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protocols::electron_density::DockIntoDensityMover Class Reference

The workhorse. More...

#include <DockIntoDensityMover.hh>

Inheritance diagram for protocols::electron_density::DockIntoDensityMover:
Inheritance graph
[legend]

Public Member Functions

 DockIntoDensityMover ()
 
void setDelR (core::Real delR)
 
void setNRsteps (core::Real nRsteps)
 
void setB (core::Real B)
 
void setTopN (core::Real topNtrans, core::Real topNfilter, core::Real topNfinal)
 
void setGridStep (core::Size gridStep)
 
void setDoRefine (bool do_refine)
 
void setMinDist (core::Real mindist)
 
void setMinBackbone (bool min_backbone)
 
void setNCyc (core::Size ncyc)
 
void setOutputSilent (std::string silent_out)
 
void setClusterRadius (core::Real cluster_radius)
 
void setPointRadius (core::Real point_radius)
 
void setTag (std::string tag)
 
void setFragDens (core::Real fragDens)
 
void setPassThrough (bool passthrough)
 
void setNormScores (bool normscores)
 
void setClusterOversamp (core::Size cluster_oversample)
 
void setMaxRotPerTrans (core::Size max_rot_per_trans)
 
void setSymminfo (DensitySymmInfo const &symminfo)
 
void setConvoluteSingleR (bool convolute_single_residue)
 
void setLaplacianOffset (core::Real laplacian_offset)
 
void predefine_search (utility::vector1< numeric::xyzVector< core::Real > > &pts_in)
 
void setCenterOnMiddleCA (bool val)
 
void setNative (core::pose::PoseOP native)
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void apply_multi (utility::vector1< core::pose::PoseOP > &poses)
 
core::Real get_radius (core::pose::Pose const &pose, numeric::xyzVector< core::Real > &com)
 
void apply_transform (core::pose::Pose &pose, RBfitResult const &transform)
 
void get_spectrum (core::pose::Pose const &pose, utility::vector1< core::Real > &pose_1dspec)
 
void map_from_spectrum (utility::vector1< core::Real > const &pose_1dspec, ObjexxFCL::FArray3D< core::Real > &rot)
 
void poseSphericalSamples (core::pose::Pose const &pose, ObjexxFCL::FArray3D< core::Real > &sigR)
 step 0: map pose to spherically sampled density More...
 
void select_points (core::pose::Pose &pose)
 step 1: select points over which to search (saved in class variable) More...
 
void density_grid_search (core::Size pose_idx, core::pose::Pose &pose, RBfitResultDB &results)
 step 2: perform the grid search, storing these results More...
 
void do_refinement (utility::vector1< core::pose::PoseOP > const &poses, RBfitResultDB &results_in, RefinementResultDB &results_out)
 step 3: local refinement of each hit empties the results_in DB More...
 
void do_filter (utility::vector1< core::pose::PoseOP > const &poses, RBfitResultDB &results_in, bool rescore)
 step 4: filter similar hits (non-refined) More...
 
void do_filter (RBfitResultDB &results_in)
 step 4: (fast) filter hits using rotation only More...
 
void do_filter (RefinementResultDB &results_in)
 step 4: filter similar hits (refined) More...
 
void print_best_rms (core::pose::Pose const &pose, RBfitResultDB const &results)
 debugging: add some stats More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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...
 

Private Attributes

core::Size topNtrans_
 
core::Size topNfilter_
 
core::Size topNfinal_
 
core::Real delR_
 
core::Real dens_wt_
 
core::Real cluster_radius_
 
core::Real point_radius_
 
core::Real fragDens_
 
core::Real mindist_
 
core::Real laplacian_offset_
 
core::Size B_
 
core::Size nRsteps_
 
core::Size gridStep_
 
bool center_on_middle_ca_
 
bool points_defined_
 
bool convolute_single_residue_
 
DensitySymmInfo symminfo_
 
core::Size cluster_oversample_
 
core::Size max_rot_per_trans_
 
bool do_refine_
 
bool min_backbone_
 
core::Size ncyc_
 
std::string silent_
 
std::string tag_
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
points_to_search_
 
bool normscores_
 
bool passthrough_
 
core::pose::PoseOP native_
 
numeric::xyzVector< core::Realnative_com_
 

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...
 
- 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...
 

Detailed Description

The workhorse.

Constructor & Destructor Documentation

protocols::electron_density::DockIntoDensityMover::DockIntoDensityMover ( )
inline

Member Function Documentation

void protocols::electron_density::DockIntoDensityMover::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References apply_multi().

void protocols::electron_density::DockIntoDensityMover::apply_multi ( utility::vector1< core::pose::PoseOP > &  poses)
void protocols::electron_density::DockIntoDensityMover::apply_transform ( core::pose::Pose pose,
RBfitResult const &  transform 
)
void protocols::electron_density::DockIntoDensityMover::density_grid_search ( core::Size  pose_idx,
core::pose::Pose pose,
RBfitResultDB results 
)
void protocols::electron_density::DockIntoDensityMover::do_filter ( utility::vector1< core::pose::PoseOP > const &  poses,
RBfitResultDB results_in,
bool  rescore 
)
void protocols::electron_density::DockIntoDensityMover::do_filter ( RBfitResultDB results_in)
void protocols::electron_density::DockIntoDensityMover::do_filter ( RefinementResultDB results_in)
void protocols::electron_density::DockIntoDensityMover::do_refinement ( utility::vector1< core::pose::PoseOP > const &  poses,
RBfitResultDB results_in,
RefinementResultDB results_out 
)
std::string protocols::electron_density::DockIntoDensityMover::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

core::Real protocols::electron_density::DockIntoDensityMover::get_radius ( core::pose::Pose const &  pose,
numeric::xyzVector< core::Real > &  com 
)
void protocols::electron_density::DockIntoDensityMover::get_spectrum ( core::pose::Pose const &  pose,
utility::vector1< core::Real > &  pose_1dspec 
)
void protocols::electron_density::DockIntoDensityMover::map_from_spectrum ( utility::vector1< core::Real > const &  pose_1dspec,
ObjexxFCL::FArray3D< core::Real > &  rot 
)
void protocols::electron_density::DockIntoDensityMover::poseSphericalSamples ( core::pose::Pose const &  pose,
ObjexxFCL::FArray3D< core::Real > &  sigR 
)
void protocols::electron_density::DockIntoDensityMover::predefine_search ( utility::vector1< numeric::xyzVector< core::Real > > &  pts_in)
void protocols::electron_density::DockIntoDensityMover::print_best_rms ( core::pose::Pose const &  pose,
RBfitResultDB const &  results 
)
void protocols::electron_density::DockIntoDensityMover::select_points ( core::pose::Pose pose)
void protocols::electron_density::DockIntoDensityMover::setB ( core::Real  B)
inline

References core::chemical::element::B, and B_.

void protocols::electron_density::DockIntoDensityMover::setCenterOnMiddleCA ( bool  val)
inline
void protocols::electron_density::DockIntoDensityMover::setClusterOversamp ( core::Size  cluster_oversample)
inline

References cluster_oversample_.

void protocols::electron_density::DockIntoDensityMover::setClusterRadius ( core::Real  cluster_radius)
inline

References cluster_radius_.

void protocols::electron_density::DockIntoDensityMover::setConvoluteSingleR ( bool  convolute_single_residue)
inline
void protocols::electron_density::DockIntoDensityMover::setDelR ( core::Real  delR)
inline

References delR_.

void protocols::electron_density::DockIntoDensityMover::setDoRefine ( bool  do_refine)
inline

References do_refine_.

void protocols::electron_density::DockIntoDensityMover::setFragDens ( core::Real  fragDens)
inline

References fragDens_.

void protocols::electron_density::DockIntoDensityMover::setGridStep ( core::Size  gridStep)
inline

References gridStep_.

void protocols::electron_density::DockIntoDensityMover::setLaplacianOffset ( core::Real  laplacian_offset)
inline

References laplacian_offset_.

void protocols::electron_density::DockIntoDensityMover::setMaxRotPerTrans ( core::Size  max_rot_per_trans)
inline

References max_rot_per_trans_.

void protocols::electron_density::DockIntoDensityMover::setMinBackbone ( bool  min_backbone)
inline

References min_backbone_.

void protocols::electron_density::DockIntoDensityMover::setMinDist ( core::Real  mindist)
inline

References mindist_.

void protocols::electron_density::DockIntoDensityMover::setNative ( core::pose::PoseOP  native)
void protocols::electron_density::DockIntoDensityMover::setNCyc ( core::Size  ncyc)
inline

References ncyc_.

void protocols::electron_density::DockIntoDensityMover::setNormScores ( bool  normscores)
inline

References normscores_.

void protocols::electron_density::DockIntoDensityMover::setNRsteps ( core::Real  nRsteps)
inline

References nRsteps_.

void protocols::electron_density::DockIntoDensityMover::setOutputSilent ( std::string  silent_out)
inline

References silent_.

void protocols::electron_density::DockIntoDensityMover::setPassThrough ( bool  passthrough)
inline

References passthrough_.

void protocols::electron_density::DockIntoDensityMover::setPointRadius ( core::Real  point_radius)
inline

References point_radius_.

void protocols::electron_density::DockIntoDensityMover::setSymminfo ( DensitySymmInfo const &  symminfo)
inline

References symminfo_.

void protocols::electron_density::DockIntoDensityMover::setTag ( std::string  tag)
inline

References tag_.

void protocols::electron_density::DockIntoDensityMover::setTopN ( core::Real  topNtrans,
core::Real  topNfilter,
core::Real  topNfinal 
)
inline

References topNfilter_, topNfinal_, and topNtrans_.

Member Data Documentation

core::Size protocols::electron_density::DockIntoDensityMover::B_
private
bool protocols::electron_density::DockIntoDensityMover::center_on_middle_ca_
private
core::Size protocols::electron_density::DockIntoDensityMover::cluster_oversample_
private

Referenced by apply_multi(), and setClusterOversamp().

core::Real protocols::electron_density::DockIntoDensityMover::cluster_radius_
private
bool protocols::electron_density::DockIntoDensityMover::convolute_single_residue_
private
core::Real protocols::electron_density::DockIntoDensityMover::delR_
private
core::Real protocols::electron_density::DockIntoDensityMover::dens_wt_
private

Referenced by do_refinement().

bool protocols::electron_density::DockIntoDensityMover::do_refine_
private

Referenced by do_refinement(), and setDoRefine().

core::Real protocols::electron_density::DockIntoDensityMover::fragDens_
private

Referenced by get_spectrum(), and setFragDens().

core::Size protocols::electron_density::DockIntoDensityMover::gridStep_
private

Referenced by select_points(), and setGridStep().

core::Real protocols::electron_density::DockIntoDensityMover::laplacian_offset_
private
core::Size protocols::electron_density::DockIntoDensityMover::max_rot_per_trans_
private
bool protocols::electron_density::DockIntoDensityMover::min_backbone_
private

Referenced by do_refinement(), and setMinBackbone().

core::Real protocols::electron_density::DockIntoDensityMover::mindist_
private

Referenced by setMinDist().

core::pose::PoseOP protocols::electron_density::DockIntoDensityMover::native_
private
numeric::xyzVector< core::Real > protocols::electron_density::DockIntoDensityMover::native_com_
private
core::Size protocols::electron_density::DockIntoDensityMover::ncyc_
private

Referenced by do_refinement(), and setNCyc().

bool protocols::electron_density::DockIntoDensityMover::normscores_
private
core::Size protocols::electron_density::DockIntoDensityMover::nRsteps_
private
bool protocols::electron_density::DockIntoDensityMover::passthrough_
private

Referenced by apply_multi(), and setPassThrough().

core::Real protocols::electron_density::DockIntoDensityMover::point_radius_
private

Referenced by select_points(), and setPointRadius().

bool protocols::electron_density::DockIntoDensityMover::points_defined_
private

Referenced by predefine_search(), and select_points().

utility::vector1< numeric::xyzVector<core::Real> > protocols::electron_density::DockIntoDensityMover::points_to_search_
private
std::string protocols::electron_density::DockIntoDensityMover::silent_
private

Referenced by apply_multi(), and setOutputSilent().

DensitySymmInfo protocols::electron_density::DockIntoDensityMover::symminfo_
private
std::string protocols::electron_density::DockIntoDensityMover::tag_
private

Referenced by apply_multi(), and setTag().

core::Size protocols::electron_density::DockIntoDensityMover::topNfilter_
private

Referenced by apply_multi(), and setTopN().

core::Size protocols::electron_density::DockIntoDensityMover::topNfinal_
private

Referenced by apply_multi(), and setTopN().

core::Size protocols::electron_density::DockIntoDensityMover::topNtrans_
private

3 stages, each with different filter numbers: 1: select points 2: select best by spharm rotation 3: select best after refinement

Referenced by select_points(), and setTopN().


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