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protocols::pockets::PocketGrid Class Reference

@ More...

#include <PocketGrid.hh>

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Public Member Functions

 PocketGrid ()
 
virtual ~PocketGrid ()
 
 PocketGrid (const PocketGrid &gr)
 
PocketGrid & operator= (const PocketGrid &gr)
 
 PocketGrid (core::conformation::Residue const &central_rsd)
 
 PocketGrid (std::vector< core::conformation::ResidueOP > const &central_rsd)
 
 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::ResidueOP > 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::ResidueOP > 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, bool targetResi=false)
 
void mark (core::Vector const &center, core::Real const &vdWd, core::Real const &buffer, bool polar=false, bool targetResi=false)
 
void clearSmallPockets (core::Size minsize)
 
void findClusters ()
 
void dumpGridToFile ()
 
void dumpGridToFile (std::string const &output_filename)
 
void fillTargetPockets ()
 
void print ()
 
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 ()
 
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::constraints::XYZ_Func const &xyz_func, Size const total_residues)
 
bool autoexpanding_pocket_eval (std::vector< core::conformation::ResidueOP > const &central_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues)
 
bool autoexpanding_pocket_eval (core::conformation::Residue const &central_rsd, core::pose::Pose const &inPose)
 
bool autoexpanding_pocket_eval (std::vector< core::conformation::ResidueOP > const &central_rsd, core::pose::Pose const &inPose)
 
bool DARC_autoexpanding_pocket_eval (core::conformation::Residue const &central_rsd, core::pose::Pose const &inPose, numeric::xyzVector< core::Real > grid_center)
 
bool DARC_autoexpanding_pocket_eval (core::conformation::Residue const &central_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues, numeric::xyzVector< core::Real > grid_center)
 
bool DARC_pocket_eval (core::conformation::Residue const &central_rsd, core::pose::Pose const &inPose, numeric::xyzVector< core::Real > grid_center)
 
bool DARC_pocket_eval (core::conformation::Residue const &central_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues, numeric::xyzVector< core::Real > grid_center)
 
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
 

Static Public Member Functions

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

Protected Types

enum  PtType {
  EMPTY, PROTEIN, TARGET, HSURFACE,
  PSURFACE, POCKET, PO_SURF, PO_BURIED,
  T_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 max1, core::Size max2, 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
 
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< core::Size > > > 		pockets_
 
core::Size xdim_
 
core::Size ydim_
 
core::Size zdim_
 
core::Real xcorn_
 
core::Real ycorn_
 
core::Real zcorn_
 
core::Real stepSize_
 
core::Real maxLen_
 
std::string tag_
 
core::Size pdbno_
 
PClusterSet clusters_
 
core::Real size_x_
 
core::Real size_y_
 
core::Real size_z_
 
core::Real spacing_
 
core::Real limit_x_
 
core::Real limit_y_
 
core::Real limit_z_
 
bool restrictSize_
 
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_
 
core::Real minPockSize_
 
core::Real maxPockSize_
 
numeric::xyzMatrix< core::Real > rot_mat_
 

Friends

class EggshellGrid
 

Detailed Description

@

Definition at line 98 of file PocketGrid.hh.

Member Enumeration Documentation

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

Definition at line 104 of file PocketGrid.hh.

Constructor & Destructor Documentation

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

Definition at line 364 of file PocketGrid.cc.

References setup_default_options().

protocols::pockets::PocketGrid::~PocketGrid ( )
virtual

Definition at line 331 of file PocketGrid.cc.

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

Definition at line 299 of file PocketGrid.cc.

References grid_, markpsp_, marksps_, minPockSize_, pdbno_, pockets_, setup_default_options(), stepSize_, tag_, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

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

Definition at line 368 of file PocketGrid.cc.

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

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

Definition at line 375 of file PocketGrid.cc.

References initialize(), markpsp_, marksps_, setup_default_options(), size_x_, size_y_, size_z_, 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 
)

Definition at line 414 of file PocketGrid.cc.

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 
)

Definition at line 421 of file PocketGrid.cc.

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 
)

Definition at line 428 of file PocketGrid.cc.

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 
)

Definition at line 447 of file PocketGrid.cc.

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 
)

Definition at line 469 of file PocketGrid.cc.

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 
)

Definition at line 512 of file PocketGrid.cc.

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

Member Function Documentation

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval ( core::conformation::Residue const &  central_rsd,
core::scoring::constraints::XYZ_Func const &  xyz_func,
Size const  total_residues 
)

Definition at line 1695 of file PocketGrid.cc.

References core::conformation::Residue::atom(), bur_dist_, findClusters(), findPockets(), findPSP(), findSPS(), initialize(), isTooSmall(), limit_x_, limit_y_, limit_z_, mark(), markEdgeDepth(), markPocketDepth(), markpsp_, marksps_, maxLen_, probe_rad_, recenter(), core::scoring::constraints::XYZ_Func::residue(), rotatePoint(), core::conformation::Residue::seqpos(), side_chains_only_, size_x_, size_y_, size_z_, spacing_, stepSize_, surf_dist_, core::conformation::Atom::type(), whatIsTooSmall(), xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval(), and move_pose_to_standard_orie().

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval ( std::vector< core::conformation::ResidueOP > const &  central_rsd,
core::scoring::constraints::XYZ_Func const &  xyz_func,
Size const  total_residues 
)

Definition at line 1686 of file PocketGrid.cc.

References autoexpanding_pocket_eval().

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval ( core::conformation::Residue const &  central_rsd,
core::pose::Pose const &  inPose 
)

Definition at line 1681 of file PocketGrid.cc.

References autoexpanding_pocket_eval(), core::pose::Pose::conformation(), and core::pose::Pose::total_residue().

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval ( std::vector< core::conformation::ResidueOP > const &  central_rsd,
core::pose::Pose const &  inPose 
)

Definition at line 1690 of file PocketGrid.cc.

References autoexpanding_pocket_eval(), core::pose::Pose::conformation(), and core::pose::Pose::total_residue().

void protocols::pockets::PocketGrid::clear ( )

Definition at line 245 of file PocketGrid.cc.

References protocols::pockets::PClusterSet::clear(), clusters_, grid_, and pockets_.

Referenced by init().

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

Definition at line 967 of file PocketGrid.cc.

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

Definition at line 1117 of file PocketGrid.cc.

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().

bool protocols::pockets::PocketGrid::DARC_autoexpanding_pocket_eval ( core::conformation::Residue const &  central_rsd,
core::pose::Pose const &  inPose,
numeric::xyzVector< core::Real >  grid_center 
)

Definition at line 1755 of file PocketGrid.cc.

References core::pose::Pose::conformation(), and core::pose::Pose::total_residue().

bool protocols::pockets::PocketGrid::DARC_autoexpanding_pocket_eval ( core::conformation::Residue const &  central_rsd,
core::scoring::constraints::XYZ_Func const &  xyz_func,
Size const  total_residues,
numeric::xyzVector< core::Real >  grid_center 
)

Definition at line 1760 of file PocketGrid.cc.

References core::conformation::Residue::atom(), bur_dist_, findClusters(), findPockets(), findPSP(), findSPS(), initialize(), isTooSmall(), limit_x_, limit_y_, limit_z_, mark(), markEdgeDepth(), markPocketDepth(), markpsp_, marksps_, maxLen_, probe_rad_, recenter(), core::scoring::constraints::XYZ_Func::residue(), rotatePoint(), core::conformation::Residue::seqpos(), side_chains_only_, size_x_, size_y_, size_z_, spacing_, stepSize_, surf_dist_, core::conformation::Atom::type(), whatIsTooSmall(), xdim_, ydim_, and zdim_.

bool protocols::pockets::PocketGrid::DARC_pocket_eval ( core::conformation::Residue const &  central_rsd,
core::pose::Pose const &  inPose,
numeric::xyzVector< core::Real >  grid_center 
)

Definition at line 1813 of file PocketGrid.cc.

References core::pose::Pose::conformation(), and core::pose::Pose::total_residue().

bool protocols::pockets::PocketGrid::DARC_pocket_eval ( core::conformation::Residue const &  central_rsd,
core::scoring::constraints::XYZ_Func const &  xyz_func,
Size const  total_residues,
numeric::xyzVector< core::Real >  grid_center 
)

Definition at line 1818 of file PocketGrid.cc.

References core::conformation::Residue::atom(), bur_dist_, findClusters(), findPockets(), findPSP(), findSPS(), mark(), markEdgeDepth(), markPocketDepth(), markpsp_, marksps_, maxLen_, probe_rad_, core::scoring::constraints::XYZ_Func::residue(), rotatePoint(), core::conformation::Residue::seqpos(), side_chains_only_, stepSize_, surf_dist_, core::conformation::Atom::type(), xdim_, ydim_, and zdim_.

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

Definition at line 984 of file PocketGrid.cc.

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

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

Definition at line 992 of file PocketGrid.cc.

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

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

Definition at line 654 of file PocketGrid.cc.

References EMPTY, grid_, POCKET, pockets_, TP_POCKET, xdim_, ydim_, and zdim_.

Referenced by fillTargetPockets().

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

Definition at line 771 of file PocketGrid.cc.

References EMPTY, fill(), grid_, pockets_, TP_POCKET, xdim_, ydim_, and zdim_.

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

Definition at line 1545 of file PocketGrid.cc.

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

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

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

Definition at line 630 of file PocketGrid.cc.

References newSearch(), and stepSize_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

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

Definition at line 638 of file PocketGrid.cc.

References newSearch(), and stepSize_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

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

Definition at line 646 of file PocketGrid.cc.

References newSearch(), and stepSize_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

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

Definition at line 224 of file PocketGrid.hh.

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

Definition at line 2024 of file PocketGrid.cc.

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

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

Definition at line 586 of file PocketGrid.cc.

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

Referenced by protocols::pockets::PocketConstraint::read_def().

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

Definition at line 251 of file PocketGrid.cc.

References clear(), EMPTY, grid_, pockets_, xdim_, ydim_, and zdim_.

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

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 
)

Definition at line 402 of file PocketGrid.cc.

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

Referenced by autoexpanding_pocket_eval(), DARC_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 
)

Definition at line 435 of file PocketGrid.cc.

References init(), markpsp_, marksps_, 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 
)

Definition at line 454 of file PocketGrid.cc.

References init(), markpsp_, marksps_, 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 
)

Definition at line 476 of file PocketGrid.cc.

References init(), markpsp_, marksps_, 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 
)

Definition at line 488 of file PocketGrid.cc.

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

void protocols::pockets::PocketGrid::initialize ( std::vector< core::conformation::ResidueOP > 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 
)

Definition at line 500 of file PocketGrid.cc.

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

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

Definition at line 1602 of file PocketGrid.cc.

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

Referenced by autoexpanding_pocket_eval(), and DARC_autoexpanding_pocket_eval().

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

Definition at line 1591 of file PocketGrid.cc.

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

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,
bool  targetResi = false 
)

Definition at line 900 of file PocketGrid.cc.

References grid_, HSURFACE, PROTEIN, PSURFACE, stepSize_, T_SURFACE, TARGET, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and mark().

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

Definition at line 896 of file PocketGrid.cc.

References 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 
)

Definition at line 1216 of file PocketGrid.cc.

References EMPTY, grid_, HSURFACE, PO_BURIED, PO_EDGE, PO_SURF, POCKET, PSURFACE, stepSize_, T_SURFACE, 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 
)

Definition at line 1201 of file PocketGrid.cc.

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

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

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 
)

Definition at line 1342 of file PocketGrid.cc.

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 
)

Definition at line 1192 of file PocketGrid.cc.

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

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

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

Definition at line 1872 of file PocketGrid.cc.

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(), setup_default_options(), stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, ycorn_, and zcorn_.

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

Definition at line 1595 of file PocketGrid.cc.

References clusters_, protocols::pockets::PClusterSet::getNetClusterSize(), maxPockSize_, minPockSize_, and stepSize_.

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

Definition at line 799 of file PocketGrid.cc.

References core::pack::dunbrack::c, EMPTY, grid_, HSURFACE, markpsp_, POCKET, PSP, PSURFACE, T_SURFACE, TP_POCKET, xdim_, ydim_, and zdim_.

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

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

Definition at line 333 of file PocketGrid.cc.

References grid_, markpsp_, marksps_, minPockSize_, pdbno_, pockets_, stepSize_, tag_, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

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

Definition at line 972 of file PocketGrid.cc.

References pockets_, xdim_, ydim_, and zdim_.

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

Definition at line 382 of file PocketGrid.cc.

References rot_mat_.

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

Definition at line 519 of file PocketGrid.cc.

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

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

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

Definition at line 528 of file PocketGrid.cc.

References core::conformation::Residue::atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), recenter(), core::conformation::Atom::type(), and core::conformation::Atom::xyz().

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

Definition at line 553 of file PocketGrid.cc.

References recenter().

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

Definition at line 582 of file PocketGrid.cc.

References recenter().

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

Definition at line 396 of file PocketGrid.cc.

References rot_mat_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and recenter().

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

Definition at line 266 of file PocketGrid.cc.

References bur_dist_, bur_score_, limit_x_, limit_y_, limit_z_, markpsp_, marksps_, maxLen_, maxPockSize_, minPockSize_, probe_rad_, restrictSize_, rot_mat_, side_chains_only_, size_x_, size_y_, size_z_, spacing_, surf_dist_, and surf_score_.

Referenced by move_pose_to_standard_orie(), and PocketGrid().

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

Definition at line 1522 of file PocketGrid.cc.

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

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

Definition at line 1490 of file PocketGrid.cc.

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

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

Definition at line 1506 of file PocketGrid.cc.

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

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

Definition at line 1474 of file PocketGrid.cc.

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

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

Definition at line 1458 of file PocketGrid.cc.

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

Definition at line 1445 of file PocketGrid.cc.

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

Definition at line 702 of file PocketGrid.cc.

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

Referenced by targetPocketHeuristicScore().

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

Definition at line 678 of file PocketGrid.cc.

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

Definition at line 692 of file PocketGrid.cc.

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

Definition at line 737 of file PocketGrid.cc.

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

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

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

Definition at line 1648 of file PocketGrid.cc.

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

Referenced by autoexpanding_pocket_eval(), and DARC_autoexpanding_pocket_eval().

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

Definition at line 392 of file PocketGrid.cc.

References rot_mat_.

Friends And Related Function Documentation

friend class EggshellGrid
friend

Definition at line 101 of file PocketGrid.hh.

Member Data Documentation

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

Definition at line 141 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and setup_default_options().

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

Definition at line 140 of file PocketGrid.hh.

Referenced by setup_default_options().

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

Definition at line 127 of file PocketGrid.hh.

Referenced by clear(), clusterPockets(), dumpGridToFile(), findClusters(), get_pocket_distance(), largestTargetPocketVolume(), markEdgeDepth(), move_pose_to_standard_orie(), netTargetPocketVolume(), and recenter().

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

Definition at line 105 of file PocketGrid.hh.

Referenced by clear(), clusterPockets(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), init(), isTooSmall(), mark(), markDepth(), markEdgeDepth(), markOneEdgeDepth(), markPocketDepth(), move_pose_to_standard_orie(), newSearch(), operator=(), PocketGrid(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesPS(), touchesSolvent(), touchesSS(), touchesSurface(), and whatIsTooSmall().

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

Definition at line 133 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and setup_default_options().

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

Definition at line 134 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and setup_default_options().

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

Definition at line 135 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and setup_default_options().

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

Definition at line 143 of file PocketGrid.hh.

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

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

Definition at line 144 of file PocketGrid.hh.

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

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

Definition at line 114 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and setup_default_options().

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

Definition at line 146 of file PocketGrid.hh.

Referenced by netTargetPocketVolume(), and setup_default_options().

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

Definition at line 145 of file PocketGrid.hh.

Referenced by dumpGridToFile(), get_pocket_distance(), largestTargetPocketVolume(), move_pose_to_standard_orie(), netTargetPocketVolume(), operator=(), PocketGrid(), and setup_default_options().

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

Definition at line 126 of file PocketGrid.hh.

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

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

Definition at line 106 of file PocketGrid.hh.

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

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

Definition at line 137 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and setup_default_options().

bool protocols::pockets::PocketGrid::restrictSize_
protected

Definition at line 136 of file PocketGrid.hh.

Referenced by setup_default_options().

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

Definition at line 147 of file PocketGrid.hh.

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

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

Definition at line 142 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and setup_default_options().

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

Definition at line 129 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), PocketGrid(), and setup_default_options().

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

Definition at line 130 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), PocketGrid(), and setup_default_options().

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

Definition at line 131 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), PocketGrid(), and setup_default_options().

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

Definition at line 132 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), PocketGrid(), and setup_default_options().

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

Definition at line 113 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), clusterPockets(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), findPockets(), findPSP(), findSPS(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), initialize(), largestTargetPocketVolume(), mark(), markDepth(), markOneEdgeDepth(), move_pose_to_standard_orie(), netTargetPocketVolume(), operator=(), PocketGrid(), recenter(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

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

Definition at line 139 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::surf_score_
protected

Definition at line 138 of file PocketGrid.hh.

Referenced by setup_default_options().

std::string protocols::pockets::PocketGrid::tag_
protected

Definition at line 115 of file PocketGrid.hh.

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

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

Definition at line 110 of file PocketGrid.hh.

Referenced by protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), mark(), move_pose_to_standard_orie(), operator=(), PocketGrid(), recenter(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

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

Definition at line 109 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), clusterPockets(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), init(), initialize(), isTooSmall(), mark(), markDepth(), markOneEdgeDepth(), markPocketDepth(), newSearch(), operator=(), PocketGrid(), print(), recenter(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesPS(), touchesSolvent(), touchesSS(), touchesSurface(), whatIsTooSmall(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

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

Definition at line 111 of file PocketGrid.hh.

Referenced by protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), mark(), move_pose_to_standard_orie(), operator=(), PocketGrid(), recenter(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

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

Definition at line 109 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), clusterPockets(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), init(), initialize(), isTooSmall(), mark(), markDepth(), markOneEdgeDepth(), markPocketDepth(), newSearch(), operator=(), PocketGrid(), print(), recenter(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesPS(), touchesSolvent(), touchesSS(), touchesSurface(), whatIsTooSmall(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

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

Definition at line 112 of file PocketGrid.hh.

Referenced by protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), mark(), move_pose_to_standard_orie(), operator=(), PocketGrid(), recenter(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

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

Definition at line 109 of file PocketGrid.hh.

Referenced by autoexpanding_pocket_eval(), clusterPockets(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), init(), initialize(), isTooSmall(), mark(), markDepth(), markOneEdgeDepth(), markPocketDepth(), newSearch(), operator=(), PocketGrid(), print(), recenter(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesPS(), touchesSolvent(), touchesSS(), touchesSurface(), whatIsTooSmall(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

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