Public Member Functions | Private Attributes | List of all members
protocols::electron_density::DockFragmentsIntoDensityMover Class Reference

The workhorse. More...

#include <DockFragmentsIntoDensityMover.hh>

Inheritance diagram for protocols::electron_density::DockFragmentsIntoDensityMover:
Inheritance graph

Public Member Functions

 DockFragmentsIntoDensityMover ()
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 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)
utility::vector1< core::pose::PoseCOPget_multi_native () const &
utility::vector1< numeric::xyzVector< core::Real > > get_multi_native_com () const
utility::vector1< numeric::xyzVector< core::Real > > get_multi_native_mca () const
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)
void map_from_spectrum (utility::vector1< core::Real > const &pose_1dspec, ObjexxFCL::FArray3D< core::Real > &rot)
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 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 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...

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 passthrough_
core::pose::PoseCOP native_
numeric::xyzVector< core::Realnative_com_
numeric::xyzVector< core::Realnative_middle_ca_

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

◆ DockFragmentsIntoDensityMover()

protocols::electron_density::DockFragmentsIntoDensityMover::DockFragmentsIntoDensityMover ( )

Member Function Documentation

◆ apply()

void protocols::electron_density::DockFragmentsIntoDensityMover::apply ( core::pose::Pose )

Main Method.

Implements protocols::moves::Mover.

References apply_multi().

◆ apply_multi()

void protocols::electron_density::DockFragmentsIntoDensityMover::apply_multi ( utility::vector1< core::pose::PoseOP > &  poses)

◆ do_refinement()

void protocols::electron_density::DockFragmentsIntoDensityMover::do_refinement ( utility::vector1< core::pose::PoseOP > const &  poses,
RBfitResultDB results_in,
RefinementResultDB results_out 

◆ get_multi_native()

utility::vector1< core::pose::PoseCOP > protocols::electron_density::DockFragmentsIntoDensityMover::get_multi_native ( ) const &

References native_.

Referenced by apply_multi().

◆ get_multi_native_com()

utility::vector1< numeric::xyzVector< core::Real > > protocols::electron_density::DockFragmentsIntoDensityMover::get_multi_native_com ( ) const

References native_, and native_com_.

Referenced by apply_multi().

◆ get_multi_native_mca()

utility::vector1< numeric::xyzVector< core::Real > > protocols::electron_density::DockFragmentsIntoDensityMover::get_multi_native_mca ( ) const

References native_, and native_middle_ca_.

Referenced by apply_multi().

◆ get_name()

std::string protocols::electron_density::DockFragmentsIntoDensityMover::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ map_from_spectrum()

void protocols::electron_density::DockFragmentsIntoDensityMover::map_from_spectrum ( utility::vector1< core::Real > const &  pose_1dspec,
ObjexxFCL::FArray3D< core::Real > &  rot 

◆ predefine_search()

void protocols::electron_density::DockFragmentsIntoDensityMover::predefine_search ( utility::vector1< numeric::xyzVector< core::Real > > &  pts_in)

◆ print_best_rms()

void protocols::electron_density::DockFragmentsIntoDensityMover::print_best_rms ( core::pose::Pose const &  pose,
RBfitResultDB const &  results 

◆ setB()

void protocols::electron_density::DockFragmentsIntoDensityMover::setB ( core::Real  B)

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

◆ setCenterOnMiddleCA()

void protocols::electron_density::DockFragmentsIntoDensityMover::setCenterOnMiddleCA ( bool  val)

◆ setClusterOversamp()

void protocols::electron_density::DockFragmentsIntoDensityMover::setClusterOversamp ( core::Size  cluster_oversample)

References cluster_oversample_.

◆ setClusterRadius()

void protocols::electron_density::DockFragmentsIntoDensityMover::setClusterRadius ( core::Real  cluster_radius)

References cluster_radius_.

◆ setConvoluteSingleR()

void protocols::electron_density::DockFragmentsIntoDensityMover::setConvoluteSingleR ( bool  convolute_single_residue)

◆ setDelR()

void protocols::electron_density::DockFragmentsIntoDensityMover::setDelR ( core::Real  delR)

References delR_.

◆ setDoRefine()

void protocols::electron_density::DockFragmentsIntoDensityMover::setDoRefine ( bool  do_refine)

References do_refine_.

◆ setFragDens()

void protocols::electron_density::DockFragmentsIntoDensityMover::setFragDens ( core::Real  fragDens)

References fragDens_.

◆ setGridStep()

void protocols::electron_density::DockFragmentsIntoDensityMover::setGridStep ( core::Size  gridStep)

References gridStep_.

◆ setLaplacianOffset()

void protocols::electron_density::DockFragmentsIntoDensityMover::setLaplacianOffset ( core::Real  laplacian_offset)

References laplacian_offset_.

◆ setMaxRotPerTrans()

void protocols::electron_density::DockFragmentsIntoDensityMover::setMaxRotPerTrans ( core::Size  max_rot_per_trans)

References max_rot_per_trans_.

◆ setMinBackbone()

void protocols::electron_density::DockFragmentsIntoDensityMover::setMinBackbone ( bool  min_backbone)

References min_backbone_.

◆ setMinDist()

void protocols::electron_density::DockFragmentsIntoDensityMover::setMinDist ( core::Real  mindist)

References mindist_.

◆ setNative()

void protocols::electron_density::DockFragmentsIntoDensityMover::setNative ( core::pose::PoseOP  native)

◆ setNCyc()

void protocols::electron_density::DockFragmentsIntoDensityMover::setNCyc ( core::Size  ncyc)

References ncyc_.

◆ setNRsteps()

void protocols::electron_density::DockFragmentsIntoDensityMover::setNRsteps ( core::Real  nRsteps)

References nRsteps_.

◆ setOutputSilent()

void protocols::electron_density::DockFragmentsIntoDensityMover::setOutputSilent ( std::string  silent_out)

References silent_.

◆ setPassThrough()

void protocols::electron_density::DockFragmentsIntoDensityMover::setPassThrough ( bool  passthrough)

References passthrough_.

◆ setPointRadius()

void protocols::electron_density::DockFragmentsIntoDensityMover::setPointRadius ( core::Real  point_radius)

References point_radius_.

◆ setSymminfo()

void protocols::electron_density::DockFragmentsIntoDensityMover::setSymminfo ( DensitySymmInfo const &  symminfo)

References symminfo_.

◆ setTag()

void protocols::electron_density::DockFragmentsIntoDensityMover::setTag ( std::string  tag)

References tag_.

◆ setTopN()

void protocols::electron_density::DockFragmentsIntoDensityMover::setTopN ( core::Real  topNtrans,
core::Real  topNfilter,
core::Real  topNfinal 

References topNfilter_, topNfinal_, and topNtrans_.

Member Data Documentation

◆ B_

core::Size protocols::electron_density::DockFragmentsIntoDensityMover::B_

Referenced by apply_multi(), and setB().

◆ center_on_middle_ca_

bool protocols::electron_density::DockFragmentsIntoDensityMover::center_on_middle_ca_

Referenced by apply_multi(), and setCenterOnMiddleCA().

◆ cluster_oversample_

core::Size protocols::electron_density::DockFragmentsIntoDensityMover::cluster_oversample_

Referenced by apply_multi(), and setClusterOversamp().

◆ cluster_radius_

core::Real protocols::electron_density::DockFragmentsIntoDensityMover::cluster_radius_

Referenced by apply_multi(), and setClusterRadius().

◆ convolute_single_residue_

bool protocols::electron_density::DockFragmentsIntoDensityMover::convolute_single_residue_

Referenced by apply_multi(), and setConvoluteSingleR().

◆ delR_

core::Real protocols::electron_density::DockFragmentsIntoDensityMover::delR_

◆ dens_wt_

core::Real protocols::electron_density::DockFragmentsIntoDensityMover::dens_wt_

Referenced by do_refinement().

◆ do_refine_

bool protocols::electron_density::DockFragmentsIntoDensityMover::do_refine_

Referenced by do_refinement(), and setDoRefine().

◆ fragDens_

core::Real protocols::electron_density::DockFragmentsIntoDensityMover::fragDens_

Referenced by apply_multi(), and setFragDens().

◆ gridStep_

core::Size protocols::electron_density::DockFragmentsIntoDensityMover::gridStep_

Referenced by apply_multi(), and setGridStep().

◆ laplacian_offset_

core::Real protocols::electron_density::DockFragmentsIntoDensityMover::laplacian_offset_

Referenced by apply_multi(), and setLaplacianOffset().

◆ max_rot_per_trans_

core::Size protocols::electron_density::DockFragmentsIntoDensityMover::max_rot_per_trans_

Referenced by apply_multi(), and setMaxRotPerTrans().

◆ min_backbone_

bool protocols::electron_density::DockFragmentsIntoDensityMover::min_backbone_

Referenced by do_refinement(), and setMinBackbone().

◆ mindist_

core::Real protocols::electron_density::DockFragmentsIntoDensityMover::mindist_

Referenced by setMinDist().

◆ native_

core::pose::PoseCOP protocols::electron_density::DockFragmentsIntoDensityMover::native_

◆ native_com_

numeric::xyzVector< core::Real > protocols::electron_density::DockFragmentsIntoDensityMover::native_com_

Referenced by get_multi_native_com(), and setNative().

◆ native_middle_ca_

numeric::xyzVector< core::Real > protocols::electron_density::DockFragmentsIntoDensityMover::native_middle_ca_

Referenced by get_multi_native_mca(), and setNative().

◆ ncyc_

core::Size protocols::electron_density::DockFragmentsIntoDensityMover::ncyc_

Referenced by do_refinement(), and setNCyc().

◆ nRsteps_

core::Size protocols::electron_density::DockFragmentsIntoDensityMover::nRsteps_

Referenced by apply_multi(), and setNRsteps().

◆ passthrough_

bool protocols::electron_density::DockFragmentsIntoDensityMover::passthrough_

Referenced by apply_multi(), and setPassThrough().

◆ point_radius_

core::Real protocols::electron_density::DockFragmentsIntoDensityMover::point_radius_

Referenced by apply_multi(), and setPointRadius().

◆ points_defined_

bool protocols::electron_density::DockFragmentsIntoDensityMover::points_defined_

Referenced by predefine_search().

◆ points_to_search_

utility::vector1< numeric::xyzVector<core::Real> > protocols::electron_density::DockFragmentsIntoDensityMover::points_to_search_

Referenced by apply_multi(), and predefine_search().

◆ silent_

std::string protocols::electron_density::DockFragmentsIntoDensityMover::silent_

Referenced by apply_multi(), and setOutputSilent().

◆ symminfo_

DensitySymmInfo protocols::electron_density::DockFragmentsIntoDensityMover::symminfo_

◆ tag_

std::string protocols::electron_density::DockFragmentsIntoDensityMover::tag_

Referenced by apply_multi(), and setTag().

◆ topNfilter_

core::Size protocols::electron_density::DockFragmentsIntoDensityMover::topNfilter_

Referenced by apply_multi(), and setTopN().

◆ topNfinal_

core::Size protocols::electron_density::DockFragmentsIntoDensityMover::topNfinal_

Referenced by apply_multi(), and setTopN().

◆ topNtrans_

core::Size protocols::electron_density::DockFragmentsIntoDensityMover::topNtrans_

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

Referenced by apply_multi(), and setTopN().

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