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protocols::hybridization::CartesianSampler Class Reference

#include <CartesianSampler.hh>

Inheritance diagram for protocols::hybridization::CartesianSampler:
Inheritance graph
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Public Member Functions

 CartesianSampler ()
 
 CartesianSampler (utility::vector1< core::fragment::FragSetOP > fragments_in)
 
void init ()
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void set_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)
 
void set_mc_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)
 
void set_fa_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void set_userpos (core::select::residue_selector::ResidueSelectorCOP 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)
 
void set_nfrags (core::Size nfrags_in)
 
void set_temp (core::Real temp_in)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool apply_frame (core::pose::Pose &pose, core::fragment::Frame &frame)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
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...
 
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...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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 mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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

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_
 
utility::vector1< std::string > fragment_bias_strategies_
 
utility::vector1
< numeric::random::WeightedSampler > 
frag_bias_
 
core::Real temp_
 
bool cumulate_prob_
 
bool exclude_residues_
 
bool include_residues_
 
core::select::residue_selector::ResidueSelectorCOP user_pos_
 
core::select::residue_selector::ResidueSelectorCOP residues_to_exclude_
 
core::select::residue_selector::ResidueSelectorCOP residues_to_include_
 
bool dump_pdb_
 
std::string dump_pdb_tag_
 
core::Real automode_scorecut_
 
core::Real score_threshold_
 
core::Size rsd_wdw_to_refine_
 
int wdw_to_freeze_
 
bool freeze_endpoints_
 
std::string selection_bias_
 
core::pose::Pose ref_model_
 
core::Real ref_cst_weight_
 
core::Real ref_cst_maxdist_
 
bool input_as_ref_
 
bool restore_csts_
 
bool debug_
 
bool fullatom_
 
bool bbmove_
 
bool recover_low_
 
char force_ss_
 
protocols::loops::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 std::list< std::string > Strings
 

Constructor & Destructor Documentation

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

References core::init::init().

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

References core::init::init().

Member Function Documentation

void protocols::hybridization::CartesianSampler::apply ( core::pose::Pose )
overridevirtual
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 
)
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
overridevirtual

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.

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

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.

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

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  )
std::string protocols::hybridization::CartesianSampler::mover_name ( )
static
void protocols::hybridization::CartesianSampler::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References core::pose::get_resnum_selector(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::hybridization::TR().

void protocols::hybridization::CartesianSampler::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::hybridization::CartesianSampler::set_bbmove ( bool  bbmove_in)
inline

References bbmove_.

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

References fa_scorefxn_.

void protocols::hybridization::CartesianSampler::set_frag_sizes ( utility::vector1< core::Size > const &  frag_sizes_in)
inline

References frag_sizes_.

void protocols::hybridization::CartesianSampler::set_fullatom ( bool  fullatom_in)
inline

References fullatom_.

void protocols::hybridization::CartesianSampler::set_mc_scorefunction ( core::scoring::ScoreFunctionOP  scorefxn_in)
inline

References mc_scorefxn_.

void protocols::hybridization::CartesianSampler::set_ncycles ( core::Size  ncycles_in)
inline

References ncycles_.

void protocols::hybridization::CartesianSampler::set_nfrags ( core::Size  nfrags_in)
inline

References nfrags_.

void protocols::hybridization::CartesianSampler::set_nminsteps ( core::Size  nminsteps_in)
inline

References nminsteps_.

void protocols::hybridization::CartesianSampler::set_overlap ( core::Size  overlap_in)
inline

References overlap_.

void protocols::hybridization::CartesianSampler::set_restore_csts ( bool  restore_csts_in)
inline

References restore_csts_.

void protocols::hybridization::CartesianSampler::set_rms_cutoff ( core::Real  rms_cutoff_in)
inline

References rms_cutoff_.

void protocols::hybridization::CartesianSampler::set_scorefunction ( core::scoring::ScoreFunctionOP  scorefxn_in)
inline

References scorefxn_.

void protocols::hybridization::CartesianSampler::set_strategy ( std::string  strategy_in)
inline
void protocols::hybridization::CartesianSampler::set_temp ( core::Real  temp_in)
inline

References temp_.

void protocols::hybridization::CartesianSampler::set_userpos ( core::select::residue_selector::ResidueSelectorCOP const &  user_pos_in)
inline
void protocols::hybridization::CartesianSampler::update_fragment_library_pointers ( )
protected

Member Data Documentation

core::Real protocols::hybridization::CartesianSampler::automode_scorecut_
private
bool protocols::hybridization::CartesianSampler::bbmove_
private

Referenced by set_bbmove().

bool protocols::hybridization::CartesianSampler::cumulate_prob_
private
bool protocols::hybridization::CartesianSampler::debug_
private
bool protocols::hybridization::CartesianSampler::dump_pdb_
private
std::string protocols::hybridization::CartesianSampler::dump_pdb_tag_
private
bool protocols::hybridization::CartesianSampler::exclude_residues_
private
core::scoring::ScoreFunctionOP protocols::hybridization::CartesianSampler::fa_scorefxn_
private

Referenced by set_fa_scorefunction().

char protocols::hybridization::CartesianSampler::force_ss_
private
utility::vector1<numeric::random::WeightedSampler> protocols::hybridization::CartesianSampler::frag_bias_
private
utility::vector1<core::Size> protocols::hybridization::CartesianSampler::frag_sizes_
private

Referenced by set_frag_sizes().

utility::vector1<std::string> protocols::hybridization::CartesianSampler::fragment_bias_strategies_
private

Referenced by set_strategy().

utility::vector1<core::fragment::FragSetOP> protocols::hybridization::CartesianSampler::fragments_
private
bool protocols::hybridization::CartesianSampler::freeze_endpoints_
private
bool protocols::hybridization::CartesianSampler::fullatom_
private

Referenced by set_fullatom().

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

Referenced by set_mc_scorefunction().

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

Referenced by set_ncycles().

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

Referenced by set_nfrags().

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

Referenced by set_nminsteps().

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

Referenced by set_overlap().

bool protocols::hybridization::CartesianSampler::recover_low_
private
core::Real protocols::hybridization::CartesianSampler::ref_cst_maxdist_
private
core::Real protocols::hybridization::CartesianSampler::ref_cst_weight_
private
core::pose::Pose protocols::hybridization::CartesianSampler::ref_model_
private
core::select::residue_selector::ResidueSelectorCOP protocols::hybridization::CartesianSampler::residues_to_exclude_
private
core::select::residue_selector::ResidueSelectorCOP protocols::hybridization::CartesianSampler::residues_to_include_
private
bool protocols::hybridization::CartesianSampler::restore_csts_
private

Referenced by set_restore_csts().

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

Referenced by set_rms_cutoff().

core::Size protocols::hybridization::CartesianSampler::rsd_wdw_to_refine_
private
core::Real protocols::hybridization::CartesianSampler::score_threshold_
private
core::scoring::ScoreFunctionOP protocols::hybridization::CartesianSampler::scorefxn_
private

Referenced by set_scorefunction().

std::string protocols::hybridization::CartesianSampler::selection_bias_
private
core::Real protocols::hybridization::CartesianSampler::temp_
private

Referenced by set_temp().

core::select::residue_selector::ResidueSelectorCOP protocols::hybridization::CartesianSampler::user_pos_
private

Referenced by set_userpos().

int protocols::hybridization::CartesianSampler::wdw_to_freeze_
private

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