Rosetta 3.4
Public Types | Public Member Functions
protocols::protein_interface_design::movers::MapHotspot Class Reference

#include <MapHotspot.hh>

Inheritance diagram for protocols::protein_interface_design::movers::MapHotspot:
Inheritance graph
[legend]
Collaboration diagram for protocols::protein_interface_design::movers::MapHotspot:
Collaboration graph
[legend]

List of all members.

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 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.
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
void MinimizeHotspots (core::pose::Pose &pose)
 minimizes rb and sc dofs for all of the hotspots
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.
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
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).
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 ()

Member Typedef Documentation

Reimplemented from protocols::moves::Mover.


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 [inline, virtual]

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 [inline, virtual]

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(), 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(), 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)

minimizes rb and sc dofs for all of the hotspots

function for minimizing the interface

References core::pose::Pose::fold_tree(), protocols::protein_interface_design::make_hotspot_foldtree(), MinimizeInterface(), core::pose::Pose::num_jump(), and core::pose::Pose::total_residue().

Referenced by GenerateMap().

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 protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), and core::pose::Pose::num_jump().


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines