Rosetta 3.4
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#include <RelaxProtocolBase.hh>
Reimplemented in protocols::relax::ClassicRelax, and protocols::relax::MiniRelax.
protocols::relax::RelaxProtocolBase::RelaxProtocolBase | ( | core::scoring::ScoreFunctionOP | score_in | ) |
References set_defaults().
protocols::relax::RelaxProtocolBase::RelaxProtocolBase | ( | std::string const & | movername = "RelaxProtocol" | ) |
References set_defaults().
protocols::relax::RelaxProtocolBase::RelaxProtocolBase | ( | std::string const & | movername, |
core::scoring::ScoreFunctionOP | score_in | ||
) |
References set_defaults().
protocols::relax::RelaxProtocolBase::~RelaxProtocolBase | ( | ) |
void protocols::relax::RelaxProtocolBase::apply_disulfides | ( | core::pose::Pose & | pose | ) |
void protocols::relax::RelaxProtocolBase::cartesian | ( | bool | newval | ) | [inline] |
References cartesian_.
bool protocols::relax::RelaxProtocolBase::cartesian | ( | ) | const [inline] |
References cartesian_.
Referenced by protocols::relax::FastRelax::parse_my_tag(), and set_default_minimization_settings().
bool protocols::relax::RelaxProtocolBase::constrain_coords | ( | ) | const [inline] |
References constrain_coords_.
Referenced by protocols::relax::FastRelax::apply(), and constrain_coords().
void protocols::relax::RelaxProtocolBase::constrain_coords | ( | bool | constrain_coords | ) | [inline] |
References constrain_coords(), and constrain_coords_.
bool protocols::relax::RelaxProtocolBase::constrain_relax_segments | ( | ) | const [inline] |
References constrain_relax_segments_.
Referenced by constrain_relax_segments(), and set_default_coordinate_settings().
void protocols::relax::RelaxProtocolBase::constrain_relax_segments | ( | bool | constrain_relax_segments | ) | [inline] |
References constrain_relax_segments(), and constrain_relax_segments_.
bool protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords | ( | ) | const [inline] |
References constrain_relax_to_native_coords_.
Referenced by constrain_relax_to_native_coords(), and set_default_coordinate_settings().
void protocols::relax::RelaxProtocolBase::constrain_relax_to_native_coords | ( | bool | constrain_relax_to_native_coords | ) | [inline] |
References constrain_relax_to_native_coords(), and constrain_relax_to_native_coords_.
bool protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords | ( | ) | const [inline] |
References constrain_relax_to_start_coords_.
Referenced by constrain_relax_to_start_coords(), and set_default_coordinate_settings().
void protocols::relax::RelaxProtocolBase::constrain_relax_to_start_coords | ( | bool | constrain_relax_to_start_coords | ) | [inline] |
References constrain_relax_to_start_coords(), and constrain_relax_to_start_coords_.
bool protocols::relax::RelaxProtocolBase::dry_run | ( | ) | const [inline] |
Referenced by protocols::relax::FastRelax::apply(), protocols::relax::FastRelax::batch_apply(), and set_defaults().
bool protocols::relax::RelaxProtocolBase::explicit_ramp_constraints | ( | ) | const [inline] |
References explicit_ramp_constraints_.
Referenced by protocols::relax::FastRelax::FastRelax().
virtual protocols::moves::MoverOP protocols::relax::RelaxProtocolBase::fresh_instance | ( | ) | const [inline, virtual] |
this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
References protocols::moves::Mover::clone().
core::kinematics::MoveMapOP protocols::relax::RelaxProtocolBase::get_movemap | ( | ) |
Referenced by protocols::relax::FastRelax::apply(), protocols::relax::ClassicRelax::apply(), protocols::relax::FastRelax::batch_apply(), protocols::relax::ClassicRelax::set_default_minimizer(), protocols::relax::ClassicRelax::set_default_moveset_phase1(), protocols::relax::ClassicRelax::set_default_moveset_phase2(), and protocols::relax::ClassicRelax::set_default_moveset_phase3().
const core::scoring::ScoreFunctionCOP protocols::relax::RelaxProtocolBase::get_scorefxn | ( | ) | const |
core::scoring::ScoreFunctionOP protocols::relax::RelaxProtocolBase::get_scorefxn | ( | ) | [protected] |
core::pack::task::TaskFactoryOP const & protocols::relax::RelaxProtocolBase::get_task_factory | ( | ) | const |
Referenced by protocols::relax::FastRelax::apply(), and protocols::relax::FastRelax::batch_apply().
void protocols::relax::RelaxProtocolBase::initialize_movemap | ( | core::pose::Pose const & | pose, |
core::kinematics::MoveMap & | movemap | ||
) | [protected] |
References core::id::D, core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_bonded(), core::conformation::Residue::mainchain_atoms(), core::pose::Pose::residue(), core::kinematics::MoveMap::set(), core::id::THETA, and core::pose::Pose::total_residue().
Referenced by protocols::relax::FastRelax::apply(), protocols::relax::ClassicRelax::apply(), and protocols::relax::FastRelax::batch_apply().
bool protocols::relax::RelaxProtocolBase::limit_aroma_chi2 | ( | ) | const [inline] |
References limit_aroma_chi2_.
Referenced by protocols::relax::FastRelax::apply(), and set_default_coordinate_settings().
void protocols::relax::RelaxProtocolBase::minimize_bond_angles | ( | bool | setting | ) |
bool protocols::relax::RelaxProtocolBase::minimize_bond_angles | ( | ) | const |
Referenced by set_default_minimization_settings().
void protocols::relax::RelaxProtocolBase::minimize_bond_lengths | ( | bool | setting | ) |
bool protocols::relax::RelaxProtocolBase::minimize_bond_lengths | ( | ) | const |
Referenced by set_default_minimization_settings().
void protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_angles | ( | bool | setting | ) |
bool protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_angles | ( | ) | const |
Referenced by set_default_minimization_settings().
void protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_lengths | ( | bool | setting | ) |
bool protocols::relax::RelaxProtocolBase::minimize_mainchain_bond_lengths | ( | ) | const |
Referenced by set_default_minimization_settings().
void protocols::relax::RelaxProtocolBase::output_debug_structure | ( | core::pose::Pose & | pose, |
std::string | prefix | ||
) | [protected] |
void protocols::relax::RelaxProtocolBase::ramp_down_constraints | ( | bool | ramp_down_constraints | ) | [inline] |
References explicit_ramp_constraints_, ramp_down_constraints(), and ramp_down_constraints_.
bool protocols::relax::RelaxProtocolBase::ramp_down_constraints | ( | ) | const [inline] |
References ramp_down_constraints_.
Referenced by protocols::relax::FastRelax::FastRelax(), and ramp_down_constraints().
void protocols::relax::RelaxProtocolBase::register_options | ( | ) | [static] |
overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method.
Reimplemented from protocols::moves::Mover.
Reimplemented in protocols::relax::ClassicRelax.
void protocols::relax::RelaxProtocolBase::set_default_coordinate_settings | ( | ) |
References constrain_coords_, constrain_relax_segments(), constrain_relax_segments_, constrain_relax_to_native_coords(), constrain_relax_to_native_coords_, constrain_relax_to_start_coords(), constrain_relax_to_start_coords_, coord_constrain_sidechains_, explicit_ramp_constraints_, limit_aroma_chi2(), limit_aroma_chi2_, and ramp_down_constraints_.
Referenced by set_defaults().
void protocols::relax::RelaxProtocolBase::set_default_minimization_settings | ( | ) |
References cartesian(), cartesian_, min_type_, minimize_bond_angles(), minimize_bond_lengths(), minimize_mainchain_bond_angles(), and minimize_mainchain_bond_lengths().
Referenced by set_defaults().
void protocols::relax::RelaxProtocolBase::set_default_movemap | ( | ) |
Referenced by protocols::relax::ClassicRelax::set_default(), and set_defaults().
void protocols::relax::RelaxProtocolBase::set_defaults | ( | ) |
References dry_run(), set_default_coordinate_settings(), set_default_minimization_settings(), and set_default_movemap().
Referenced by RelaxProtocolBase().
void protocols::relax::RelaxProtocolBase::set_dry_run | ( | bool | setting | ) | [inline] |
void protocols::relax::RelaxProtocolBase::set_min_type | ( | std::string | min_type | ) |
References min_type_.
Referenced by protocols::comparative_modeling::hybridize::HybridizeProtocol::apply().
void protocols::relax::RelaxProtocolBase::set_movemap | ( | core::kinematics::MoveMapOP | movemap | ) |
void protocols::relax::RelaxProtocolBase::set_scorefxn | ( | core::scoring::ScoreFunctionOP | score | ) |
void protocols::relax::RelaxProtocolBase::set_task_factory | ( | core::pack::task::TaskFactoryOP | taskf | ) |
void protocols::relax::RelaxProtocolBase::set_up_constraints | ( | core::pose::Pose & | pose, |
core::kinematics::MoveMap & | local_movemap | ||
) | [protected] |
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::add_constraint(), core::pose::Pose::append_residue_by_jump(), core::scoring::atom_pair_constraint, core::scoring::calpha_superimpose_pose(), constrain_coords_, constrain_relax_segments_, constrain_relax_to_native_coords_, coord_constrain_sidechains_, core::scoring::coordinate_constraint, core::conformation::ResidueFactory::create_residue(), protocols::relax::derive_sc_sc_restraints(), core::pose::Pose::fold_tree(), protocols::moves::Mover::get_native_pose(), get_scorefxn(), core::chemical::ResidueTypeSet::name_map(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::num_jump(), ramp_down_constraints_, core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::kinematics::FoldTree::root(), core::kinematics::MoveMap::set_jump(), and core::pose::Pose::total_residue().
Referenced by protocols::relax::FastRelax::apply(), and protocols::relax::ClassicRelax::apply().
bool protocols::relax::RelaxProtocolBase::cartesian_ [protected] |
Do cartesian-space minimization?
Referenced by cartesian(), protocols::relax::FastRelax::do_minimize(), and set_default_minimization_settings().
Referenced by constrain_coords(), set_default_coordinate_settings(), and set_up_constraints().
Referenced by constrain_relax_segments(), set_default_coordinate_settings(), and set_up_constraints().
Referenced by constrain_relax_to_native_coords(), set_default_coordinate_settings(), and set_up_constraints().
Referenced by constrain_relax_to_start_coords(), and set_default_coordinate_settings().
Referenced by set_default_coordinate_settings(), and set_up_constraints().
Referenced by explicit_ramp_constraints(), ramp_down_constraints(), and set_default_coordinate_settings().
Referenced by limit_aroma_chi2(), and set_default_coordinate_settings().
std::string protocols::relax::RelaxProtocolBase::min_type_ [protected] |