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

#include <DockPDBIntoDensityMover.hh>

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

Public Member Functions

 DockPDBIntoDensityMover ()
 
void setDelR (core::Real delR)
 
void setNRsteps (core::Real nRsteps)
 
void set_nRsteps_from_pose (core::pose::Pose const &pose)
 
void setB (core::Real B)
 
void setTopN (core::Size const topNtrans, core::Size const topNfilter, core::Size const topNfinal)
 
core::Size get_top_N_filter () const
 
void setGridStep (core::Size gridStep)
 
void setNCyc (core::Size ncyc)
 
void setPointRadius (core::Real point_radius)
 
void setClusterOversamp (core::Size cluster_oversample)
 
void setFragDens (core::Real fragDens)
 
void setConvoluteSingleR (bool convolute_single_residue)
 
void setGaussianBlur (bool gaussian_blur)
 
void setLaplacianOffset (core::Real laplacian_offset)
 
void setPointsToSearchFname (std::string const &pts_fname)
 
void setPointsToSearchPDBFname (std::string const &pts_fname)
 
void setRotateSeqCenter (bool rot_seq_center)
 
void setRotateMiddleCA (bool rot_middle_ca)
 
void setRotateOnSeqCenter (bool val)
 
void setStartModel (std::string const &startmodel)
 
void setConstrainRefinement (core::Real constrain_refinement)
 
void setCartRef (core::Real cart_ref)
 
void setDoRefine (bool do_refine)
 
void setMinBackbone (bool min_backbone)
 
void setMultiNative (utility::vector1< core::pose::PoseOP > const &)
 
void setScoreNatives (bool score_natives)
 
void setCentroidSilentOut (bool centroid_silent_out)
 
void setClusterRadius (core::Real cluster_radius)
 
void setDumpInter (bool dump_inter)
 
void setDumpInterSilent (bool dump_inter_silent)
 
void setMaxRotPerTrans (core::Size max_rot_per_trans)
 
void setOutputSilent (std::string silent_out)
 
void setOverwrite (bool overwrite)
 
void setPassThrough (bool passthrough)
 
void setSymminfo (DensitySymmInfo const &symminfo)
 
void setTag (std::string tag)
 
void setFinalChain (std::string const &final_chain)
 
void setCoreIdx (utility::vector1< core::Size > core_idx)
 
void setRefineEnd (core::Size refine_end)
 
void setRefineStart (core::Size refine_start)
 
void setSearchEnd (core::Size point_search_end)
 
void setSearchStart (core::Size point_search_start)
 
void setPointSearchResultsFname (std::string const &point_search_results_fname)
 
void setCombinedSearchResultsFname (std::string const &combined_search_results_fname)
 
void predefine_search (utility::vector1< numeric::xyzVector< core::Real > > &pts_in)
 
void setCheatNativeCOM (bool cheat_native_com)
 
void setCheatNativeMCA (bool cheat_native_mca)
 
core::Real get_radius (core::pose::Pose const &)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void score_and_dump_natives ()
 
void read_in_points_to_search ()
 Read in points to search. More...
 
core::Real compare_and_align_poses (core::pose::Pose &, core::pose::Pose const &)
 
RBfitResultDB read_in_partial_search_results (utility::vector1< std::string > const &) const
 
void refine_partial_RBfitResultDB (utility::vector1< core::pose::PoseOP > const &, RBfitResultDB &, RevRefinementResultDB &)
 
void set_search_responsibilities ()
 
void dump_RBfitDB_to_pdbs (RBfitResultDB &resultDB, core::pose::PoseOP const &) const
 
void set_refinement_responsibilities (RBfitResultDB &)
 
void check_for_existing_output_file (std::string const &) const
 
void import_refinement_silent_files (utility::vector1< std::string > const &, RevRefinementResultDB &)
 
void cluster_RevRefinementDB (RevRefinementResultDB &, core::Size)
 
void minimize_poseOP_into_density (core::pose::PoseOP const, MinimizePoseIntoDensityOptions const &params, utility::vector1< core::Real > &)
 
void refine_RBfitResultDB (core::pose::PoseOP const &, RBfitResultDB &, RevRefinementResultDB &)
 step 3: local refinement of each hit empties the results_in DB More...
 
utility::vector1< numeric::xyzVector< core::Real > > get_points_to_search (core::pose::PoseOP const)
 
RBfitResultDB apply_search (core::pose::Pose &pose, core::Size const result_size)
 
void combine_search (utility::vector1< std::string > const &, core::pose::Pose const &, RBfitResultDB &)
 
void search_results_to_pdb (utility::vector1< std::string > const &, core::pose::PoseOP const &)
 
void manual_refine_pdb (core::pose::PoseOP const &)
 
RevRefinementResultDB apply_refinement (utility::vector1< std::string > const &, core::pose::PoseOP const, RBfitResultDB &, bool const)
 
void combine_refinement (utility::vector1< std::string > const &, RevRefinementResultDB &refinement_results)
 
void cluster_silent (utility::vector1< std::string > const &)
 
void analyze_RefinementDB (RevRefinementResultDB)
 
void run_aio (core::pose::PoseOP const)
 
void apply (core::pose::Pose &) override
 Main Method. 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 Strings & info ()
 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_
 
bool rot_seq_center_
 
bool rot_middle_ca_
 
bool points_defined_
 
bool convolute_single_residue_
 
bool gaussian_blur_
 
core::Real delR_
 
core::Real dens_wt_
 
core::Real cluster_radius_
 
core::Real point_radius_
 
core::Real fragDens_
 
core::Real laplacian_offset_
 
core::Size nRsteps_
 
core::Size gridStep_
 
core::Size B_
 
std::string points_to_search_fname_
 
std::string points_to_search_pdb_fname_
 
std::string start_model_
 
utility::vector1< numeric::xyzVector< core::Real > > points_to_search_
 
DensitySymmInfo symminfo_
 
core::Size cluster_oversample_
 
core::Size max_rot_per_trans_
 
bool do_refine_
 
bool min_backbone_
 
bool centroid_silent_out_
 
bool dump_inter_
 
bool dump_inter_silent_
 
bool cart_ref_
 
core::Size ncyc_
 
core::Real constrain_refinement_
 
std::string silent_
 
std::string tag_
 
std::string final_chain_
 
std::string point_search_results_fname_
 
std::string combined_search_results_fname_
 
bool passthrough_
 
utility::vector1< core::pose::PoseOP > all_natives_
 
utility::vector1< numeric::xyzVector< core::Real > > all_native_com_
 
utility::vector1< numeric::xyzVector< core::Real > > all_native_mca_
 
utility::vector1< numeric::xyzVector< core::Real > > all_native_seq_center_
 
bool cheat_native_com_
 
bool cheat_native_mca_
 
bool score_natives_
 
core::Size point_search_start_
 
core::Size point_search_end_
 
core::Size refine_start_
 
core::Size refine_end_
 
utility::vector1< core::Size > core_idx_
 
bool overwrite_
 

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...
 

Constructor & Destructor Documentation

◆ DockPDBIntoDensityMover()

protocols::electron_density::DockPDBIntoDensityMover::DockPDBIntoDensityMover ( )
inline

References B_, cart_ref_, centroid_silent_out_, cheat_native_com_, cheat_native_mca_, cluster_oversample_, cluster_radius_, constrain_refinement_, convolute_single_residue_, delR_, dens_wt_, do_refine_, dump_inter_, dump_inter_silent_, final_chain_, fragDens_, gaussian_blur_, gridStep_, laplacian_offset_, max_rot_per_trans_, min_backbone_, ncyc_, nRsteps_, overwrite_, passthrough_, point_radius_, points_defined_, points_to_search_fname_, points_to_search_pdb_fname_, rot_middle_ca_, rot_seq_center_, score_natives_, start_model_, topNfilter_, topNfinal_, and topNtrans_.

Member Function Documentation

◆ analyze_RefinementDB()

void protocols::electron_density::DockPDBIntoDensityMover::analyze_RefinementDB ( RevRefinementResultDB  resultDB)

References all_natives_, protocols::electron_density::get_rms(), protocols::electron_density::ResultDB< T, Tcomp >::pop(), protocols::electron_density::RefinementResult::pose_, core::scoring::rms, protocols::electron_density::RefinementResult::score_, protocols::electron_density::ResultDB< T, Tcomp >::size(), symminfo_, and protocols::electron_density::TR().

Referenced by cluster_silent(), and run_aio().

◆ apply()

void protocols::electron_density::DockPDBIntoDensityMover::apply ( core::pose::Pose &  )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::Pose::sequence(), and protocols::electron_density::TR().

◆ apply_refinement()

RevRefinementResultDB protocols::electron_density::DockPDBIntoDensityMover::apply_refinement ( utility::vector1< std::string > const &  local_result_filenames,
core::pose::PoseOP const  poseOP,
RBfitResultDB &  results_to_refine,
bool const  write_to_file 
)

References all_natives_, check_for_existing_output_file(), protocols::electron_density::dump_RefinementDB_to_silent(), final_chain_, protocols::electron_density::ResultDB< T, Tcomp >::pop(), read_in_partial_search_results(), refine_end_, refine_RBfitResultDB(), refine_start_, set_refinement_responsibilities(), silent_, protocols::electron_density::ResultDB< T, Tcomp >::size(), symminfo_, topNfilter_, and protocols::simple_filters::write_to_file().

Referenced by run_aio().

◆ apply_search()

RBfitResultDB protocols::electron_density::DockPDBIntoDensityMover::apply_search ( core::pose::Pose &  pose,
core::Size const  result_size 
)

References all_native_com_, all_native_mca_, all_natives_, B_, cluster_radius_, convolute_single_residue_, delR_, protocols::electron_density::density_grid_search(), fragDens_, protocols::electron_density::get_spectrum(), laplacian_offset_, max_rot_per_trans_, nRsteps_, point_search_end_, point_search_results_fname_, point_search_start_, points_to_search_, read_in_points_to_search(), rot_middle_ca_, set_search_responsibilities(), and symminfo_.

Referenced by run_aio().

◆ check_for_existing_output_file()

void protocols::electron_density::DockPDBIntoDensityMover::check_for_existing_output_file ( std::string const &  mode) const

References protocols::electron_density::check_if_file_exists(), overwrite_, and silent_.

Referenced by apply_refinement(), cluster_silent(), and combine_refinement().

◆ cluster_RevRefinementDB()

void protocols::electron_density::DockPDBIntoDensityMover::cluster_RevRefinementDB ( RevRefinementResultDB &  results,
core::Size  target_size = 0 
)

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), cluster_radius_, protocols::electron_density::get_rms(), protocols::electron_density::ResultDB< T, Tcomp >::pop(), protocols::electron_density::ResultDB< T, Tcomp >::size(), and symminfo_.

Referenced by cluster_silent(), and combine_refinement().

◆ cluster_silent()

void protocols::electron_density::DockPDBIntoDensityMover::cluster_silent ( utility::vector1< std::string > const &  final_result_filenames)

References all_natives_, analyze_RefinementDB(), check_for_existing_output_file(), cluster_RevRefinementDB(), protocols::electron_density::dump_RefinementDB_to_silent(), final_chain_, import_refinement_silent_files(), protocols::electron_density::ResultDB< T, Tcomp >::pop(), silent_, protocols::electron_density::ResultDB< T, Tcomp >::size(), symminfo_, topNfilter_, topNfinal_, and protocols::electron_density::TR().

◆ combine_refinement()

void protocols::electron_density::DockPDBIntoDensityMover::combine_refinement ( utility::vector1< std::string > const &  refinement_result_filenames,
RevRefinementResultDB &  refinement_results 
)

References all_natives_, check_for_existing_output_file(), cluster_RevRefinementDB(), protocols::electron_density::dump_RefinementDB_to_silent(), final_chain_, import_refinement_silent_files(), protocols::electron_density::ResultDB< T, Tcomp >::pop(), silent_, protocols::electron_density::ResultDB< T, Tcomp >::size(), symminfo_, topNfilter_, topNfinal_, and protocols::electron_density::TR().

Referenced by run_aio().

◆ combine_search()

void protocols::electron_density::DockPDBIntoDensityMover::combine_search ( utility::vector1< std::string > const &  local_result_filenames,
core::pose::Pose const &  pose,
RBfitResultDB &  all_results 
)

References all_native_com_, all_native_mca_, all_natives_, cluster_radius_, protocols::electron_density::cluster_RBfitResultDB_fast(), combined_search_results_fname_, protocols::electron_density::compare_RBfitDB_to_native(), delR_, core::scoring::electron_density::getDensityMap(), nRsteps_, read_in_partial_search_results(), rot_middle_ca_, protocols::electron_density::ResultDB< T, Tcomp >::size(), symminfo_, topNfilter_, protocols::electron_density::TR(), and protocols::electron_density::write_RBfitResultDB().

Referenced by run_aio().

◆ compare_and_align_poses()

core::Real protocols::electron_density::DockPDBIntoDensityMover::compare_and_align_poses ( core::pose::Pose &  query,
core::pose::Pose const &  native 
)

References core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::chemical::element::N, core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::Pose::size(), core::scoring::superimpose_pose(), and protocols::electron_density::TR().

◆ dump_RBfitDB_to_pdbs()

void protocols::electron_density::DockPDBIntoDensityMover::dump_RBfitDB_to_pdbs ( RBfitResultDB &  resultDB,
core::pose::PoseOP const &  poseOP 
) const

References protocols::electron_density::apply_transform(), protocols::electron_density::ResultDB< T, Tcomp >::pop(), protocols::electron_density::ResultDB< T, Tcomp >::size(), and core::id::to_string().

Referenced by search_results_to_pdb().

◆ get_name()

std::string protocols::electron_density::DockPDBIntoDensityMover::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ get_points_to_search()

utility::vector1< numeric::xyzVector< core::Real > > protocols::electron_density::DockPDBIntoDensityMover::get_points_to_search ( core::pose::PoseOP const  poseOP)

References all_native_com_, all_native_mca_, all_natives_, B_, cheat_native_com_, cheat_native_mca_, convolute_single_residue_, delR_, protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), fragDens_, core::scoring::electron_density::getDensityMap(), gridStep_, laplacian_offset_, nRsteps_, point_radius_, points_to_search_, points_to_search_fname_, points_to_search_pdb_fname_, core::import_pose::pose_from_file(), predefine_search(), protocols::electron_density::remove_occupied_density_from_density(), rot_middle_ca_, score_and_dump_natives(), score_natives_, protocols::electron_density::select_density_points(), start_model_, symminfo_, topNtrans_, and protocols::electron_density::TR().

Referenced by run_aio().

◆ get_radius()

core::Real protocols::electron_density::DockPDBIntoDensityMover::get_radius ( core::pose::Pose const &  pose)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::pose::get_center_of_mass(), protocols::mean_field::max(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by set_nRsteps_from_pose().

◆ get_top_N_filter()

core::Size protocols::electron_density::DockPDBIntoDensityMover::get_top_N_filter ( ) const
inline

References topNfilter_.

◆ import_refinement_silent_files()

void protocols::electron_density::DockPDBIntoDensityMover::import_refinement_silent_files ( utility::vector1< std::string > const &  refinement_result_filenames,
RevRefinementResultDB &  refinement_results 
)

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), core::sequence::end, core::io::silent::SilentFileData::read_file(), protocols::hybridization::score, and protocols::electron_density::TR().

Referenced by cluster_silent(), and combine_refinement().

◆ manual_refine_pdb()

void protocols::electron_density::DockPDBIntoDensityMover::manual_refine_pdb ( core::pose::PoseOP const &  poseOP)

References protocols::electron_density::create_minimize_pose_into_density_options(), dens_wt_, and minimize_poseOP_into_density().

◆ minimize_poseOP_into_density()

void protocols::electron_density::DockPDBIntoDensityMover::minimize_poseOP_into_density ( core::pose::PoseOP const  posecopy,
MinimizePoseIntoDensityOptions const &  params,
utility::vector1< core::Real > &  scores_vector 
)

References core::chemical::aa_vrt, core::pose::addVirtualResAsRoot(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::electron_density::MinimizePoseIntoDensityOptions::bbmin, constrain_refinement_, do_refine_, dump_inter_, dump_inter_silent_, protocols::electron_density::dump_to_silent(), core::chemical::FA_STANDARD, core::pose::get_center_of_mass(), min_backbone_, ncyc_, protocols::electron_density::MinimizePoseIntoDensityOptions::packer, protocols::electron_density::MinimizePoseIntoDensityOptions::rbmin, protocols::electron_density::MinimizePoseIntoDensityOptions::scorefxn_dens, protocols::electron_density::MinimizePoseIntoDensityOptions::scorefxn_refine, protocols::electron_density::TR(), and core::conformation::Residue::xyz().

Referenced by manual_refine_pdb(), and refine_RBfitResultDB().

◆ predefine_search()

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

References core::scoring::electron_density::ElectronDensity::cart2idx(), core::scoring::electron_density::getDensityMap(), points_defined_, and points_to_search_.

Referenced by get_points_to_search().

◆ read_in_partial_search_results()

RBfitResultDB protocols::electron_density::DockPDBIntoDensityMover::read_in_partial_search_results ( utility::vector1< std::string > const &  local_result_filenames) const

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), protocols::hybridization::score, and protocols::electron_density::ResultDB< T, Tcomp >::size().

Referenced by apply_refinement(), combine_search(), and search_results_to_pdb().

◆ read_in_points_to_search()

void protocols::electron_density::DockPDBIntoDensityMover::read_in_points_to_search ( )

Read in points to search.

References protocols::electron_density::check_if_file_exists(), points_to_search_, points_to_search_fname_, and silent_.

Referenced by apply_search().

◆ refine_partial_RBfitResultDB()

void protocols::electron_density::DockPDBIntoDensityMover::refine_partial_RBfitResultDB ( utility::vector1< core::pose::PoseOP > const &  ,
RBfitResultDB &  ,
RevRefinementResultDB &   
)

◆ refine_RBfitResultDB()

void protocols::electron_density::DockPDBIntoDensityMover::refine_RBfitResultDB ( core::pose::PoseOP const &  poseOP,
RBfitResultDB &  results_in,
RevRefinementResultDB &  results_out 
)

step 3: local refinement of each hit empties the results_in DB

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), core::pose::addVirtualResAsRoot(), all_natives_, protocols::electron_density::apply_transform(), constrain_refinement_, protocols::electron_density::create_minimize_pose_into_density_options(), dens_wt_, dump_inter_, dump_inter_silent_, protocols::electron_density::dump_to_silent(), protocols::electron_density::get_gdt(), protocols::electron_density::get_rms(), minimize_poseOP_into_density(), protocols::electron_density::ResultDB< T, Tcomp >::pop(), refine_end_, refine_start_, core::scoring::rms, protocols::electron_density::ResultDB< T, Tcomp >::size(), symminfo_, core::id::to_string(), and protocols::electron_density::TR().

Referenced by apply_refinement().

◆ run_aio()

void protocols::electron_density::DockPDBIntoDensityMover::run_aio ( core::pose::PoseOP const  poseOP)

References analyze_RefinementDB(), apply_refinement(), apply_search(), combine_refinement(), combine_search(), core_idx_, get_points_to_search(), point_search_end_, point_search_start_, and points_to_search_.

◆ score_and_dump_natives()

void protocols::electron_density::DockPDBIntoDensityMover::score_and_dump_natives ( )

References core::io::silent::SilentStruct::add_energy(), all_natives_, protocols::simple_moves::SwitchResidueTypeSetMover::apply(), centroid_silent_out_, core::io::silent::SilentStruct::clear_energies(), core::scoring::elec_dens_whole_structure_allatom, protocols::hybridization::score, silent_, core::id::to_string(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by get_points_to_search().

◆ search_results_to_pdb()

void protocols::electron_density::DockPDBIntoDensityMover::search_results_to_pdb ( utility::vector1< std::string > const &  local_result_filenames,
core::pose::PoseOP const &  poseOP 
)

References dump_RBfitDB_to_pdbs(), and read_in_partial_search_results().

◆ set_nRsteps_from_pose()

void protocols::electron_density::DockPDBIntoDensityMover::set_nRsteps_from_pose ( core::pose::Pose const &  pose)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), protocols::membrane::com(), delR_, fragDens_, core::pose::get_center_of_mass(), get_radius(), core::conformation::Residue::nheavyatoms(), nRsteps_, point_radius_, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

◆ set_refinement_responsibilities()

void protocols::electron_density::DockPDBIntoDensityMover::set_refinement_responsibilities ( RBfitResultDB &  resultDB)

References core_idx_, refine_end_, refine_start_, protocols::electron_density::ResultDB< T, Tcomp >::size(), and protocols::electron_density::TR().

Referenced by apply_refinement().

◆ set_search_responsibilities()

void protocols::electron_density::DockPDBIntoDensityMover::set_search_responsibilities ( )

References core_idx_, point_search_end_, point_search_start_, points_to_search_, and protocols::electron_density::TR().

Referenced by apply_search().

◆ setB()

void protocols::electron_density::DockPDBIntoDensityMover::setB ( core::Real  B)
inline

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

◆ setCartRef()

void protocols::electron_density::DockPDBIntoDensityMover::setCartRef ( core::Real  cart_ref)
inline

References cart_ref_.

◆ setCentroidSilentOut()

void protocols::electron_density::DockPDBIntoDensityMover::setCentroidSilentOut ( bool  centroid_silent_out)
inline

References centroid_silent_out_.

◆ setCheatNativeCOM()

void protocols::electron_density::DockPDBIntoDensityMover::setCheatNativeCOM ( bool  cheat_native_com)
inline

References cheat_native_com_.

◆ setCheatNativeMCA()

void protocols::electron_density::DockPDBIntoDensityMover::setCheatNativeMCA ( bool  cheat_native_mca)
inline

References cheat_native_mca_.

◆ setClusterOversamp()

void protocols::electron_density::DockPDBIntoDensityMover::setClusterOversamp ( core::Size  cluster_oversample)
inline

References cluster_oversample_.

◆ setClusterRadius()

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

References cluster_radius_.

◆ setCombinedSearchResultsFname()

void protocols::electron_density::DockPDBIntoDensityMover::setCombinedSearchResultsFname ( std::string const &  combined_search_results_fname)
inline

References combined_search_results_fname_.

◆ setConstrainRefinement()

void protocols::electron_density::DockPDBIntoDensityMover::setConstrainRefinement ( core::Real  constrain_refinement)
inline

References constrain_refinement_.

◆ setConvoluteSingleR()

void protocols::electron_density::DockPDBIntoDensityMover::setConvoluteSingleR ( bool  convolute_single_residue)
inline

References convolute_single_residue_.

◆ setCoreIdx()

void protocols::electron_density::DockPDBIntoDensityMover::setCoreIdx ( utility::vector1< core::Size >  core_idx)
inline

References core_idx_.

◆ setDelR()

void protocols::electron_density::DockPDBIntoDensityMover::setDelR ( core::Real  delR)
inline

References delR_.

◆ setDoRefine()

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

References do_refine_.

◆ setDumpInter()

void protocols::electron_density::DockPDBIntoDensityMover::setDumpInter ( bool  dump_inter)
inline

References dump_inter_.

◆ setDumpInterSilent()

void protocols::electron_density::DockPDBIntoDensityMover::setDumpInterSilent ( bool  dump_inter_silent)
inline

References dump_inter_silent_.

◆ setFinalChain()

void protocols::electron_density::DockPDBIntoDensityMover::setFinalChain ( std::string const &  final_chain)
inline

References final_chain_.

◆ setFragDens()

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

References fragDens_.

◆ setGaussianBlur()

void protocols::electron_density::DockPDBIntoDensityMover::setGaussianBlur ( bool  gaussian_blur)
inline

References gaussian_blur_.

◆ setGridStep()

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

References gridStep_.

◆ setLaplacianOffset()

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

References laplacian_offset_.

◆ setMaxRotPerTrans()

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

References max_rot_per_trans_.

◆ setMinBackbone()

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

References min_backbone_.

◆ setMultiNative()

void protocols::electron_density::DockPDBIntoDensityMover::setMultiNative ( utility::vector1< core::pose::PoseOP > const &  all_natives)

References protocols::cluster::calibur::aa, core::chemical::aa_vrt, core::pose::addVirtualResAsRoot(), all_native_com_, all_native_mca_, all_native_seq_center_, all_natives_, protocols::stepwise::modeler::is_protein(), core::chemical::element::N, protocols::electron_density::TR(), and protocols::kinmatch::xyz().

◆ setNCyc()

void protocols::electron_density::DockPDBIntoDensityMover::setNCyc ( core::Size  ncyc)
inline

References ncyc_.

◆ setNRsteps()

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

References nRsteps_.

◆ setOutputSilent()

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

References silent_.

◆ setOverwrite()

void protocols::electron_density::DockPDBIntoDensityMover::setOverwrite ( bool  overwrite)
inline

References overwrite_.

◆ setPassThrough()

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

References passthrough_.

◆ setPointRadius()

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

References point_radius_.

◆ setPointSearchResultsFname()

void protocols::electron_density::DockPDBIntoDensityMover::setPointSearchResultsFname ( std::string const &  point_search_results_fname)
inline

References point_search_results_fname_.

◆ setPointsToSearchFname()

void protocols::electron_density::DockPDBIntoDensityMover::setPointsToSearchFname ( std::string const &  pts_fname)
inline

References points_to_search_fname_.

◆ setPointsToSearchPDBFname()

void protocols::electron_density::DockPDBIntoDensityMover::setPointsToSearchPDBFname ( std::string const &  pts_fname)
inline

References points_to_search_pdb_fname_.

◆ setRefineEnd()

void protocols::electron_density::DockPDBIntoDensityMover::setRefineEnd ( core::Size  refine_end)
inline

References refine_end_.

◆ setRefineStart()

void protocols::electron_density::DockPDBIntoDensityMover::setRefineStart ( core::Size  refine_start)
inline

References refine_start_.

◆ setRotateMiddleCA()

void protocols::electron_density::DockPDBIntoDensityMover::setRotateMiddleCA ( bool  rot_middle_ca)
inline

References rot_middle_ca_.

◆ setRotateOnSeqCenter()

void protocols::electron_density::DockPDBIntoDensityMover::setRotateOnSeqCenter ( bool  val)
inline

References rot_seq_center_, and protocols::hybridization::val.

◆ setRotateSeqCenter()

void protocols::electron_density::DockPDBIntoDensityMover::setRotateSeqCenter ( bool  rot_seq_center)
inline

References rot_seq_center_.

◆ setScoreNatives()

void protocols::electron_density::DockPDBIntoDensityMover::setScoreNatives ( bool  score_natives)
inline

References score_natives_.

◆ setSearchEnd()

void protocols::electron_density::DockPDBIntoDensityMover::setSearchEnd ( core::Size  point_search_end)
inline

References point_search_end_.

◆ setSearchStart()

void protocols::electron_density::DockPDBIntoDensityMover::setSearchStart ( core::Size  point_search_start)
inline

References point_search_start_.

◆ setStartModel()

void protocols::electron_density::DockPDBIntoDensityMover::setStartModel ( std::string const &  startmodel)
inline

References start_model_.

◆ setSymminfo()

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

References symminfo_.

◆ setTag()

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

References tag_.

◆ setTopN()

void protocols::electron_density::DockPDBIntoDensityMover::setTopN ( core::Size const  topNtrans,
core::Size const  topNfilter,
core::Size const  topNfinal 
)
inline

References topNfilter_, topNfinal_, and topNtrans_.

Member Data Documentation

◆ all_native_com_

utility::vector1< numeric::xyzVector< core::Real > > protocols::electron_density::DockPDBIntoDensityMover::all_native_com_
private

Referenced by apply_search(), combine_search(), get_points_to_search(), and setMultiNative().

◆ all_native_mca_

utility::vector1< numeric::xyzVector< core::Real > > protocols::electron_density::DockPDBIntoDensityMover::all_native_mca_
private

Referenced by apply_search(), combine_search(), get_points_to_search(), and setMultiNative().

◆ all_native_seq_center_

utility::vector1< numeric::xyzVector< core::Real > > protocols::electron_density::DockPDBIntoDensityMover::all_native_seq_center_
private

Referenced by setMultiNative().

◆ all_natives_

utility::vector1< core::pose::PoseOP > protocols::electron_density::DockPDBIntoDensityMover::all_natives_
private

Referenced by analyze_RefinementDB(), apply_refinement(), apply_search(), cluster_silent(), combine_refinement(), combine_search(), get_points_to_search(), refine_RBfitResultDB(), score_and_dump_natives(), and setMultiNative().

◆ B_

core::Size protocols::electron_density::DockPDBIntoDensityMover::B_
private

Referenced by apply_search(), DockPDBIntoDensityMover(), get_points_to_search(), and setB().

◆ cart_ref_

bool protocols::electron_density::DockPDBIntoDensityMover::cart_ref_
private

Referenced by DockPDBIntoDensityMover(), and setCartRef().

◆ centroid_silent_out_

bool protocols::electron_density::DockPDBIntoDensityMover::centroid_silent_out_
private

Referenced by DockPDBIntoDensityMover(), score_and_dump_natives(), and setCentroidSilentOut().

◆ cheat_native_com_

bool protocols::electron_density::DockPDBIntoDensityMover::cheat_native_com_
private

Referenced by DockPDBIntoDensityMover(), get_points_to_search(), and setCheatNativeCOM().

◆ cheat_native_mca_

bool protocols::electron_density::DockPDBIntoDensityMover::cheat_native_mca_
private

Referenced by DockPDBIntoDensityMover(), get_points_to_search(), and setCheatNativeMCA().

◆ cluster_oversample_

core::Size protocols::electron_density::DockPDBIntoDensityMover::cluster_oversample_
private

Referenced by DockPDBIntoDensityMover(), and setClusterOversamp().

◆ cluster_radius_

core::Real protocols::electron_density::DockPDBIntoDensityMover::cluster_radius_
private

Referenced by apply_search(), cluster_RevRefinementDB(), combine_search(), DockPDBIntoDensityMover(), and setClusterRadius().

◆ combined_search_results_fname_

std::string protocols::electron_density::DockPDBIntoDensityMover::combined_search_results_fname_
private

Referenced by combine_search(), and setCombinedSearchResultsFname().

◆ constrain_refinement_

core::Real protocols::electron_density::DockPDBIntoDensityMover::constrain_refinement_
private

Referenced by DockPDBIntoDensityMover(), minimize_poseOP_into_density(), refine_RBfitResultDB(), and setConstrainRefinement().

◆ convolute_single_residue_

bool protocols::electron_density::DockPDBIntoDensityMover::convolute_single_residue_
private

Referenced by apply_search(), DockPDBIntoDensityMover(), get_points_to_search(), and setConvoluteSingleR().

◆ core_idx_

utility::vector1< core::Size > protocols::electron_density::DockPDBIntoDensityMover::core_idx_
private

Referenced by run_aio(), set_refinement_responsibilities(), set_search_responsibilities(), and setCoreIdx().

◆ delR_

core::Real protocols::electron_density::DockPDBIntoDensityMover::delR_
private

Referenced by apply_search(), combine_search(), DockPDBIntoDensityMover(), get_points_to_search(), set_nRsteps_from_pose(), and setDelR().

◆ dens_wt_

core::Real protocols::electron_density::DockPDBIntoDensityMover::dens_wt_
private

Referenced by DockPDBIntoDensityMover(), manual_refine_pdb(), and refine_RBfitResultDB().

◆ do_refine_

bool protocols::electron_density::DockPDBIntoDensityMover::do_refine_
private

Referenced by DockPDBIntoDensityMover(), minimize_poseOP_into_density(), and setDoRefine().

◆ dump_inter_

bool protocols::electron_density::DockPDBIntoDensityMover::dump_inter_
private

Referenced by DockPDBIntoDensityMover(), minimize_poseOP_into_density(), refine_RBfitResultDB(), and setDumpInter().

◆ dump_inter_silent_

bool protocols::electron_density::DockPDBIntoDensityMover::dump_inter_silent_
private

Referenced by DockPDBIntoDensityMover(), minimize_poseOP_into_density(), refine_RBfitResultDB(), and setDumpInterSilent().

◆ final_chain_

std::string protocols::electron_density::DockPDBIntoDensityMover::final_chain_
private

Referenced by apply_refinement(), cluster_silent(), combine_refinement(), DockPDBIntoDensityMover(), and setFinalChain().

◆ fragDens_

core::Real protocols::electron_density::DockPDBIntoDensityMover::fragDens_
private

Referenced by apply_search(), DockPDBIntoDensityMover(), get_points_to_search(), set_nRsteps_from_pose(), and setFragDens().

◆ gaussian_blur_

bool protocols::electron_density::DockPDBIntoDensityMover::gaussian_blur_
private

Referenced by DockPDBIntoDensityMover(), and setGaussianBlur().

◆ gridStep_

core::Size protocols::electron_density::DockPDBIntoDensityMover::gridStep_
private

Referenced by DockPDBIntoDensityMover(), get_points_to_search(), and setGridStep().

◆ laplacian_offset_

core::Real protocols::electron_density::DockPDBIntoDensityMover::laplacian_offset_
private

Referenced by apply_search(), DockPDBIntoDensityMover(), get_points_to_search(), and setLaplacianOffset().

◆ max_rot_per_trans_

core::Size protocols::electron_density::DockPDBIntoDensityMover::max_rot_per_trans_
private

Referenced by apply_search(), DockPDBIntoDensityMover(), and setMaxRotPerTrans().

◆ min_backbone_

bool protocols::electron_density::DockPDBIntoDensityMover::min_backbone_
private

Referenced by DockPDBIntoDensityMover(), minimize_poseOP_into_density(), and setMinBackbone().

◆ ncyc_

core::Size protocols::electron_density::DockPDBIntoDensityMover::ncyc_
private

Referenced by DockPDBIntoDensityMover(), minimize_poseOP_into_density(), and setNCyc().

◆ nRsteps_

core::Size protocols::electron_density::DockPDBIntoDensityMover::nRsteps_
private

Referenced by apply_search(), combine_search(), DockPDBIntoDensityMover(), get_points_to_search(), set_nRsteps_from_pose(), and setNRsteps().

◆ overwrite_

bool protocols::electron_density::DockPDBIntoDensityMover::overwrite_
private

Referenced by check_for_existing_output_file(), DockPDBIntoDensityMover(), and setOverwrite().

◆ passthrough_

bool protocols::electron_density::DockPDBIntoDensityMover::passthrough_
private

Referenced by DockPDBIntoDensityMover(), and setPassThrough().

◆ point_radius_

core::Real protocols::electron_density::DockPDBIntoDensityMover::point_radius_
private

Referenced by DockPDBIntoDensityMover(), get_points_to_search(), set_nRsteps_from_pose(), and setPointRadius().

◆ point_search_end_

core::Size protocols::electron_density::DockPDBIntoDensityMover::point_search_end_
private

Referenced by apply_search(), run_aio(), set_search_responsibilities(), and setSearchEnd().

◆ point_search_results_fname_

std::string protocols::electron_density::DockPDBIntoDensityMover::point_search_results_fname_
private

Referenced by apply_search(), and setPointSearchResultsFname().

◆ point_search_start_

core::Size protocols::electron_density::DockPDBIntoDensityMover::point_search_start_
private

Referenced by apply_search(), run_aio(), set_search_responsibilities(), and setSearchStart().

◆ points_defined_

bool protocols::electron_density::DockPDBIntoDensityMover::points_defined_
private

Referenced by DockPDBIntoDensityMover(), and predefine_search().

◆ points_to_search_

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

Referenced by apply_search(), get_points_to_search(), predefine_search(), read_in_points_to_search(), run_aio(), and set_search_responsibilities().

◆ points_to_search_fname_

std::string protocols::electron_density::DockPDBIntoDensityMover::points_to_search_fname_
private

Referenced by DockPDBIntoDensityMover(), get_points_to_search(), read_in_points_to_search(), and setPointsToSearchFname().

◆ points_to_search_pdb_fname_

std::string protocols::electron_density::DockPDBIntoDensityMover::points_to_search_pdb_fname_
private

Referenced by DockPDBIntoDensityMover(), get_points_to_search(), and setPointsToSearchPDBFname().

◆ refine_end_

core::Size protocols::electron_density::DockPDBIntoDensityMover::refine_end_
private

Referenced by apply_refinement(), refine_RBfitResultDB(), set_refinement_responsibilities(), and setRefineEnd().

◆ refine_start_

core::Size protocols::electron_density::DockPDBIntoDensityMover::refine_start_
private

Referenced by apply_refinement(), refine_RBfitResultDB(), set_refinement_responsibilities(), and setRefineStart().

◆ rot_middle_ca_

bool protocols::electron_density::DockPDBIntoDensityMover::rot_middle_ca_
private

Referenced by apply_search(), combine_search(), DockPDBIntoDensityMover(), get_points_to_search(), and setRotateMiddleCA().

◆ rot_seq_center_

bool protocols::electron_density::DockPDBIntoDensityMover::rot_seq_center_
private

Referenced by DockPDBIntoDensityMover(), setRotateOnSeqCenter(), and setRotateSeqCenter().

◆ score_natives_

bool protocols::electron_density::DockPDBIntoDensityMover::score_natives_
private

Referenced by DockPDBIntoDensityMover(), get_points_to_search(), and setScoreNatives().

◆ silent_

std::string protocols::electron_density::DockPDBIntoDensityMover::silent_
private

Referenced by apply_refinement(), check_for_existing_output_file(), cluster_silent(), combine_refinement(), read_in_points_to_search(), score_and_dump_natives(), and setOutputSilent().

◆ start_model_

std::string protocols::electron_density::DockPDBIntoDensityMover::start_model_
private

Referenced by DockPDBIntoDensityMover(), get_points_to_search(), and setStartModel().

◆ symminfo_

DensitySymmInfo protocols::electron_density::DockPDBIntoDensityMover::symminfo_
private

Referenced by analyze_RefinementDB(), apply_refinement(), apply_search(), cluster_RevRefinementDB(), cluster_silent(), combine_refinement(), combine_search(), get_points_to_search(), refine_RBfitResultDB(), and setSymminfo().

◆ tag_

std::string protocols::electron_density::DockPDBIntoDensityMover::tag_
private

Referenced by setTag().

◆ topNfilter_

core::Size protocols::electron_density::DockPDBIntoDensityMover::topNfilter_
private

Referenced by apply_refinement(), cluster_silent(), combine_refinement(), combine_search(), DockPDBIntoDensityMover(), get_top_N_filter(), and setTopN().

◆ topNfinal_

core::Size protocols::electron_density::DockPDBIntoDensityMover::topNfinal_
private

Referenced by cluster_silent(), combine_refinement(), DockPDBIntoDensityMover(), and setTopN().

◆ topNtrans_

core::Size protocols::electron_density::DockPDBIntoDensityMover::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 DockPDBIntoDensityMover(), get_points_to_search(), and setTopN().

The documentation for this class was generated from the following files:
Generated on Mon Sep 4 2023 10:56:57 for Rosetta by doxygen 1.9.1