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Rosetta 3.5
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Rosetta 3.5
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This is the complete list of members for protocols::pockets::PocketGrid, including all inherited members.
| autoexpanding_pocket_eval(core::conformation::Residue const ¢ral_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues) | protocols::pockets::PocketGrid | |
| autoexpanding_pocket_eval(std::vector< core::conformation::ResidueOP > const ¢ral_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues) | protocols::pockets::PocketGrid | |
| autoexpanding_pocket_eval(core::conformation::Residue const ¢ral_rsd, core::pose::Pose const &inPose) | protocols::pockets::PocketGrid | |
| autoexpanding_pocket_eval(std::vector< core::conformation::ResidueOP > const ¢ral_rsd, core::pose::Pose const &inPose) | protocols::pockets::PocketGrid | |
| bur_dist_ | protocols::pockets::PocketGrid | protected |
| bur_score_ | protocols::pockets::PocketGrid | protected |
| clear() | protocols::pockets::PocketGrid | |
| clearSmallPockets(core::Size minsize) | protocols::pockets::PocketGrid | |
| clusterPockets() | protocols::pockets::PocketGrid | |
| clusters_ | protocols::pockets::PocketGrid | protected |
| DARC_autoexpanding_pocket_eval(core::conformation::Residue const ¢ral_rsd, core::pose::Pose const &inPose, numeric::xyzVector< core::Real > grid_center) | protocols::pockets::PocketGrid | |
| DARC_autoexpanding_pocket_eval(core::conformation::Residue const ¢ral_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues, numeric::xyzVector< core::Real > grid_center) | protocols::pockets::PocketGrid | |
| DARC_pocket_eval(core::conformation::Residue const ¢ral_rsd, core::pose::Pose const &inPose, numeric::xyzVector< core::Real > grid_center) | protocols::pockets::PocketGrid | |
| DARC_pocket_eval(core::conformation::Residue const ¢ral_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues, numeric::xyzVector< core::Real > grid_center) | protocols::pockets::PocketGrid | |
| dumpGridToFile() | protocols::pockets::PocketGrid | |
| dumpGridToFile(std::string const &output_filename) | protocols::pockets::PocketGrid | |
| EGGSHELL enum value | protocols::pockets::PocketGrid | protected |
| EGGSHELL_SURROUNDING enum value | protocols::pockets::PocketGrid | protected |
| EggshellGrid class | protocols::pockets::PocketGrid | friend |
| EMPTY enum value | protocols::pockets::PocketGrid | protected |
| fill(core::Size x, core::Size y, core::Size z) | protocols::pockets::PocketGrid | protected |
| fillTargetPockets() | protocols::pockets::PocketGrid | |
| findClusters() | 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_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 | |
| 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 |
| 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::ResidueOP > 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 | |
| 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 |
| mark(core::Real x, core::Real y, core::Real z, core::Real const &vdWd, core::Real const &buffer, bool polar=false, bool targetResi=false) | protocols::pockets::PocketGrid | |
| mark(core::Vector const ¢er, core::Real const &vdWd, core::Real const &buffer, bool polar=false, bool targetResi=false) | protocols::pockets::PocketGrid | |
| 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 |
| maxLen_ | protocols::pockets::PocketGrid | protected |
| maxPockSize_ | 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 max1, core::Size max2, bool psp=false, bool sps=false) | protocols::pockets::PocketGrid | protected |
| operator=(const PocketGrid &gr) | protocols::pockets::PocketGrid | |
| 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() | protocols::pockets::PocketGrid | |
| PocketGrid(const PocketGrid &gr) | protocols::pockets::PocketGrid | |
| PocketGrid(core::conformation::Residue const ¢ral_rsd) | protocols::pockets::PocketGrid | |
| PocketGrid(std::vector< core::conformation::ResidueOP > const ¢ral_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 ¢er, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false) | 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() | protocols::pockets::PocketGrid | |
| probe_rad_ | protocols::pockets::PocketGrid | protected |
| PROTEIN enum value | protocols::pockets::PocketGrid | protected |
| PSP enum value | protocols::pockets::PocketGrid | protected |
| PSURFACE enum value | protocols::pockets::PocketGrid | protected |
| PtType enum name | protocols::pockets::PocketGrid | protected |
| 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::ResidueOP > const ¢ral_rsds) | protocols::pockets::PocketGrid | |
| recenter(core::Vector const ¢er) | protocols::pockets::PocketGrid | |
| 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 |
| 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 |
| spacing_ | protocols::pockets::PocketGrid | protected |
| stepSize_ | protocols::pockets::PocketGrid | protected |
| surf_dist_ | protocols::pockets::PocketGrid | protected |
| surf_score_ | protocols::pockets::PocketGrid | protected |
| 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 |
| whatIsTooSmall() const | 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() | protocols::pockets::PocketGrid | virtual |
1.8.4