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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)
 
PocketGridoperator= (const PocketGrid &gr)
 
numeric::xyzVector< core::Realdim () 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 findClusters ()
 
void findExemplars (core::pose::Pose const &inPose, core::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, core::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, core::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::RealgetBounds ()
 
core::Size GetExemplarNumClusters () const
 
core::Size GetExemplarNumAtoms () const
 
core::Size GetExemplarNumPolarAtoms () const
 
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::ResidueCOPgetRelaxResidues (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::RealrotatePoint (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::Realmid_
 
numeric::xyzVector< core::Sizedim_
 
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::Realrot_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

◆ PtType

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

◆ PocketGrid() [1/12]

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

◆ ~PocketGrid()

protocols::pockets::PocketGrid::~PocketGrid ( )
overridedefault

◆ PocketGrid() [2/12]

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

◆ PocketGrid() [3/12]

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

◆ PocketGrid() [4/12]

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

◆ PocketGrid() [5/12]

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

◆ PocketGrid() [6/12]

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

◆ PocketGrid() [7/12]

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 
)

◆ PocketGrid() [8/12]

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 
)

◆ PocketGrid() [9/12]

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 
)

◆ PocketGrid() [10/12]

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 
)

◆ PocketGrid() [11/12]

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

◆ PocketGrid() [12/12]

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 
)

Member Function Documentation

◆ alter_espGrid()

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

◆ alter_espGrid_with_bound_ligand()

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

◆ autoexpanding_pocket_eval() [1/4]

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 
)

◆ autoexpanding_pocket_eval() [2/4]

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

◆ autoexpanding_pocket_eval() [3/4]

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 
)

◆ autoexpanding_pocket_eval() [4/4]

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

◆ clear()

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

◆ clusterCPockets()

void protocols::pockets::PocketGrid::clusterCPockets ( )

◆ clusterPockets()

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

◆ dim()

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

References dim_.

◆ dumpExemplarToFile() [1/2]

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

◆ dumpExemplarToFile() [2/2]

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

◆ dumpGridToFile() [1/2]

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

◆ dumpGridToFile() [2/2]

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

◆ dumpTargetPocketsToFile() [1/2]

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

◆ dumpTargetPocketsToFile() [2/2]

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 
)

◆ dumpTargetPocketsToPDB() [1/2]

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

◆ dumpTargetPocketsToPDB() [2/2]

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 
)

◆ fill()

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

◆ fillTargetPockets()

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

◆ findClusters()

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

◆ findClustersByExemplars()

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

◆ findExemplars()

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

◆ findPockets()

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

◆ findPSP()

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

◆ findSPS()

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

◆ get_connolly_surfacePoints()

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

◆ get_connolly_surfacePoints_within_grid()

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

◆ get_pocket_distance() [1/2]

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

References get_pocket_distance().

Referenced by get_pocket_distance().

◆ get_pocket_distance() [2/2]

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

◆ getBounds()

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

◆ GetExemplarNumAtoms()

core::Size protocols::pockets::PocketGrid::GetExemplarNumAtoms ( ) const

◆ GetExemplarNumClusters()

core::Size protocols::pockets::PocketGrid::GetExemplarNumClusters ( ) const

◆ GetExemplarNumPolarAtoms()

core::Size protocols::pockets::PocketGrid::GetExemplarNumPolarAtoms ( ) const

◆ getRelaxResidues()

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

◆ init()

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

◆ initialize() [1/6]

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 
)

◆ initialize() [2/6]

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 
)

◆ initialize() [3/6]

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 
)

◆ initialize() [4/6]

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 
)

◆ initialize() [5/6]

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

◆ initialize() [6/6]

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 
)

◆ isDeepTargetPocketPoint()

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().

◆ isProteinPoint()

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().

◆ isSurfacePoint()

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().

◆ isTargetPocketPoint()

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().

◆ isTooSmall()

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

◆ largestTargetPocketVolume()

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

◆ linkExemplarsThroughSolvent()

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

◆ mark() [1/2]

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 
)

◆ mark() [2/2]

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

◆ markDepth()

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

◆ markEdgeDepth()

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

◆ markOneEdgeDepth()

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 
)

◆ markPocketDepth()

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

◆ move_pose_to_standard_orie()

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

◆ netTargetPocketVolume()

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

◆ newSearch()

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

◆ operator=()

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

◆ operator==()

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

◆ print()

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

◆ randomAngle()

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

References rot_mat_.

◆ recenter() [1/4]

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

◆ recenter() [2/4]

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

◆ recenter() [3/4]

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

◆ recenter() [4/4]

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

◆ rotatePoint()

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

◆ same_type_as_me()

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

◆ setup_default_options()

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

◆ spacing()

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

◆ targetPocketHeuristicScore()

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

◆ targetPocketHydrophobicProteinSurface()

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

◆ targetPocketPolarProteinSurface()

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

◆ targetPocketProteinSurface()

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

◆ targetPocketSolventSurface()

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

◆ targetPocketVolume()

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

◆ touchesPS()

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().

◆ touchesSolvent()

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().

◆ touchesSS()

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().

◆ touchesSurface()

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

◆ whatIsTooSmall()

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

◆ write_pocketGrid_to_pdb()

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

◆ zeroAngle()

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

References rot_mat_.

Friends And Related Function Documentation

◆ ComparisonGrid

friend class ComparisonGrid
friend

◆ EggshellGrid

friend class EggshellGrid
friend

◆ ElectrostaticpotentialGrid

friend class ElectrostaticpotentialGrid
friend

◆ NonPlaidFingerprint

friend class NonPlaidFingerprint
friend

◆ TargetPocketGrid

friend class TargetPocketGrid
friend

Member Data Documentation

◆ bur_dist_

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

◆ bur_score_

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

◆ c_clusters_

CClusterSet protocols::pockets::PocketGrid::c_clusters_
protected

◆ c_grid_

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

◆ clusters_

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

◆ dim_

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

◆ dumpExemplars_

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

◆ exemplarRestriction_

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

◆ expdbno_

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

◆ filterExemplars_

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

◆ grid_

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

◆ ignoreBuriedPockets_

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

◆ ignoreExposedPockets_

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

◆ limit_x_

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

◆ limit_y_

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

◆ limit_z_

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

◆ limitExemplars_

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

◆ markpsp_

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

◆ marksps_

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

◆ MAX_TARGETS

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

◆ maxLen_

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

◆ maxPockSize_

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

Referenced by netTargetPocketVolume().

◆ mid_

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

◆ minPockSize_

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

◆ numTargets_

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

◆ pdbno_

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

◆ pockets_

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

◆ probe_rad_

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

◆ restrictSize_

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

◆ rot_mat_

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

◆ search13_

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

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

◆ side_chains_only_

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

◆ size_x_

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

◆ size_y_

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

◆ size_z_

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

◆ spacing_

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

◆ static_grid_

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

◆ stepSize_

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

◆ surf_dist_

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

◆ surf_score_

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

◆ tag_

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

◆ xcorn_

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

◆ xdim_

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

◆ ycorn_

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

◆ ydim_

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

◆ zcorn_

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

◆ zdim_

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

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