rots_
 
Real prob_to_accumulate_buried_
 
Real prob_to_accumulate_nonburied_
 
utility::vector1< boolrotwell_exists_
 
bool packed_rotno_conversion_data_current_
 
utility::vector1< Sizerotno_2_packed_rotno_
 
utility::vector1< Sizepacked_rotno_2_rotno_
 
utility::vector1
< utility::vector1< Size > > 
packed_rotno_2_rotwell_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::pack::dunbrack::SingleResidueDunbrackLibrary::SingleResidueDunbrackLibrary ( AA const  aa,
Size const  n_rotameric_chi,
bool  dun02 
)
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
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
virtual DunbrackRotamerSampleData core::pack::dunbrack::SingleResidueDunbrackLibrary::get_rotamer ( Real  phi,
Real  psi,
Size  rot_ind 
) const
pure virtual
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.

References core::chemical::aa_ala, core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::find_another_representative_for_unlikely_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_probability_for_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_probability_for_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::memory_usage_dynamic(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::memory_usage_dynamic(), memory_usage_in_bytes(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::memory_usage_static(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::memory_usage_static(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::n_rotamer_bins(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::n_rotamer_bins(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::nchi(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::nchi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_binary(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_from_binary(), core::pack::RG, core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv(), scratch, utility_exit_with_message, core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::write_to_binary(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::write_to_binary(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::write_to_file(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::write_to_file().

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
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
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
void core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa ( chemical::AA const  aa,
RotVector rot 
)
static
void core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa_02 ( chemical::AA const  aa,
RotVector rot 
)
static
void core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_bins_for_aa ( chemical::AA const  aa,
RotVector rot,
bool  dun02 
)
static
virtual Size core::pack::dunbrack::SingleResidueDunbrackLibrary::nchi ( ) const
pure virtual
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
utility::vector1< Size > const & core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell ( Size const  packed_rotno) const
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)
void core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate_nonburied ( Real  nonburied)
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
void core::pack::dunbrack::SingleResidueDunbrackLibrary::read_options ( )
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

Member Data Documentation

AA const core::pack::dunbrack::SingleResidueDunbrackLibrary::aa_
private
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
utility::vector1< Size > core::pack::dunbrack::SingleResidueDunbrackLibrary::n_chi_products_
private
Size core::pack::dunbrack::SingleResidueDunbrackLibrary::n_packed_rots_
private
Size core::pack::dunbrack::SingleResidueDunbrackLibrary::n_possible_rots_
private
Size const core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotameric_chi_
private
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
utility::vector1< utility::vector1< Size > > core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell_
private
bool core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_conversion_data_current_
private
Real core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate_buried_
private
Real core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate_nonburied_
private
utility::vector1< Size > core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno_
private
utility::vector1< bool > core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_exists_
private

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