Rosetta 3.4
Public Member Functions
protocols::comparative_modeling::LoopRelaxMover Class Reference

#include <LoopRelaxMover.hh>

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List of all members.

Public Member Functions

 LoopRelaxMover ()
 LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::Loops loops)
 Alternative constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.
 ~LoopRelaxMover ()
void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void scorefxns (core::scoring::ScoreFunctionOP cen_scorefxn, core::scoring::ScoreFunctionOP fa_scorefxn)
void fa_scorefxn (core::scoring::ScoreFunctionOP fa_scorefxn)
void cen_scorefxn (core::scoring::ScoreFunctionOP cen_scorefxn)
void cmd_line_csts (bool setting)
void copy_sidechains (bool setting)
void rebuild_filter (core::Real setting)
void n_rebuild_tries (core::Size setting)
void remodel (std::string val)
void intermedrelax (std::string val)
void refine (std::string val)
void relax (std::string val)
void loops (protocols::loops::LoopsOP const val)
void frag_libs (utility::vector1< core::fragment::FragSetOP > new_libs)
bool cmd_line_csts () const
bool copy_sidechains () const
core::Size n_rebuild_tries () const
core::Real rebuild_filter () const
protocols::loops::LoopsOP get_loops () const
std::string remodel () const
std::string relax () const
std::string intermedrelax () const
std::string refine () const
utility::vector1
< core::fragment::FragSetOP
frag_libs () const
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
protocols::moves::MoverOP fresh_instance () const
 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).
void compute_rmsd (bool const c)
bool compute_rmsd () const
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Constructor & Destructor Documentation

protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover ( )
protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover ( std::string const &  remodel,
std::string const &  intermedrelax,
std::string const &  refine,
std::string const &  relax,
loops::Loops  loops 
)

Alternative constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.

protocols::comparative_modeling::LoopRelaxMover::~LoopRelaxMover ( )

Member Function Documentation

void protocols::comparative_modeling::LoopRelaxMover::apply ( core::pose::Pose pose) [virtual]

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::viewer::add_conformation_viewer(), core::pose::Pose::add_constraint(), core::scoring::constraints::add_constraints_from_cmdline(), core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::util::add_cutpoint_variants(), core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), protocols::loops::loop_mover::LoopMover::add_fragments(), core::scoring::angle_constraint, core::pose::Pose::annotated_sequence(), core::pose::Pose::append_residue_by_jump(), protocols::relax::MiniRelax::apply(), protocols::idealize::IdealizeMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::relax::FastRelax::apply(), protocols::simple_moves::PackRotamersMover::apply(), protocols::LoopRebuild::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::scoring::atom_pair_constraint, core::scoring::big_bin_constraint, core::id::BOGUS_ATOM_ID, core::scoring::CA_rmsd(), core::pose::Pose::center(), core::chemical::CENTROID, core::scoring::chainbreak, protocols::checkpoint::CheckPointer::checkpoint(), cmd_line_csts(), compute_rmsd(), core::pose::Pose::conformation(), core::scoring::constant_constraint, core::scoring::coordinate_constraint, copy_sidechains(), core::pack::task::TaskFactory::create_packer_task(), core::conformation::ResidueFactory::create_residue(), protocols::checkpoint::CheckPointer::debug(), core::pack::interaction_graph::debug, core::conformation::Conformation::detect_bonds(), core::scoring::dihedral_constraint, core::io::raw_data::DisulfideFile::disulfides(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::chemical::FA_STANDARD, protocols::moves::FAIL_RETRY, protocols::idealize::IdealizeMover::fast(), core::conformation::Conformation::fix_disulfides(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), frag_libs(), protocols::relax::generate_relax_from_cmd(), protocols::loops::loop_mover::LoopMover::get_checkpoints(), protocols::moves::Mover::get_current_tag(), protocols::loops::LoopMoverFactory::get_instance(), protocols::evaluation::EvaluatorFactory::get_instance(), get_loops(), core::chemical::ResidueType::has(), core::pose::initialize_atomid_map(), intermedrelax(), core::pose::Pose::is_fullatom(), protocols::loops::Loops::is_loop_residue(), core::conformation::Residue::is_polymer(), core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), core::scoring::linear_chainbreak, protocols::loops::loop_rmsd(), loops(), core::pose::symmetry::make_residue_mask_symmetric(), core::pose::symmetry::make_symmetric_movemap(), protocols::moves::MS_SUCCESS, n_rebuild_tries(), core::chemical::ResidueTypeSet::name_map(), core::scoring::native_CA_rmsd(), protocols::loops::native_loop_core_CA_rmsd(), core::conformation::Residue::natoms(), core::scoring::overlap_chainbreak, core::scoring::pair, protocols::comparative_modeling::pick_loops_chainbreak(), core::import_pose::pose_from_pdb(), rebuild_filter(), protocols::checkpoint::CheckPointer::recover_checkpoint(), refine(), relax(), remodel(), core::util::remove_cutpoint_variants(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::residue_type_set(), core::kinematics::FoldTree::root(), core::optimization::AtomTreeMinimizer::run(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), protocols::loops::loop_mover::IndependentLoopMover::set_accept_aborted_loops_(), protocols::loops::loop_mover::IndependentLoopMover::set_build_all_loops_(), protocols::loops::loop_mover::IndependentLoopMover::set_build_attempts_(), protocols::moves::Mover::set_current_tag(), protocols::loops::loop_mover::IndependentLoopMover::set_grow_attempts_(), protocols::moves::Mover::set_last_move_status(), protocols::loops::loop_mover::IndependentLoopMover::set_loop_combine_rate_(), protocols::moves::Mover::set_native_pose(), protocols::loops::loop_mover::IndependentLoopMover::set_random_order_(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), core::pose::set_ss_from_phipsi(), protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops(), core::pose::Pose::set_xyz(), core::pose::setPoseExtraScores(), core::scoring::superimpose_pose(), core::util::switch_to_residue_type_set(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), protocols::TR(), and core::conformation::Atom::xyz().

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), and protocols::loop_build::LoopBuild_main().

void protocols::comparative_modeling::LoopRelaxMover::cen_scorefxn ( core::scoring::ScoreFunctionOP  cen_scorefxn)

Referenced by parse_my_tag(), and scorefxns().

protocols::moves::MoverOP protocols::comparative_modeling::LoopRelaxMover::clone ( ) const [virtual]

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. 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.

Reimplemented from protocols::moves::Mover.

References LoopRelaxMover().

bool protocols::comparative_modeling::LoopRelaxMover::cmd_line_csts ( ) const [inline]

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::cmd_line_csts ( bool  setting) [inline]
void protocols::comparative_modeling::LoopRelaxMover::compute_rmsd ( bool const  c) [inline]
bool protocols::comparative_modeling::LoopRelaxMover::compute_rmsd ( ) const [inline]

Referenced by apply(), and parse_my_tag().

bool protocols::comparative_modeling::LoopRelaxMover::copy_sidechains ( ) const [inline]

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::copy_sidechains ( bool  setting) [inline]
void protocols::comparative_modeling::LoopRelaxMover::fa_scorefxn ( core::scoring::ScoreFunctionOP  fa_scorefxn)
utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::LoopRelaxMover::frag_libs ( ) const

Referenced by apply().

void protocols::comparative_modeling::LoopRelaxMover::frag_libs ( utility::vector1< core::fragment::FragSetOP new_libs)
protocols::moves::MoverOP protocols::comparative_modeling::LoopRelaxMover::fresh_instance ( ) const [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 LoopRelaxMover().

protocols::loops::LoopsOP protocols::comparative_modeling::LoopRelaxMover::get_loops ( ) const [inline]

Referenced by apply().

std::string protocols::comparative_modeling::LoopRelaxMover::get_name ( ) const [virtual]

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

void protocols::comparative_modeling::LoopRelaxMover::intermedrelax ( std::string  val) [inline]
std::string protocols::comparative_modeling::LoopRelaxMover::intermedrelax ( ) const [inline]

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::loops ( protocols::loops::LoopsOP const  val) [inline]
core::Size protocols::comparative_modeling::LoopRelaxMover::n_rebuild_tries ( ) const [inline]

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::n_rebuild_tries ( core::Size  setting) [inline]
void protocols::comparative_modeling::LoopRelaxMover::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
) [virtual]

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References cen_scorefxn(), cmd_line_csts(), compute_rmsd(), copy_sidechains(), fa_scorefxn(), intermedrelax(), loops(), protocols::loops::loop_mover::loops_set_chainbreak_weight(), n_rebuild_tries(), protocols::rosetta_scripts::parse_resnum(), protocols::rosetta_scripts::parse_score_function(), protocols::loops::read_loop_fragments(), rebuild_filter(), refine(), relax(), remodel(), and core::pose::Pose::total_residue().

void protocols::comparative_modeling::LoopRelaxMover::rebuild_filter ( core::Real  setting) [inline]
core::Real protocols::comparative_modeling::LoopRelaxMover::rebuild_filter ( ) const [inline]

Referenced by apply(), and parse_my_tag().

std::string protocols::comparative_modeling::LoopRelaxMover::refine ( ) const [inline]

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::refine ( std::string  val) [inline]
std::string protocols::comparative_modeling::LoopRelaxMover::relax ( ) const [inline]

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::relax ( std::string  val) [inline]
void protocols::comparative_modeling::LoopRelaxMover::remodel ( std::string  val) [inline]
std::string protocols::comparative_modeling::LoopRelaxMover::remodel ( ) const [inline]

Referenced by apply(), and parse_my_tag().

void protocols::comparative_modeling::LoopRelaxMover::scorefxns ( core::scoring::ScoreFunctionOP  cen_scorefxn,
core::scoring::ScoreFunctionOP  fa_scorefxn 
)

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