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protocols::protein_interface_design::movers::MapHotspot Class Reference

#include <MapHotspot.hh>

Inheritance diagram for protocols::protein_interface_design::movers::MapHotspot:
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Collaboration diagram for protocols::protein_interface_design::movers::MapHotspot:
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Public Types

typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef core::pose::Pose Pose
 
typedef core::conformation::Residue Residue
 
typedef
core::pack::rotamer_set::RotamerSetOP 
RotamerSetOP
 
typedef std::map< core::Size,
protocols::filters::FilterCOP
SizeFilter_map
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 

Public Member Functions

 MapHotspot ()
 
void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void GenerateMap (core::pose::Pose const &start_pose, core::pose::Pose &curr_pose, core::Size const jump_number)
 this is the recursive function where the functionality takes place More...
 
void MinimizeHotspots (core::pose::Pose &pose)
 minimizes rb and sc dofs for all of the hotspots More...
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void output_pose (core::pose::Pose const &pose) const
 
RotamerSetOP create_rotamer_set (core::pose::Pose const &, core::Size const hotspot_resnum, core::Size const explosion) const
 
virtual ~MapHotspot ()
 
- 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
 
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
 this function informs 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
 this function informs 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
 

Private Attributes

bool clash_check_
 
std::map< core::Size, core::Sizeexplosion_
 
SizeFilter_map jump_filters_
 
std::map< core::Size, std::string > allowed_aas_per_jump_
 
std::map< core::Size,
core::scoring::ScoreFunctionCOP
minimization_scorefxns_
 
std::map< core::Size,
protocols::moves::MoverOP
jump_movers_
 
std::string file_name_prefix_
 

Additional Inherited Members

- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 
- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::MapHotspot::MapHotspot ( )

Referenced by clone().

protocols::protein_interface_design::movers::MapHotspot::~MapHotspot ( )
virtual

Member Function Documentation

void protocols::protein_interface_design::movers::MapHotspot::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::protein_interface_design::movers::MapHotspot::clone ( ) const
inlinevirtual

clone has to be overridden only if clone invocation is expected.

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 MapHotspot().

core::pack::rotamer_set::RotamerSetOP protocols::protein_interface_design::movers::MapHotspot::create_rotamer_set ( core::pose::Pose const &  pose,
core::Size const  hotspot_resnum,
core::Size const  explosion 
) const
protocols::moves::MoverOP protocols::protein_interface_design::movers::MapHotspot::fresh_instance ( ) const
inlinevirtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

void protocols::protein_interface_design::movers::MapHotspot::GenerateMap ( core::pose::Pose const &  start_pose,
core::pose::Pose curr_pose,
core::Size const  jump_number 
)

this is the recursive function where the functionality takes place

A function that recursively goes over all jumps. Within each function, the residue-identities related to that jump are cycled, and for each of those, it iterates over the rotamer set. for each residue type, the best-energy (score12) rotamer, that fulfills all of the user-defined filters is chosen and then we move deeper into the recursion with the next jump. Stopping condition is the final iteration over the final jump at which point a decoy is output, or if no rotamer for the particular residue identity meets all filters (exit with no decoy generation).

References core::chemical::aa_from_oneletter_code(), allowed_aas_per_jump_, core::conformation::Conformation::chain_begin(), protocols::simple_filters::ScoreTypeFilter::compute(), core::pose::Pose::conformation(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), create_rotamer_set(), core::scoring::ScoreFunctionFactory::create_score_function(), explosion_, jump_filters_, jump_movers_, MinimizeHotspots(), core::chemical::name_from_aa(), core::pose::Pose::num_jump(), output_pose(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), rot(), core::scoring::SCORE12_PATCH, core::scoring::STANDARD_WTS, and core::scoring::total_score.

Referenced by apply().

std::string protocols::protein_interface_design::movers::MapHotspot::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

References protocols::protein_interface_design::movers::MapHotspotCreator::mover_name().

void protocols::protein_interface_design::movers::MapHotspot::MinimizeHotspots ( core::pose::Pose pose)
void protocols::protein_interface_design::movers::MapHotspot::output_pose ( core::pose::Pose const &  pose) const
void protocols::protein_interface_design::movers::MapHotspot::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::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 allowed_aas_per_jump_, clash_check_, explosion_, file_name_prefix_, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), jump_filters_, jump_movers_, minimization_scorefxns_, and core::pose::Pose::num_jump().

Member Data Documentation

std::map< core::Size, std::string > protocols::protein_interface_design::movers::MapHotspot::allowed_aas_per_jump_
private

Referenced by GenerateMap(), and parse_my_tag().

bool protocols::protein_interface_design::movers::MapHotspot::clash_check_
private

Referenced by parse_my_tag().

std::map< core::Size, core::Size > protocols::protein_interface_design::movers::MapHotspot::explosion_
private

Referenced by GenerateMap(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::MapHotspot::file_name_prefix_
private

Referenced by output_pose(), and parse_my_tag().

SizeFilter_map protocols::protein_interface_design::movers::MapHotspot::jump_filters_
private

Referenced by GenerateMap(), and parse_my_tag().

std::map< core::Size, protocols::moves::MoverOP > protocols::protein_interface_design::movers::MapHotspot::jump_movers_
private

Referenced by GenerateMap(), and parse_my_tag().

std::map< core::Size, core::scoring::ScoreFunctionCOP > protocols::protein_interface_design::movers::MapHotspot::minimization_scorefxns_
private

Referenced by MinimizeHotspots(), and parse_my_tag().


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