core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary Class Reference

#include <SingleResidueCenrotLibrary.hh>

Public Types
typedef chemical::AA	AA

Public Member Functions
	SingleResidueCenrotLibrary (AA const aa)
virtual	~SingleResidueCenrotLibrary ()
AA	aa () const
std::string	read_from_file (utility::io::izstream &infile, bool first_line_three_letter_code_already_read)
const utility::vector1 < CentroidRotamerSampleData >	get_rotamer_samples (conformation::Residue const &rsd) const
virtual Real	rotamer_energy (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const
	Virtual functions required by the base classes. More...
virtual Real	rotamer_energy_deriv (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const
Real	eval_rotameric_energy_deriv (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, bool eval_deriv) const
Real	eval_rotameric_energy_bb_dof_deriv (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const
virtual Real	best_rotamer_energy (conformation::Residue const &rsd, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const
	Returns the energy of the lowest-energy rotamer accessible to the given residue (based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue's current rotamer (local optimum); otherwise, consider all rotamers (global optimum). More...
virtual void	assign_random_rotamer_with_bias (conformation::Residue const &rsd, pose::Pose const &pose, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const
	Pick a rotamer for the input residue according to the rotamer probability distribution and assign chi angles to the input rsd. – currently no perturbation allowed. More...
virtual void	fill_rotamer_vector (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, RotamerVector &rotamers) const
virtual void	write_to_file (utility::io::ozstream &out) const
CentroidRotamerSampleData const &	get_closest_rotamer (conformation::Residue const &rsd, Size &nrot, Real &dis) const
Public Member Functions inherited from core::pack::dunbrack::SingleResidueRotamerLibrary
virtual	~SingleResidueRotamerLibrary ()

Static Protected Attributes
static Size const	N_PHIPSI_BINS = 36
static Real const	PHIPSI_BINRANGE = 10.0
static Size const	RSD_PHI_INDEX = 1
static Size const	RSD_PSI_INDEX = 2
static Real const	NEUTRAL_PHI = -90
static Real const	NEUTRAL_PSI = 130
static Real const	MAX_ROT_ENERGY = 16
static Real const	MIN_ROT_PROB = 1e-6

Private Member Functions
void	get_phipsi_bins (Real phi, Real psi, Size &phibin, Size &psibin, Size &phibin_next, Size &psibin_next, Real &phi_alpha, Real &psi_alpha) const
void	get_phipsi_bins (Real phi, Real psi, Size &phibin, Size &psibin) const
Real	get_phi_from_rsd (conformation::Residue const &rsd) const
Real	get_psi_from_rsd (conformation::Residue const &rsd) const
void	verify_phipsi_bins (Real phi, Real psi, Size const phibin, Size const psibin, Size const phibin_next, Size const psibin_next) const
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...
void	setup_entropy_correction ()
	E_ref is the same as shannon entropy. More...

Private Attributes
ObjexxFCL::FArray2D < utility::vector1 < CentroidRotamerSampleData > >	all_rots_bb_
utility::vector1 < CentroidRotamerSampleData >	dummy_sample_
AA	aa_
Size	max_rot_num
Real	ref_energy_
ObjexxFCL::FArray2D< Real >	entropy_

Member Typedef Documentation

typedef chemical::AA core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::AA

Constructor & Destructor Documentation

core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::SingleResidueCenrotLibrary

(

AA const

aa

)

References all_rots_bb_, entropy_, N_PHIPSI_BINS, and option.

core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::~SingleResidueCenrotLibrary ( )

virtual

Member Function Documentation

AA core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::aa ( ) const

inline

References aa_.

Referenced by read_from_file(), and verify_phipsi_bins().

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

virtual

Pick a rotamer for the input residue according to the rotamer probability distribution and assign chi angles to the input rsd. – currently no perturbation allowed.

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

References core::pack::dunbrack::cenrot::TR.

Real core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::best_rotamer_energy ( conformation::Residue const &  rsd, bool  curr_rotamer_only, RotamerLibraryScratchSpace &  scratch  ) const

virtual

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

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

void core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::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

inlineprivate

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().

Referenced by get_phipsi_bins().

Real core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_bb_dof_deriv	(	conformation::Residue const &	rsd,
		RotamerLibraryScratchSpace &	scratch
	)		const

References core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::data_, core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::deriv_phi_, core::pack::dunbrack::cenrot::CentroidRotamerSampleData::deriv_psi_, entropy_, get_phi_from_rsd(), get_phipsi_bins(), get_psi_from_rsd(), get_rotamer_samples(), basic::interpolate_bilinear_by_value(), log(), MAX_ROT_ENERGY, max_rot_num, MIN_ROT_PROB, option, PHIPSI_BINRANGE, core::pack::dunbrack::cenrot::CentroidRotamerSampleData::prob(), ref_energy_, RSD_PHI_INDEX, RSD_PSI_INDEX, core::pack::dunbrack::cenrot::TR, and utility_exit.

Real core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_deriv	(	conformation::Residue const &	rsd,
		RotamerLibraryScratchSpace &	scratch,
		bool	eval_deriv
	)		const

References core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi(), entropy_, get_phi_from_rsd(), get_phipsi_bins(), get_psi_from_rsd(), get_rotamer_samples(), basic::interpolate_bilinear_by_value(), log(), MAX_ROT_ENERGY, max_rot_num, MIN_ROT_PROB, core::conformation::Residue::name(), option, PHIPSI_BINRANGE, ref_energy_, core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_ang(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_dih(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_dis(), core::conformation::Residue::seqpos(), core::pack::dunbrack::cenrot::TR, and utility_exit.

Referenced by rotamer_energy(), and rotamer_energy_deriv().

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

virtual

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

References core::chemical::aa_ala, core::chemical::aa_gly, core::conformation::Residue::atom(), core::pack::dunbrack::c, numeric::xyzMatrix< class >::col_x(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), get_rotamer_samples(), core::kinematics::Stub::M, max_rot_num, MIN_ROT_PROB, option, core::pack::task::ResidueLevelTask::preserve_c_beta(), core::pack::task::PackerTask::residue_task(), core::conformation::Residue::seqpos(), core::conformation::Residue::set_xyz(), core::kinematics::Stub::v, numeric::x_rotation_matrix_radians(), core::conformation::Atom::xyz(), and numeric::z_rotation_matrix_radians().

CentroidRotamerSampleData const & core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_closest_rotamer	(	conformation::Residue const &	rsd,
		Size &	nrot,
		Real &	dis
	)		const

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, dummy_sample_, get_rotamer_samples(), and max_rot_num.

Real core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_phi_from_rsd ( conformation::Residue const &  rsd ) const

private

References core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::mainchain_torsion(), NEUTRAL_PHI, and RSD_PHI_INDEX.

Referenced by eval_rotameric_energy_bb_dof_deriv(), eval_rotameric_energy_deriv(), and get_rotamer_samples().

void core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_phipsi_bins ( Real  phi, Real  psi, Size &  phibin, Size &  psibin, Size &  phibin_next, Size &  psibin_next, Real &  phi_alpha, Real &  psi_alpha  ) const

private

References bin_angle(), N_PHIPSI_BINS, basic::periodic_range(), PHIPSI_BINRANGE, and verify_phipsi_bins().

Referenced by eval_rotameric_energy_bb_dof_deriv(), eval_rotameric_energy_deriv(), get_phipsi_bins(), get_rotamer_samples(), and read_from_file().

void core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_phipsi_bins ( Real  phi, Real  psi, Size &  phibin, Size &  psibin  ) const

private

References get_phipsi_bins().

Real core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_psi_from_rsd ( conformation::Residue const &  rsd ) const

private

References core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::mainchain_torsion(), NEUTRAL_PSI, and RSD_PSI_INDEX.

Referenced by eval_rotameric_energy_bb_dof_deriv(), eval_rotameric_energy_deriv(), and get_rotamer_samples().

const utility::vector1< CentroidRotamerSampleData > core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_rotamer_samples

(

conformation::Residue const &

rsd

)

const

References all_rots_bb_, get_phi_from_rsd(), get_phipsi_bins(), get_psi_from_rsd(), basic::interpolate_bilinear_by_value(), max_rot_num, PHIPSI_BINRANGE, numeric::constants::r::pi_over_180, and numeric::constants::r::radians_to_degrees.

Referenced by eval_rotameric_energy_bb_dof_deriv(), eval_rotameric_energy_deriv(), fill_rotamer_vector(), and get_closest_rotamer().

std::string core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::read_from_file	(	utility::io::izstream &	infile,
		bool	first_line_three_letter_code_already_read
	)

References aa(), all_rots_bb_, dummy_sample_, get_phipsi_bins(), utility::io::izstream::getline(), log(), max_rot_num, core::chemical::name_from_aa(), option, utility::io::izstream::peek(), numeric::constants::r::pi_over_180, ref_energy_, setup_entropy_correction(), core::io::serialization::size(), and core::pack::dunbrack::cenrot::TR.

Real core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::rotamer_energy ( conformation::Residue const &  rsd, RotamerLibraryScratchSpace &  scratch  ) const

virtual

Virtual functions required by the base classes.

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

References eval_rotameric_energy_deriv().

Real core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::rotamer_energy_deriv ( conformation::Residue const &  rsd, RotamerLibraryScratchSpace &  scratch  ) const

virtual

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

References eval_rotameric_energy_deriv().

void core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::setup_entropy_correction ( )

private

E_ref is the same as shannon entropy.

References all_rots_bb_, entropy_, max_rot_num, N_PHIPSI_BINS, and core::scoring::packstat::old::nphi.

Referenced by read_from_file().

void core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::verify_phipsi_bins ( Real  phi, Real  psi, Size const  phibin, Size const  psibin, Size const  phibin_next, Size const  psibin_next  ) const

private

References aa(), and utility_exit.

Referenced by get_phipsi_bins().

void core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::write_to_file ( utility::io::ozstream &  out ) const

virtual

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

References core::pack::dunbrack::cenrot::TR.

Member Data Documentation

AA core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::aa_

private

Referenced by aa().

ObjexxFCL::FArray2D< utility::vector1< CentroidRotamerSampleData > > core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::all_rots_bb_

private

Referenced by get_rotamer_samples(), read_from_file(), setup_entropy_correction(), and SingleResidueCenrotLibrary().

utility::vector1< CentroidRotamerSampleData > core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::dummy_sample_

private

Referenced by get_closest_rotamer(), and read_from_file().

ObjexxFCL::FArray2D< Real > core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::entropy_

private

Referenced by eval_rotameric_energy_bb_dof_deriv(), eval_rotameric_energy_deriv(), setup_entropy_correction(), and SingleResidueCenrotLibrary().

Real const core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::MAX_ROT_ENERGY = 16

staticprotected

Referenced by eval_rotameric_energy_bb_dof_deriv(), and eval_rotameric_energy_deriv().

Size core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::max_rot_num

private

Referenced by eval_rotameric_energy_bb_dof_deriv(), eval_rotameric_energy_deriv(), fill_rotamer_vector(), get_closest_rotamer(), get_rotamer_samples(), read_from_file(), and setup_entropy_correction().

Real const core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::MIN_ROT_PROB = 1e-6

staticprotected

Referenced by eval_rotameric_energy_bb_dof_deriv(), eval_rotameric_energy_deriv(), and fill_rotamer_vector().

Size const core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::N_PHIPSI_BINS = 36

staticprotected

Referenced by get_phipsi_bins(), setup_entropy_correction(), and SingleResidueCenrotLibrary().

Real const core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::NEUTRAL_PHI = -90

staticprotected

Referenced by get_phi_from_rsd().

Real const core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::NEUTRAL_PSI = 130

staticprotected

Referenced by get_psi_from_rsd().

Real const core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::PHIPSI_BINRANGE = 10.0

staticprotected

Referenced by eval_rotameric_energy_bb_dof_deriv(), eval_rotameric_energy_deriv(), get_phipsi_bins(), and get_rotamer_samples().

Real core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::ref_energy_

private

Referenced by eval_rotameric_energy_bb_dof_deriv(), eval_rotameric_energy_deriv(), and read_from_file().

Size const core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::RSD_PHI_INDEX = 1

staticprotected

Referenced by eval_rotameric_energy_bb_dof_deriv(), and get_phi_from_rsd().

Size const core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::RSD_PSI_INDEX = 2

staticprotected

Referenced by eval_rotameric_energy_bb_dof_deriv(), and get_psi_from_rsd().

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

• src/core/pack/dunbrack/cenrot/SingleResidueCenrotLibrary.hh
• src/core/pack/dunbrack/cenrot/SingleResidueCenrotLibrary.cc