| alter_espGrid(std::string const &espGrid_filename) | protocols::pockets::PocketGrid | |
| alter_espGrid_with_bound_ligand(std::string const &espGrid_filename, core::pose::Pose const &protein_pose) | protocols::pockets::PocketGrid | |
| assign_esp_for_atom_grid_points(numeric::xyzVector< core::Real > atom_coord, core::Real const &inflated_radius) | protocols::pockets::ElectrostaticpotentialGrid | |
| assign_esp_for_protein_grid_points(core::pose::Pose const &protein_pose, std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list) | protocols::pockets::ElectrostaticpotentialGrid | |
| assign_esp_for_surface_grid_points(std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list) | protocols::pockets::ElectrostaticpotentialGrid | |
| assign_esp_for_surface_grid_points_by_nn(std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list) | protocols::pockets::ElectrostaticpotentialGrid | |
| autoexpanding_pocket_eval(core::conformation::Residue const ¢ral_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) | protocols::pockets::PocketGrid | |
| autoexpanding_pocket_eval(std::vector< core::conformation::ResidueCOP > const ¢ral_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) | protocols::pockets::PocketGrid | |
| autoexpanding_pocket_eval(core::conformation::Residue const ¢ral_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) | protocols::pockets::PocketGrid | |
| autoexpanding_pocket_eval(std::vector< core::conformation::ResidueCOP > const ¢ral_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) | protocols::pockets::PocketGrid | |
| bur_dist_ | protocols::pockets::PocketGrid | protected |
| bur_score_ | protocols::pockets::PocketGrid | protected |
| c_clusters_ | protocols::pockets::PocketGrid | protected |
| c_grid_ | protocols::pockets::PocketGrid | protected |
| cap_espGrid() | protocols::pockets::ElectrostaticpotentialGrid | |
| change_espGrid_for_darc(std::string const &espGrid_filename, core::pose::Pose const &protein_pose, PocketGrid const &pocket_grid) | protocols::pockets::ElectrostaticpotentialGrid | |
| clear() | protocols::pockets::PocketGrid | |
| clearSmallPockets(core::Size minsize) | protocols::pockets::PocketGrid | |
| clusterCPockets() | protocols::pockets::PocketGrid | |
| clusterPockets() | protocols::pockets::PocketGrid | |
| clusters_ | protocols::pockets::PocketGrid | protected |
| dim() const | protocols::pockets::PocketGrid | inline |
| dim_ | protocols::pockets::PocketGrid | protected |
| dumpExemplars_ | protocols::pockets::PocketGrid | protected |
| dumpExemplarToFile() | protocols::pockets::PocketGrid | |
| dumpExemplarToFile(std::string const &output_filename) | protocols::pockets::PocketGrid | |
| dumpGridToFile() | protocols::pockets::PocketGrid | |
| dumpGridToFile(std::string const &output_filename) | protocols::pockets::PocketGrid | |
| dumpTargetPocketsToFile(std::string const &output_filename) | protocols::pockets::PocketGrid | |
| dumpTargetPocketsToFile(std::string const &output_filename, numeric::xyzMatrix< core::Real > rot1, numeric::xyzMatrix< core::Real > rot2, numeric::xyzMatrix< core::Real > rot3) | protocols::pockets::PocketGrid | |
| dumpTargetPocketsToPDB(std::string const &output_filename, bool minipock=false) | protocols::pockets::PocketGrid | |
| dumpTargetPocketsToPDB(std::string const &output_filename, numeric::xyzMatrix< core::Real > rot1, numeric::xyzMatrix< core::Real > rot2, numeric::xyzMatrix< core::Real > rot3) | protocols::pockets::PocketGrid | |
| EGGSHELL enum value | protocols::pockets::PocketGrid | protected |
| EGGSHELL_SURROUNDING enum value | protocols::pockets::PocketGrid | protected |
| ElectrostaticpotentialGrid() | protocols::pockets::ElectrostaticpotentialGrid | inline |
| ElectrostaticpotentialGrid(std::string const &input_espGrid_filename, core::pose::Pose const &protein_pose, PocketGrid const &pocket_grid, bool delphi=false) | protocols::pockets::ElectrostaticpotentialGrid | |
| EMPTY enum value | protocols::pockets::PocketGrid | protected |
| espGrid_ | protocols::pockets::ElectrostaticpotentialGrid | |
| espGrid_dim_ | protocols::pockets::ElectrostaticpotentialGrid | private |
| espGrid_mid_ | protocols::pockets::ElectrostaticpotentialGrid | private |
| espGrid_point_list() const | protocols::pockets::ElectrostaticpotentialGrid | inline |
| espGrid_points_list_ | protocols::pockets::ElectrostaticpotentialGrid | private |
| espGrid_spacing_ | protocols::pockets::ElectrostaticpotentialGrid | private |
| exemplarRestriction_ | protocols::pockets::PocketGrid | protected |
| expdbno_ | protocols::pockets::PocketGrid | protected |
| fill(core::Size x, core::Size y, core::Size z) | protocols::pockets::PocketGrid | protected |
| fill_espGrid_values(std::string const &input_OEgrid_filename) | protocols::pockets::ElectrostaticpotentialGrid | |
| fill_espGrid_values_with_type(std::string const &input_OEgrid_filename) | protocols::pockets::ElectrostaticpotentialGrid | |
| fillTargetPockets() | protocols::pockets::PocketGrid | |
| filterExemplars_ | protocols::pockets::PocketGrid | protected |
| findClusters() | protocols::pockets::PocketGrid | |
| findClustersByExemplars() | protocols::pockets::PocketGrid | |
| findExemplars(core::pose::Pose const &inPose, core::Size const total_residues) | protocols::pockets::PocketGrid | |
| findPockets(core::Size thr, core::Real max) | protocols::pockets::PocketGrid | |
| findPSP(core::Size thr, core::Real max) | protocols::pockets::PocketGrid | |
| findSPS(core::Size thr, core::Real max) | protocols::pockets::PocketGrid | |
| get_atom_dist_from_connolly_surface(numeric::xyzVector< core::Real > atom_coord, std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list) | protocols::pockets::ElectrostaticpotentialGrid | |
| get_connolly_surfacePoints(core::pose::Pose const &protein_pose) const | protocols::pockets::PocketGrid | |
| get_connolly_surfacePoints_within_grid(std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list) | protocols::pockets::PocketGrid | |
| get_DELPHI_espGrid_values(std::string const &input_espGrid_filename) | protocols::pockets::ElectrostaticpotentialGrid | |
| get_oegrid_dimensions(std::string const &input_OEgrid_filename) | protocols::pockets::ElectrostaticpotentialGrid | |
| get_pocket_distance(PocketGrid const &template_pocket) const | protocols::pockets::PocketGrid | inline |
| get_pocket_distance(PocketGrid const &template_pocket, std::string const &comparison_pdbname) const | protocols::pockets::PocketGrid | |
| get_ZAP_espGrid_values(std::string const &input_espGrid_filename) | protocols::pockets::ElectrostaticpotentialGrid | |
| get_ZAP_espGrid_values_with_type(std::string const &input_espGrid_filename) | protocols::pockets::ElectrostaticpotentialGrid | |
| getBounds() | protocols::pockets::PocketGrid | |
| GetExemplarNumAtoms() const | protocols::pockets::PocketGrid | |
| GetExemplarNumClusters() const | protocols::pockets::PocketGrid | |
| GetExemplarNumPolarAtoms() const | protocols::pockets::PocketGrid | |
| getRelaxResidues(core::pose::Pose const &input_pose, std::string const &resids) | protocols::pockets::PocketGrid | static |
| grid_ | protocols::pockets::PocketGrid | protected |
| HSURFACE enum value | protocols::pockets::PocketGrid | protected |
| ignoreBuriedPockets_ | protocols::pockets::PocketGrid | protected |
| ignoreExposedPockets_ | protocols::pockets::PocketGrid | protected |
| init() | protocols::pockets::PocketGrid | protected |
| 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) | 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) | protocols::pockets::PocketGrid | |
| initialize(core::Vector const ¢er, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false) | protocols::pockets::PocketGrid | |
| initialize(core::Vector const ¢er, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false) | protocols::pockets::PocketGrid | |
| initialize(core::conformation::Residue const ¢ral_rsd, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false) | protocols::pockets::PocketGrid | |
| initialize(std::vector< core::conformation::ResidueCOP > const ¢ral_rsd, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false) | protocols::pockets::PocketGrid | |
| initialize_espGrid() | protocols::pockets::ElectrostaticpotentialGrid | |
| initialize_typGrid() | protocols::pockets::ElectrostaticpotentialGrid | |
| isDeepTargetPocketPoint(core::Size x, core::Size y, core::Size z) const | protocols::pockets::PocketGrid | inlineprotected |
| isProteinPoint(core::Size x, core::Size y, core::Size z) const | protocols::pockets::PocketGrid | inlineprotected |
| isSurfacePoint(core::Size x, core::Size y, core::Size z) const | protocols::pockets::PocketGrid | protected |
| isTargetPocketPoint(core::Size x, core::Size y, core::Size z) const | protocols::pockets::PocketGrid | inlineprotected |
| isTooSmall() const | protocols::pockets::PocketGrid | |
| largestTargetPocketVolume() | protocols::pockets::PocketGrid | |
| limit_x_ | protocols::pockets::PocketGrid | protected |
| limit_y_ | protocols::pockets::PocketGrid | protected |
| limit_z_ | protocols::pockets::PocketGrid | protected |
| limitExemplars_ | protocols::pockets::PocketGrid | protected |
| linkExemplarsThroughSolvent() | 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) | protocols::pockets::PocketGrid | |
| mark(core::Vector const ¢er, core::Real const &vdWd, core::Real const &buffer, bool polar=false, int targetResi=0) | protocols::pockets::PocketGrid | |
| mark_atom_espGrid_points(numeric::xyzVector< core::Real > atom_coord, core::Real const &vdWd) | protocols::pockets::ElectrostaticpotentialGrid | |
| mark_buried_solvent_points(core::pose::Pose const &protein_pose, std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list) | protocols::pockets::ElectrostaticpotentialGrid | |
| mark_protein_espGrid_points(core::pose::Pose const &protein_pose) | protocols::pockets::ElectrostaticpotentialGrid | |
| markDepth(core::Size x, core::Size y, core::Size z, core::Real const &surf_d, core::Real const &bur_d) | protocols::pockets::PocketGrid | |
| markEdgeDepth(core::Real const &surf_d, core::Real const &bur_d) | 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) | protocols::pockets::PocketGrid | |
| markPocketDepth(core::Real const &surf_d, core::Real const &bur_d) | protocols::pockets::PocketGrid | |
| markpsp_ | protocols::pockets::PocketGrid | protected |
| marksps_ | protocols::pockets::PocketGrid | protected |
| MAX_TARGETS | protocols::pockets::PocketGrid | protectedstatic |
| maxLen_ | protocols::pockets::PocketGrid | protected |
| maxPockSize_ | protocols::pockets::PocketGrid | protected |
| mid_ | protocols::pockets::PocketGrid | protected |
| minPockSize_ | protocols::pockets::PocketGrid | protected |
| move_pose_to_standard_orie(core::Size const ¢ral_seqpos, core::pose::Pose &pose) | protocols::pockets::PocketGrid | |
| netTargetPocketVolume() | 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) | protocols::pockets::PocketGrid | protected |
| NonPlaidFingerprint class | protocols::pockets::ElectrostaticpotentialGrid | friend |
| numTargets_ | protocols::pockets::PocketGrid | protected |
| operator=(const PocketGrid &gr) | protocols::pockets::PocketGrid | |
| operator==(PocketGrid const &other) const override | protocols::pockets::ElectrostaticpotentialGrid | virtual |
| pdbno_ | protocols::pockets::PocketGrid | protected |
| PO_BURIED enum value | protocols::pockets::PocketGrid | protected |
| PO_EDGE enum value | protocols::pockets::PocketGrid | protected |
| PO_SURF enum value | protocols::pockets::PocketGrid | protected |
| POCKET enum value | protocols::pockets::PocketGrid | protected |
| PocketGrid class | protocols::pockets::ElectrostaticpotentialGrid | friend |
| protocols::pockets::PocketGrid::PocketGrid() | protocols::pockets::PocketGrid | |
| protocols::pockets::PocketGrid::PocketGrid(const PocketGrid &gr) | protocols::pockets::PocketGrid | |
| protocols::pockets::PocketGrid::PocketGrid(core::conformation::Residue const ¢ral_rsd) | protocols::pockets::PocketGrid | |
| protocols::pockets::PocketGrid::PocketGrid(std::vector< core::conformation::ResidueCOP > const ¢ral_rsd) | protocols::pockets::PocketGrid | |
| protocols::pockets::PocketGrid::PocketGrid(core::conformation::Residue const ¢ral_rsd, core::Real x, core::Real y, core::Real z) | protocols::pockets::PocketGrid | |
| protocols::pockets::PocketGrid::PocketGrid(std::vector< core::conformation::ResidueCOP > const ¢ral_rsd, core::Real x, core::Real y, core::Real z) | protocols::pockets::PocketGrid | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| protocols::pockets::PocketGrid::PocketGrid(core::Vector const ¢er, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false) | protocols::pockets::PocketGrid | |
| protocols::pockets::PocketGrid::PocketGrid(core::Vector const ¢er, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false) | protocols::pockets::PocketGrid | |
| pockets_ | protocols::pockets::PocketGrid | protected |
| print() const | protocols::pockets::PocketGrid | |
| print_to_oegrid(std::string const &output_OEgrid_filename) | protocols::pockets::ElectrostaticpotentialGrid | |
| probe_rad_ | protocols::pockets::PocketGrid | protected |
| PROTEIN enum value | protocols::pockets::ElectrostaticpotentialGrid | |
| PSEUDO_PROTEIN enum value | protocols::pockets::ElectrostaticpotentialGrid | |
| PSP enum value | protocols::pockets::PocketGrid | protected |
| PSURFACE enum value | protocols::pockets::PocketGrid | protected |
| PtType enum name | protocols::pockets::ElectrostaticpotentialGrid | |
| randomAngle() | protocols::pockets::PocketGrid | |
| recenter(core::Real const &xc, core::Real const &yc, core::Real const &zc) | protocols::pockets::PocketGrid | |
| recenter(core::conformation::Residue const ¢ral_rsd) | protocols::pockets::PocketGrid | |
| recenter(std::vector< core::conformation::ResidueCOP > const ¢ral_rsds) | protocols::pockets::PocketGrid | |
| recenter(core::Vector const ¢er) | protocols::pockets::PocketGrid | |
| resize_espGrid_to_match_pocketGrid(std::string const &espGrid_filename, PocketGrid const &pg) | protocols::pockets::ElectrostaticpotentialGrid | |
| restrictSize_ | protocols::pockets::PocketGrid | protected |
| rot_mat_ | protocols::pockets::PocketGrid | protected |
| rotatePoint(core::Real x, core::Real y, core::Real z) | protocols::pockets::PocketGrid | protected |
| same_type_as_me(PocketGrid const &other) const override | protocols::pockets::ElectrostaticpotentialGrid | virtual |
| search13_ | protocols::pockets::PocketGrid | protected |
| set_protein_esp_to_zero() | protocols::pockets::ElectrostaticpotentialGrid | |
| set_surface_esp_to_zero() | protocols::pockets::ElectrostaticpotentialGrid | |
| setup_default_options() | protocols::pockets::PocketGrid | protected |
| side_chains_only_ | protocols::pockets::PocketGrid | protected |
| size_x_ | protocols::pockets::PocketGrid | protected |
| size_y_ | protocols::pockets::PocketGrid | protected |
| size_z_ | protocols::pockets::PocketGrid | protected |
| SOLVENT enum value | protocols::pockets::ElectrostaticpotentialGrid | |
| spacing() const | protocols::pockets::PocketGrid | inline |
| spacing_ | protocols::pockets::PocketGrid | protected |
| ST_SURFACE enum value | protocols::pockets::PocketGrid | protected |
| static_grid_ | protocols::pockets::PocketGrid | protected |
| stepSize_ | protocols::pockets::PocketGrid | protected |
| SUBTARGET enum value | protocols::pockets::PocketGrid | protected |
| surf_dist_ | protocols::pockets::PocketGrid | protected |
| surf_score_ | protocols::pockets::PocketGrid | protected |
| SURFACE enum value | protocols::pockets::ElectrostaticpotentialGrid | |
| T_SURFACE enum value | protocols::pockets::PocketGrid | protected |
| tag_ | protocols::pockets::PocketGrid | protected |
| TARGET enum value | protocols::pockets::PocketGrid | protected |
| targetPocketHeuristicScore() const | protocols::pockets::PocketGrid | |
| targetPocketHydrophobicProteinSurface() const | protocols::pockets::PocketGrid | |
| targetPocketPolarProteinSurface() const | protocols::pockets::PocketGrid | |
| targetPocketProteinSurface() const | protocols::pockets::PocketGrid | |
| targetPocketSolventSurface() const | protocols::pockets::PocketGrid | |
| targetPocketVolume(core::Real const &surf_sc, core::Real const &bur_sc) const | protocols::pockets::PocketGrid | |
| touchesPS(core::Size x, core::Size y, core::Size z) const | protocols::pockets::PocketGrid | protected |
| touchesSolvent(core::Size x, core::Size y, core::Size z) const | protocols::pockets::PocketGrid | protected |
| touchesSS(core::Size x, core::Size y, core::Size z) const | protocols::pockets::PocketGrid | protected |
| touchesSurface(core::Size x, core::Size y, core::Size z, bool polar, bool either=false) const | protocols::pockets::PocketGrid | protected |
| TP_BURIED enum value | protocols::pockets::PocketGrid | protected |
| TP_EDGE enum value | protocols::pockets::PocketGrid | protected |
| TP_POCKET enum value | protocols::pockets::PocketGrid | protected |
| TP_SURF enum value | protocols::pockets::PocketGrid | protected |
| typGrid_ | protocols::pockets::ElectrostaticpotentialGrid | |
| whatIsTooSmall() const | protocols::pockets::PocketGrid | |
| write_connollySurface_to_pdb(std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list, std::string const &output_pdbname) const | protocols::pockets::ElectrostaticpotentialGrid | |
| write_espGrid_to_pdb(std::string const &output_pdbname) const | protocols::pockets::ElectrostaticpotentialGrid | |
| write_pocketGrid_to_pdb(std::string const &output_filename) | protocols::pockets::PocketGrid | |
| xcorn_ | protocols::pockets::PocketGrid | protected |
| xdim_ | protocols::pockets::PocketGrid | protected |
| ycorn_ | protocols::pockets::PocketGrid | protected |
| ydim_ | protocols::pockets::PocketGrid | protected |
| zcorn_ | protocols::pockets::PocketGrid | protected |
| zdim_ | protocols::pockets::PocketGrid | protected |
| zeroAngle() | protocols::pockets::PocketGrid | |
| ~PocketGrid() override | protocols::pockets::PocketGrid | |
1.8.7