#include <SingleResidueCenrotLibrary.hh>

Inheritance diagram for core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary:

Public Types
typedef chemical::AA	AA

Public Member Functions
	SingleResidueCenrotLibrary (AA const aa)

	~SingleResidueCenrotLibrary () override

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

Real	rotamer_energy (conformation::Residue const &rsd, pose::Pose const &pose, core::pack::rotamers::TorsionEnergy &tenergy) const override
	Virtual functions required by the base classes. More...

void	rotamer_energy_deriv (conformation::Residue const &rsd, pose::Pose const &pose, id::TorsionID const &tor_id, core::pack::rotamers::TorsionEnergy &tderiv) const override

std::set< id::PartialAtomID >	atoms_w_dof_derivatives (conformation::Residue const &rsd, pose::Pose const &pose) const override
	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...

Real	eval_rotameric_energy_deriv (conformation::Residue const &rsd, Real4 &dis_ang_dih, bool eval_deriv) const

Real	eval_rotameric_energy_bb_dof_deriv (conformation::Residue const &rsd, id::TorsionID const &tor_id) const

Real	best_rotamer_energy (conformation::Residue const &rsd, pose::Pose const &pose, bool curr_rotamer_only) const override
	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...

void	assign_random_rotamer_with_bias (conformation::Residue const &rsd, pose::Pose const &pose, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const override
	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...

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, rotamers::RotamerVector &rotamers) const override

void	write_to_file (utility::io::ozstream &out) const override

CentroidRotamerSampleData const &	get_closest_rotamer (conformation::Residue const &rsd, Size &nrot, Real &dis) const

Public Member Functions inherited from core::pack::rotamers::SingleResidueRotamerLibrary
	SingleResidueRotamerLibrary ()

	~SingleResidueRotamerLibrary () override

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 bool	operator== (SingleResidueRotamerLibrary const &) const
	Equality test for equivalence. Two SingleResidueRotamerLibraries test equal if and only if they represent the exact same behavior. More...

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

◆ AA

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

Constructor & Destructor Documentation

◆ SingleResidueCenrotLibrary()

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

References all_rots_bb_, entropy_, and N_PHIPSI_BINS.

◆ ~SingleResidueCenrotLibrary()

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

overridedefault

Member Function Documentation

◆ aa()

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

inline

References aa_.

Referenced by read_from_file(), and verify_phipsi_bins().

◆ assign_random_rotamer_with_bias()

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

overridevirtual

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::rotamers::SingleResidueRotamerLibrary.

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

◆ atoms_w_dof_derivatives()

std::set< id::PartialAtomID > core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::atoms_w_dof_derivatives	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose
	)		const

overridevirtual

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.

Implements core::pack::rotamers::SingleResidueRotamerLibrary.

References core::conformation::insert_partial_atom_ids_for_mainchain_torsion(), RSD_PHI_INDEX, and RSD_PSI_INDEX.

◆ best_rotamer_energy()

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

overridevirtual

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::rotamers::SingleResidueRotamerLibrary.

◆ bin_angle()

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...

Referenced by get_phipsi_bins().

◆ eval_rotameric_energy_bb_dof_deriv()

Real core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_bb_dof_deriv	(	conformation::Residue const &	rsd,
		id::TorsionID const &	tor_id
	)		const

◆ eval_rotameric_energy_deriv()

Real core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_deriv	(	conformation::Residue const &	rsd,
		Real4 &	dis_ang_dih,
		bool	eval_deriv
	)		const

References entropy_, get_phi_from_rsd(), get_phipsi_bins(), get_psi_from_rsd(), get_rotamer_samples(), MAX_ROT_ENERGY, max_rot_num, MIN_ROT_PROB, core::conformation::Residue::name(), 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(), and core::pack::dunbrack::cenrot::TR().

Referenced by rotamer_energy().

◆ fill_rotamer_vector()

void core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::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,
		rotamers::RotamerVector &	rotamers
	)		const

overridevirtual

Implements core::pack::rotamers::SingleResidueRotamerLibrary.

References core::pose::motif::a(), core::chemical::aa_ala, core::chemical::aa_gly, protocols::match::upstream::b, core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), get_rotamer_samples(), core::kinematics::Stub::M, max_rot_num, MIN_ROT_PROB, core::pack::task::ResidueLevelTask::preserve_c_beta(), core::pack::task::PackerTask::residue_task(), core::conformation::Residue::seqpos(), and core::kinematics::Stub::v.

◆ get_closest_rotamer()

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.

◆ get_phi_from_rsd()

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().

◆ get_phipsi_bins() [1/2]

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

private

References get_phipsi_bins().

◆ get_phipsi_bins() [2/2]

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, 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().

◆ get_psi_from_rsd()

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().

◆ 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(), max_rot_num, and PHIPSI_BINRANGE.

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

◆ read_from_file()

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(), max_rot_num, core::chemical::name_from_aa(), ref_energy_, setup_entropy_correction(), and core::pack::dunbrack::cenrot::TR().

◆ rotamer_energy()

Real core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::rotamer_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		core::pack::rotamers::TorsionEnergy &	tenergy
	)		const

overridevirtual

Virtual functions required by the base classes.

Implements core::pack::rotamers::SingleResidueRotamerLibrary.

References eval_rotameric_energy_deriv(), and core::pack::rotamers::TorsionEnergy::tot.

◆ rotamer_energy_deriv()

void core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::rotamer_energy_deriv	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		id::TorsionID const &	tor_id,
		core::pack::rotamers::TorsionEnergy &	tderiv
	)		const

overridevirtual

Implements core::pack::rotamers::SingleResidueRotamerLibrary.

◆ setup_entropy_correction()

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().

◆ verify_phipsi_bins()

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().

Referenced by get_phipsi_bins().

◆ write_to_file()

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

overridevirtual

Implements core::pack::rotamers::SingleResidueRotamerLibrary.

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

Member Data Documentation

◆ aa_

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

private

Referenced by aa().

◆ all_rots_bb_

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().

◆ dummy_sample_

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

private

Referenced by get_closest_rotamer(), and read_from_file().

◆ entropy_

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().

◆ MAX_ROT_ENERGY

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().

◆ max_rot_num

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().

◆ MIN_ROT_PROB

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().

◆ N_PHIPSI_BINS

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

staticprotected

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

◆ NEUTRAL_PHI

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

staticprotected

Referenced by get_phi_from_rsd().

◆ NEUTRAL_PSI

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

staticprotected

Referenced by get_psi_from_rsd().

◆ PHIPSI_BINRANGE

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().

◆ ref_energy_

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

private

Referenced by eval_rotameric_energy_deriv(), and read_from_file().

◆ RSD_PHI_INDEX

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

staticprotected

Referenced by atoms_w_dof_derivatives(), eval_rotameric_energy_bb_dof_deriv(), and get_phi_from_rsd().

◆ RSD_PSI_INDEX

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

staticprotected

Referenced by atoms_w_dof_derivatives(), eval_rotameric_energy_bb_dof_deriv(), and get_psi_from_rsd().

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

Public Types

Public Member Functions

Static Protected Attributes

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ AA

Constructor & Destructor Documentation

◆ SingleResidueCenrotLibrary()

◆ ~SingleResidueCenrotLibrary()

Member Function Documentation

◆ aa()

◆ assign_random_rotamer_with_bias()

◆ atoms_w_dof_derivatives()

◆ best_rotamer_energy()

◆ bin_angle()

◆ eval_rotameric_energy_bb_dof_deriv()

◆ eval_rotameric_energy_deriv()

◆ fill_rotamer_vector()

◆ get_closest_rotamer()

◆ get_phi_from_rsd()

◆ get_phipsi_bins() [1/2]

◆ get_phipsi_bins() [2/2]

◆ get_psi_from_rsd()

◆ get_rotamer_samples()

◆ read_from_file()

◆ rotamer_energy()

◆ rotamer_energy_deriv()

◆ setup_entropy_correction()

◆ verify_phipsi_bins()

◆ write_to_file()

Member Data Documentation

◆ aa_

◆ all_rots_bb_

◆ dummy_sample_

◆ entropy_

◆ MAX_ROT_ENERGY

◆ max_rot_num

◆ MIN_ROT_PROB

◆ N_PHIPSI_BINS

◆ NEUTRAL_PHI

◆ NEUTRAL_PSI

◆ PHIPSI_BINRANGE

◆ ref_energy_

◆ RSD_PHI_INDEX

◆ RSD_PSI_INDEX