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protocols::pockets::PocketGrid Class Reference

@ More...

#include <PocketGrid.hh>

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

 PocketGrid ()
 
virtual ~PocketGrid ()
 
 PocketGrid (const PocketGrid &gr)
 
PocketGridoperator= (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::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< 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::Realrot_mat_
 

Friends

class EggshellGrid
 

Detailed Description

@

Member Enumeration Documentation

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 

Constructor & Destructor Documentation

protocols::pockets::PocketGrid::PocketGrid ( )
protocols::pockets::PocketGrid::~PocketGrid ( )
virtual
protocols::pockets::PocketGrid::PocketGrid ( const PocketGrid gr)
protocols::pockets::PocketGrid::PocketGrid ( core::conformation::Residue const &  central_rsd)
protocols::pockets::PocketGrid::PocketGrid ( std::vector< core::conformation::ResidueOP > const &  central_rsd)
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 
)
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 
)
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 
)
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 
)
protocols::pockets::PocketGrid::PocketGrid ( core::Vector const &  center,
core::Real  x,
core::Real const &  stepSize = 1,
bool  psp = false,
bool  sps = false 
)
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

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 
)
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 
)
bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval ( core::conformation::Residue const &  central_rsd,
core::pose::Pose const &  inPose 
)
bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval ( std::vector< core::conformation::ResidueOP > const &  central_rsd,
core::pose::Pose const &  inPose 
)
void protocols::pockets::PocketGrid::clear ( )
void protocols::pockets::PocketGrid::clearSmallPockets ( core::Size  minsize)
void protocols::pockets::PocketGrid::clusterPockets ( )
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 
)
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 
)
bool protocols::pockets::PocketGrid::DARC_pocket_eval ( core::conformation::Residue const &  central_rsd,
core::pose::Pose const &  inPose,
numeric::xyzVector< core::Real grid_center 
)
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 
)
void protocols::pockets::PocketGrid::dumpGridToFile ( )
void protocols::pockets::PocketGrid::dumpGridToFile ( std::string const &  output_filename)
bool protocols::pockets::PocketGrid::fill ( core::Size  x,
core::Size  y,
core::Size  z 
)
protected

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

Referenced by fillTargetPockets().

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

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

void protocols::pockets::PocketGrid::findClusters ( )
void protocols::pockets::PocketGrid::findPockets ( core::Size  thr,
core::Real  max 
)
void protocols::pockets::PocketGrid::findPSP ( core::Size  thr,
core::Real  max 
)
void protocols::pockets::PocketGrid::findSPS ( core::Size  thr,
core::Real  max 
)
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
std::vector< core::conformation::ResidueOP > protocols::pockets::PocketGrid::getRelaxResidues ( core::pose::Pose const &  input_pose,
std::string const &  resids 
)
static
void protocols::pockets::PocketGrid::init ( void  )
protected
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 
)
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 
)
void protocols::pockets::PocketGrid::initialize ( core::Vector const &  center,
core::Real  x,
core::Real const &  stepSize = 1,
bool  psp = false,
bool  sps = false 
)
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 
)
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 
)
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 
)
bool protocols::pockets::PocketGrid::isTooSmall ( ) const
core::Real protocols::pockets::PocketGrid::largestTargetPocketVolume ( )
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 
)
void protocols::pockets::PocketGrid::mark ( core::Vector const &  center,
core::Real const &  vdWd,
core::Real const &  buffer,
bool  polar = false,
bool  targetResi = false 
)

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 
)
void protocols::pockets::PocketGrid::markEdgeDepth ( core::Real const &  surf_d,
core::Real const &  bur_d 
)
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 
)
void protocols::pockets::PocketGrid::markPocketDepth ( core::Real const &  surf_d,
core::Real const &  bur_d 
)
void protocols::pockets::PocketGrid::move_pose_to_standard_orie ( core::Size const &  central_seqpos,
core::pose::Pose pose 
)
core::Real protocols::pockets::PocketGrid::netTargetPocketVolume ( )
void protocols::pockets::PocketGrid::newSearch ( core::Size  thr1,
core::Size  thr2,
core::Size  max1,
core::Size  max2,
bool  psp = false,
bool  sps = false 
)
protected
PocketGrid & protocols::pockets::PocketGrid::operator= ( const PocketGrid gr)
void protocols::pockets::PocketGrid::print ( )

References pockets_, 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 
)
void protocols::pockets::PocketGrid::recenter ( core::conformation::Residue const &  central_rsd)
void protocols::pockets::PocketGrid::recenter ( std::vector< core::conformation::ResidueOP > const &  central_rsds)

References recenter().

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

References recenter().

numeric::xyzVector< core::Real > protocols::pockets::PocketGrid::rotatePoint ( core::Real  x,
core::Real  y,
core::Real  z 
)
protected
void protocols::pockets::PocketGrid::setup_default_options ( )
protected
core::Real protocols::pockets::PocketGrid::targetPocketHeuristicScore ( ) const
core::Real protocols::pockets::PocketGrid::targetPocketHydrophobicProteinSurface ( ) const
core::Real protocols::pockets::PocketGrid::targetPocketPolarProteinSurface ( ) const
core::Real protocols::pockets::PocketGrid::targetPocketProteinSurface ( ) const
core::Real protocols::pockets::PocketGrid::targetPocketSolventSurface ( ) const
core::Real protocols::pockets::PocketGrid::targetPocketVolume ( core::Real const &  surf_sc,
core::Real const &  bur_sc 
) const
bool protocols::pockets::PocketGrid::touchesPS ( core::Size  x,
core::Size  y,
core::Size  z 
) const
protected
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
core::Vector protocols::pockets::PocketGrid::whatIsTooSmall ( ) const
void protocols::pockets::PocketGrid::zeroAngle ( )

References rot_mat_.

Friends And Related Function Documentation

friend class EggshellGrid
friend

Member Data Documentation

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

Referenced by setup_default_options().

PClusterSet protocols::pockets::PocketGrid::clusters_
protected
std::vector< std::vector < std::vector <PtType> > > protocols::pockets::PocketGrid::grid_
protected
core::Real protocols::pockets::PocketGrid::limit_x_
protected
core::Real protocols::pockets::PocketGrid::limit_y_
protected
core::Real protocols::pockets::PocketGrid::limit_z_
protected
bool protocols::pockets::PocketGrid::markpsp_
protected
bool protocols::pockets::PocketGrid::marksps_
protected
core::Real protocols::pockets::PocketGrid::maxLen_
protected
core::Real protocols::pockets::PocketGrid::maxPockSize_
protected
core::Real protocols::pockets::PocketGrid::minPockSize_
protected
core::Size protocols::pockets::PocketGrid::pdbno_
protected
std::vector< std::vector < std::vector <core::Size> > > protocols::pockets::PocketGrid::pockets_
protected
core::Real protocols::pockets::PocketGrid::probe_rad_
protected
bool protocols::pockets::PocketGrid::restrictSize_
protected

Referenced by setup_default_options().

numeric::xyzMatrix<core::Real> protocols::pockets::PocketGrid::rot_mat_
protected
bool protocols::pockets::PocketGrid::side_chains_only_
protected
core::Real protocols::pockets::PocketGrid::size_x_
protected
core::Real protocols::pockets::PocketGrid::size_y_
protected
core::Real protocols::pockets::PocketGrid::size_z_
protected
core::Real protocols::pockets::PocketGrid::spacing_
protected
core::Real protocols::pockets::PocketGrid::stepSize_
protected
core::Real protocols::pockets::PocketGrid::surf_dist_
protected
core::Real protocols::pockets::PocketGrid::surf_score_
protected

Referenced by setup_default_options().

std::string protocols::pockets::PocketGrid::tag_
protected
core::Real protocols::pockets::PocketGrid::xcorn_
protected
core::Size protocols::pockets::PocketGrid::xdim_
protected
core::Real protocols::pockets::PocketGrid::ycorn_
protected
core::Size protocols::pockets::PocketGrid::ydim_
protected
core::Real protocols::pockets::PocketGrid::zcorn_
protected
core::Size protocols::pockets::PocketGrid::zdim_
protected

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