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protocols::pockets::TargetPocketGrid Member List

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

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
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)protocols::pockets::PocketGrid
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)protocols::pockets::PocketGrid
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)protocols::pockets::PocketGrid
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)protocols::pockets::PocketGrid
bur_dist_protocols::pockets::PocketGridprotected
bur_score_protocols::pockets::PocketGridprotected
c_clusters_protocols::pockets::PocketGridprotected
c_grid_protocols::pockets::PocketGridprotected
clear()protocols::pockets::PocketGrid
clearSmallPockets(core::Size minsize)protocols::pockets::PocketGrid
clusterCPockets()protocols::pockets::PocketGrid
clusterPockets()protocols::pockets::PocketGrid
clusters_protocols::pockets::PocketGridprotected
dim() const protocols::pockets::PocketGridinline
dim_protocols::pockets::PocketGridprotected
dumpExemplars_protocols::pockets::PocketGridprotected
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::TargetPocketGrid
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 valueprotocols::pockets::PocketGridprotected
EGGSHELL_SURROUNDING enum valueprotocols::pockets::PocketGridprotected
EMPTY enum valueprotocols::pockets::PocketGridprotected
exemplarRestriction_protocols::pockets::PocketGridprotected
expdbno_protocols::pockets::PocketGridprotected
fill(core::Size x, core::Size y, core::Size z)protocols::pockets::PocketGridprotected
fillTargetPockets()protocols::pockets::PocketGrid
filterExemplars_protocols::pockets::PocketGridprotected
findClusters()protocols::pockets::TargetPocketGrid
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_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_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
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::PocketGridstatic
grid_protocols::pockets::PocketGridprotected
HSURFACE enum valueprotocols::pockets::PocketGridprotected
ignoreBuriedPockets_protocols::pockets::PocketGridprotected
ignoreExposedPockets_protocols::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::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)protocols::pockets::PocketGrid
isDeepTargetPocketPoint(core::Size x, core::Size y, core::Size z) const protocols::pockets::PocketGridinlineprotected
isProteinPoint(core::Size x, core::Size y, core::Size z) const protocols::pockets::PocketGridinlineprotected
isSurfacePoint(core::Size x, core::Size y, core::Size z) const protocols::pockets::PocketGridprotected
isTargetPocketPoint(core::Size x, core::Size y, core::Size z) const protocols::pockets::PocketGridinlineprotected
isTooSmall() const protocols::pockets::PocketGrid
largestTargetPocketVolume()protocols::pockets::PocketGrid
limit_x_protocols::pockets::PocketGridprotected
limit_y_protocols::pockets::PocketGridprotected
limit_z_protocols::pockets::PocketGridprotected
limitExemplars_protocols::pockets::PocketGridprotected
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 &center, core::Real const &vdWd, core::Real const &buffer, bool polar=false, int targetResi=0)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
MAX_TARGETSprotocols::pockets::PocketGridprotectedstatic
maxLen_protocols::pockets::PocketGridprotected
maxPockSize_protocols::pockets::PocketGridprotected
mid_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 thr3, core::Size max1, core::Size max2, core::Size max3, bool psp=false, bool sps=false)protocols::pockets::PocketGridprotected
numTargets_protocols::pockets::PocketGridprotected
operator=(const PocketGrid &gr)protocols::pockets::PocketGrid
operator==(PocketGrid const &other) const protocols::pockets::PocketGridvirtual
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::ResidueCOP > const &central_rsd)protocols::pockets::PocketGrid
PocketGrid(core::conformation::Residue const &central_rsd, core::Real x, core::Real y, core::Real z)protocols::pockets::PocketGrid
PocketGrid(std::vector< core::conformation::ResidueCOP > const &central_rsd, 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)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() const 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::ResidueCOP > 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
same_type_as_me(PocketGrid const &other) const overrideprotocols::pockets::TargetPocketGridvirtual
search13_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() const protocols::pockets::PocketGridinline
spacing_protocols::pockets::PocketGridprotected
ST_SURFACE enum valueprotocols::pockets::PocketGridprotected
static_grid_protocols::pockets::PocketGridprotected
stepSize_protocols::pockets::PocketGridprotected
SUBTARGET enum valueprotocols::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
TargetPocketGrid(const PocketGrid &gr)protocols::pockets::TargetPocketGrid
TargetPocketGrid(std::string const &fname)protocols::pockets::TargetPocketGrid
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_pocketGrid_to_pdb(std::string const &output_filename)protocols::pockets::PocketGrid
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() overrideprotocols::pockets::PocketGrid