A fixed library of conformations for some residue type (doesn't have to be a ligand). More...

#include <SingleLigandRotamerLibrary.hh>

Inheritance diagram for core::pack::rotamers::SingleLigandRotamerLibrary:

Public Member Functions
	SingleLigandRotamerLibrary ()

	~SingleLigandRotamerLibrary () override

virtual void	init_from_file (std::string const &filename, chemical::ResidueType const &restype)
	Reads conformers from PDB-format file (must be separated by TER records!) More...

void	init_from_vector (utility::vector1< NamePosMap > const &coordinates)
	Reads conformers from a vector of name:coordinate maps. More...

void	rotamer_energy_deriv (conformation::Residue const &rsd, pose::Pose const &pose, core::id::TorsionID const &tor_id, TorsionEnergy &tderiv) const override
	Adheres to the contract from SingleLigandRotamerLibrary. More...

Real	rotamer_energy (conformation::Residue const &rsd, pose::Pose const &pose, TorsionEnergy &tenergy) const override
	Adheres to the contract from SingleLigandRotamerLibrary. More...

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

void	assign_random_rotamer_with_bias (conformation::Residue const &, pose::Pose const &, numeric::random::RandomGenerator &, dunbrack::ChiVector &, bool) const override
	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...

void	fill_rotamer_vector (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, utility::graph::GraphCOP, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, RotamerVector &rotamers) const override
	Adheres to the contract from SingleLigandRotamerLibrary. More...

void	write_to_file (utility::io::ozstream &out) const override
	Adheres to the contract from SingleLigandRotamerLibrary. More...

Real	get_reference_energy () const

void	set_reference_energy (Real ref_E_in)

void	build_base_rotamers (chemical::ResidueType const &restype, RotamerVector &base_rotamers) const
	Build a set of rotamers for the given ResidueType. More...

utility::vector1< NamePosMap > const &	get_atom_positions () const
	@ brief getter for our contained data. Not meant for use by Rosetta proper; this enables a simpler unit test. More...

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...

Private Member Functions
void	fill_missing_atoms (utility::vector1< bool > missing, conformation::ResidueOP rsd, utility::vector1< bool > &missed) const
	Fills in missing hydrogens/virtual atoms from library load. More...

Private Attributes
utility::vector1< NamePosMap >	atom_positions_

Real	ref_energy_

Detailed Description

A fixed library of conformations for some residue type (doesn't have to be a ligand).

Reads residue conformations in PDB format separated by mandatory TER records. "Included" from a residue .params file with the PDB_ROTAMERS keyword.

Constructor & Destructor Documentation

◆ SingleLigandRotamerLibrary()

core::pack::rotamers::SingleLigandRotamerLibrary::SingleLigandRotamerLibrary ( )

◆ ~SingleLigandRotamerLibrary()

core::pack::rotamers::SingleLigandRotamerLibrary::~SingleLigandRotamerLibrary ( )

overridedefault

Member Function Documentation

◆ assign_random_rotamer_with_bias()

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

inlineoverridevirtual

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.

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

◆ atoms_w_dof_derivatives()

std::set< id::PartialAtomID > core::pack::rotamers::SingleLigandRotamerLibrary::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.

◆ best_rotamer_energy()

Real core::pack::rotamers::SingleLigandRotamerLibrary::best_rotamer_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		bool	curr_rotamer_only
	)		const

overridevirtual

Not currently implemented – returns 0. For most things, it's actually quite hard to correctly rank the conformers by energy. Thus, I've chosen not to introduce noise by attempting to rank them and doing it badly.

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

References ref_energy_.

◆ build_base_rotamers()

void core::pack::rotamers::SingleLigandRotamerLibrary::build_base_rotamers	(	chemical::ResidueType const &	restype,
		RotamerVector &	base_rotamers
	)		const

Build a set of rotamers for the given ResidueType.

References atom_positions_, core::conformation::ResidueFactory::create_residue(), fill_missing_atoms(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::natoms(), core::conformation::set_chi_according_to_coordinates(), and core::pack::rotamers::TR().

Referenced by fill_rotamer_vector().

◆ fill_missing_atoms()

void core::pack::rotamers::SingleLigandRotamerLibrary::fill_missing_atoms	(	utility::vector1< bool >	missing,
		conformation::ResidueOP	rsd,
		utility::vector1< bool > &	missed
	)		const

private

Fills in missing hydrogens/virtual atoms from library load.

"missing" is the vector for atoms missing for the current "rsd"

References core::chemical::ICoorAtomID::atomno(), core::chemical::AtomICoor::build(), core::chemical::AtomICoor::stub_atom(), core::id::to_string(), and core::pack::rotamers::TR().

Referenced by build_base_rotamers().

◆ fill_rotamer_vector()

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

overridevirtual

Adheres to the contract from SingleLigandRotamerLibrary.

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

References build_base_rotamers(), core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(), core::pose::Pose::conformation(), core::pack::rotamers::dup_residue(), core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(), core::pack::task::PackerTask::residue_task(), core::conformation::Residue::seqpos(), and core::pack::rotamers::TR().

◆ get_atom_positions()

utility::vector1< NamePosMap > const& core::pack::rotamers::SingleLigandRotamerLibrary::get_atom_positions ( ) const

inline

@ brief getter for our contained data. Not meant for use by Rosetta proper; this enables a simpler unit test.

References atom_positions_.

◆ get_reference_energy()

Real core::pack::rotamers::SingleLigandRotamerLibrary::get_reference_energy ( ) const

inline

References ref_energy_.

◆ init_from_file()

void core::pack::rotamers::SingleLigandRotamerLibrary::init_from_file	(	std::string const &	filename,
		chemical::ResidueType const &	restype
	)

virtual

Reads conformers from PDB-format file (must be separated by TER records!)

Reads conformers from PDB-format file. Chain ID, residue name and number, etc are all ignored – must have TER records.

References atom_positions_, protocols::abinitio::filename(), ref_energy_, core::pack::rotamers::rotamer_information_from_PDB_stream(), and core::pack::rotamers::TR().

◆ init_from_vector()

void core::pack::rotamers::SingleLigandRotamerLibrary::init_from_vector ( utility::vector1< NamePosMap > const & coordinates )

Reads conformers from a vector of name:coordinate maps.

References atom_positions_.

◆ rotamer_energy()

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

overridevirtual

Adheres to the contract from SingleLigandRotamerLibrary.

Not currently implemented – returns 0. For most things, it's actually quite hard to correctly rank the conformers by energy. Thus, I've chosen not to introduce noise by attempting to rank them and doing it badly.

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

References ref_energy_, and core::pack::rotamers::TorsionEnergy::tot.

◆ rotamer_energy_deriv()

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

overridevirtual

Adheres to the contract from SingleLigandRotamerLibrary.

Not currently implemented – returns 0.

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

◆ set_reference_energy()

void core::pack::rotamers::SingleLigandRotamerLibrary::set_reference_energy ( Real ref_E_in )

inline

References ref_energy_.

◆ write_to_file()

void core::pack::rotamers::SingleLigandRotamerLibrary::write_to_file ( utility::io::ozstream & out ) const

overridevirtual

Adheres to the contract from SingleLigandRotamerLibrary.

Not implemented – will cause program termination. Is this only used by coarse representations?

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

Member Data Documentation

◆ atom_positions_

utility::vector1< NamePosMap > core::pack::rotamers::SingleLigandRotamerLibrary::atom_positions_

private

Referenced by build_base_rotamers(), get_atom_positions(), init_from_file(), and init_from_vector().

◆ ref_energy_

Real core::pack::rotamers::SingleLigandRotamerLibrary::ref_energy_

private

Referenced by best_rotamer_energy(), get_reference_energy(), init_from_file(), rotamer_energy(), and set_reference_energy().

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

src/core/pack/rotamers/SingleLigandRotamerLibrary.hh
src/core/pack/rotamers/SingleLigandRotamerLibrary.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SingleLigandRotamerLibrary()

◆ ~SingleLigandRotamerLibrary()

Member Function Documentation

◆ assign_random_rotamer_with_bias()

◆ atoms_w_dof_derivatives()

◆ best_rotamer_energy()

◆ build_base_rotamers()

◆ fill_missing_atoms()

◆ fill_rotamer_vector()

◆ get_atom_positions()

◆ get_reference_energy()

◆ init_from_file()

◆ init_from_vector()

◆ rotamer_energy()

◆ rotamer_energy_deriv()

◆ set_reference_energy()

◆ write_to_file()

Member Data Documentation

◆ atom_positions_

◆ ref_energy_