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core::pack::rotamers::SingleBasicRotamerLibrary Class Reference

A simple Rotamer library, which serves as a default for ResidueTypes which don't have some other more specific rotamer library. More...

#include <SingleBasicRotamerLibrary.hh>

Inheritance diagram for core::pack::rotamers::SingleBasicRotamerLibrary:
Inheritance graph
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Public Member Functions

 SingleBasicRotamerLibrary ()
 
 ~SingleBasicRotamerLibrary () override
 
Real rotamer_energy_deriv (conformation::Residue const &rsd, pose::Pose const &pose, dunbrack::RotamerLibraryScratchSpace &scratch) const override
 Adheres to the contract from SingleBasicRotamerLibrary. More...
 
Real rotamer_energy (conformation::Residue const &rsd, pose::Pose const &pose, dunbrack::RotamerLibraryScratchSpace &scratch) const override
 Adheres to the contract from SingleBasicRotamerLibrary. More...
 
Real best_rotamer_energy (conformation::Residue const &rsd, pose::Pose const &pose, bool curr_rotamer_only, dunbrack::RotamerLibraryScratchSpace &scratch) const override
 
void assign_random_rotamer_with_bias (conformation::Residue const &, pose::Pose const &, dunbrack::RotamerLibraryScratchSpace &, 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, rotamers::RotamerVector &rotamers) const override
 Adheres to the contract from SingleBasicRotamerLibrary. More...
 
void write_to_file (utility::io::ozstream &out) const override
 Adheres to the contract from SingleBasicRotamerLibrary. 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...
 

Detailed Description

A simple Rotamer library, which serves as a default for ResidueTypes which don't have some other more specific rotamer library.

In practice just diversifies the proton chi records.

Constructor & Destructor Documentation

core::pack::rotamers::SingleBasicRotamerLibrary::SingleBasicRotamerLibrary ( )
default
core::pack::rotamers::SingleBasicRotamerLibrary::~SingleBasicRotamerLibrary ( )
overridedefault

Member Function Documentation

void core::pack::rotamers::SingleBasicRotamerLibrary::assign_random_rotamer_with_bias ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
dunbrack::RotamerLibraryScratchSpace scratch,
numeric::random::RandomGenerator &  RG,
dunbrack::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. 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.

Real core::pack::rotamers::SingleBasicRotamerLibrary::best_rotamer_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
bool  curr_rotamer_only,
dunbrack::RotamerLibraryScratchSpace scratch 
) const
overridevirtual

Single rotamer - best is zero

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

void core::pack::rotamers::SingleBasicRotamerLibrary::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,
rotamers::RotamerVector rotamers 
) const
overridevirtual
Real core::pack::rotamers::SingleBasicRotamerLibrary::rotamer_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
dunbrack::RotamerLibraryScratchSpace scratch 
) const
overridevirtual

Adheres to the contract from SingleBasicRotamerLibrary.

Single rotamer - energy is zero

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

Real core::pack::rotamers::SingleBasicRotamerLibrary::rotamer_energy_deriv ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
dunbrack::RotamerLibraryScratchSpace scratch 
) const
overridevirtual

Adheres to the contract from SingleBasicRotamerLibrary.

Single rotamer - no derivative

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

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

Adheres to the contract from SingleBasicRotamerLibrary.

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

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


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