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protocols::hybridization::CartesianHybridize Class Reference

#include <CartesianHybridize.hh>

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

 CartesianHybridize ()
 
 CartesianHybridize (utility::vector1< core::pose::PoseOP > const &templates_in, utility::vector1< core::Real > const &template_wts_in, utility::vector1< protocols::loops::Loops > const &template_chunks_in, utility::vector1< protocols::loops::Loops > const &template_contigs_in, core::fragment::FragSetOP fragments9_in)
 
void init ()
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void set_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)
 
void set_min_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)
 
void set_pack_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)
 
void set_increase_cycles (core::Real increase_cycles_in)
 
void set_no_global_frame (bool no_global_frame_in)
 
void set_linmin_only (bool linmin_only_in)
 
void set_cartfrag_overlap (core::Size cartfrag_overlap_in)
 
void set_seqfrags_only (bool seqfrags_only_in)
 
void set_skip_long_min (bool skip_long_min_in)
 
void set_cenrot (bool cenrot_in)
 
void set_temperature (core::Real temp_in)
 
void set_fragment_probs (core::Real prob, core::Real randprob)
 
void set_max_insertion (int max_in)
 
void set_per_residue_controls (utility::vector1< bool > const &residue_sample_template_in, utility::vector1< bool > const &residue_sample_abinitio_in)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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...
 
- 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 

Protected Member Functions

void apply_frag (core::pose::Pose &pose, core::pose::Pose &templ, protocols::loops::Loop &frag, bool superpose=true)
 
void apply_frame (core::pose::Pose &pose, core::fragment::Frame &frame)
 
- 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

bool align_templates_to_pose_
 
core::Real increase_cycles_
 
core::Size ncycles_
 
core::Size cartfrag_overlap_
 
bool no_global_frame_
 
bool linmin_only_
 
bool seqfrags_only_
 
bool skip_long_min_
 
bool cenrot_
 
core::Real temperature_
 
int max_contig_insertion_
 
core::Real fragprob_
 
core::Real randfragprob_
 
utility::vector1
< core::pose::PoseOP
templates_
 
utility::vector1< core::Realtemplate_wts_
 
utility::vector1
< protocols::loops::Loops
template_contigs_
 
core::fragment::FragSetOP fragments9_
 
boost::unordered_map
< core::Size,
core::fragment::Frame
library_
 
utility::vector1< boolresidue_sample_template_
 
utility::vector1< boolresidue_sample_abinitio_
 
core::scoring::ScoreFunctionOP lowres_scorefxn_
 
core::scoring::ScoreFunctionOP min_scorefxn_
 
core::scoring::ScoreFunctionOP cenrot_repack_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
 
- 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::CartesianHybridize::CartesianHybridize ( )

References init().

protocols::hybridization::CartesianHybridize::CartesianHybridize ( utility::vector1< core::pose::PoseOP > const &  templates_in,
utility::vector1< core::Real > const &  template_wts_in,
utility::vector1< protocols::loops::Loops > const &  template_chunks_in,
utility::vector1< protocols::loops::Loops > const &  template_contigs_in,
core::fragment::FragSetOP  fragments9_in 
)

Member Function Documentation

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

Main Method.

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, apply_frag(), apply_frame(), core::conformation::Residue::atom(), core::scoring::atom_pair_constraint, core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::cart_bonded_torsion, cenrot_, cenrot_repack_scorefxn_, core::chemical::CENTROID, core::chemical::CENTROID_ROT, core::pose::Pose::conformation(), core::pose::Pose::data(), core::pose::Pose::fold_tree(), fragprob_, protocols::hybridization::get_num_residues_nonvirt(), increase_cycles_, core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_protein(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), library_, linmin_only_, lowres_scorefxn_, core::pose::symmetry::make_symmetric_movemap(), protocols::mean_field::max(), max_contig_insertion_, core::optimization::MinimizerOptions::max_iter(), protocols::mean_field::min(), min_scorefxn_, ncycles_, no_global_frame_, core::pack::pack_rotamers(), randfragprob_, core::pose::Pose::residue(), residue_sample_abinitio_, residue_sample_template_, core::pose::Pose::residue_type(), seqfrags_only_, protocols::hybridization::TemplateHistory::set(), core::kinematics::MoveMap::set_bb(), core::pose::Pose::size(), skip_long_min_, protocols::loops::start, protocols::loops::stop, temperature_, template_contigs_, templates_, protocols::hybridization::TR(), core::scoring::vdw, and core::conformation::Atom::xyz().

void protocols::hybridization::CartesianHybridize::apply_frag ( core::pose::Pose pose,
core::pose::Pose templ,
protocols::loops::Loop frag,
bool  superpose = true 
)
protected
void protocols::hybridization::CartesianHybridize::apply_frame ( core::pose::Pose pose,
core::fragment::Frame frame 
)
protected
protocols::moves::MoverOP protocols::hybridization::CartesianHybridize::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.

protocols::moves::MoverOP protocols::hybridization::CartesianHybridize::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::CartesianHybridize::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

void protocols::hybridization::CartesianHybridize::init ( void  )
void protocols::hybridization::CartesianHybridize::set_cartfrag_overlap ( core::Size  cartfrag_overlap_in)
inline

References cartfrag_overlap_.

void protocols::hybridization::CartesianHybridize::set_cenrot ( bool  cenrot_in)
inline

References cenrot_.

void protocols::hybridization::CartesianHybridize::set_fragment_probs ( core::Real  prob,
core::Real  randprob 
)
inline

References fragprob_, and randfragprob_.

void protocols::hybridization::CartesianHybridize::set_increase_cycles ( core::Real  increase_cycles_in)
inline

References increase_cycles_.

void protocols::hybridization::CartesianHybridize::set_linmin_only ( bool  linmin_only_in)
inline

References linmin_only_.

void protocols::hybridization::CartesianHybridize::set_max_insertion ( int  max_in)
inline

References max_contig_insertion_.

void protocols::hybridization::CartesianHybridize::set_min_scorefunction ( core::scoring::ScoreFunctionOP  scorefxn_in)

References min_scorefxn_.

Referenced by init().

void protocols::hybridization::CartesianHybridize::set_no_global_frame ( bool  no_global_frame_in)
inline

References no_global_frame_.

void protocols::hybridization::CartesianHybridize::set_pack_scorefunction ( core::scoring::ScoreFunctionOP  scorefxn_in)

References cenrot_repack_scorefxn_.

Referenced by init().

void protocols::hybridization::CartesianHybridize::set_per_residue_controls ( utility::vector1< bool > const &  residue_sample_template_in,
utility::vector1< bool > const &  residue_sample_abinitio_in 
)
inline
void protocols::hybridization::CartesianHybridize::set_scorefunction ( core::scoring::ScoreFunctionOP  scorefxn_in)
void protocols::hybridization::CartesianHybridize::set_seqfrags_only ( bool  seqfrags_only_in)
inline

References seqfrags_only_.

void protocols::hybridization::CartesianHybridize::set_skip_long_min ( bool  skip_long_min_in)
inline

References skip_long_min_.

void protocols::hybridization::CartesianHybridize::set_temperature ( core::Real  temp_in)
inline

References temperature_.

Member Data Documentation

bool protocols::hybridization::CartesianHybridize::align_templates_to_pose_
private

Referenced by init().

core::Size protocols::hybridization::CartesianHybridize::cartfrag_overlap_
private
bool protocols::hybridization::CartesianHybridize::cenrot_
private

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

core::scoring::ScoreFunctionOP protocols::hybridization::CartesianHybridize::cenrot_repack_scorefxn_
private
core::fragment::FragSetOP protocols::hybridization::CartesianHybridize::fragments9_
private

Referenced by CartesianHybridize().

core::Real protocols::hybridization::CartesianHybridize::fragprob_
private

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

core::Real protocols::hybridization::CartesianHybridize::increase_cycles_
private

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

boost::unordered_map<core::Size, core::fragment::Frame> protocols::hybridization::CartesianHybridize::library_
private

Referenced by apply(), and CartesianHybridize().

bool protocols::hybridization::CartesianHybridize::linmin_only_
private

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

core::scoring::ScoreFunctionOP protocols::hybridization::CartesianHybridize::lowres_scorefxn_
private

Referenced by apply(), and set_scorefunction().

int protocols::hybridization::CartesianHybridize::max_contig_insertion_
private

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

core::scoring::ScoreFunctionOP protocols::hybridization::CartesianHybridize::min_scorefxn_
private
core::Size protocols::hybridization::CartesianHybridize::ncycles_
private

Referenced by apply().

bool protocols::hybridization::CartesianHybridize::no_global_frame_
private

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

core::Real protocols::hybridization::CartesianHybridize::randfragprob_
private

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

utility::vector1<bool> protocols::hybridization::CartesianHybridize::residue_sample_abinitio_
private

Referenced by apply(), and set_per_residue_controls().

utility::vector1<bool> protocols::hybridization::CartesianHybridize::residue_sample_template_
private

Referenced by apply(), and set_per_residue_controls().

bool protocols::hybridization::CartesianHybridize::seqfrags_only_
private

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

bool protocols::hybridization::CartesianHybridize::skip_long_min_
private

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

core::Real protocols::hybridization::CartesianHybridize::temperature_
private

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

utility::vector1< protocols::loops::Loops > protocols::hybridization::CartesianHybridize::template_contigs_
private

Referenced by apply(), and CartesianHybridize().

utility::vector1< core::Real > protocols::hybridization::CartesianHybridize::template_wts_
private

Referenced by CartesianHybridize().

utility::vector1< core::pose::PoseOP > protocols::hybridization::CartesianHybridize::templates_
private

Referenced by apply(), and CartesianHybridize().


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