Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::ncbb::oop::OopCreatorMover Class Reference

#include <OopCreatorMover.hh>

Public Member Functions

 OopCreatorMover ()
 
 OopCreatorMover (utility::vector1< core::Size > oop_plus_positions, utility::vector1< core::Size > oop_minus_positions, utility::vector1< core::Size > oop_d_plus_positions, utility::vector1< core::Size > oop_d_minus_positions, utility::vector1< core::Size > oop_low_e_puck_positions, core::Size prepend_n_residues, core::Size append_n_residues, bool final_repack, bool final_minimize, bool final_mc, bool final_correct_oop_post)
 
virtual ~OopCreatorMover ()
 
virtual void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
void parse_my_tag (utility::tag::TagCOP, basic::datacache::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. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
void set_type (std::string const &setting)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
void set_current_tag (std::string const &new_tag)
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Attributes

utility::vector1< core::Sizeoop_plus_positions_
 
utility::vector1< core::Sizeoop_minus_positions_
 
utility::vector1< core::Sizeoop_d_plus_positions_
 
utility::vector1< core::Sizeoop_d_minus_positions_
 
utility::vector1< core::Sizeoop_low_e_puck_positions_
 
core::Size prepend_n_residues_
 
core::Size append_n_residues_
 
bool final_repack_
 
bool final_minimize_
 
bool final_mc_
 
bool final_correct_oop_post_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Constructor & Destructor Documentation

protocols::ncbb::oop::OopCreatorMover::OopCreatorMover ( )
protocols::ncbb::oop::OopCreatorMover::OopCreatorMover ( utility::vector1< core::Size oop_plus_positions,
utility::vector1< core::Size oop_minus_positions,
utility::vector1< core::Size oop_d_plus_positions,
utility::vector1< core::Size oop_d_minus_positions,
utility::vector1< core::Size oop_low_e_puck_positions,
core::Size  prepend_n_residues,
core::Size  append_n_residues,
bool  final_repack,
bool  final_minimize,
bool  final_mc,
bool  final_correct_oop_post 
)
virtual protocols::ncbb::oop::OopCreatorMover::~OopCreatorMover ( )
inlinevirtual

Member Function Documentation

void protocols::ncbb::oop::OopCreatorMover::apply ( core::pose::Pose pose)
virtual

Implements protocols::moves::Mover.

References core::pose::Pose::add_constraint(), protocols::moves::MoverContainer::add_mover(), protocols::simple_moves::BackboneMover::angle_max(), append_n_residues_, protocols::simple_moves::PackRotamersMover::apply(), protocols::simple_moves::MinMover::apply(), protocols::moves::TrialMover::apply(), atom_pair_constraint, BB, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), dihedral_constraint, final_correct_oop_post_, final_mc_, final_minimize_, final_repack_, core::conformation::Conformation::get_torsion_angle_atom_ids(), core::conformation::Residue::has_variant_type(), protocols::simple_moves::chiral::is_d_chiral(), protocols::simple_moves::chiral::is_l_chiral(), core::chemical::ResidueType::name(), oop_d_minus_positions_, oop_d_plus_positions_, oop_low_e_puck_positions_, oop_minus_positions_, oop_plus_positions_, option, core::pack::task::TaskFactory::push_back(), radians(), protocols::moves::MonteCarlo::recover_low(), packing::resfile, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::residue_type_set(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(), protocols::simple_moves::PackRotamersMover::score_function(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::simple_moves::PackRotamersMover::task_factory(), core::pose::Pose::torsion(), core::pose::Pose::total_residue(), protocols::TR, core::conformation::Conformation::update_polymeric_connection(), and user.

protocols::moves::MoverOP protocols::ncbb::oop::OopCreatorMover::clone ( ) const
virtual

Return a clone of the Mover object.

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 OopCreatorMover().

protocols::moves::MoverOP protocols::ncbb::oop::OopCreatorMover::fresh_instance ( ) const
inlinevirtual

Generates a new Mover object freshly created with the default ctor.

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.

virtual std::string protocols::ncbb::oop::OopCreatorMover::get_name ( ) const
inlinevirtual

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

Implements protocols::moves::Mover.

void protocols::ncbb::oop::OopCreatorMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::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 append_n_residues_, final_correct_oop_post_, final_mc_, final_minimize_, final_repack_, core::pose::get_resnum_list(), oop_d_minus_positions_, oop_d_plus_positions_, oop_low_e_puck_positions_, oop_minus_positions_, oop_plus_positions_, and prepend_n_residues_.

Member Data Documentation

core::Size protocols::ncbb::oop::OopCreatorMover::append_n_residues_
private

Referenced by apply(), and parse_my_tag().

bool protocols::ncbb::oop::OopCreatorMover::final_correct_oop_post_
private

Referenced by apply(), and parse_my_tag().

bool protocols::ncbb::oop::OopCreatorMover::final_mc_
private

Referenced by apply(), and parse_my_tag().

bool protocols::ncbb::oop::OopCreatorMover::final_minimize_
private

Referenced by apply(), and parse_my_tag().

bool protocols::ncbb::oop::OopCreatorMover::final_repack_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<core::Size> protocols::ncbb::oop::OopCreatorMover::oop_d_minus_positions_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<core::Size> protocols::ncbb::oop::OopCreatorMover::oop_d_plus_positions_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<core::Size> protocols::ncbb::oop::OopCreatorMover::oop_low_e_puck_positions_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<core::Size> protocols::ncbb::oop::OopCreatorMover::oop_minus_positions_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<core::Size> protocols::ncbb::oop::OopCreatorMover::oop_plus_positions_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::ncbb::oop::OopCreatorMover::prepend_n_residues_
private

Referenced by parse_my_tag().


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