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protocols::pockets::ElectrostaticpotentialGrid Class Reference

#include <PocketGrid.hh>

Inheritance diagram for protocols::pockets::ElectrostaticpotentialGrid:
Inheritance graph
[legend]

Public Types

enum  PtType { PROTEIN, SURFACE, SOLVENT, PSEUDO_PROTEIN }
 

Public Member Functions

 ElectrostaticpotentialGrid ()
 
void initialize_espGrid ()
 
void initialize_typGrid ()
 
 ElectrostaticpotentialGrid (std::string const &input_espGrid_filename, core::pose::Pose const &protein_pose, PocketGrid const &pocket_grid, bool delphi=false)
 
void mark_protein_espGrid_points (core::pose::Pose const &protein_pose)
 
void mark_atom_espGrid_points (numeric::xyzVector< core::Real > atom_coord, core::Real const &vdWd)
 
std::list< utility::vector1
< core::Real > > const & 
espGrid_point_list () const
 
void write_espGrid_to_pdb (std::string const &output_pdbname) const
 
void write_connollySurface_to_pdb (std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list, std::string const &output_pdbname) const
 
void get_oegrid_dimensions (std::string const &input_OEgrid_filename)
 
void fill_espGrid_values (std::string const &input_OEgrid_filename)
 
void fill_espGrid_values_with_type (std::string const &input_OEgrid_filename)
 
void print_to_oegrid (std::string const &output_OEgrid_filename)
 
void resize_espGrid_to_match_pocketGrid (std::string const &espGrid_filename, PocketGrid const &pg)
 
void assign_esp_for_protein_grid_points (core::pose::Pose const &protein_pose, std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)
 
void assign_esp_for_atom_grid_points (numeric::xyzVector< core::Real > atom_coord, core::Real const &inflated_radius)
 
void assign_esp_for_surface_grid_points (std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)
 
void assign_esp_for_surface_grid_points_by_nn (std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)
 
core::Real get_atom_dist_from_connolly_surface (numeric::xyzVector< core::Real > atom_coord, std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)
 
void mark_buried_solvent_points (core::pose::Pose const &protein_pose, std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)
 
void get_ZAP_espGrid_values (std::string const &input_espGrid_filename)
 
void get_ZAP_espGrid_values_with_type (std::string const &input_espGrid_filename)
 
void get_DELPHI_espGrid_values (std::string const &input_espGrid_filename)
 
void change_espGrid_for_darc (std::string const &espGrid_filename, core::pose::Pose const &protein_pose, PocketGrid const &pocket_grid)
 
void set_surface_esp_to_zero ()
 
void set_protein_esp_to_zero ()
 
void cap_espGrid ()
 
bool operator== (PocketGrid const &other) const override
 
bool same_type_as_me (PocketGrid const &other) const override
 
- Public Member Functions inherited from protocols::pockets::PocketGrid
 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 clearSmallPockets (core::Size minsize)
 
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)
 

Public Attributes

std::vector< std::vector
< std::vector< core::Real > > > 
espGrid_
 
std::vector< std::vector
< std::vector< PtType > > > 
typGrid_
 

Private Attributes

numeric::xyzVector< core::SizeespGrid_dim_
 
numeric::xyzVector< core::RealespGrid_mid_
 
core::Real espGrid_spacing_
 
std::list< utility::vector1
< core::Real > > 
espGrid_points_list_
 

Friends

class NonPlaidFingerprint
 
class PocketGrid
 

Additional Inherited Members

- Static Public Member Functions inherited from protocols::pockets::PocketGrid
static std::vector
< core::conformation::ResidueCOP
getRelaxResidues (core::pose::Pose const &input_pose, std::string const &resids)
 
- Protected Types inherited from protocols::pockets::PocketGrid
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 inherited from protocols::pockets::PocketGrid
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 inherited from protocols::pockets::PocketGrid
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 inherited from protocols::pockets::PocketGrid
static const core::Size MAX_TARGETS =2
 

Member Enumeration Documentation

Enumerator
PROTEIN 
SURFACE 
SOLVENT 
PSEUDO_PROTEIN 

Constructor & Destructor Documentation

protocols::pockets::ElectrostaticpotentialGrid::ElectrostaticpotentialGrid ( )
inline
protocols::pockets::ElectrostaticpotentialGrid::ElectrostaticpotentialGrid ( std::string const &  input_espGrid_filename,
core::pose::Pose const &  protein_pose,
PocketGrid const &  pocket_grid,
bool  delphi = false 
)

Member Function Documentation

void protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_atom_grid_points ( numeric::xyzVector< core::Real atom_coord,
core::Real const &  inflated_radius 
)
void protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points ( core::pose::Pose const &  protein_pose,
std::list< numeric::xyzVector< core::Real > > const &  surfacePoints_list 
)
void protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_surface_grid_points ( std::list< numeric::xyzVector< core::Real > > const &  surfacePoints_list)
void protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_surface_grid_points_by_nn ( std::list< numeric::xyzVector< core::Real > > const &  surfacePoints_list)
void protocols::pockets::ElectrostaticpotentialGrid::cap_espGrid ( )

References espGrid_, and espGrid_dim_.

Referenced by change_espGrid_for_darc().

void protocols::pockets::ElectrostaticpotentialGrid::change_espGrid_for_darc ( std::string const &  espGrid_filename,
core::pose::Pose const &  protein_pose,
PocketGrid const &  pocket_grid 
)
std::list< utility::vector1<core::Real> > const& protocols::pockets::ElectrostaticpotentialGrid::espGrid_point_list ( ) const
inline

References espGrid_points_list_.

void protocols::pockets::ElectrostaticpotentialGrid::fill_espGrid_values ( std::string const &  input_OEgrid_filename)
void protocols::pockets::ElectrostaticpotentialGrid::fill_espGrid_values_with_type ( std::string const &  input_OEgrid_filename)
core::Real protocols::pockets::ElectrostaticpotentialGrid::get_atom_dist_from_connolly_surface ( numeric::xyzVector< core::Real atom_coord,
std::list< numeric::xyzVector< core::Real > > const &  surfacePoints_list 
)
void protocols::pockets::ElectrostaticpotentialGrid::get_DELPHI_espGrid_values ( std::string const &  input_espGrid_filename)
void protocols::pockets::ElectrostaticpotentialGrid::get_oegrid_dimensions ( std::string const &  input_OEgrid_filename)
void protocols::pockets::ElectrostaticpotentialGrid::get_ZAP_espGrid_values ( std::string const &  input_espGrid_filename)
void protocols::pockets::ElectrostaticpotentialGrid::get_ZAP_espGrid_values_with_type ( std::string const &  input_espGrid_filename)
void protocols::pockets::ElectrostaticpotentialGrid::initialize_espGrid ( )
void protocols::pockets::ElectrostaticpotentialGrid::initialize_typGrid ( )
void protocols::pockets::ElectrostaticpotentialGrid::mark_atom_espGrid_points ( numeric::xyzVector< core::Real atom_coord,
core::Real const &  vdWd 
)
void protocols::pockets::ElectrostaticpotentialGrid::mark_buried_solvent_points ( core::pose::Pose const &  protein_pose,
std::list< numeric::xyzVector< core::Real > > const &  surfacePoints_list 
)
void protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points ( core::pose::Pose const &  protein_pose)
bool protocols::pockets::ElectrostaticpotentialGrid::operator== ( PocketGrid const &  other) const
overridevirtual
void protocols::pockets::ElectrostaticpotentialGrid::print_to_oegrid ( std::string const &  output_OEgrid_filename)
void protocols::pockets::ElectrostaticpotentialGrid::resize_espGrid_to_match_pocketGrid ( std::string const &  espGrid_filename,
PocketGrid const &  pg 
)
bool protocols::pockets::ElectrostaticpotentialGrid::same_type_as_me ( PocketGrid const &  other) const
overridevirtual

Reimplemented from protocols::pockets::PocketGrid.

void protocols::pockets::ElectrostaticpotentialGrid::set_protein_esp_to_zero ( )

References espGrid_, espGrid_dim_, PROTEIN, and typGrid_.

Referenced by change_espGrid_for_darc().

void protocols::pockets::ElectrostaticpotentialGrid::set_surface_esp_to_zero ( )

References espGrid_, espGrid_dim_, SURFACE, and typGrid_.

Referenced by change_espGrid_for_darc().

void protocols::pockets::ElectrostaticpotentialGrid::write_connollySurface_to_pdb ( std::list< numeric::xyzVector< core::Real > > const &  surfacePoints_list,
std::string const &  output_pdbname 
) const
void protocols::pockets::ElectrostaticpotentialGrid::write_espGrid_to_pdb ( std::string const &  output_pdbname) const

Friends And Related Function Documentation

friend class NonPlaidFingerprint
friend
friend class PocketGrid
friend

Member Data Documentation

std::vector< std::vector < std::vector <core::Real> > > protocols::pockets::ElectrostaticpotentialGrid::espGrid_
numeric::xyzVector<core::Size> protocols::pockets::ElectrostaticpotentialGrid::espGrid_dim_
private
numeric::xyzVector<core::Real> protocols::pockets::ElectrostaticpotentialGrid::espGrid_mid_
private
std::list< utility::vector1<core::Real> > protocols::pockets::ElectrostaticpotentialGrid::espGrid_points_list_
private

Referenced by espGrid_point_list(), and operator==().

core::Real protocols::pockets::ElectrostaticpotentialGrid::espGrid_spacing_
private
std::vector< std::vector < std::vector <PtType> > > protocols::pockets::ElectrostaticpotentialGrid::typGrid_

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