Rosetta 3.4
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typedef utility::pointer::access_ptr< FastRelax const > protocols::relax::FastRelaxCAP |
typedef utility::pointer::owning_ptr< FastRelax const > protocols::relax::FastRelaxCOP |
typedef utility::pointer::access_ptr< RelaxProtocolBase const > protocols::relax::RelaxProtocolBaseCAP |
typedef utility::pointer::owning_ptr< RelaxProtocolBase const > protocols::relax::RelaxProtocolBaseCOP |
typedef utility::pointer::owning_ptr< WorkUnit_BatchRelax const > protocols::relax::WorkUnit_BatchRelaxCOP |
void protocols::relax::add_coordinate_constraints_to_pose | ( | core::pose::Pose & | pose, |
const core::pose::Pose & | constraint_target_pose, | ||
protocols::loops::Loops & | exclude_regions | ||
) |
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::add_constraint(), core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), protocols::loops::Loops::invert(), core::chemical::ResidueTypeSet::name_map(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::kinematics::FoldTree::root(), and core::pose::Pose::total_residue().
Referenced by fix_worst_bad_ramas().
void protocols::relax::add_virtual_residue_to_cterm | ( | core::pose::Pose & | pose | ) |
void protocols::relax::coordinate_constrain_selection | ( | core::pose::Pose & | pose, |
core::sequence::SequenceAlignment | aln, | ||
core::Real | coord_sdev | ||
) |
References core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), generate_bb_coordinate_constraints(), make_table_of_pilot_apps::name, core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::sequence::SequenceAlignment::sequence_mapping(), core::sequence::SequenceAlignment::size(), core::pose::Pose::total_residue(), and tr().
Referenced by protocols::relax::MiniRelax::apply().
void protocols::relax::delete_virtual_residues | ( | core::pose::Pose & | pose | ) |
References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().
Referenced by protocols::relax::MiniRelax::apply(), and protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps().
void protocols::relax::derive_sc_sc_restraints | ( | core::pose::Pose & | pose, |
core::Real const | upper_dist_cutoff | ||
) |
References core::pose::Pose::add_constraint(), core::kinematics::distance(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), tr(), and core::conformation::Residue::xyz().
Referenced by protocols::relax::RelaxProtocolBase::set_up_constraints().
void protocols::relax::fix_worst_bad_ramas | ( | core::pose::Pose & | original_pose, |
core::Size | how_many, | ||
core::Real | skip_prob, | ||
core::Real | limit_RMS, | ||
core::Real | limit_rama | ||
) |
References core::chemical::aa_pro, add_coordinate_constraints_to_pose(), core::id::BB, core::scoring::CA_rmsd(), core::scoring::coordinate_constraint, core::scoring::omega, core::id::omega_torsion(), core::id::phi_torsion(), core::scoring::rama, rama_list_pred(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::scoring::ScoreFunction::set_weight(), core::pose::Pose::total_residue(), and TR().
Referenced by protocols::relax::FastRelax::apply(), and protocols::relax::FastRelax::batch_apply().
core::scoring::constraints::ConstraintSetOP protocols::relax::generate_bb_coordinate_constraints | ( | core::pose::Pose & | pose, |
utility::vector1< core::Real > const & | coord_sdevs | ||
) |
Generate a set of coordinate constraints to backbone atoms using the given standard deviations, with one sd per-reside. If no constraint should be applied to a given residue, give a -1 for the value of the sdev.
References core::pose::Pose::residue(), and core::pose::Pose::total_residue().
Referenced by protocols::relax::MiniRelax::apply(), and coordinate_constrain_selection().
RelaxProtocolBaseOP protocols::relax::generate_relax_from_cmd | ( | bool | NULL_if_no_flag | ) |
References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), core::scoring::getScoreFunction(), script, and tr().
Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::wum::MPI_Relax::register_work_units(), Relax_main(), relax_pose(), and protocols::abinitio::AbrelaxMover::set_defaults().
utility::vector1< core::Real > protocols::relax::get_per_residue_scores | ( | core::pose::Pose & | pose, |
core::scoring::ScoreType | scoretype | ||
) |
bool protocols::relax::rama_list_pred | ( | const std::pair< core::Size, core::Real > & | left, |
const std::pair< core::Size, core::Real > & | right | ||
) |
Referenced by fix_worst_bad_ramas().
void protocols::relax::relax_pose | ( | pose::Pose & | pose, |
core::scoring::ScoreFunctionOP | scorefxn, | ||
std::string const & | tag | ||
) |
void protocols::relax::setup_membrane_topology | ( | pose::Pose & | pose, |
std::string | spanfile | ||
) |
static basic::Tracer protocols::relax::TR | ( | "WorkUnit_BatchRelax" | ) | [static] |
Referenced by protocols::relax::FastRelax::apply(), protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::FastRelax::cmd_accept_to_best(), fix_worst_bad_ramas(), protocols::relax::FastRelax::makeDnaRigid(), protocols::relax::WorkUnit_BatchRelax::post_process(), protocols::relax::WorkUnit_BatchRelax::pre_process(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::relax::ClassicRelax::set_default(), protocols::relax::FastRelax::set_script_to_batchrelax_default(), and protocols::relax::ClassicRelax::set_tolerance().