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::dunbrack::SingleLigandRotamerLibrary:

Collaboration diagram for core::pack::dunbrack::SingleLigandRotamerLibrary:

Public Member Functions
	SingleLigandRotamerLibrary ()

virtual	~SingleLigandRotamerLibrary ()

	SingleLigandRotamerLibrary (utility::vector1< conformation::ResidueOP > &rotamers_in, Real ref_E_in)
	explicit constructor More...

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

virtual Real	rotamer_energy_deriv (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const
	Adheres to the contract from SingleLigandRotamerLibrary. More...

virtual Real	rotamer_energy (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const
	Adheres to the contract from SingleLigandRotamerLibrary. More...

virtual Real	best_rotamer_energy (conformation::Residue const &rsd, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const

virtual void	assign_random_rotamer_with_bias (conformation::Residue const &, RotamerLibraryScratchSpace &, numeric::random::RandomGenerator &, ChiVector &, bool) const
	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, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, RotamerVector &rotamers) const
	Adheres to the contract from SingleLigandRotamerLibrary. More...

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

Real	get_reference_energy () const

void	set_reference_energy (Real ref_E_in)

void	set_rotamers (utility::vector1< conformation::ResidueOP > &rotamers_in)

utility::vector1 < conformation::ResidueOP > const &	get_rotamers () const

Public Member Functions inherited from core::pack::dunbrack::SingleResidueRotamerLibrary
virtual	~SingleResidueRotamerLibrary ()

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 < conformation::ResidueOP >	rotamers_

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.

Definition at line 39 of file SingleLigandRotamerLibrary.hh.

Constructor & Destructor Documentation

core::pack::dunbrack::SingleLigandRotamerLibrary::SingleLigandRotamerLibrary ( )

Definition at line 76 of file SingleLigandRotamerLibrary.cc.

core::pack::dunbrack::SingleLigandRotamerLibrary::~SingleLigandRotamerLibrary ( )

virtual

Definition at line 86 of file SingleLigandRotamerLibrary.cc.

core::pack::dunbrack::SingleLigandRotamerLibrary::SingleLigandRotamerLibrary	(	utility::vector1< conformation::ResidueOP > &	rotamers_in,
		Real	ref_E_in
	)

explicit constructor

Definition at line 90 of file SingleLigandRotamerLibrary.cc.

Member Function Documentation

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

inlinevirtual

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::dunbrack::SingleResidueRotamerLibrary.

Definition at line 91 of file SingleLigandRotamerLibrary.hh.

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

virtual

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::dunbrack::SingleResidueRotamerLibrary.

Definition at line 220 of file SingleLigandRotamerLibrary.cc.

References ref_energy_.

void core::pack::dunbrack::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"

Definition at line 418 of file SingleLigandRotamerLibrary.cc.

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

Referenced by init_from_file().

void core::pack::dunbrack::SingleLigandRotamerLibrary::fill_rotamer_vector	(	pose::Pose const &	pose,
		scoring::ScoreFunction const &	scorefxn,
		pack::task::PackerTask const &	task,
		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

virtual

Adheres to the contract from SingleLigandRotamerLibrary.

Assumes that rotamers is already empty or doesn't need to be cleared...

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

Definition at line 306 of file SingleLigandRotamerLibrary.cc.

References core::pose::Pose::conformation(), core::pack::dunbrack::dup_residue(), core::pack::dunbrack::expand_proton_chi(), core::pack::task::PackerTask::residue_task(), rotamers_, core::conformation::Residue::seqpos(), and core::pack::dunbrack::TR().

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

inline

Definition at line 129 of file SingleLigandRotamerLibrary.hh.

References ref_energy_.

utility::vector1< conformation::ResidueOP > const& core::pack::dunbrack::SingleLigandRotamerLibrary::get_rotamers ( ) const

inline

Definition at line 142 of file SingleLigandRotamerLibrary.hh.

References rotamers_.

void core::pack::dunbrack::SingleLigandRotamerLibrary::init_from_file	(	std::string const &	filename,
		chemical::ResidueTypeCOP	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.

Definition at line 101 of file SingleLigandRotamerLibrary.cc.

References core::conformation::ResidueFactory::create_residue(), fill_missing_atoms(), ref_energy_, rotamers_, core::conformation::set_chi_according_to_coordinates(), and core::pack::dunbrack::TR().

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

virtual

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::dunbrack::SingleResidueRotamerLibrary.

Definition at line 207 of file SingleLigandRotamerLibrary.cc.

References ref_energy_.

Referenced by rotamer_energy_deriv().

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