Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::hybridization::CartesianSampler Class Reference

#include <CartesianSampler.hh>

Public Member Functions

 CartesianSampler ()
 
 CartesianSampler (utility::vector1< core::fragment::FragSetOP > fragments_in)
 
void init ()
 
void apply (core::pose::Pose &pose)
 
void set_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)
 
void set_fa_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)
 
std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, filters::Filters_map const &, moves::Movers_map const &, core::pose::Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
void set_userpos (std::set< core::Size > const &user_pos_in)
 
void set_strategy (std::string strategy_in)
 
void set_rms_cutoff (core::Real rms_cutoff_in)
 
void set_fullatom (bool fullatom_in)
 
void set_bbmove (bool bbmove_in)
 
void set_restore_csts (bool restore_csts_in)
 
void set_frag_sizes (utility::vector1< core::Size > const &frag_sizes_in)
 
void set_nminsteps (core::Size nminsteps_in)
 
void set_ncycles (core::Size ncycles_in)
 
void set_overlap (core::Size overlap_in)
 
- 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...
 

Protected Member Functions

bool apply_frame (core::pose::Pose &pose, core::fragment::Frame &frame)
 
void compute_fragment_bias (core::pose::Pose &pose)
 
void update_fragment_library_pointers ()
 
void apply_constraints (core::pose::Pose &pose)
 
core::Real get_transform (core::pose::Pose const &pose, core::pose::Pose const &frag, core::Size startpos, core::Vector &preT, core::Vector &postT, numeric::xyzMatrix< core::Real > &R)
 
void apply_transform (core::pose::Pose &frag, core::Vector const &preT, core::Vector const &postT, numeric::xyzMatrix< core::Real > const &R)
 
void apply_fragcsts (core::pose::Pose &working_frag, core::pose::Pose const &pose, core::Size start)
 
- 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...
 

Private Attributes

core::Size ncycles_
 
core::Size overlap_
 
core::Size nminsteps_
 
core::Real rms_cutoff_
 
utility::vector1< core::Sizefrag_sizes_
 
core::Size nfrags_
 
utility::vector1
< core::fragment::FragSetOP
fragments_
 
utility::vector1
< boost::unordered_map
< core::Size,
core::fragment::Frame > > 
library_
 
std::string fragment_bias_strategy_
 
utility::vector1
< numeric::random::WeightedSampler
frag_bias_
 
std::set< core::Sizeuser_pos_
 
core::Real temp_
 
std::string selection_bias_
 
core::pose::Pose ref_model_
 
core::Real ref_cst_weight_
 
bool input_as_ref_
 
bool restore_csts_
 
bool fullatom_
 
bool bbmove_
 
bool recover_low_
 
char force_ss_
 
LoopsOP loops_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP fa_scorefxn_
 
core::scoring::ScoreFunctionOP mc_scorefxn_
 

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...
 

Constructor & Destructor Documentation

protocols::hybridization::CartesianSampler::CartesianSampler ( )

References init().

Referenced by clone(), and fresh_instance().

protocols::hybridization::CartesianSampler::CartesianSampler ( utility::vector1< core::fragment::FragSetOP fragments_in)

Member Function Documentation

void protocols::hybridization::CartesianSampler::apply ( core::pose::Pose pose)
virtual
void protocols::hybridization::CartesianSampler::apply_constraints ( core::pose::Pose pose)
protected
void protocols::hybridization::CartesianSampler::apply_fragcsts ( core::pose::Pose working_frag,
core::pose::Pose const &  pose,
core::Size  start 
)
protected
bool protocols::hybridization::CartesianSampler::apply_frame ( core::pose::Pose pose,
core::fragment::Frame frame 
)
protected

References core::pose::addVirtualResAsRoot(), core::pose::Pose::append_residue_by_bond(), core::fragment::Frame::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::PackRotamersMover::apply(), apply_fragcsts(), apply_transform(), core::scoring::symmetry::asymmetrize_scorefunction(), bbmove_, core::pose::Pose::conformation(), core::scoring::coordinate_constraint, core::pose::Pose::data(), core::scoring::elec_dens_fast, fa_scorefxn_, fullatom_, basic::datacache::BasicDataCache::get_ptr(), get_transform(), basic::datacache::BasicDataCache::has(), core::conformation::idealize_position(), core::pose::symmetry::is_symmetric(), core::fragment::Frame::length(), core::optimization::MinimizerOptions::max_iter(), core::pose::datacache::CacheableDataType::NCS_RESIDUE_MAPPING, core::fragment::Frame::nr_frags(), overlap_, core::pack::task::TaskFactory::push_back(), numeric::random::random_range(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), rms, rms_cutoff_, core::optimization::AtomTreeMinimizer::run(), runtime_assert, protocols::simple_moves::PackRotamersMover::score_function(), scorefxn_, selection_bias_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::fragment::Frame::shift_to(), core::fragment::Frame::start(), protocols::loops::start, protocols::simple_moves::PackRotamersMover::task_factory(), protocols::hybridization::TR, and utility_exit_with_message.

Referenced by apply().

void protocols::hybridization::CartesianSampler::apply_transform ( core::pose::Pose frag,
core::Vector const &  preT,
core::Vector const &  postT,
numeric::xyzMatrix< core::Real > const &  R 
)
protected
protocols::moves::MoverOP protocols::hybridization::CartesianSampler::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 CartesianSampler().

void protocols::hybridization::CartesianSampler::compute_fragment_bias ( core::pose::Pose pose)
protected
protocols::moves::MoverOP protocols::hybridization::CartesianSampler::fresh_instance ( ) const
virtual

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.

References CartesianSampler().

std::string protocols::hybridization::CartesianSampler::get_name ( ) const
inlinevirtual

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

Implements protocols::moves::Mover.

core::Real protocols::hybridization::CartesianSampler::get_transform ( core::pose::Pose const &  pose,
core::pose::Pose const &  frag,
core::Size  startpos,
core::Vector preT,
core::Vector postT,
numeric::xyzMatrix< core::Real > &  R 
)
protected
void protocols::hybridization::CartesianSampler::init ( void  )
void protocols::hybridization::CartesianSampler::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
filters::Filters_map const &  filters,
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 bbmove_, force_ss_, frag_sizes_, fragment_bias_strategy_, fragments_, fullatom_, basic::datacache::DataMap::get(), core::pose::get_resnum_list(), basic::datacache::DataMap::has(), input_as_ref_, loops_, mc_scorefxn_, ncycles_, nfrags_, nminsteps_, overlap_, core::import_pose::pose_from_pdb(), recover_low_, ref_cst_weight_, ref_model_, rms_cutoff_, runtime_assert, selection_bias_, set_fa_scorefunction(), set_scorefunction(), utility::string_split(), temp_, update_fragment_library_pointers(), and user_pos_.

void protocols::hybridization::CartesianSampler::set_bbmove ( bool  bbmove_in)
inline
void protocols::hybridization::CartesianSampler::set_fa_scorefunction ( core::scoring::ScoreFunctionOP  scorefxn_in)
inline

Referenced by init(), and parse_my_tag().

void protocols::hybridization::CartesianSampler::set_frag_sizes ( utility::vector1< core::Size > const &  frag_sizes_in)
inline
void protocols::hybridization::CartesianSampler::set_fullatom ( bool  fullatom_in)
inline
void protocols::hybridization::CartesianSampler::set_ncycles ( core::Size  ncycles_in)
inline
void protocols::hybridization::CartesianSampler::set_nminsteps ( core::Size  nminsteps_in)
inline
void protocols::hybridization::CartesianSampler::set_overlap ( core::Size  overlap_in)
inline
void protocols::hybridization::CartesianSampler::set_restore_csts ( bool  restore_csts_in)
inline
void protocols::hybridization::CartesianSampler::set_rms_cutoff ( core::Real  rms_cutoff_in)
inline
void protocols::hybridization::CartesianSampler::set_scorefunction ( core::scoring::ScoreFunctionOP  scorefxn_in)
inline

Referenced by init(), and parse_my_tag().

void protocols::hybridization::CartesianSampler::set_strategy ( std::string  strategy_in)
inline
void protocols::hybridization::CartesianSampler::set_userpos ( std::set< core::Size > const &  user_pos_in)
inline
void protocols::hybridization::CartesianSampler::update_fragment_library_pointers ( )
protected

References begin, fragments_, and library_.

Referenced by apply(), CartesianSampler(), and parse_my_tag().

Member Data Documentation

bool protocols::hybridization::CartesianSampler::bbmove_
private

Referenced by apply_frame(), init(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::hybridization::CartesianSampler::fa_scorefxn_
private

Referenced by apply(), and apply_frame().

char protocols::hybridization::CartesianSampler::force_ss_
private

Referenced by apply(), init(), and parse_my_tag().

utility::vector1<numeric::random::WeightedSampler> protocols::hybridization::CartesianSampler::frag_bias_
private

Referenced by apply(), and compute_fragment_bias().

utility::vector1<core::Size> protocols::hybridization::CartesianSampler::frag_sizes_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::hybridization::CartesianSampler::fragment_bias_strategy_
private
utility::vector1<core::fragment::FragSetOP> protocols::hybridization::CartesianSampler::fragments_
private
bool protocols::hybridization::CartesianSampler::fullatom_
private

Referenced by apply(), apply_frame(), init(), and parse_my_tag().

bool protocols::hybridization::CartesianSampler::input_as_ref_
private

Referenced by apply(), init(), and parse_my_tag().

utility::vector1<boost::unordered_map<core::Size, core::fragment::Frame> > protocols::hybridization::CartesianSampler::library_
private
LoopsOP protocols::hybridization::CartesianSampler::loops_
private
core::scoring::ScoreFunctionOP protocols::hybridization::CartesianSampler::mc_scorefxn_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::hybridization::CartesianSampler::ncycles_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::CartesianSampler::nfrags_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::CartesianSampler::nminsteps_
private

Referenced by apply(), init(), and parse_my_tag().

core::Size protocols::hybridization::CartesianSampler::overlap_
private
bool protocols::hybridization::CartesianSampler::recover_low_
private

Referenced by apply(), init(), and parse_my_tag().

core::Real protocols::hybridization::CartesianSampler::ref_cst_weight_
private
core::pose::Pose protocols::hybridization::CartesianSampler::ref_model_
private
bool protocols::hybridization::CartesianSampler::restore_csts_
private

Referenced by apply(), and init().

core::Real protocols::hybridization::CartesianSampler::rms_cutoff_
private

Referenced by apply_frame(), init(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::hybridization::CartesianSampler::scorefxn_
private

Referenced by apply(), and apply_frame().

std::string protocols::hybridization::CartesianSampler::selection_bias_
private

Referenced by apply_frame(), init(), and parse_my_tag().

core::Real protocols::hybridization::CartesianSampler::temp_
private

Referenced by apply(), init(), and parse_my_tag().

std::set<core::Size> protocols::hybridization::CartesianSampler::user_pos_
private

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