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

#include <CartesianHybridize.hh>

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 setup_for_parser ()
 
void apply (core::pose::Pose &pose)
 
void set_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_nofragbias (bool nofragbias_in)
 
void set_skip_long_min (bool skip_long_min_in)
 
std::string get_name () const
 Each derived class must specify its name. The class name. 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...
 
virtual void parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &, Filters_map const &, Movers_map const &, 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...
 

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

HybridizeSetupOP hybridize_setup_
 
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 nofragbias_
 
bool skip_long_min_
 
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 bonds_scorefxn_
 
core::scoring::ScoreFunctionOP nocst_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::CartesianHybridize::CartesianHybridize ( )
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 pose)
virtual

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, action, align_templates_to_pose_, protocols::moves::Mover::apply(), apply_frag(), apply_frame(), core::conformation::Residue::atom(), core::scoring::atom_pair_constraint, bonds_scorefxn_, core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::cart_bonded_torsion, corrections::score::cenrot, core::chemical::CENTROID, core::chemical::CENTROID_ROT, core::pose::Pose::conformation(), cst_weight, core::pose::Pose::data(), numeric::xyzVector< class >::distance(), core::pose::Pose::fold_tree(), protocols::hybridization::get_num_residues_nonvirt(), basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), hybridize_setup_, increase_cycles_, core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), library_, linmin_only_, lowres_scorefxn_, core::pose::symmetry::make_symmetric_movemap(), core::optimization::MinimizerOptions::max_iter(), max_poses, mc, min_scorefxn_, ncycles_, no_global_frame_, nocst_scorefxn_, nofragbias_, nres, ntrials, option, options, pack_rotamers(), core::pack::task::TaskFactory::push_back(), numeric::random::random_range(), core::pose::Pose::residue(), residue_sample_abinitio_, residue_sample_template_, core::pose::Pose::residue_type(), runtime_assert, seqfrags_only_, protocols::hybridization::TemplateHistory::set(), core::kinematics::MoveMap::set_bb(), setup_for_parser(), skip_long_min_, cm::hybridize::stage2_temperature, protocols::loops::start, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), template_contigs_, templates_, core::pose::Pose::total_residue(), protocols::hybridization::TR, numeric::random::uniform(), 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
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 CartesianHybridize().

protocols::moves::MoverOP protocols::hybridization::CartesianHybridize::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 CartesianHybridize().

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

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

Implements protocols::moves::Mover.

void protocols::hybridization::CartesianHybridize::init ( void  )
void protocols::hybridization::CartesianHybridize::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
filters::Filters_map const &  filters,
moves::Movers_map const &  movers,
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 align_templates_to_pose_, core::pack::task::ResidueLevelTask::being_designed(), core::pack::task::ResidueLevelTask::being_packed(), core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), basic::datacache::DataMap::get(), hybridize_setup_, protocols::rosetta_scripts::parse_task_operations(), residue_sample_abinitio_, residue_sample_template_, core::pack::task::PackerTask::residue_task(), set_cartfrag_overlap(), set_increase_cycles(), set_linmin_only(), set_no_global_frame(), set_scorefunction(), and utility_exit_with_message.

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

Referenced by parse_my_tag().

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

Referenced by parse_my_tag().

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

Referenced by parse_my_tag().

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

Referenced by parse_my_tag().

void protocols::hybridization::CartesianHybridize::set_nofragbias ( bool  nofragbias_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
void protocols::hybridization::CartesianHybridize::set_skip_long_min ( bool  skip_long_min_in)
inline
void protocols::hybridization::CartesianHybridize::setup_for_parser ( )

Member Data Documentation

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

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

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

Referenced by apply(), and set_scorefunction().

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

Referenced by apply_frame(), and init().

core::fragment::FragSetOP protocols::hybridization::CartesianHybridize::fragments9_
private
HybridizeSetupOP protocols::hybridization::CartesianHybridize::hybridize_setup_
private
core::Real protocols::hybridization::CartesianHybridize::increase_cycles_
private

Referenced by apply(), and init().

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

Referenced by apply(), and init().

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

Referenced by apply(), and set_scorefunction().

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

Referenced by apply(), and set_scorefunction().

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

Referenced by apply().

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

Referenced by apply(), and init().

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

Referenced by apply(), and set_scorefunction().

bool protocols::hybridization::CartesianHybridize::nofragbias_
private

Referenced by apply(), and init().

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

Referenced by apply(), and parse_my_tag().

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

Referenced by apply(), and parse_my_tag().

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

Referenced by apply(), and init().

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

Referenced by apply(), and init().

utility::vector1< protocols::loops::Loops > protocols::hybridization::CartesianHybridize::template_contigs_
private
utility::vector1< core::Real > protocols::hybridization::CartesianHybridize::template_wts_
private
utility::vector1< core::pose::PoseOP > protocols::hybridization::CartesianHybridize::templates_
private

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