Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::hybridization::CartesianHybridize Class Reference

#include <CartesianHybridize.hh>

Inheritance diagram for protocols::hybridization::CartesianHybridize:
Inheritance graph

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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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::PoseOPtemplates_
utility::vector1< core::Realtemplate_wts_
utility::vector1< protocols::loops::Loopstemplate_contigs_
core::fragment::FragSetOP fragments9_
boost::unordered_map< core::Size, core::fragment::Framelibrary_
utility::vector1< bool > residue_sample_template_
utility::vector1< bool > residue_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

◆ CartesianHybridize() [1/2]

protocols::hybridization::CartesianHybridize::CartesianHybridize ( )

References init().

◆ CartesianHybridize() [2/2]

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

◆ apply()

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

Main Method.

Implements protocols::moves::Mover.

Reimplemented in protocols::rbsegment_relax::ConfChangeMover.

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::scoring::ScoreFunctionFactory::create_score_function(), 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(), core::optimization::CartesianMinimizer::run(), seqfrags_only_, protocols::hybridization::TemplateHistory::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), 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().

◆ apply_frag()

void protocols::hybridization::CartesianHybridize::apply_frag ( core::pose::Pose pose,
core::pose::Pose templ,
protocols::loops::Loop frag,
bool  superpose = true 

◆ apply_frame()

void protocols::hybridization::CartesianHybridize::apply_frame ( core::pose::Pose pose,
core::fragment::Frame frame 

◆ clone()

protocols::moves::MoverOP protocols::hybridization::CartesianHybridize::clone ( ) const

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.

Reimplemented in protocols::rbsegment_relax::ConfChangeMover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::hybridization::CartesianHybridize::fresh_instance ( ) const

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.

◆ get_name()

std::string protocols::hybridization::CartesianHybridize::get_name ( ) const

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

Implements protocols::moves::Mover.

Reimplemented in protocols::rbsegment_relax::ConfChangeMover.

◆ init()

void protocols::hybridization::CartesianHybridize::init ( void  )

◆ set_cartfrag_overlap()

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

References cartfrag_overlap_.

◆ set_cenrot()

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

References cenrot_.

◆ set_fragment_probs()

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

References fragprob_, and randfragprob_.

◆ set_increase_cycles()

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

References increase_cycles_.

◆ set_linmin_only()

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

References linmin_only_.

◆ set_max_insertion()

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

References max_contig_insertion_.

◆ set_min_scorefunction()

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

References min_scorefxn_.

◆ set_no_global_frame()

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

References no_global_frame_.

◆ set_pack_scorefunction()

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

◆ set_per_residue_controls()

void protocols::hybridization::CartesianHybridize::set_per_residue_controls ( utility::vector1< bool > const &  residue_sample_template_in,
utility::vector1< bool > const &  residue_sample_abinitio_in 

◆ set_scorefunction()

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

◆ set_seqfrags_only()

void protocols::hybridization::CartesianHybridize::set_seqfrags_only ( bool  seqfrags_only_in)

References seqfrags_only_.

◆ set_skip_long_min()

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

References skip_long_min_.

◆ set_temperature()

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

References temperature_.

Member Data Documentation

◆ align_templates_to_pose_

bool protocols::hybridization::CartesianHybridize::align_templates_to_pose_

Referenced by init().

◆ cartfrag_overlap_

core::Size protocols::hybridization::CartesianHybridize::cartfrag_overlap_

◆ cenrot_

bool protocols::hybridization::CartesianHybridize::cenrot_

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

◆ cenrot_repack_scorefxn_

core::scoring::ScoreFunctionOP protocols::hybridization::CartesianHybridize::cenrot_repack_scorefxn_

◆ fragments9_

core::fragment::FragSetOP protocols::hybridization::CartesianHybridize::fragments9_

Referenced by CartesianHybridize().

◆ fragprob_

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

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

◆ increase_cycles_

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

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

◆ library_

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

Referenced by apply(), and CartesianHybridize().

◆ linmin_only_

bool protocols::hybridization::CartesianHybridize::linmin_only_

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

◆ lowres_scorefxn_

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

Referenced by apply(), and set_scorefunction().

◆ max_contig_insertion_

int protocols::hybridization::CartesianHybridize::max_contig_insertion_

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

◆ min_scorefxn_

core::scoring::ScoreFunctionOP protocols::hybridization::CartesianHybridize::min_scorefxn_

◆ ncycles_

core::Size protocols::hybridization::CartesianHybridize::ncycles_

Referenced by apply().

◆ no_global_frame_

bool protocols::hybridization::CartesianHybridize::no_global_frame_

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

◆ randfragprob_

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

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

◆ residue_sample_abinitio_

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

Referenced by apply(), and set_per_residue_controls().

◆ residue_sample_template_

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

Referenced by apply(), and set_per_residue_controls().

◆ seqfrags_only_

bool protocols::hybridization::CartesianHybridize::seqfrags_only_

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

◆ skip_long_min_

bool protocols::hybridization::CartesianHybridize::skip_long_min_

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

◆ temperature_

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

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

◆ template_contigs_

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

Referenced by apply(), and CartesianHybridize().

◆ template_wts_

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

Referenced by CartesianHybridize().

◆ templates_

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

Referenced by apply(), and CartesianHybridize().

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