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protocols::pockets::EggshellGrid Member List

This is the complete list of members for protocols::pockets::EggshellGrid, including all inherited members.

autoexpanding_pocket_eval(core::conformation::Residue const &central_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 &central_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues)protocols::pockets::PocketGrid
autoexpanding_pocket_eval(core::conformation::Residue const &central_rsd, core::pose::Pose const &inPose)protocols::pockets::PocketGrid
autoexpanding_pocket_eval(std::vector< core::conformation::ResidueOP > const &central_rsd, core::pose::Pose const &inPose)protocols::pockets::PocketGrid
bur_dist_protocols::pockets::PocketGridprotected
bur_score_protocols::pockets::PocketGridprotected
calculate_center_xyz(std::list< numeric::xyzVector< core::Real > > const &pocketshell_coord_list)protocols::pockets::EggshellGrid
clear()protocols::pockets::PocketGrid
clearSmallPockets(core::Size minsize)protocols::pockets::PocketGrid
clusterPockets()protocols::pockets::PocketGrid
clusters_protocols::pockets::PocketGridprotected
DARC_autoexpanding_pocket_eval(core::conformation::Residue const &central_rsd, core::pose::Pose const &inPose, numeric::xyzVector< core::Real > grid_center)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)protocols::pockets::PocketGrid
DARC_pocket_eval(core::conformation::Residue const &central_rsd, core::pose::Pose const &inPose, numeric::xyzVector< core::Real > grid_center)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)protocols::pockets::PocketGrid
dump_eggshell(std::string const &fname) const protocols::pockets::EggshellGrid
dumpGridToFile()protocols::pockets::PocketGrid
dumpGridToFile(std::string const &output_filename)protocols::pockets::PocketGrid
EGGSHELL enum valueprotocols::pockets::PocketGridprotected
eggshell_CoM_protocols::pockets::EggshellGridprivate
eggshell_coord_list() const protocols::pockets::EggshellGridinline
eggshell_coord_list_protocols::pockets::EggshellGridprivate
EGGSHELL_SURROUNDING enum valueprotocols::pockets::PocketGridprotected
EggshellGrid(const PocketGrid &gr)protocols::pockets::EggshellGrid
EggshellGrid(const PocketGrid &ext_grd, std::list< numeric::xyzVector< core::Real > > const &eggshell_coord_list)protocols::pockets::EggshellGrid
EggshellGrid(std::string const &fname)protocols::pockets::EggshellGrid
EMPTY enum valueprotocols::pockets::PocketGridprotected
extra_coord_list() const protocols::pockets::EggshellGridinline
extra_coord_list_protocols::pockets::EggshellGridprivate
fill(core::Size x, core::Size y, core::Size z)protocols::pockets::PocketGridprotected
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_eggshell_distance(EggshellGrid const &template_eggshell) const protocols::pockets::EggshellGridinline
get_eggshell_distance(EggshellGrid const &template_eggshell, std::string const &comparison_pdbname) const protocols::pockets::EggshellGrid
get_pocket_distance(PocketGrid const &template_pocket) const protocols::pockets::PocketGridinline
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::PocketGridstatic
grid_protocols::pockets::PocketGridprotected
HSURFACE enum valueprotocols::pockets::PocketGridprotected
init()protocols::pockets::PocketGridprotected
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 &center, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false)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)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)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)protocols::pockets::PocketGrid
isTooSmall() const protocols::pockets::PocketGrid
largestTargetPocketVolume()protocols::pockets::PocketGrid
limit_x_protocols::pockets::PocketGridprotected
limit_y_protocols::pockets::PocketGridprotected
limit_z_protocols::pockets::PocketGridprotected
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 &center, 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::PocketGridprotected
marksps_protocols::pockets::PocketGridprotected
maxLen_protocols::pockets::PocketGridprotected
maxPockSize_protocols::pockets::PocketGridprotected
minPockSize_protocols::pockets::PocketGridprotected
move_pose_to_standard_orie(core::Size const &central_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::PocketGridprotected
NonPlaidFingerprint classprotocols::pockets::EggshellGridfriend
operator=(const PocketGrid &gr)protocols::pockets::PocketGrid
pdbno_protocols::pockets::PocketGridprotected
PO_BURIED enum valueprotocols::pockets::PocketGridprotected
PO_EDGE enum valueprotocols::pockets::PocketGridprotected
PO_SURF enum valueprotocols::pockets::PocketGridprotected
POCKET enum valueprotocols::pockets::PocketGridprotected
PocketGrid()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)protocols::pockets::PocketGrid
pockets_protocols::pockets::PocketGridprotected
print()protocols::pockets::PocketGrid
probe_rad_protocols::pockets::PocketGridprotected
PROTEIN enum valueprotocols::pockets::PocketGridprotected
PSP enum valueprotocols::pockets::PocketGridprotected
PSURFACE enum valueprotocols::pockets::PocketGridprotected
PtType enum nameprotocols::pockets::PocketGridprotected
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 &central_rsd)protocols::pockets::PocketGrid
recenter(std::vector< core::conformation::ResidueOP > const &central_rsds)protocols::pockets::PocketGrid
recenter(core::Vector const &center)protocols::pockets::PocketGrid
restrictSize_protocols::pockets::PocketGridprotected
rot_mat_protocols::pockets::PocketGridprotected
rotatePoint(core::Real x, core::Real y, core::Real z)protocols::pockets::PocketGridprotected
setup_default_options()protocols::pockets::PocketGridprotected
side_chains_only_protocols::pockets::PocketGridprotected
size_x_protocols::pockets::PocketGridprotected
size_y_protocols::pockets::PocketGridprotected
size_z_protocols::pockets::PocketGridprotected
spacing_protocols::pockets::PocketGridprotected
stepSize_protocols::pockets::PocketGridprotected
surf_dist_protocols::pockets::PocketGridprotected
surf_score_protocols::pockets::PocketGridprotected
T_SURFACE enum valueprotocols::pockets::PocketGridprotected
tag_protocols::pockets::PocketGridprotected
TARGET enum valueprotocols::pockets::PocketGridprotected
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::PocketGridprotected
touchesSolvent(core::Size x, core::Size y, core::Size z) const protocols::pockets::PocketGridprotected
touchesSS(core::Size x, core::Size y, core::Size z) const protocols::pockets::PocketGridprotected
touchesSurface(core::Size x, core::Size y, core::Size z, bool polar, bool either=false) const protocols::pockets::PocketGridprotected
TP_BURIED enum valueprotocols::pockets::PocketGridprotected
TP_EDGE enum valueprotocols::pockets::PocketGridprotected
TP_POCKET enum valueprotocols::pockets::PocketGridprotected
TP_SURF enum valueprotocols::pockets::PocketGridprotected
whatIsTooSmall() const protocols::pockets::PocketGrid
write_eggshell_to_pdb(std::string const &output_pdbname) const protocols::pockets::EggshellGrid
write_grid_to_pdb(const PocketGrid &gr, std::string const &output_pdbname) const protocols::pockets::EggshellGrid
xcorn_protocols::pockets::PocketGridprotected
xdim_protocols::pockets::PocketGridprotected
ycorn_protocols::pockets::PocketGridprotected
ydim_protocols::pockets::PocketGridprotected
zcorn_protocols::pockets::PocketGridprotected
zdim_protocols::pockets::PocketGridprotected
zeroAngle()protocols::pockets::PocketGrid
~PocketGrid()protocols::pockets::PocketGridvirtual
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