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protocols::pockets::PocketGrid Class Reference

@ More...

#include <PocketGrid.hh>

Inheritance diagram for protocols::pockets::PocketGrid:
Inheritance graph
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Public Member Functions

 PocketGrid ()
 
 ~PocketGrid () override
 
 PocketGrid (const PocketGrid &gr)
 
PocketGrid & operator= (const PocketGrid &gr)
 
numeric::xyzVector< core::Real > dim () const
 
core::Real spacing () const
 
 PocketGrid (core::conformation::Residue const &central_rsd)
 
 PocketGrid (std::vector< core::conformation::ResidueCOP > const &central_rsd)
 
 PocketGrid (core::conformation::Residue const &central_rsd, core::Real x, core::Real y, core::Real z)
 
 PocketGrid (std::vector< core::conformation::ResidueCOP > const &central_rsd, core::Real x, core::Real y, core::Real z)
 
 PocketGrid (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real x, core::Real y, core::Real z, core::Real const &stepSize)
 
 PocketGrid (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real x, core::Real y, core::Real z)
 
 PocketGrid (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real x, core::Real y, core::Real z, core::Real const &stepSize, bool psp, bool sps)
 
 PocketGrid (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false)
 
 PocketGrid (core::Vector const &center, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false)
 
 PocketGrid (core::Vector const &center, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false)
 
void initialize (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real const size_x, core::Real const size_y, core::Real const size_z, core::Real const &stepSize=1, bool psp=false, bool sps=false)
 
void initialize (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false)
 
void initialize (core::Vector const &center, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false)
 
void initialize (core::Vector const &center, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false)
 
void initialize (core::conformation::Residue const &central_rsd, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false)
 
void initialize (std::vector< core::conformation::ResidueCOP > const &central_rsd, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false)
 
void clear ()
 
void recenter (core::Real const &xc, core::Real const &yc, core::Real const &zc)
 
void recenter (core::conformation::Residue const &central_rsd)
 
void recenter (std::vector< core::conformation::ResidueCOP > const &central_rsds)
 
void recenter (core::Vector const &center)
 
void findPockets (core::Size thr, core::Real max)
 
void findPSP (core::Size thr, core::Real max)
 
void findSPS (core::Size thr, core::Real max)
 
void mark (core::Real x, core::Real y, core::Real z, core::Real const &vdWd, core::Real const &buffer, bool polar=false, int targetResi=0)
 
void mark (core::Vector const &center, core::Real const &vdWd, core::Real const &buffer, bool polar=false, int targetResi=0)
 
void clearSmallPockets (core::Size minsize)
 
void findClusters ()
 
void findExemplars (core::pose::Pose const &inPose, Size const total_residues)
 
void findClustersByExemplars ()
 
void linkExemplarsThroughSolvent ()
 
void dumpGridToFile ()
 
void dumpGridToFile (std::string const &output_filename)
 
void dumpExemplarToFile ()
 
void dumpExemplarToFile (std::string const &output_filename)
 
void dumpTargetPocketsToFile (std::string const &output_filename)
 
void dumpTargetPocketsToFile (std::string const &output_filename, numeric::xyzMatrix< core::Real > rot1, numeric::xyzMatrix< core::Real > rot2, numeric::xyzMatrix< core::Real > rot3)
 
void dumpTargetPocketsToPDB (std::string const &output_filename, bool minipock=false)
 
void dumpTargetPocketsToPDB (std::string const &output_filename, numeric::xyzMatrix< core::Real > rot1, numeric::xyzMatrix< core::Real > rot2, numeric::xyzMatrix< core::Real > rot3)
 
void fillTargetPockets ()
 
void print () const
 
core::Real targetPocketVolume (core::Real const &surf_sc, core::Real const &bur_sc) const
 
core::Real largestTargetPocketVolume ()
 
void markPocketDepth (core::Real const &surf_d, core::Real const &bur_d)
 
void markEdgeDepth (core::Real const &surf_d, core::Real const &bur_d)
 
core::Real netTargetPocketVolume ()
 
void markDepth (core::Size x, core::Size y, core::Size z, core::Real const &surf_d, core::Real const &bur_d)
 
bool markOneEdgeDepth (core::Size x, core::Size y, core::Size z, core::Real const &surf_d, core::Real const &bur_d, bool isTarget)
 
void clusterPockets ()
 
void clusterCPockets ()
 
core::Real targetPocketSolventSurface () const
 
core::Real targetPocketProteinSurface () const
 
core::Real targetPocketHydrophobicProteinSurface () const
 
core::Real targetPocketPolarProteinSurface () const
 
core::Real targetPocketHeuristicScore () const
 
bool isTooSmall () const
 
core::Vector whatIsTooSmall () const
 
bool autoexpanding_pocket_eval (core::conformation::Residue const &central_rsd, core::scoring::func::XYZ_Func const &xyz_func, Size const total_residues, bool center_target=true, core::Real x=0.0, core::Real y=0.0, core::Real z=0.0)
 
bool autoexpanding_pocket_eval (std::vector< core::conformation::ResidueCOP > const &central_rsd, core::scoring::func::XYZ_Func const &xyz_func, Size const total_residues, bool center_target=true, core::Real x=0.0, core::Real y=0.0, core::Real z=0.0)
 
bool autoexpanding_pocket_eval (core::conformation::Residue const &central_rsd, core::pose::Pose const &inPose, bool center_target=true, core::Real x=0.0, core::Real y=0.0, core::Real z=0.0)
 
bool autoexpanding_pocket_eval (std::vector< core::conformation::ResidueCOP > const &central_rsd, core::pose::Pose const &inPose, bool center_target=true, core::Real x=0.0, core::Real y=0.0, core::Real z=0.0)
 
void move_pose_to_standard_orie (core::Size const &central_seqpos, core::pose::Pose &pose)
 
void randomAngle ()
 
void zeroAngle ()
 
core::Real get_pocket_distance (PocketGrid const &template_pocket) const
 
core::Real get_pocket_distance (PocketGrid const &template_pocket, std::string const &comparison_pdbname) const
 
utility::vector1< core::Real > getBounds ()
 
void write_pocketGrid_to_pdb (std::string const &output_filename)
 
void alter_espGrid (std::string const &espGrid_filename)
 
void alter_espGrid_with_bound_ligand (std::string const &espGrid_filename, core::pose::Pose const &protein_pose)
 
std::list< numeric::xyzVector
< core::Real > > 		get_connolly_surfacePoints (core::pose::Pose const &protein_pose) const
 
std::list< numeric::xyzVector
< core::Real > > 		get_connolly_surfacePoints_within_grid (std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)
 
virtual bool operator== (PocketGrid const &other) const
 
virtual bool same_type_as_me (PocketGrid const &other) const
 

Static Public Member Functions

static std::vector
< core::conformation::ResidueCOP > 		getRelaxResidues (core::pose::Pose const &input_pose, std::string const &resids)
 

Protected Types

enum  PtType {
  EMPTY, PROTEIN, TARGET, SUBTARGET,
  HSURFACE, PSURFACE, POCKET, PO_SURF,
  PO_BURIED, T_SURFACE, ST_SURFACE, TP_POCKET,
  TP_SURF, TP_BURIED, PO_EDGE, TP_EDGE,
  PSP, EGGSHELL, EGGSHELL_SURROUNDING
}
 

Protected Member Functions

void init ()
 
void setup_default_options ()
 
void newSearch (core::Size thr1, core::Size thr2, core::Size thr3, core::Size max1, core::Size max2, core::Size max3, bool psp=false, bool sps=false)
 
bool fill (core::Size x, core::Size y, core::Size z)
 
bool touchesSolvent (core::Size x, core::Size y, core::Size z) const
 
bool touchesSS (core::Size x, core::Size y, core::Size z) const
 
bool touchesPS (core::Size x, core::Size y, core::Size z) const
 
bool touchesSurface (core::Size x, core::Size y, core::Size z, bool polar, bool either=false) const
 
bool isSurfacePoint (core::Size x, core::Size y, core::Size z) const
 
bool isTargetPocketPoint (core::Size x, core::Size y, core::Size z) const
 
bool isDeepTargetPocketPoint (core::Size x, core::Size y, core::Size z) const
 
bool isProteinPoint (core::Size x, core::Size y, core::Size z) const
 
numeric::xyzVector< core::Real > rotatePoint (core::Real x, core::Real y, core::Real z)
 

Protected Attributes

std::vector< std::vector
< std::vector< PtType > > > 		grid_
 
std::vector< std::vector
< std::vector< PtType > > > 		c_grid_
 
std::vector< std::vector
< std::vector< core::Size > > > 		pockets_
 
core::Size xdim_
 
core::Size ydim_
 
core::Size zdim_
 
core::Real xcorn_
 
core::Real ycorn_
 
core::Real zcorn_
 
core::Real spacing_
 
core::Real stepSize_
 
numeric::xyzVector< core::Real > mid_
 
numeric::xyzVector< core::Size > dim_
 
core::Real maxLen_
 
std::string tag_
 
core::Size pdbno_
 
core::Size expdbno_
 
core::Size numTargets_
 
PClusterSet clusters_
 
CClusterSet c_clusters_
 
core::Real size_x_
 
core::Real size_y_
 
core::Real size_z_
 
core::Real limit_x_
 
core::Real limit_y_
 
core::Real limit_z_
 
bool restrictSize_
 
bool ignoreBuriedPockets_
 
bool ignoreExposedPockets_
 
core::Real probe_rad_
 
core::Real surf_score_
 
core::Real surf_dist_
 
core::Real bur_score_
 
core::Real bur_dist_
 
bool side_chains_only_
 
bool markpsp_
 
bool marksps_
 
bool exemplarRestriction_
 
bool dumpExemplars_
 
bool filterExemplars_
 
bool limitExemplars_
 
bool search13_
 
core::Real minPockSize_
 
core::Real maxPockSize_
 
numeric::xyzMatrix< core::Real > rot_mat_
 
bool static_grid_
 

Static Protected Attributes

static const core::Size MAX_TARGETS =2
 

Friends

class EggshellGrid
 
class ElectrostaticpotentialGrid
 
class TargetPocketGrid
 
class ComparisonGrid
 
class NonPlaidFingerprint
 

Detailed Description

@

Member Enumeration Documentation

enum protocols::pockets::PocketGrid::PtType
protected
Enumerator
EMPTY 
PROTEIN 
TARGET 
SUBTARGET 
HSURFACE 
PSURFACE 
POCKET 
PO_SURF 
PO_BURIED 
T_SURFACE 
ST_SURFACE 
TP_POCKET 
TP_SURF 
TP_BURIED 
PO_EDGE 
TP_EDGE 
PSP 
EGGSHELL 
EGGSHELL_SURROUNDING 

Constructor & Destructor Documentation

protocols::pockets::PocketGrid::PocketGrid ( )

References core::pose::metrics::CalculatorFactory::Instance(), core::pose::metrics::CalculatorFactory::register_calculator(), and setup_default_options().

protocols::pockets::PocketGrid::~PocketGrid ( )
overridedefault
protocols::pockets::PocketGrid::PocketGrid ( const PocketGrid &  gr)

References c_grid_, dumpExemplars_, exemplarRestriction_, expdbno_, filterExemplars_, grid_, limitExemplars_, markpsp_, marksps_, minPockSize_, pdbno_, pockets_, search13_, setup_default_options(), static_grid_, stepSize_, tag_, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

protocols::pockets::PocketGrid::PocketGrid ( core::conformation::Residue const &  central_rsd)

References core::pose::metrics::CalculatorFactory::check_calculator_exists(), initialize(), core::pose::metrics::CalculatorFactory::Instance(), markpsp_, marksps_, core::pose::metrics::CalculatorFactory::register_calculator(), setup_default_options(), size_x_, size_y_, size_z_, spacing_, and tag_.

protocols::pockets::PocketGrid::PocketGrid ( std::vector< core::conformation::ResidueCOP > const &  central_rsd)

References core::pose::metrics::CalculatorFactory::check_calculator_exists(), initialize(), core::pose::metrics::CalculatorFactory::Instance(), markpsp_, marksps_, core::pose::metrics::CalculatorFactory::register_calculator(), setup_default_options(), size_x_, size_y_, size_z_, spacing_, and tag_.

protocols::pockets::PocketGrid::PocketGrid ( core::conformation::Residue const &  central_rsd,
core::Real  x,
core::Real  y,
core::Real  z 
)

References core::pose::metrics::CalculatorFactory::check_calculator_exists(), initialize(), core::pose::metrics::CalculatorFactory::Instance(), markpsp_, marksps_, core::pose::metrics::CalculatorFactory::register_calculator(), setup_default_options(), spacing_, and tag_.

protocols::pockets::PocketGrid::PocketGrid ( std::vector< core::conformation::ResidueCOP > const &  central_rsd,
core::Real  x,
core::Real  y,
core::Real  z 
)

References core::pose::metrics::CalculatorFactory::check_calculator_exists(), initialize(), core::pose::metrics::CalculatorFactory::Instance(), markpsp_, marksps_, core::pose::metrics::CalculatorFactory::register_calculator(), setup_default_options(), spacing_, and tag_.

protocols::pockets::PocketGrid::PocketGrid ( core::Real const &  xc,
core::Real const &  yc,
core::Real const &  zc,
core::Real  x,
core::Real  y,
core::Real  z,
core::Real const &  stepSize 
)

References initialize(), markpsp_, marksps_, setup_default_options(), and tag_.

protocols::pockets::PocketGrid::PocketGrid ( core::Real const &  xc,
core::Real const &  yc,
core::Real const &  zc,
core::Real  x,
core::Real  y,
core::Real  z 
)

References initialize(), markpsp_, marksps_, setup_default_options(), spacing_, and tag_.

protocols::pockets::PocketGrid::PocketGrid ( core::Real const &  xc,
core::Real const &  yc,
core::Real const &  zc,
core::Real  x,
core::Real  y,
core::Real  z,
core::Real const &  stepSize,
bool  psp,
bool  sps 
)

References initialize(), setup_default_options(), and tag_.

protocols::pockets::PocketGrid::PocketGrid ( core::Real const &  xc,
core::Real const &  yc,
core::Real const &  zc,
core::Real  x,
core::Real const &  stepSize = 1,
bool  psp = false,
bool  sps = false 
)

References initialize(), setup_default_options(), and tag_.

protocols::pockets::PocketGrid::PocketGrid ( core::Vector const &  center,
core::Real  x,
core::Real const &  stepSize = 1,
bool  psp = false,
bool  sps = false 
)

References initialize(), setup_default_options(), and tag_.

protocols::pockets::PocketGrid::PocketGrid ( core::Vector const &  center,
core::Real const &  x,
core::Real const &  y,
core::Real const &  z,
core::Real const &  stepSize = 1,
bool  psp = false,
bool  sps = false 
)

References initialize(), setup_default_options(), and tag_.

Member Function Documentation

void protocols::pockets::PocketGrid::alter_espGrid ( std::string const &  espGrid_filename)

References protocols::pockets::ElectrostaticpotentialGrid::espGrid_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_dim_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_mid_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_spacing_, protocols::pockets::ElectrostaticpotentialGrid::fill_espGrid_values(), protocols::pockets::ElectrostaticpotentialGrid::get_oegrid_dimensions(), grid_, HSURFACE, core::conformation::membrane::out, PO_BURIED, PO_EDGE, PO_SURF, POCKET, protocols::pockets::ElectrostaticpotentialGrid::print_to_oegrid(), PSURFACE, spacing_, ST_SURFACE, stepSize_, T_SURFACE, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

void protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand ( std::string const &  espGrid_filename,
core::pose::Pose const &  protein_pose 
)

References core::conformation::Residue::atom(), core::conformation::Residue::atom_is_hydrogen(), protocols::pockets::ElectrostaticpotentialGrid::espGrid_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_dim_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_mid_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_spacing_, protocols::pockets::ElectrostaticpotentialGrid::fill_espGrid_values(), get_connolly_surfacePoints(), protocols::pockets::ElectrostaticpotentialGrid::get_oegrid_dimensions(), core::conformation::Residue::is_protein(), core::conformation::Residue::natoms(), core::conformation::membrane::out, protocols::pockets::ElectrostaticpotentialGrid::print_to_oegrid(), core::pose::Pose::residue(), core::pose::Pose::size(), spacing_, stepSize_, protocols::pockets::ElectrostaticpotentialGrid::write_espGrid_to_pdb(), xcorn_, xdim_, core::conformation::Atom::xyz(), ycorn_, ydim_, zcorn_, and zdim_.

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval ( core::conformation::Residue const &  central_rsd,
core::scoring::func::XYZ_Func const &  xyz_func,
Size const  total_residues,
bool  center_target = true,
core::Real  x = 0.0,
core::Real  y = 0.0,
core::Real  z = 0.0 
)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::clone(), core::conformation::Residue::is_terminus(), and core::scoring::func::XYZ_Func::residue().

Referenced by autoexpanding_pocket_eval(), and move_pose_to_standard_orie().

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval ( std::vector< core::conformation::ResidueCOP > const &  central_rsd,
core::scoring::func::XYZ_Func const &  xyz_func,
Size const  total_residues,
bool  center_target = true,
core::Real  x = 0.0,
core::Real  y = 0.0,
core::Real  z = 0.0 
)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), autoexpanding_pocket_eval(), core::conformation::Residue::is_terminus(), and core::scoring::func::XYZ_Func::residue().

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval ( core::conformation::Residue const &  central_rsd,
core::pose::Pose const &  inPose,
bool  center_target = true,
core::Real  x = 0.0,
core::Real  y = 0.0,
core::Real  z = 0.0 
)

References autoexpanding_pocket_eval(), and core::conformation::Residue::clone().

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval ( std::vector< core::conformation::ResidueCOP > const &  central_rsd,
core::pose::Pose const &  inPose,
bool  center_target = true,
core::Real  x = 0.0,
core::Real  y = 0.0,
core::Real  z = 0.0 
)

References bur_dist_, core::pose::Pose::conformation(), dumpExemplars_, exemplarRestriction_, findClusters(), findClustersByExemplars(), findExemplars(), findPockets(), findPSP(), findSPS(), initialize(), isTooSmall(), limit_x_, limit_y_, limit_z_, mark(), markPocketDepth(), markpsp_, marksps_, MAX_TARGETS, maxLen_, probe_rad_, recenter(), core::conformation::Conformation::residue(), rotatePoint(), side_chains_only_, core::pose::Pose::size(), size_x_, size_y_, size_z_, spacing_, static_grid_, stepSize_, surf_dist_, whatIsTooSmall(), xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::clear ( )
void protocols::pockets::PocketGrid::clearSmallPockets ( core::Size  minsize)
void protocols::pockets::PocketGrid::clusterCPockets ( )

References protocols::pockets::PClusterSet::add(), c_grid_, protocols::pockets::PClusterSet::clusters_, clusters_, protocols::pockets::PClusterSet::join(), PO_BURIED, PO_EDGE, POCKET, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, xdim_, ydim_, and zdim_.

Referenced by findClustersByExemplars(), and linkExemplarsThroughSolvent().

void protocols::pockets::PocketGrid::clusterPockets ( )

References protocols::pockets::PClusterSet::add(), protocols::pockets::PClusterSet::clusters_, clusters_, grid_, protocols::pockets::PClusterSet::join(), PO_BURIED, PO_EDGE, POCKET, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, xdim_, ydim_, and zdim_.

Referenced by findClusters(), and protocols::pockets::TargetPocketGrid::findClusters().

numeric::xyzVector<core::Real> protocols::pockets::PocketGrid::dim ( ) const
inline

References dim_.

void protocols::pockets::PocketGrid::dumpExemplarToFile ( )

References expdbno_, protocols::abinitio::filename(), and tag_.

void protocols::pockets::PocketGrid::dumpExemplarToFile ( std::string const &  output_filename)

References c_clusters_, protocols::pockets::CClusterSet::clusters_, limitExemplars_, numTargets_, core::conformation::membrane::out, stepSize_, xcorn_, ycorn_, and zcorn_.

void protocols::pockets::PocketGrid::dumpGridToFile ( )

References protocols::abinitio::filename(), pdbno_, and tag_.

void protocols::pockets::PocketGrid::dumpGridToFile ( std::string const &  output_filename)

References protocols::pockets::PClusterSet::clusters_, clusters_, EMPTY, grid_, HSURFACE, minPockSize_, core::conformation::membrane::out, PO_BURIED, PO_EDGE, PO_SURF, POCKET, PROTEIN, PSP, PSURFACE, ST_SURFACE, stepSize_, SUBTARGET, T_SURFACE, TARGET, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

void protocols::pockets::PocketGrid::dumpTargetPocketsToFile ( std::string const &  output_filename)

References protocols::pockets::PClusterSet::clusters_, clusters_, grid_, minPockSize_, numTargets_, core::conformation::membrane::out, stepSize_, TP_BURIED, TP_POCKET, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

void protocols::pockets::PocketGrid::dumpTargetPocketsToFile ( std::string const &  output_filename,
numeric::xyzMatrix< core::Real >  rot1,
numeric::xyzMatrix< core::Real >  rot2,
numeric::xyzMatrix< core::Real >  rot3 
)

References protocols::pockets::PClusterSet::clusters_, clusters_, grid_, minPockSize_, numTargets_, core::conformation::membrane::out, stepSize_, TP_BURIED, TP_POCKET, xcorn_, ycorn_, and zcorn_.

void protocols::pockets::PocketGrid::dumpTargetPocketsToPDB ( std::string const &  output_filename,
bool  minipock = false 
)

References protocols::pockets::PClusterSet::clusters_, clusters_, EMPTY, grid_, minPockSize_, numTargets_, core::conformation::membrane::out, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

void protocols::pockets::PocketGrid::dumpTargetPocketsToPDB ( std::string const &  output_filename,
numeric::xyzMatrix< core::Real >  rot1,
numeric::xyzMatrix< core::Real >  rot2,
numeric::xyzMatrix< core::Real >  rot3 
)

References protocols::pockets::PClusterSet::clusters_, clusters_, grid_, minPockSize_, numTargets_, core::conformation::membrane::out, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, ycorn_, and zcorn_.

bool protocols::pockets::PocketGrid::fill ( core::Size  x,
core::Size  y,
core::Size  z 
)
protected

References EMPTY, grid_, protocols::mean_field::min(), POCKET, pockets_, TP_POCKET, xdim_, ydim_, and zdim_.

Referenced by fillTargetPockets().

void protocols::pockets::PocketGrid::fillTargetPockets ( )

References EMPTY, fill(), grid_, protocols::mean_field::min(), pockets_, TP_POCKET, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::findClusters ( )

References clusterPockets(), protocols::pockets::PClusterSet::clusters_, clusters_, EMPTY, grid_, numTargets_, PO_BURIED, PO_EDGE, PO_SURF, POCKET, ST_SURFACE, T_SURFACE, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval().

void protocols::pockets::PocketGrid::findClustersByExemplars ( )

References c_clusters_, c_grid_, protocols::pockets::PClusterSet::clear(), clusterCPockets(), protocols::pockets::CClusterSet::clusters_, clusters_, grid_, numTargets_, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval().

void protocols::pockets::PocketGrid::findExemplars ( core::pose::Pose const &  inPose,
Size const  total_residues 
)

References protocols::pockets::CClusterSet::add(), core::pack::dunbrack::c, c_clusters_, protocols::pockets::CClusterSet::clear(), protocols::pockets::PClusterSet::clusters_, protocols::pockets::CClusterSet::clusters_, clusters_, core::pose::Pose::conformation(), EMPTY, filterExemplars_, protocols::pockets::CClusterSet::findClusters(), grid_, isDeepTargetPocketPoint(), isProteinPoint(), isTargetPocketPoint(), core::pose::Pose::metric(), minPockSize_, numTargets_, PO_SURF, core::conformation::Conformation::residue(), core::chemical::RING_HYBRID, rotatePoint(), core::chemical::SP2_HYBRID, core::chemical::SP3_HYBRID, core::kinematics::Stub::spherical(), ST_SURFACE, stepSize_, T_SURFACE, TP_SURF, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

Referenced by autoexpanding_pocket_eval().

void protocols::pockets::PocketGrid::findPockets ( core::Size  thr,
core::Real  max 
)

References newSearch(), and stepSize_.

Referenced by autoexpanding_pocket_eval().

void protocols::pockets::PocketGrid::findPSP ( core::Size  thr,
core::Real  max 
)

References newSearch(), and stepSize_.

Referenced by autoexpanding_pocket_eval().

void protocols::pockets::PocketGrid::findSPS ( core::Size  thr,
core::Real  max 
)

References newSearch(), and stepSize_.

Referenced by autoexpanding_pocket_eval().

std::list< numeric::xyzVector< core::Real > > protocols::pockets::PocketGrid::get_connolly_surfacePoints ( core::pose::Pose const &  protein_pose) const

References core::pack::task::TaskFactory::create_packer_task(), and core::scoring::sc::MolecularSurfaceCalculator::Init().

Referenced by alter_espGrid_with_bound_ligand(), protocols::pockets::ElectrostaticpotentialGrid::change_espGrid_for_darc(), and protocols::pockets::EggshellGrid::EggshellGrid().

std::list< numeric::xyzVector< core::Real > > protocols::pockets::PocketGrid::get_connolly_surfacePoints_within_grid ( std::list< numeric::xyzVector< core::Real > > const &  surfacePoints_list)

References protocols::pockets::convert_cartesian_to_grid(), dim_, mid_, and spacing_.

core::Real protocols::pockets::PocketGrid::get_pocket_distance ( PocketGrid const &  template_pocket) const
inline

References get_pocket_distance().

Referenced by get_pocket_distance().

core::Real protocols::pockets::PocketGrid::get_pocket_distance ( PocketGrid const &  template_pocket,
std::string const &  comparison_pdbname 
) const

References protocols::pockets::PClusterSet::clusters_, clusters_, grid_, minPockSize_, core::conformation::membrane::out, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, protocols::pockets::TR(), xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

utility::vector1< core::Real > protocols::pockets::PocketGrid::getBounds ( )

References protocols::pockets::PClusterSet::clusters_, clusters_, grid_, minPockSize_, numTargets_, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, xcorn_, ycorn_, and zcorn_.

std::vector< core::conformation::ResidueCOP > protocols::pockets::PocketGrid::getRelaxResidues ( core::pose::Pose const &  input_pose,
std::string const &  resids 
)
static

References core::conformation::Residue::clone(), core::pose::Pose::conformation(), MAX_TARGETS, core::pose::Pose::pdb_info(), core::conformation::Conformation::residue(), and core::pose::Pose::size().

Referenced by protocols::pockets::PocketExemplarMultifunc::PocketExemplarMultifunc(), and protocols::pockets::PocketConstraint::read_def().

void protocols::pockets::PocketGrid::init ( void  )
protected

Referenced by protocols::pockets::EggshellGrid::EggshellGrid(), protocols::pockets::ElectrostaticpotentialGrid::get_DELPHI_espGrid_values(), initialize(), move_pose_to_standard_orie(), recenter(), and protocols::pockets::TargetPocketGrid::TargetPocketGrid().

void protocols::pockets::PocketGrid::initialize ( core::Real const &  xc,
core::Real const &  yc,
core::Real const &  zc,
core::Real const  size_x,
core::Real const  size_y,
core::Real const  size_z,
core::Real const &  stepSize = 1,
bool  psp = false,
bool  sps = false 
)

References expdbno_, init(), markpsp_, marksps_, numTargets_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval(), and PocketGrid().

void protocols::pockets::PocketGrid::initialize ( core::Real const &  xc,
core::Real const &  yc,
core::Real const &  zc,
core::Real  x,
core::Real const &  stepSize = 1,
bool  psp = false,
bool  sps = false 
)

References expdbno_, init(), markpsp_, marksps_, numTargets_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::initialize ( core::Vector const &  center,
core::Real  x,
core::Real const &  stepSize = 1,
bool  psp = false,
bool  sps = false 
)

References core::conformation::membrane::center, expdbno_, init(), markpsp_, marksps_, numTargets_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::initialize ( core::Vector const &  center,
core::Real const &  x,
core::Real const &  y,
core::Real const &  z,
core::Real const &  stepSize = 1,
bool  psp = false,
bool  sps = false 
)

References expdbno_, init(), markpsp_, marksps_, numTargets_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::initialize ( core::conformation::Residue const &  central_rsd,
core::Real const &  x,
core::Real const &  y,
core::Real const &  z,
core::Real const &  stepSize = 1,
bool  psp = false,
bool  sps = false 
)

References expdbno_, init(), markpsp_, marksps_, numTargets_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::initialize ( std::vector< core::conformation::ResidueCOP > const &  central_rsd,
core::Real const &  x,
core::Real const &  y,
core::Real const &  z,
core::Real const &  stepSize = 1,
bool  psp = false,
bool  sps = false 
)

References expdbno_, init(), markpsp_, marksps_, numTargets_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

bool protocols::pockets::PocketGrid::isDeepTargetPocketPoint ( core::Size  x,
core::Size  y,
core::Size  z 
) const
inlineprotected

References grid_, TP_BURIED, and TP_POCKET.

Referenced by findExemplars().

bool protocols::pockets::PocketGrid::isProteinPoint ( core::Size  x,
core::Size  y,
core::Size  z 
) const
inlineprotected

References grid_, PROTEIN, SUBTARGET, and TARGET.

Referenced by findExemplars().

bool protocols::pockets::PocketGrid::isSurfacePoint ( core::Size  x,
core::Size  y,
core::Size  z 
) const
protected

References grid_, HSURFACE, PSURFACE, ST_SURFACE, and T_SURFACE.

Referenced by markDepth(), newSearch(), and touchesPS().

bool protocols::pockets::PocketGrid::isTargetPocketPoint ( core::Size  x,
core::Size  y,
core::Size  z 
) const
inlineprotected

References grid_, TP_BURIED, TP_EDGE, TP_POCKET, and TP_SURF.

Referenced by findExemplars().

bool protocols::pockets::PocketGrid::isTooSmall ( ) const

References grid_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval().

core::Real protocols::pockets::PocketGrid::largestTargetPocketVolume ( )

References clusters_, protocols::pockets::PClusterSet::getLargestClusterSize(), ignoreBuriedPockets_, ignoreExposedPockets_, minPockSize_, numTargets_, and stepSize_.

void protocols::pockets::PocketGrid::linkExemplarsThroughSolvent ( )

References c_clusters_, clusterCPockets(), protocols::pockets::PClusterSet::clusters_, protocols::pockets::CClusterSet::clusters_, clusters_, EMPTY, grid_, protocols::mean_field::min(), minPockSize_, numTargets_, POCKET, PROTEIN, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, ycorn_, and zcorn_.

void protocols::pockets::PocketGrid::mark ( core::Real  x,
core::Real  y,
core::Real  z,
core::Real const &  vdWd,
core::Real const &  buffer,
bool  polar = false,
int  targetResi = 0 
)

References grid_, HSURFACE, protocols::mean_field::max(), protocols::mean_field::min(), PROTEIN, PSURFACE, ST_SURFACE, stepSize_, SUBTARGET, T_SURFACE, TARGET, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

Referenced by autoexpanding_pocket_eval(), and mark().

void protocols::pockets::PocketGrid::mark ( core::Vector const &  center,
core::Real const &  vdWd,
core::Real const &  buffer,
bool  polar = false,
int  targetResi = 0 
)

References core::conformation::membrane::center, and mark().

void protocols::pockets::PocketGrid::markDepth ( core::Size  x,
core::Size  y,
core::Size  z,
core::Real const &  surf_d,
core::Real const &  bur_d 
)

References EMPTY, grid_, isSurfacePoint(), PO_BURIED, PO_EDGE, PO_SURF, POCKET, stepSize_, TP_BURIED, TP_EDGE, TP_SURF, xdim_, ydim_, and zdim_.

Referenced by markPocketDepth().

void protocols::pockets::PocketGrid::markEdgeDepth ( core::Real const &  surf_d,
core::Real const &  bur_d 
)

References protocols::pockets::PClusterSet::clusters_, clusters_, grid_, markOneEdgeDepth(), numTargets_, PO_EDGE, and TP_EDGE.

bool protocols::pockets::PocketGrid::markOneEdgeDepth ( core::Size  x,
core::Size  y,
core::Size  z,
core::Real const &  surf_d,
core::Real const &  bur_d,
bool  isTarget 
)

References EMPTY, grid_, HSURFACE, PO_BURIED, PO_EDGE, PO_SURF, POCKET, PSURFACE, stepSize_, TP_BURIED, TP_POCKET, TP_SURF, xdim_, ydim_, and zdim_.

Referenced by markEdgeDepth().

void protocols::pockets::PocketGrid::markPocketDepth ( core::Real const &  surf_d,
core::Real const &  bur_d 
)

References grid_, markDepth(), POCKET, TP_POCKET, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval().

void protocols::pockets::PocketGrid::move_pose_to_standard_orie ( core::Size const &  central_seqpos,
core::pose::Pose &  pose 
)

References core::pose::Pose::apply_transform_Rx_plus_v(), autoexpanding_pocket_eval(), protocols::pockets::PClusterSet::clusters_, clusters_, core::pose::Pose::conformation(), grid_, init(), minPockSize_, core::conformation::Conformation::residue(), protocols::forge::remodel::rot_mat(), setup_default_options(), stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, ycorn_, and zcorn_.

core::Real protocols::pockets::PocketGrid::netTargetPocketVolume ( )

References clusters_, protocols::pockets::PClusterSet::getNetClusterSize(), ignoreBuriedPockets_, ignoreExposedPockets_, maxPockSize_, protocols::mean_field::min(), minPockSize_, numTargets_, and stepSize_.

void protocols::pockets::PocketGrid::newSearch ( core::Size  thr1,
core::Size  thr2,
core::Size  thr3,
core::Size  max1,
core::Size  max2,
core::Size  max3,
bool  psp = false,
bool  sps = false 
)
protected

References core::pack::dunbrack::c, EMPTY, grid_, isSurfacePoint(), markpsp_, protocols::mean_field::max(), POCKET, PSP, search13_, ST_SURFACE, T_SURFACE, TP_POCKET, protocols::pockets::TR(), xdim_, ydim_, and zdim_.

Referenced by findPockets(), findPSP(), and findSPS().

PocketGrid & protocols::pockets::PocketGrid::operator= ( const PocketGrid &  gr)

References c_grid_, dumpExemplars_, exemplarRestriction_, expdbno_, filterExemplars_, grid_, limitExemplars_, markpsp_, marksps_, minPockSize_, pdbno_, pockets_, search13_, stepSize_, tag_, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

bool protocols::pockets::PocketGrid::operator== ( PocketGrid const &  other) const
virtual

Reimplemented in protocols::pockets::ElectrostaticpotentialGrid, and protocols::pockets::EggshellGrid.

References same_type_as_me(), size_x_, size_y_, size_z_, spacing_, xcorn_, ycorn_, and zcorn_.

void protocols::pockets::PocketGrid::print ( ) const

References pockets_, protocols::pockets::TR(), xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::randomAngle ( )

References rot_mat_.

void protocols::pockets::PocketGrid::recenter ( core::Real const &  xc,
core::Real const &  yc,
core::Real const &  zc 
)

References protocols::pockets::PClusterSet::clear(), clusters_, dim_, init(), mid_, rotatePoint(), stepSize_, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

Referenced by autoexpanding_pocket_eval(), initialize(), and recenter().

void protocols::pockets::PocketGrid::recenter ( core::conformation::Residue const &  central_rsd)

References core::conformation::Residue::atom(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::membrane::center, core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), recenter(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

void protocols::pockets::PocketGrid::recenter ( std::vector< core::conformation::ResidueCOP > const &  central_rsds)

References core::conformation::membrane::center, core::sequence::left, MAX_TARGETS, recenter(), stepSize_, protocols::pockets::TR(), xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::recenter ( core::Vector const &  center)

References core::conformation::membrane::center, and recenter().

numeric::xyzVector< core::Real > protocols::pockets::PocketGrid::rotatePoint ( core::Real  x,
core::Real  y,
core::Real  z 
)
protected

References rot_mat_.

Referenced by autoexpanding_pocket_eval(), findExemplars(), and recenter().

bool protocols::pockets::PocketGrid::same_type_as_me ( PocketGrid const &  other) const
virtual

Reimplemented in protocols::pockets::ElectrostaticpotentialGrid, protocols::pockets::EggshellGrid, and protocols::pockets::TargetPocketGrid.

Referenced by operator==().

void protocols::pockets::PocketGrid::setup_default_options ( )
protected

References protocols::pockets::CCluster::filterExemplars_.

Referenced by move_pose_to_standard_orie(), and PocketGrid().

core::Real protocols::pockets::PocketGrid::spacing ( ) const
inline

References spacing_.

Referenced by protocols::pockets::ElectrostaticpotentialGrid::get_DELPHI_espGrid_values(), and protocols::pockets::ElectrostaticpotentialGrid::get_oegrid_dimensions().

core::Real protocols::pockets::PocketGrid::targetPocketHeuristicScore ( ) const

References grid_, stepSize_, touchesPS(), touchesSS(), TP_POCKET, xdim_, ydim_, and zdim_.

core::Real protocols::pockets::PocketGrid::targetPocketHydrophobicProteinSurface ( ) const

References grid_, stepSize_, touchesSurface(), TP_POCKET, xdim_, ydim_, and zdim_.

core::Real protocols::pockets::PocketGrid::targetPocketPolarProteinSurface ( ) const

References grid_, stepSize_, touchesSurface(), TP_POCKET, xdim_, ydim_, and zdim_.

core::Real protocols::pockets::PocketGrid::targetPocketProteinSurface ( ) const

References grid_, stepSize_, touchesSurface(), TP_POCKET, xdim_, ydim_, and zdim_.

core::Real protocols::pockets::PocketGrid::targetPocketSolventSurface ( ) const

References grid_, stepSize_, touchesSolvent(), TP_POCKET, xdim_, ydim_, and zdim_.

core::Real protocols::pockets::PocketGrid::targetPocketVolume ( core::Real const &  surf_sc,
core::Real const &  bur_sc 
) const

References grid_, stepSize_, TP_BURIED, TP_POCKET, TP_SURF, xdim_, ydim_, and zdim_.

bool protocols::pockets::PocketGrid::touchesPS ( core::Size  x,
core::Size  y,
core::Size  z 
) const
protected

References isSurfacePoint(), xdim_, ydim_, and zdim_.

Referenced by targetPocketHeuristicScore().

bool protocols::pockets::PocketGrid::touchesSolvent ( core::Size  x,
core::Size  y,
core::Size  z 
) const
protected

References EMPTY, grid_, xdim_, ydim_, and zdim_.

Referenced by targetPocketSolventSurface().

bool protocols::pockets::PocketGrid::touchesSS ( core::Size  x,
core::Size  y,
core::Size  z 
) const
protected

References EMPTY, grid_, xdim_, ydim_, and zdim_.

Referenced by targetPocketHeuristicScore().

bool protocols::pockets::PocketGrid::touchesSurface ( core::Size  x,
core::Size  y,
core::Size  z,
bool  polar,
bool  either = false 
) const
protected

References grid_, HSURFACE, PSURFACE, xdim_, ydim_, and zdim_.

Referenced by targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), and targetPocketProteinSurface().

core::Vector protocols::pockets::PocketGrid::whatIsTooSmall ( ) const

References grid_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval().

void protocols::pockets::PocketGrid::write_pocketGrid_to_pdb ( std::string const &  output_filename)

References EMPTY, grid_, HSURFACE, core::conformation::membrane::out, PO_BURIED, PO_EDGE, PO_SURF, POCKET, PROTEIN, PSP, PSURFACE, ST_SURFACE, stepSize_, SUBTARGET, T_SURFACE, TARGET, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

void protocols::pockets::PocketGrid::zeroAngle ( )

References rot_mat_.

Friends And Related Function Documentation

friend class ComparisonGrid
friend
friend class EggshellGrid
friend
friend class ElectrostaticpotentialGrid
friend
friend class NonPlaidFingerprint
friend
friend class TargetPocketGrid
friend

Member Data Documentation

core::Real protocols::pockets::PocketGrid::bur_dist_
protected

Referenced by autoexpanding_pocket_eval().

core::Real protocols::pockets::PocketGrid::bur_score_
protected
CClusterSet protocols::pockets::PocketGrid::c_clusters_
protected

Referenced by dumpExemplarToFile(), findClustersByExemplars(), findExemplars(), and linkExemplarsThroughSolvent().

std::vector< std::vector < std::vector <PtType> > > protocols::pockets::PocketGrid::c_grid_
protected

Referenced by clusterCPockets(), findClustersByExemplars(), operator=(), and PocketGrid().

PClusterSet protocols::pockets::PocketGrid::clusters_
protected

Referenced by clusterCPockets(), clusterPockets(), protocols::pockets::ComparisonGrid::compareCoverage(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), findClusters(), protocols::pockets::TargetPocketGrid::findClusters(), findClustersByExemplars(), findExemplars(), get_pocket_distance(), getBounds(), largestTargetPocketVolume(), linkExemplarsThroughSolvent(), markEdgeDepth(), move_pose_to_standard_orie(), netTargetPocketVolume(), and recenter().

numeric::xyzVector<core::Size> protocols::pockets::PocketGrid::dim_
protected

Referenced by dim(), protocols::pockets::EggshellGrid::get_connolly_eggshell(), protocols::pockets::EggshellGrid::get_connolly_eggshell_on_grid(), get_connolly_surfacePoints_within_grid(), recenter(), protocols::pockets::ElectrostaticpotentialGrid::resize_espGrid_to_match_pocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand(), and protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand().

bool protocols::pockets::PocketGrid::dumpExemplars_
protected

Referenced by autoexpanding_pocket_eval(), operator=(), and PocketGrid().

bool protocols::pockets::PocketGrid::exemplarRestriction_
protected

Referenced by autoexpanding_pocket_eval(), operator=(), and PocketGrid().

core::Size protocols::pockets::PocketGrid::expdbno_
protected

Referenced by dumpExemplarToFile(), initialize(), operator=(), and PocketGrid().

bool protocols::pockets::PocketGrid::filterExemplars_
protected

Referenced by findExemplars(), operator=(), and PocketGrid().

std::vector< std::vector < std::vector <PtType> > > protocols::pockets::PocketGrid::grid_
protected

Referenced by alter_espGrid(), clusterPockets(), protocols::pockets::ComparisonGrid::compareCoverage(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), findClustersByExemplars(), findExemplars(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), getBounds(), isDeepTargetPocketPoint(), isProteinPoint(), isSurfacePoint(), isTargetPocketPoint(), isTooSmall(), linkExemplarsThroughSolvent(), mark(), protocols::pockets::ComparisonGrid::mark(), markDepth(), markEdgeDepth(), markOneEdgeDepth(), markPocketDepth(), move_pose_to_standard_orie(), newSearch(), operator=(), PocketGrid(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesSolvent(), touchesSS(), touchesSurface(), whatIsTooSmall(), and write_pocketGrid_to_pdb().

bool protocols::pockets::PocketGrid::ignoreBuriedPockets_
protected

Referenced by largestTargetPocketVolume(), and netTargetPocketVolume().

bool protocols::pockets::PocketGrid::ignoreExposedPockets_
protected

Referenced by largestTargetPocketVolume(), and netTargetPocketVolume().

core::Real protocols::pockets::PocketGrid::limit_x_
protected

Referenced by autoexpanding_pocket_eval().

core::Real protocols::pockets::PocketGrid::limit_y_
protected

Referenced by autoexpanding_pocket_eval().

core::Real protocols::pockets::PocketGrid::limit_z_
protected

Referenced by autoexpanding_pocket_eval().

bool protocols::pockets::PocketGrid::limitExemplars_
protected

Referenced by dumpExemplarToFile(), operator=(), and PocketGrid().

bool protocols::pockets::PocketGrid::markpsp_
protected

Referenced by autoexpanding_pocket_eval(), initialize(), newSearch(), operator=(), and PocketGrid().

bool protocols::pockets::PocketGrid::marksps_
protected

Referenced by autoexpanding_pocket_eval(), initialize(), operator=(), and PocketGrid().

const core::Size protocols::pockets::PocketGrid::MAX_TARGETS =2
staticprotected

Referenced by autoexpanding_pocket_eval(), getRelaxResidues(), and recenter().

core::Real protocols::pockets::PocketGrid::maxLen_
protected

Referenced by autoexpanding_pocket_eval().

core::Real protocols::pockets::PocketGrid::maxPockSize_
protected

Referenced by netTargetPocketVolume().

numeric::xyzVector<core::Real> protocols::pockets::PocketGrid::mid_
protected

Referenced by protocols::pockets::EggshellGrid::get_connolly_eggshell(), protocols::pockets::EggshellGrid::get_connolly_eggshell_on_grid(), get_connolly_surfacePoints_within_grid(), recenter(), protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand(), and protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand().

core::Real protocols::pockets::PocketGrid::minPockSize_
protected

Referenced by protocols::pockets::ComparisonGrid::compareCoverage(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), findExemplars(), get_pocket_distance(), getBounds(), largestTargetPocketVolume(), linkExemplarsThroughSolvent(), move_pose_to_standard_orie(), netTargetPocketVolume(), operator=(), and PocketGrid().

core::Size protocols::pockets::PocketGrid::numTargets_
protected

Referenced by dumpExemplarToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), findClusters(), findClustersByExemplars(), findExemplars(), getBounds(), initialize(), largestTargetPocketVolume(), linkExemplarsThroughSolvent(), markEdgeDepth(), and netTargetPocketVolume().

core::Size protocols::pockets::PocketGrid::pdbno_
protected

Referenced by dumpGridToFile(), initialize(), operator=(), and PocketGrid().

std::vector< std::vector < std::vector <core::Size> > > protocols::pockets::PocketGrid::pockets_
protected

Referenced by fill(), fillTargetPockets(), operator=(), PocketGrid(), and print().

core::Real protocols::pockets::PocketGrid::probe_rad_
protected

Referenced by autoexpanding_pocket_eval().

bool protocols::pockets::PocketGrid::restrictSize_
protected
numeric::xyzMatrix<core::Real> protocols::pockets::PocketGrid::rot_mat_
protected

Referenced by randomAngle(), rotatePoint(), and zeroAngle().

bool protocols::pockets::PocketGrid::search13_
protected

Referenced by newSearch(), operator=(), and PocketGrid().

bool protocols::pockets::PocketGrid::side_chains_only_
protected

Referenced by autoexpanding_pocket_eval().

core::Real protocols::pockets::PocketGrid::size_x_
protected

Referenced by autoexpanding_pocket_eval(), operator==(), and PocketGrid().

core::Real protocols::pockets::PocketGrid::size_y_
protected

Referenced by autoexpanding_pocket_eval(), operator==(), and PocketGrid().

core::Real protocols::pockets::PocketGrid::size_z_
protected

Referenced by autoexpanding_pocket_eval(), operator==(), and PocketGrid().

core::Real protocols::pockets::PocketGrid::spacing_
protected

Referenced by alter_espGrid(), alter_espGrid_with_bound_ligand(), autoexpanding_pocket_eval(), protocols::pockets::EggshellGrid::get_connolly_eggshell(), protocols::pockets::EggshellGrid::get_connolly_eggshell_on_grid(), get_connolly_surfacePoints_within_grid(), operator==(), PocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand(), and spacing().

bool protocols::pockets::PocketGrid::static_grid_
protected

Referenced by autoexpanding_pocket_eval(), and PocketGrid().

core::Real protocols::pockets::PocketGrid::stepSize_
protected

Referenced by alter_espGrid(), alter_espGrid_with_bound_ligand(), autoexpanding_pocket_eval(), clusterCPockets(), clusterPockets(), protocols::pockets::ComparisonGrid::compareCoverage(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpExemplarToFile(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), findClustersByExemplars(), findExemplars(), findPockets(), findPSP(), findSPS(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), getBounds(), initialize(), largestTargetPocketVolume(), linkExemplarsThroughSolvent(), mark(), protocols::pockets::ComparisonGrid::mark(), markDepth(), markOneEdgeDepth(), move_pose_to_standard_orie(), netTargetPocketVolume(), operator=(), PocketGrid(), recenter(), protocols::pockets::ElectrostaticpotentialGrid::resize_espGrid_to_match_pocketGrid(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), protocols::pockets::EggshellGrid::write_Grid_to_pdb(), and write_pocketGrid_to_pdb().

core::Real protocols::pockets::PocketGrid::surf_dist_
protected

Referenced by autoexpanding_pocket_eval().

core::Real protocols::pockets::PocketGrid::surf_score_
protected
std::string protocols::pockets::PocketGrid::tag_
protected

Referenced by dumpExemplarToFile(), dumpGridToFile(), operator=(), and PocketGrid().

core::Real protocols::pockets::PocketGrid::xcorn_
protected

Referenced by alter_espGrid(), alter_espGrid_with_bound_ligand(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpExemplarToFile(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), findExemplars(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), getBounds(), linkExemplarsThroughSolvent(), mark(), protocols::pockets::ComparisonGrid::mark(), move_pose_to_standard_orie(), operator=(), operator==(), PocketGrid(), recenter(), protocols::pockets::ElectrostaticpotentialGrid::resize_espGrid_to_match_pocketGrid(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), protocols::pockets::EggshellGrid::write_Grid_to_pdb(), and write_pocketGrid_to_pdb().

core::Size protocols::pockets::PocketGrid::xdim_
protected

Referenced by alter_espGrid(), alter_espGrid_with_bound_ligand(), autoexpanding_pocket_eval(), clusterCPockets(), clusterPockets(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), findClustersByExemplars(), findExemplars(), protocols::pockets::EggshellGrid::get_connolly_eggshell_on_grid(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), initialize(), isTooSmall(), mark(), protocols::pockets::ComparisonGrid::mark(), markDepth(), markOneEdgeDepth(), markPocketDepth(), newSearch(), operator=(), PocketGrid(), print(), recenter(), protocols::pockets::ElectrostaticpotentialGrid::resize_espGrid_to_match_pocketGrid(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesPS(), touchesSolvent(), touchesSS(), touchesSurface(), whatIsTooSmall(), protocols::pockets::EggshellGrid::write_Grid_to_pdb(), and write_pocketGrid_to_pdb().

core::Real protocols::pockets::PocketGrid::ycorn_
protected

Referenced by alter_espGrid(), alter_espGrid_with_bound_ligand(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpExemplarToFile(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), findExemplars(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), getBounds(), linkExemplarsThroughSolvent(), mark(), protocols::pockets::ComparisonGrid::mark(), move_pose_to_standard_orie(), operator=(), operator==(), PocketGrid(), recenter(), protocols::pockets::ElectrostaticpotentialGrid::resize_espGrid_to_match_pocketGrid(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), protocols::pockets::EggshellGrid::write_Grid_to_pdb(), and write_pocketGrid_to_pdb().

core::Size protocols::pockets::PocketGrid::ydim_
protected

Referenced by alter_espGrid(), alter_espGrid_with_bound_ligand(), autoexpanding_pocket_eval(), clusterCPockets(), clusterPockets(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), findClustersByExemplars(), findExemplars(), protocols::pockets::EggshellGrid::get_connolly_eggshell_on_grid(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), initialize(), isTooSmall(), mark(), protocols::pockets::ComparisonGrid::mark(), markDepth(), markOneEdgeDepth(), markPocketDepth(), newSearch(), operator=(), PocketGrid(), print(), recenter(), protocols::pockets::ElectrostaticpotentialGrid::resize_espGrid_to_match_pocketGrid(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesPS(), touchesSolvent(), touchesSS(), touchesSurface(), whatIsTooSmall(), protocols::pockets::EggshellGrid::write_Grid_to_pdb(), and write_pocketGrid_to_pdb().

core::Real protocols::pockets::PocketGrid::zcorn_
protected

Referenced by alter_espGrid(), alter_espGrid_with_bound_ligand(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpExemplarToFile(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), findExemplars(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), getBounds(), linkExemplarsThroughSolvent(), mark(), protocols::pockets::ComparisonGrid::mark(), move_pose_to_standard_orie(), operator=(), operator==(), PocketGrid(), recenter(), protocols::pockets::ElectrostaticpotentialGrid::resize_espGrid_to_match_pocketGrid(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), protocols::pockets::EggshellGrid::write_Grid_to_pdb(), and write_pocketGrid_to_pdb().

core::Size protocols::pockets::PocketGrid::zdim_
protected

Referenced by alter_espGrid(), alter_espGrid_with_bound_ligand(), autoexpanding_pocket_eval(), clusterCPockets(), clusterPockets(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), findClustersByExemplars(), findExemplars(), protocols::pockets::EggshellGrid::get_connolly_eggshell_on_grid(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), initialize(), isTooSmall(), mark(), protocols::pockets::ComparisonGrid::mark(), markDepth(), markOneEdgeDepth(), markPocketDepth(), newSearch(), operator=(), PocketGrid(), print(), recenter(), protocols::pockets::ElectrostaticpotentialGrid::resize_espGrid_to_match_pocketGrid(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesPS(), touchesSolvent(), touchesSS(), touchesSurface(), whatIsTooSmall(), protocols::pockets::EggshellGrid::write_Grid_to_pdb(), and write_pocketGrid_to_pdb().

The documentation for this class was generated from the following files:
Generated on Thu Mar 28 2019 04:35:49 for Rosetta by   doxygen 1.8.7