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>
Public Member Functions | |
| SingleBasicRotamerLibrary () | |
| ~SingleBasicRotamerLibrary () override | |
| 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 SingleBasicRotamerLibrary. More... | |
| Real | rotamer_energy (conformation::Residue const &rsd, pose::Pose const &pose, TorsionEnergy &energy) const override |
| Adheres to the contract from SingleBasicRotamerLibrary. 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, 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
◆ SingleBasicRotamerLibrary()
|
default |
◆ ~SingleBasicRotamerLibrary()
|
overridedefault |
Member Function Documentation
◆ assign_random_rotamer_with_bias()
|
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.
◆ atoms_w_dof_derivatives()
|
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()
|
overridevirtual |
Single rotamer - best is zero
Implements core::pack::rotamers::SingleResidueRotamerLibrary.
◆ fill_rotamer_vector()
|
overridevirtual |
Adheres to the contract from SingleBasicRotamerLibrary.
Implements core::pack::rotamers::SingleResidueRotamerLibrary.
References core::conformation::Residue::atom_name(), core::conformation::Residue::chi(), core::chemical::ResidueType::chi_atoms(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::nchi(), core::pack::task::PackerTask::residue_task(), core::conformation::Residue::seqpos(), core::pack::rotamers::TR(), and core::conformation::Residue::type().
◆ rotamer_energy()
|
overridevirtual |
Adheres to the contract from SingleBasicRotamerLibrary.
Single rotamer - energy is zero
Implements core::pack::rotamers::SingleResidueRotamerLibrary.
◆ rotamer_energy_deriv()
|
overridevirtual |
Adheres to the contract from SingleBasicRotamerLibrary.
Single rotamer - no derivative
Implements core::pack::rotamers::SingleResidueRotamerLibrary.
◆ write_to_file()
|
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:
- src/core/pack/rotamers/SingleBasicRotamerLibrary.hh
- src/core/pack/rotamers/SingleBasicRotamerLibrary.cc
