pockets

Bindings for protocols::pockets namespace

class pyrosetta.rosetta.protocols.pockets.CCluster

Bases: pybind11_object

@ Cluster of exemplar points

class Cxyz

Bases: pybind11_object

property absX

property absY

property absZ

assign(self: pyrosetta.rosetta.protocols.pockets.CCluster.Cxyz, : pyrosetta.rosetta.protocols.pockets.CCluster.Cxyz) → pyrosetta.rosetta.protocols.pockets.CCluster.Cxyz

C++: protocols::pockets::CCluster::Cxyz::operator=(const struct protocols::pockets::CCluster::Cxyz &) –> struct protocols::pockets::CCluster::Cxyz &

property atom_type

property x

property y

property z

add(*args, **kwargs)

Overloaded function.

1. add(self: pyrosetta.rosetta.protocols.pockets.CCluster, x: int, y: int, z: int, atype: str) -> None

2. add(self: pyrosetta.rosetta.protocols.pockets.CCluster, x: int, y: int, z: int, atype: str, absX: float) -> None

3. add(self: pyrosetta.rosetta.protocols.pockets.CCluster, x: int, y: int, z: int, atype: str, absX: float, absY: float) -> None

4. add(self: pyrosetta.rosetta.protocols.pockets.CCluster, x: int, y: int, z: int, atype: str, absX: float, absY: float, absZ: float) -> None

C++: protocols::pockets::CCluster::add(unsigned long, unsigned long, unsigned long, std::string, double, double, double) –> void

property filterExemplars_

isClose(self: pyrosetta.rosetta.protocols.pockets.CCluster, c2: pyrosetta.rosetta.protocols.pockets.CCluster) → bool

C++: protocols::pockets::CCluster::isClose(const class protocols::pockets::CCluster &) const –> bool

isSolventExposed(self: pyrosetta.rosetta.protocols.pockets.CCluster) → bool

C++: protocols::pockets::CCluster::isSolventExposed() const –> bool

isTarget(*args, **kwargs)

Overloaded function.

1. isTarget(self: pyrosetta.rosetta.protocols.pockets.CCluster) -> bool

2. isTarget(self: pyrosetta.rosetta.protocols.pockets.CCluster, numTargets: int) -> bool

C++: protocols::pockets::CCluster::isTarget(unsigned long) const –> bool

property points_

size(self: pyrosetta.rosetta.protocols.pockets.CCluster) → int

C++: protocols::pockets::CCluster::size() const –> int

testNeighbor(self: pyrosetta.rosetta.protocols.pockets.CCluster, c2: pyrosetta.rosetta.protocols.pockets.CCluster) → bool

C++: protocols::pockets::CCluster::testNeighbor(class protocols::pockets::CCluster &) –> bool

class pyrosetta.rosetta.protocols.pockets.CClusterSet

Bases: pybind11_object

@ Set of clusters of exemplar points

assign(self: pyrosetta.rosetta.protocols.pockets.CClusterSet, old: pyrosetta.rosetta.protocols.pockets.CClusterSet) → pyrosetta.rosetta.protocols.pockets.CClusterSet

C++: protocols::pockets::CClusterSet::operator=(const class protocols::pockets::CClusterSet &) –> class protocols::pockets::CClusterSet &

clear(self: pyrosetta.rosetta.protocols.pockets.CClusterSet) → None

C++: protocols::pockets::CClusterSet::clear() –> void

findClusters(self: pyrosetta.rosetta.protocols.pockets.CClusterSet) → None

C++: protocols::pockets::CClusterSet::findClusters() –> void

getLargestClusterSize(self: pyrosetta.rosetta.protocols.pockets.CClusterSet, stepSize: float, minClusterSize: float, numTargets: int, ignoreBuried: bool, ignoreSurface: bool) → float

C++: protocols::pockets::CClusterSet::getLargestClusterSize(const double &, const double &, const unsigned long &, bool, bool) –> double

getNetClusterSize(self: pyrosetta.rosetta.protocols.pockets.CClusterSet, stepSize: float, minClusterSize: float, numTargets: int, ignoreBuried: bool, ignoreSurface: bool) → float

C++: protocols::pockets::CClusterSet::getNetClusterSize(const double &, const double &, const unsigned long &, bool, bool) –> double

size(self: pyrosetta.rosetta.protocols.pockets.CClusterSet) → int

C++: protocols::pockets::CClusterSet::size() –> unsigned long

class pyrosetta.rosetta.protocols.pockets.ComparisonGrid

Bases: pybind11_object

@

compareCoverage(self: pyrosetta.rosetta.protocols.pockets.ComparisonGrid, gr: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::ComparisonGrid::compareCoverage(const class protocols::pockets::PocketGrid &) –> double

mark(self: pyrosetta.rosetta.protocols.pockets.ComparisonGrid, gr: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, penalty: float) → float

C++: protocols::pockets::ComparisonGrid::mark(const class protocols::pockets::PocketGrid &, double, double, double, const double &, const double &) –> double

class pyrosetta.rosetta.protocols.pockets.DarcParticleSwarmMinimizer

Bases: ParticleSwarmMinimizer

assign(self: pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer, : pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer) → pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer

C++: core::optimization::ParticleSwarmMinimizer::operator=(const class core::optimization::ParticleSwarmMinimizer &) –> class core::optimization::ParticleSwarmMinimizer &

class pyrosetta.rosetta.protocols.pockets.EggshellGrid

Bases: PocketGrid

@

GetExemplarNumAtoms(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumAtoms() const –> unsigned long

GetExemplarNumClusters(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumClusters() const –> unsigned long

GetExemplarNumPolarAtoms(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumPolarAtoms() const –> unsigned long

alter_espGrid(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, espGrid_filename: str) → None

C++: protocols::pockets::PocketGrid::alter_espGrid(const std::string &) –> void

alter_espGrid_with_bound_ligand(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, espGrid_filename: str, protein_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(const std::string &, const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, : pyrosetta.rosetta.protocols.pockets.EggshellGrid) → pyrosetta.rosetta.protocols.pockets.EggshellGrid

C++: protocols::pockets::EggshellGrid::operator=(const class protocols::pockets::EggshellGrid &) –> class protocols::pockets::EggshellGrid &

autoexpanding_pocket_eval(*args, **kwargs)

Overloaded function.

1. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int) -> bool

2. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool) -> bool

3. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float) -> bool

4. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float) -> bool

5. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class core::conformation::Residue &, const class core::scoring::func::XYZ_Func &, const unsigned long, bool, double, double, double) –> bool

6. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int) -> bool

7. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool) -> bool

8. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float) -> bool

9. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float) -> bool

10. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::scoring::func::XYZ_Func &, const unsigned long, bool, double, double, double) –> bool

11. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose) -> bool

12. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool) -> bool

13. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float) -> bool

14. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float) -> bool

15. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class core::conformation::Residue &, const class core::pose::Pose &, bool, double, double, double) –> bool

16. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose) -> bool

17. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool) -> bool

18. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float) -> bool

19. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float) -> bool

20. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::pose::Pose &, bool, double, double, double) –> bool

calculate_center_xyz(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, pocketshell_coord_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::EggshellGrid::calculate_center_xyz(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> class numeric::xyzVector<double>

clear(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clear() –> void

clusterCPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clusterCPockets() –> void

clusterPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clusterPockets() –> void

dim(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::PocketGrid::dim() const –> class numeric::xyzVector<double>

dumpExemplarToFile(*args, **kwargs)

Overloaded function.

1. dumpExemplarToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None

C++: protocols::pockets::PocketGrid::dumpExemplarToFile() –> void

2. dumpExemplarToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpExemplarToFile(const std::string &) –> void

dumpGridToFile(*args, **kwargs)

Overloaded function.

1. dumpGridToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None

C++: protocols::pockets::PocketGrid::dumpGridToFile() –> void

2. dumpGridToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpGridToFile(const std::string &) –> void

dumpTargetPocketsToFile(*args, **kwargs)

Overloaded function.

1. dumpTargetPocketsToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToFile(const std::string &) –> void

2. dumpTargetPocketsToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str, rot1: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot2: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot3: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToFile(const std::string &, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>) –> void

dumpTargetPocketsToPDB(*args, **kwargs)

Overloaded function.

1. dumpTargetPocketsToPDB(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

2. dumpTargetPocketsToPDB(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str, minipock: bool) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToPDB(const std::string &, bool) –> void

3. dumpTargetPocketsToPDB(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str, rot1: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot2: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot3: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToPDB(const std::string &, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>) –> void

dump_eggshell(*args, **kwargs)

Overloaded function.

1. dump_eggshell(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, fname: str) -> None

C++: protocols::pockets::EggshellGrid::dump_eggshell(const std::string &) const –> void

2. dump_eggshell(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, fname: str, rot1: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot2: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot3: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

C++: protocols::pockets::EggshellGrid::dump_eggshell(const std::string &, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>) const –> void

eggshell_coord_list(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::EggshellGrid::eggshell_coord_list() const –> const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &

extra_coord_list(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::EggshellGrid::extra_coord_list() const –> const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &

fillTargetPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::fillTargetPockets() –> void

findClusters(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::findClusters() –> void

findClustersByExemplars(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::findClustersByExemplars() –> void

findExemplars(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, inPose: pyrosetta.rosetta.core.pose.Pose, total_residues: int) → None

C++: protocols::pockets::PocketGrid::findExemplars(const class core::pose::Pose &, const unsigned long) –> void

findPSP(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findPSP(unsigned long, double) –> void

findPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findPockets(unsigned long, double) –> void

findSPS(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findSPS(unsigned long, double) –> void

getBounds(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::pockets::PocketGrid::getBounds() –> class utility::vector1<double, class std::allocator<double> >

static getRelaxResidues(input_pose: pyrosetta.rosetta.core.pose.Pose, resids: str) → pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t

C++: protocols::pockets::PocketGrid::getRelaxResidues(const class core::pose::Pose &, const std::string &) –> class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

get_connolly_eggshell(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t, eggGrid: pyrosetta.rosetta.protocols.pockets.PocketGrid, extGrid: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::EggshellGrid::get_connolly_eggshell(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class protocols::pockets::PocketGrid &, const class protocols::pockets::PocketGrid &) –> void

get_connolly_eggshell_on_grid(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t, eggGrid: pyrosetta.rosetta.protocols.pockets.PocketGrid, extGrid: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::EggshellGrid::get_connolly_eggshell_on_grid(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class protocols::pockets::PocketGrid &, const class protocols::pockets::PocketGrid &) –> void

get_connolly_surfacePoints(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, protein_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::PocketGrid::get_connolly_surfacePoints(const class core::pose::Pose &) const –> class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

get_connolly_surfacePoints_within_grid(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::PocketGrid::get_connolly_surfacePoints_within_grid(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

get_eggshell_distance(*args, **kwargs)

Overloaded function.

1. get_eggshell_distance(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, template_eggshell: pyrosetta.rosetta.protocols.pockets.EggshellGrid) -> float

C++: protocols::pockets::EggshellGrid::get_eggshell_distance(const class protocols::pockets::EggshellGrid &) const –> double

2. get_eggshell_distance(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, template_eggshell: pyrosetta.rosetta.protocols.pockets.EggshellGrid, comparison_pdbname: str) -> float

C++: protocols::pockets::EggshellGrid::get_eggshell_distance(const class protocols::pockets::EggshellGrid &, const std::string &) const –> double

get_pocket_distance(*args, **kwargs)

Overloaded function.

1. get_pocket_distance(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, template_pocket: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> float

C++: protocols::pockets::PocketGrid::get_pocket_distance(const class protocols::pockets::PocketGrid &) const –> double

2. get_pocket_distance(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, template_pocket: pyrosetta.rosetta.protocols.pockets.PocketGrid, comparison_pdbname: str) -> float

C++: protocols::pockets::PocketGrid::get_pocket_distance(const class protocols::pockets::PocketGrid &, const std::string &) const –> double

initialize(*args, **kwargs)

Overloaded function.

1. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float) -> None

2. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float) -> None

3. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float, psp: bool) -> None

4. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const double &, const double &, const double &, const double, const double, const double, const double &, bool, bool) –> void

5. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float) -> None

6. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float) -> None

7. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float, psp: bool) -> None

8. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const double &, const double &, const double &, double, const double &, bool, bool) –> void

9. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float) -> None

10. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float) -> None

11. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float, psp: bool) -> None

12. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class numeric::xyzVector<double> &, double, const double &, bool, bool) –> void

13. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float) -> None

14. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float) -> None

15. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

16. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class numeric::xyzVector<double> &, const double &, const double &, const double &, const double &, bool, bool) –> void

17. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float) -> None

18. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float) -> None

19. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

20. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class core::conformation::Residue &, const double &, const double &, const double &, const double &, bool, bool) –> void

21. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float) -> None

22. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float) -> None

23. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

24. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const double &, const double &, const double &, const double &, bool, bool) –> void

isTooSmall(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → bool

C++: protocols::pockets::PocketGrid::isTooSmall() const –> bool

largestTargetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::largestTargetPocketVolume() –> double

linkExemplarsThroughSolvent(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::linkExemplarsThroughSolvent() –> void

mark(*args, **kwargs)

Overloaded function.

1. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float) -> None

2. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float, polar: bool) -> None

3. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float, polar: bool, targetResi: int) -> None

C++: protocols::pockets::PocketGrid::mark(double, double, double, const double &, const double &, bool, int) –> void

4. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float) -> None

5. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float, polar: bool) -> None

6. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float, polar: bool, targetResi: int) -> None

C++: protocols::pockets::PocketGrid::mark(const class numeric::xyzVector<double> &, const double &, const double &, bool, int) –> void

markDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: int, y: int, z: int, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markDepth(unsigned long, unsigned long, unsigned long, const double &, const double &) –> void

markEdgeDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markEdgeDepth(const double &, const double &) –> void

markOneEdgeDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: int, y: int, z: int, surf_d: float, bur_d: float, isTarget: bool) → bool

C++: protocols::pockets::PocketGrid::markOneEdgeDepth(unsigned long, unsigned long, unsigned long, const double &, const double &, bool) –> bool

markPocketDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markPocketDepth(const double &, const double &) –> void

move_pose_to_standard_orie(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_seqpos: int, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::PocketGrid::move_pose_to_standard_orie(const unsigned long &, class core::pose::Pose &) –> void

netTargetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::netTargetPocketVolume() –> double

print(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::print() const –> void

randomAngle(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::randomAngle() –> void

recenter(*args, **kwargs)

Overloaded function.

1. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float) -> None

C++: protocols::pockets::PocketGrid::recenter(const double &, const double &, const double &) –> void

2. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

C++: protocols::pockets::PocketGrid::recenter(const class core::conformation::Residue &) –> void

3. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsds: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t) -> None

C++: protocols::pockets::PocketGrid::recenter(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) –> void

4. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::PocketGrid::recenter(const class numeric::xyzVector<double> &) –> void

same_type_as_me(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, other: pyrosetta.rosetta.protocols.pockets.PocketGrid) → bool

C++: protocols::pockets::EggshellGrid::same_type_as_me(const class protocols::pockets::PocketGrid &) const –> bool

spacing(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::spacing() const –> double

targetPocketHeuristicScore(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketHeuristicScore() const –> double

targetPocketHydrophobicProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketHydrophobicProteinSurface() const –> double

targetPocketPolarProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketPolarProteinSurface() const –> double

targetPocketProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketProteinSurface() const –> double

targetPocketSolventSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketSolventSurface() const –> double

targetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_sc: float, bur_sc: float) → float

C++: protocols::pockets::PocketGrid::targetPocketVolume(const double &, const double &) const –> double

whatIsTooSmall(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::PocketGrid::whatIsTooSmall() const –> class numeric::xyzVector<double>

write_Grid_to_pdb(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, gr: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_pdbname: str) → None

C++: protocols::pockets::EggshellGrid::write_Grid_to_pdb(const class protocols::pockets::PocketGrid &, const std::string &) const –> void

write_eggshell_to_pdb(*args, **kwargs)

Overloaded function.

1. write_eggshell_to_pdb(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, output_pdbname: str) -> None

C++: protocols::pockets::EggshellGrid::write_eggshell_to_pdb(const std::string &) const –> void

2. write_eggshell_to_pdb(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, output_pdbname: str, rot1: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot2: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot3: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

C++: protocols::pockets::EggshellGrid::write_eggshell_to_pdb(const std::string &, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>) const –> void

write_pocketGrid_to_pdb(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) → None

C++: protocols::pockets::PocketGrid::write_pocketGrid_to_pdb(const std::string &) –> void

zeroAngle(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::zeroAngle() –> void

class pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid

Bases: PocketGrid

GetExemplarNumAtoms(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumAtoms() const –> unsigned long

GetExemplarNumClusters(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumClusters() const –> unsigned long

GetExemplarNumPolarAtoms(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumPolarAtoms() const –> unsigned long

PROTEIN = <PtType.PROTEIN: 0>

PSEUDO_PROTEIN = <PtType.PSEUDO_PROTEIN: 3>

class PtType

Bases: pybind11_object

Members:

PROTEIN

SURFACE

SOLVENT

PSEUDO_PROTEIN

PROTEIN = <PtType.PROTEIN: 0>

PSEUDO_PROTEIN = <PtType.PSEUDO_PROTEIN: 3>

SOLVENT = <PtType.SOLVENT: 2>

SURFACE = <PtType.SURFACE: 1>

property name

property value

SOLVENT = <PtType.SOLVENT: 2>

SURFACE = <PtType.SURFACE: 1>

alter_espGrid(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, espGrid_filename: str) → None

C++: protocols::pockets::PocketGrid::alter_espGrid(const std::string &) –> void

alter_espGrid_with_bound_ligand(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, espGrid_filename: str, protein_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(const std::string &, const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, : pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid) → pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid

C++: protocols::pockets::ElectrostaticpotentialGrid::operator=(const class protocols::pockets::ElectrostaticpotentialGrid &) –> class protocols::pockets::ElectrostaticpotentialGrid &

assign_esp_for_atom_grid_points(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, atom_coord: pyrosetta.rosetta.numeric.xyzVector_double_t, inflated_radius: float) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_atom_grid_points(class numeric::xyzVector<double>, const double &) –> void

assign_esp_for_protein_grid_points(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, protein_pose: pyrosetta.rosetta.core.pose.Pose, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points(const class core::pose::Pose &, const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

assign_esp_for_surface_grid_points(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_surface_grid_points(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

assign_esp_for_surface_grid_points_by_nn(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_surface_grid_points_by_nn(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

autoexpanding_pocket_eval(*args, **kwargs)

Overloaded function.

1. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int) -> bool

2. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool) -> bool

3. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float) -> bool

4. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float) -> bool

5. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class core::conformation::Residue &, const class core::scoring::func::XYZ_Func &, const unsigned long, bool, double, double, double) –> bool

6. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int) -> bool

7. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool) -> bool

8. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float) -> bool

9. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float) -> bool

10. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::scoring::func::XYZ_Func &, const unsigned long, bool, double, double, double) –> bool

11. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose) -> bool

12. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool) -> bool

13. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float) -> bool

14. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float) -> bool

15. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class core::conformation::Residue &, const class core::pose::Pose &, bool, double, double, double) –> bool

16. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose) -> bool

17. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool) -> bool

18. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float) -> bool

19. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float) -> bool

20. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::pose::Pose &, bool, double, double, double) –> bool

cap_espGrid(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::cap_espGrid() –> void

change_espGrid_for_darc(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, espGrid_filename: str, protein_pose: pyrosetta.rosetta.core.pose.Pose, pocket_grid: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::change_espGrid_for_darc(const std::string &, const class core::pose::Pose &, const class protocols::pockets::PocketGrid &) –> void

clear(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clear() –> void

clusterCPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clusterCPockets() –> void

clusterPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clusterPockets() –> void

dim(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::PocketGrid::dim() const –> class numeric::xyzVector<double>

dumpExemplarToFile(*args, **kwargs)

Overloaded function.

1. dumpExemplarToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None

C++: protocols::pockets::PocketGrid::dumpExemplarToFile() –> void

2. dumpExemplarToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpExemplarToFile(const std::string &) –> void

dumpGridToFile(*args, **kwargs)

Overloaded function.

1. dumpGridToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None

C++: protocols::pockets::PocketGrid::dumpGridToFile() –> void

2. dumpGridToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpGridToFile(const std::string &) –> void

dumpTargetPocketsToFile(*args, **kwargs)

Overloaded function.

1. dumpTargetPocketsToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToFile(const std::string &) –> void

2. dumpTargetPocketsToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str, rot1: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot2: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot3: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToFile(const std::string &, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>) –> void

dumpTargetPocketsToPDB(*args, **kwargs)

Overloaded function.

1. dumpTargetPocketsToPDB(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

2. dumpTargetPocketsToPDB(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str, minipock: bool) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToPDB(const std::string &, bool) –> void

3. dumpTargetPocketsToPDB(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str, rot1: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot2: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot3: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToPDB(const std::string &, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>) –> void

property espGrid_

espGrid_point_list(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid) → pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t

C++: protocols::pockets::ElectrostaticpotentialGrid::espGrid_point_list() const –> const class std::list<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &

fillTargetPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::fillTargetPockets() –> void

fill_espGrid_values(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_OEgrid_filename: str) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::fill_espGrid_values(const std::string &) –> void

fill_espGrid_values_with_type(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_OEgrid_filename: str) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::fill_espGrid_values_with_type(const std::string &) –> void

findClusters(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::findClusters() –> void

findClustersByExemplars(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::findClustersByExemplars() –> void

findExemplars(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, inPose: pyrosetta.rosetta.core.pose.Pose, total_residues: int) → None

C++: protocols::pockets::PocketGrid::findExemplars(const class core::pose::Pose &, const unsigned long) –> void

findPSP(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findPSP(unsigned long, double) –> void

findPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findPockets(unsigned long, double) –> void

findSPS(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findSPS(unsigned long, double) –> void

getBounds(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::pockets::PocketGrid::getBounds() –> class utility::vector1<double, class std::allocator<double> >

static getRelaxResidues(input_pose: pyrosetta.rosetta.core.pose.Pose, resids: str) → pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t

C++: protocols::pockets::PocketGrid::getRelaxResidues(const class core::pose::Pose &, const std::string &) –> class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

get_DELPHI_espGrid_values(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_espGrid_filename: str) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::get_DELPHI_espGrid_values(const std::string &) –> void

get_ZAP_espGrid_values(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_espGrid_filename: str) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::get_ZAP_espGrid_values(const std::string &) –> void

get_ZAP_espGrid_values_with_type(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_espGrid_filename: str) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::get_ZAP_espGrid_values_with_type(const std::string &) –> void

get_atom_dist_from_connolly_surface(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, atom_coord: pyrosetta.rosetta.numeric.xyzVector_double_t, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → float

C++: protocols::pockets::ElectrostaticpotentialGrid::get_atom_dist_from_connolly_surface(class numeric::xyzVector<double>, const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> double

get_connolly_surfacePoints(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, protein_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::PocketGrid::get_connolly_surfacePoints(const class core::pose::Pose &) const –> class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

get_connolly_surfacePoints_within_grid(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::PocketGrid::get_connolly_surfacePoints_within_grid(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

get_oegrid_dimensions(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_OEgrid_filename: str) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::get_oegrid_dimensions(const std::string &) –> void

get_pocket_distance(*args, **kwargs)

Overloaded function.

1. get_pocket_distance(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, template_pocket: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> float

C++: protocols::pockets::PocketGrid::get_pocket_distance(const class protocols::pockets::PocketGrid &) const –> double

2. get_pocket_distance(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, template_pocket: pyrosetta.rosetta.protocols.pockets.PocketGrid, comparison_pdbname: str) -> float

C++: protocols::pockets::PocketGrid::get_pocket_distance(const class protocols::pockets::PocketGrid &, const std::string &) const –> double

initialize(*args, **kwargs)

Overloaded function.

1. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float) -> None

2. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float) -> None

3. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float, psp: bool) -> None

4. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const double &, const double &, const double &, const double, const double, const double, const double &, bool, bool) –> void

5. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float) -> None

6. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float) -> None

7. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float, psp: bool) -> None

8. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const double &, const double &, const double &, double, const double &, bool, bool) –> void

9. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float) -> None

10. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float) -> None

11. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float, psp: bool) -> None

12. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class numeric::xyzVector<double> &, double, const double &, bool, bool) –> void

13. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float) -> None

14. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float) -> None

15. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

16. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class numeric::xyzVector<double> &, const double &, const double &, const double &, const double &, bool, bool) –> void

17. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float) -> None

18. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float) -> None

19. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

20. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class core::conformation::Residue &, const double &, const double &, const double &, const double &, bool, bool) –> void

21. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float) -> None

22. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float) -> None

23. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

24. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const double &, const double &, const double &, const double &, bool, bool) –> void

initialize_espGrid(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::initialize_espGrid() –> void

initialize_typGrid(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::initialize_typGrid() –> void

isTooSmall(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → bool

C++: protocols::pockets::PocketGrid::isTooSmall() const –> bool

largestTargetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::largestTargetPocketVolume() –> double

linkExemplarsThroughSolvent(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::linkExemplarsThroughSolvent() –> void

mark(*args, **kwargs)

Overloaded function.

1. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float) -> None

2. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float, polar: bool) -> None

3. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float, polar: bool, targetResi: int) -> None

C++: protocols::pockets::PocketGrid::mark(double, double, double, const double &, const double &, bool, int) –> void

4. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float) -> None

5. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float, polar: bool) -> None

6. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float, polar: bool, targetResi: int) -> None

C++: protocols::pockets::PocketGrid::mark(const class numeric::xyzVector<double> &, const double &, const double &, bool, int) –> void

markDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: int, y: int, z: int, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markDepth(unsigned long, unsigned long, unsigned long, const double &, const double &) –> void

markEdgeDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markEdgeDepth(const double &, const double &) –> void

markOneEdgeDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: int, y: int, z: int, surf_d: float, bur_d: float, isTarget: bool) → bool

C++: protocols::pockets::PocketGrid::markOneEdgeDepth(unsigned long, unsigned long, unsigned long, const double &, const double &, bool) –> bool

markPocketDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markPocketDepth(const double &, const double &) –> void

mark_atom_espGrid_points(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, atom_coord: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::mark_atom_espGrid_points(class numeric::xyzVector<double>, const double &) –> void

mark_buried_solvent_points(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, protein_pose: pyrosetta.rosetta.core.pose.Pose, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::mark_buried_solvent_points(const class core::pose::Pose &, const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

mark_protein_espGrid_points(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, protein_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points(const class core::pose::Pose &) –> void

move_pose_to_standard_orie(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_seqpos: int, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::PocketGrid::move_pose_to_standard_orie(const unsigned long &, class core::pose::Pose &) –> void

netTargetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::netTargetPocketVolume() –> double

print(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::print() const –> void

print_to_oegrid(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, output_OEgrid_filename: str) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::print_to_oegrid(const std::string &) –> void

randomAngle(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::randomAngle() –> void

recenter(*args, **kwargs)

Overloaded function.

1. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float) -> None

C++: protocols::pockets::PocketGrid::recenter(const double &, const double &, const double &) –> void

2. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

C++: protocols::pockets::PocketGrid::recenter(const class core::conformation::Residue &) –> void

3. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsds: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t) -> None

C++: protocols::pockets::PocketGrid::recenter(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) –> void

4. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::PocketGrid::recenter(const class numeric::xyzVector<double> &) –> void

resize_espGrid_to_match_pocketGrid(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, espGrid_filename: str, pg: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::resize_espGrid_to_match_pocketGrid(const std::string &, const class protocols::pockets::PocketGrid &) –> void

same_type_as_me(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, other: pyrosetta.rosetta.protocols.pockets.PocketGrid) → bool

C++: protocols::pockets::ElectrostaticpotentialGrid::same_type_as_me(const class protocols::pockets::PocketGrid &) const –> bool

set_protein_esp_to_zero(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::set_protein_esp_to_zero() –> void

set_surface_esp_to_zero(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::set_surface_esp_to_zero() –> void

spacing(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::spacing() const –> double

targetPocketHeuristicScore(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketHeuristicScore() const –> double

targetPocketHydrophobicProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketHydrophobicProteinSurface() const –> double

targetPocketPolarProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketPolarProteinSurface() const –> double

targetPocketProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketProteinSurface() const –> double

targetPocketSolventSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketSolventSurface() const –> double

targetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_sc: float, bur_sc: float) → float

C++: protocols::pockets::PocketGrid::targetPocketVolume(const double &, const double &) const –> double

property typGrid_

whatIsTooSmall(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::PocketGrid::whatIsTooSmall() const –> class numeric::xyzVector<double>

write_connollySurface_to_pdb(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t, output_pdbname: str) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::write_connollySurface_to_pdb(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const std::string &) const –> void

write_espGrid_to_pdb(self: pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid, output_pdbname: str) → None

C++: protocols::pockets::ElectrostaticpotentialGrid::write_espGrid_to_pdb(const std::string &) const –> void

write_pocketGrid_to_pdb(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) → None

C++: protocols::pockets::PocketGrid::write_pocketGrid_to_pdb(const std::string &) –> void

zeroAngle(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::zeroAngle() –> void

pyrosetta.rosetta.protocols.pockets.Find_Closest_Intersect_SQ(phiAngle: float, psiAngle: float, atomX: float, atomY: float, atomZ: float, atom_radius: float) → float

C++: protocols::pockets::Find_Closest_Intersect_SQ(const double &, const double &, const double &, const double &, const double &, const double &) –> double

class pyrosetta.rosetta.protocols.pockets.FingerprintBase

Bases: pybind11_object

CHEAT_CoM(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, inp_CoM: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::pockets::FingerprintBase::CHEAT_CoM(const class numeric::xyzVector<double> &) –> void

CoM(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::FingerprintBase::CoM() const –> class numeric::xyzVector<double>

assign(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, : pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.protocols.pockets.FingerprintBase

C++: protocols::pockets::FingerprintBase::operator=(const class protocols::pockets::FingerprintBase &) –> class protocols::pockets::FingerprintBase &

multi_origin_list(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: protocols::pockets::FingerprintBase::multi_origin_list() const –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

num_origins(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → int

C++: protocols::pockets::FingerprintBase::num_origins() const –> unsigned long

origin(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::FingerprintBase::origin() const –> class numeric::xyzVector<double>

property pocketGrid_dim_

property pocketGrid_mid_

property pocketGrid_spacing_

print_to_file(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, output_filename: str) → None

C++: protocols::pockets::FingerprintBase::print_to_file(const std::string &) const –> void

print_to_pdb(*args, **kwargs)

Overloaded function.

1. print_to_pdb(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, output_pdbname: str) -> None

C++: protocols::pockets::FingerprintBase::print_to_pdb(const std::string &) const –> void

2. print_to_pdb(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, output_pdbname: str, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::FingerprintBase::print_to_pdb(const std::string &, const class numeric::xyzVector<double> &) const –> void

triplet_fingerprint_data(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t

C++: protocols::pockets::FingerprintBase::triplet_fingerprint_data() const –> const class std::list<struct protocols::pockets::spherical_coor_triplet, class std::allocator<struct protocols::pockets::spherical_coor_triplet> > &

class pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc

Bases: Multifunc

Atom tree multifunction class

abort_min(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double) → bool

Christophe added the following to allow premature end of minimization

If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!

C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

dfunc(self: pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::pockets::FingerprintMultifunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dump(*args, **kwargs)

Overloaded function.

1. dump(self: pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.utility.vector1_double) -> None

2. dump(self: pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc, vars: pyrosetta.rosetta.utility.vector1_double) -> None

Error state reached; dump out current pdb.

C++: protocols::pockets::FingerprintMultifunc::dump(const class utility::vector1<double, class std::allocator<double> > &) const –> void

class pyrosetta.rosetta.protocols.pockets.GenPharmacophore

Bases: pybind11_object

ReplaceString(self: pyrosetta.rosetta.protocols.pockets.GenPharmacophore, subject: str, search: str, replace: str) → str

C++: protocols::pockets::GenPharmacophore::ReplaceString(std::string, const std::string &, const std::string &) –> std::string

assign(self: pyrosetta.rosetta.protocols.pockets.GenPharmacophore, : pyrosetta.rosetta.protocols.pockets.GenPharmacophore) → pyrosetta.rosetta.protocols.pockets.GenPharmacophore

C++: protocols::pockets::GenPharmacophore::operator=(const class protocols::pockets::GenPharmacophore &) –> class protocols::pockets::GenPharmacophore &

cluster_KeyFeatures(self: pyrosetta.rosetta.protocols.pockets.GenPharmacophore, input_filename: str, output_filename: str) → None

C++: protocols::pockets::GenPharmacophore::cluster_KeyFeatures(const std::string &, const std::string &) const –> void

extract_Hbond_atoms_from_protein_rna_complex(self: pyrosetta.rosetta.protocols.pockets.GenPharmacophore, protein_pose: pyrosetta.rosetta.core.pose.Pose, rna_pose: pyrosetta.rosetta.core.pose.Pose) → str

C++: protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(const class core::pose::Pose &, const class core::pose::Pose &) –> std::string

extract_rna_rings_from_protein_rna_complex(self: pyrosetta.rosetta.protocols.pockets.GenPharmacophore, protein_pose: pyrosetta.rosetta.core.pose.Pose, rna_pose: pyrosetta.rosetta.core.pose.Pose) → str

C++: protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(const class core::pose::Pose &, const class core::pose::Pose &) –> std::string

get_RNAring_sasa(self: pyrosetta.rosetta.protocols.pockets.GenPharmacophore, rsd: pyrosetta.rosetta.core.conformation.Residue, rsdno: int, pose_atom_sasa: pyrosetta.rosetta.core.id.AtomID_Map_double_t) → float

C++: protocols::pockets::GenPharmacophore::get_RNAring_sasa(const class core::conformation::Residue &, const int &, const class core::id::AtomID_Map<double> &) –> double

get_ideal_hydrogenBond_atoms(self: pyrosetta.rosetta.protocols.pockets.GenPharmacophore, protein_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(const class core::pose::Pose &) –> void

is_buried_ring(self: pyrosetta.rosetta.protocols.pockets.GenPharmacophore, rsd: pyrosetta.rosetta.core.conformation.Residue, ring_sasa: float, sasa_cutoff: float) → bool

C++: protocols::pockets::GenPharmacophore::is_buried_ring(const class core::conformation::Residue &, const double &, const double &) –> bool

make_compatible_with_ROCS_custom_ForceField(self: pyrosetta.rosetta.protocols.pockets.GenPharmacophore, input_filename: str) → str

C++: protocols::pockets::GenPharmacophore::make_compatible_with_ROCS_custom_ForceField(std::string &) –> std::string

print_string_to_PDBfile(self: pyrosetta.rosetta.protocols.pockets.GenPharmacophore, input_filename: str, output_filename: str) → None

C++: protocols::pockets::GenPharmacophore::print_string_to_PDBfile(const std::string &, const std::string &) const –> void

class pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint

Bases: FingerprintBase

CHEAT_CoM(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, inp_CoM: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::pockets::FingerprintBase::CHEAT_CoM(const class numeric::xyzVector<double> &) –> void

CoM(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::FingerprintBase::CoM() const –> class numeric::xyzVector<double>

assign(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, : pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint) → pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint

C++: protocols::pockets::NonPlaidFingerprint::operator=(const class protocols::pockets::NonPlaidFingerprint &) –> class protocols::pockets::NonPlaidFingerprint &

calculate_protein_CoM(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(const class core::pose::Pose &) –> class numeric::xyzVector<double>

change_CoM_to_ligandCoM(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, ligandCoM: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::pockets::NonPlaidFingerprint::change_CoM_to_ligandCoM(const class numeric::xyzVector<double> &) –> void

choose_origin_with_lowest_eggshell_ruggedness(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose, egg_and_extra_shell: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → None

C++: protocols::pockets::NonPlaidFingerprint::choose_origin_with_lowest_eggshell_ruggedness(const class core::pose::Pose &, const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

combine_xyz_lists(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, xyz_list_1: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t, xyz_list_2: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::NonPlaidFingerprint::combine_xyz_lists(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

convert_cart_to_spherical_and_round(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, xyz_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t

C++: protocols::pockets::NonPlaidFingerprint::convert_cart_to_spherical_and_round(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> class std::list<struct protocols::pockets::spherical_coor_triplet, class std::allocator<struct protocols::pockets::spherical_coor_triplet> >

convert_spherical_list_to_cartesian_list(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, unique_triplet: pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::NonPlaidFingerprint::convert_spherical_list_to_cartesian_list(const class std::list<struct protocols::pockets::spherical_coor_triplet, class std::allocator<struct protocols::pockets::spherical_coor_triplet> > &) –> class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

property egg_and_ext_list_

property eggshell_list_

property espGrid_

property esp_dim_

property esp_mid_

property esp_spacing_

property extshell_list_

get_Rvalue(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose, egg_and_extra_shell: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t, set_origin_option: int) → float

C++: protocols::pockets::NonPlaidFingerprint::get_Rvalue(const class core::pose::Pose &, const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const unsigned long &) –> double

get_electrostatics_energy(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, ligand_pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy(const class core::pose::Pose &) –> double

get_interpolated_esp_energy(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, ligand_atom: pyrosetta.rosetta.numeric.xyzVector_double_t, atom_charge: float) → float

C++: protocols::pockets::NonPlaidFingerprint::get_interpolated_esp_energy(const class numeric::xyzVector<double> &, const double &) –> double

get_interpolated_esp_energy_with_type(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, ligand_atom: pyrosetta.rosetta.numeric.xyzVector_double_t, atom_charge: float) → float

C++: protocols::pockets::NonPlaidFingerprint::get_interpolated_esp_energy_with_type(const class numeric::xyzVector<double> &, const double &) –> double

get_nearest_neighbour_esp_energy(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, ligand_atom: pyrosetta.rosetta.numeric.xyzVector_double_t, atom_charge: float) → float

C++: protocols::pockets::NonPlaidFingerprint::get_nearest_neighbour_esp_energy(const class numeric::xyzVector<double> &, const double &) –> double

get_pose_resnum(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, pdbnum: int, pdbchn: str, ps: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::pockets::NonPlaidFingerprint::get_pose_resnum(const int, const char, const class core::pose::Pose &) –> unsigned long

get_surface_esp(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t, inp_espGrid_fname: str) → float

C++: protocols::pockets::NonPlaidFingerprint::get_surface_esp(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const std::string &) –> double

include_eggshell_points_based_on_known_ligand(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, known_ligand_pose: pyrosetta.rosetta.core.pose.Pose, trim_dist: float) → None

C++: protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(const class core::pose::Pose &, const double &) –> void

multi_origin_list(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: protocols::pockets::FingerprintBase::multi_origin_list() const –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

num_origins(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → int

C++: protocols::pockets::FingerprintBase::num_origins() const –> unsigned long

origin(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::FingerprintBase::origin() const –> class numeric::xyzVector<double>

place_origin_point(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, angle: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::NonPlaidFingerprint::place_origin_point(const double &) –> class numeric::xyzVector<double>

property pocketGrid_dim_

property pocketGrid_mid_

property pocketGrid_spacing_

property pocket_CoM_

print_to_file(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, output_filename: str) → None

C++: protocols::pockets::FingerprintBase::print_to_file(const std::string &) const –> void

print_to_pdb(*args, **kwargs)

Overloaded function.

1. print_to_pdb(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, output_pdbname: str) -> None

C++: protocols::pockets::FingerprintBase::print_to_pdb(const std::string &) const –> void

2. print_to_pdb(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, output_pdbname: str, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::FingerprintBase::print_to_pdb(const std::string &, const class numeric::xyzVector<double> &) const –> void

remove_duplicate_phi_psi(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, rounded_triplet: pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t) → pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t

C++: protocols::pockets::NonPlaidFingerprint::remove_duplicate_phi_psi(const class std::list<struct protocols::pockets::spherical_coor_triplet, class std::allocator<struct protocols::pockets::spherical_coor_triplet> > &) –> class std::list<struct protocols::pockets::spherical_coor_triplet, class std::allocator<struct protocols::pockets::spherical_coor_triplet> >

set_multiple_origin(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose, egg_and_extra_shell: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → None

C++: protocols::pockets::NonPlaidFingerprint::set_multiple_origin(const class core::pose::Pose &, const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

set_origin(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose, egg_and_extra_shell: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → None

C++: protocols::pockets::NonPlaidFingerprint::set_origin(const class core::pose::Pose &, const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

set_origin_away_from_eggshell(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, egg_and_extra_shell: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t, protein_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::NonPlaidFingerprint::set_origin_away_from_eggshell(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class core::pose::Pose &) –> void

set_origin_away_from_eggshell_plane(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, egg_and_extra_shell: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t, protein_pose: pyrosetta.rosetta.core.pose.Pose, set_origin_option: int) → None

C++: protocols::pockets::NonPlaidFingerprint::set_origin_away_from_eggshell_plane(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class core::pose::Pose &, const unsigned long &) –> void

set_origin_away_from_protein_center(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::NonPlaidFingerprint::set_origin_away_from_protein_center(const class core::pose::Pose &) –> void

set_origin_from_option_(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose, egg_and_extra_shell: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t, set_origin_option: int) → None

C++: protocols::pockets::NonPlaidFingerprint::set_origin_from_option_(const class core::pose::Pose &, const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const unsigned long &) –> void

set_origin_from_residue(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::NonPlaidFingerprint::set_origin_from_residue(const class core::pose::Pose &) –> void

set_rho_to_zero(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, rounded_triplet: pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t) → pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t

C++: protocols::pockets::NonPlaidFingerprint::set_rho_to_zero(const class std::list<struct protocols::pockets::spherical_coor_triplet, class std::allocator<struct protocols::pockets::spherical_coor_triplet> > &) –> class std::list<struct protocols::pockets::spherical_coor_triplet, class std::allocator<struct protocols::pockets::spherical_coor_triplet> >

setup_from_ConnollySurface(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose, pocket_grid: pyrosetta.rosetta.protocols.pockets.PocketGrid, grid_for_extshell: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface(const class core::pose::Pose &, const class protocols::pockets::PocketGrid &, const class protocols::pockets::PocketGrid &) –> void

setup_from_EggshellGrid(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint) → None

C++: protocols::pockets::NonPlaidFingerprint::setup_from_EggshellGrid() –> void

setup_from_PlaidFingerprint(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, pfp: protocols::pockets::PlaidFingerprint) → None

C++: protocols::pockets::NonPlaidFingerprint::setup_from_PlaidFingerprint(const class protocols::pockets::PlaidFingerprint &) –> void

setup_from_PocketGrid(*args, **kwargs)

Overloaded function.

1. setup_from_PocketGrid(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose, pocket_grid: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None

C++: protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(const class core::pose::Pose &, const class protocols::pockets::PocketGrid &) –> void

2. setup_from_PocketGrid(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose, pocket_grid: pyrosetta.rosetta.protocols.pockets.PocketGrid, grid_for_extshell: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None

C++: protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(const class core::pose::Pose &, const class protocols::pockets::PocketGrid &, const class protocols::pockets::PocketGrid &) –> void

setup_from_PocketGrid_and_known_ligand(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose, pocket_grid: pyrosetta.rosetta.protocols.pockets.PocketGrid, grid_for_extshell: pyrosetta.rosetta.protocols.pockets.PocketGrid, known_ligand_pose: pyrosetta.rosetta.core.pose.Pose, trim_dist: float) → None

C++: protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand(const class core::pose::Pose &, const class protocols::pockets::PocketGrid &, const class protocols::pockets::PocketGrid &, const class core::pose::Pose &, const double &) –> void

setup_from_PocketGrid_using_bound_ligand(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose: pyrosetta.rosetta.core.pose.Pose, pocket_grid: pyrosetta.rosetta.protocols.pockets.PocketGrid, grid_for_extshell: pyrosetta.rosetta.protocols.pockets.PocketGrid, known_ligand_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand(const class core::pose::Pose &, const class protocols::pockets::PocketGrid &, const class protocols::pockets::PocketGrid &, const class core::pose::Pose &) –> void

setup_from_eggshell_pdb_file(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, input_filename: str) → None

C++: protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_pdb_file(const std::string &) –> void

setup_from_eggshell_triplet_file(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, input_filename: str) → None

C++: protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file(const std::string &) –> void

setup_from_espGrid(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, input_filename: str, protein_pose: pyrosetta.rosetta.core.pose.Pose, delphi: bool) → None

C++: protocols::pockets::NonPlaidFingerprint::setup_from_espGrid(const std::string &, const class core::pose::Pose &, bool) –> void

trim_based_on_known_ligand(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, known_ligand_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::NonPlaidFingerprint::trim_based_on_known_ligand(const class core::pose::Pose &) –> void

triplet_fingerprint_data(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t

C++: protocols::pockets::FingerprintBase::triplet_fingerprint_data() const –> const class std::list<struct protocols::pockets::spherical_coor_triplet, class std::allocator<struct protocols::pockets::spherical_coor_triplet> > &

property typGrid_

write_eggshell_to_pdb_file(self: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, output_eggshell_name: str) → None

C++: protocols::pockets::NonPlaidFingerprint::write_eggshell_to_pdb_file(const std::string &) const –> void

class pyrosetta.rosetta.protocols.pockets.PCluster

Bases: pybind11_object

@ Cluster of Pocket points

class Cxyz

Bases: pybind11_object

property x

property y

property z

add(self: pyrosetta.rosetta.protocols.pockets.PCluster, x: int, y: int, z: int) → None

C++: protocols::pockets::PCluster::add(unsigned long, unsigned long, unsigned long) –> void

isClose(self: pyrosetta.rosetta.protocols.pockets.PCluster, c2: pyrosetta.rosetta.protocols.pockets.PCluster) → bool

C++: protocols::pockets::PCluster::isClose(const class protocols::pockets::PCluster &) const –> bool

isSolventExposed(self: pyrosetta.rosetta.protocols.pockets.PCluster) → bool

C++: protocols::pockets::PCluster::isSolventExposed() const –> bool

isTarget(*args, **kwargs)

Overloaded function.

1. isTarget(self: pyrosetta.rosetta.protocols.pockets.PCluster) -> bool

2. isTarget(self: pyrosetta.rosetta.protocols.pockets.PCluster, numTargets: int) -> bool

C++: protocols::pockets::PCluster::isTarget(unsigned long) const –> bool

property points_

size(self: pyrosetta.rosetta.protocols.pockets.PCluster) → int

C++: protocols::pockets::PCluster::size() const –> int

testNeighbor(self: pyrosetta.rosetta.protocols.pockets.PCluster, c2: pyrosetta.rosetta.protocols.pockets.PCluster) → bool

C++: protocols::pockets::PCluster::testNeighbor(class protocols::pockets::PCluster &) –> bool

class pyrosetta.rosetta.protocols.pockets.PClusterSet

Bases: pybind11_object

@ Set of cluster of pocket points

assign(self: pyrosetta.rosetta.protocols.pockets.PClusterSet, old: pyrosetta.rosetta.protocols.pockets.PClusterSet) → pyrosetta.rosetta.protocols.pockets.PClusterSet

C++: protocols::pockets::PClusterSet::operator=(const class protocols::pockets::PClusterSet &) –> class protocols::pockets::PClusterSet &

clear(self: pyrosetta.rosetta.protocols.pockets.PClusterSet) → None

C++: protocols::pockets::PClusterSet::clear() –> void

findClusters(self: pyrosetta.rosetta.protocols.pockets.PClusterSet) → None

C++: protocols::pockets::PClusterSet::findClusters() –> void

getLargestClusterSize(self: pyrosetta.rosetta.protocols.pockets.PClusterSet, stepSize: float, minClusterSize: float, numTargets: int, ignoreBuried: bool, ignoreSurface: bool) → float

C++: protocols::pockets::PClusterSet::getLargestClusterSize(const double &, const double &, const unsigned long &, bool, bool) –> double

getNetClusterSize(self: pyrosetta.rosetta.protocols.pockets.PClusterSet, stepSize: float, minClusterSize: float, numTargets: int, ignoreBuried: bool, ignoreSurface: bool) → float

C++: protocols::pockets::PClusterSet::getNetClusterSize(const double &, const double &, const unsigned long &, bool, bool) –> double

size(self: pyrosetta.rosetta.protocols.pockets.PClusterSet) → int

C++: protocols::pockets::PClusterSet::size() –> unsigned long

class pyrosetta.rosetta.protocols.pockets.PlaidFingerprint

Bases: FingerprintBase

CHEAT_CoM(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, inp_CoM: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::pockets::FingerprintBase::CHEAT_CoM(const class numeric::xyzVector<double> &) –> void

CoM(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::FingerprintBase::CoM() const –> class numeric::xyzVector<double>

assign(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, : pyrosetta.rosetta.protocols.pockets.PlaidFingerprint) → pyrosetta.rosetta.protocols.pockets.PlaidFingerprint

C++: protocols::pockets::PlaidFingerprint::operator=(const class protocols::pockets::PlaidFingerprint &) –> class protocols::pockets::PlaidFingerprint &

calculate_ligand_CoM(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, ligand_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::PlaidFingerprint::calculate_ligand_CoM(const class core::pose::Pose &) –> class numeric::xyzVector<double>

compute_ligand_natoms(*args, **kwargs)

Overloaded function.

1. compute_ligand_natoms(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, pose: pyrosetta.rosetta.core.pose.Pose) -> int

C++: protocols::pockets::PlaidFingerprint::compute_ligand_natoms(const class core::pose::Pose &) const –> unsigned long

2. compute_ligand_natoms(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint) -> int

C++: protocols::pockets::PlaidFingerprint::compute_ligand_natoms() const –> unsigned long

compute_ligand_natoms_with_hydrogens(*args, **kwargs)

Overloaded function.

1. compute_ligand_natoms_with_hydrogens(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, pose: pyrosetta.rosetta.core.pose.Pose) -> int

C++: protocols::pockets::PlaidFingerprint::compute_ligand_natoms_with_hydrogens(const class core::pose::Pose &) const –> unsigned long

2. compute_ligand_natoms_with_hydrogens(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint) -> int

C++: protocols::pockets::PlaidFingerprint::compute_ligand_natoms_with_hydrogens() const –> unsigned long

compute_ligand_nconformers(*args, **kwargs)

Overloaded function.

1. compute_ligand_nconformers(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, pose: pyrosetta.rosetta.core.pose.Pose) -> int

C++: protocols::pockets::PlaidFingerprint::compute_ligand_nconformers(const class core::pose::Pose &) const –> unsigned long

2. compute_ligand_nconformers(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint) -> int

C++: protocols::pockets::PlaidFingerprint::compute_ligand_nconformers() const –> unsigned long

compute_ligand_resnum(*args, **kwargs)

Overloaded function.

1. compute_ligand_resnum(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, pose: pyrosetta.rosetta.core.pose.Pose) -> int

C++: protocols::pockets::PlaidFingerprint::compute_ligand_resnum(const class core::pose::Pose &) const –> unsigned long

2. compute_ligand_resnum(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint) -> int

C++: protocols::pockets::PlaidFingerprint::compute_ligand_resnum() const –> unsigned long

dump_oriented_pose_and_fp_to_pdb(*args, **kwargs)

Overloaded function.

1. dump_oriented_pose_and_fp_to_pdb(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, pose_filename: str, fp_filename: str, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, angle1_offset: float, angle2_offset: float, angle3_offset: float) -> None

C++: protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(const std::string &, const std::string &, class protocols::pockets::FingerprintBase &, const double &, const double &, const double &) –> void

2. dump_oriented_pose_and_fp_to_pdb(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, pose_filename: str, fp_filename: str, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, angle1_offset: float, angle2_offset: float, angle3_offset: float, original_pocket_angle_transform: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(const std::string &, const std::string &, class protocols::pockets::FingerprintBase &, const double &, const double &, const double &, const class utility::vector1<double, class std::allocator<double> > &) –> void

3. dump_oriented_pose_and_fp_to_pdb(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, pose_filename: str, fp_filename: str, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, angle1_offset: float, angle2_offset: float, angle3_offset: float, CoM_offset: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(const std::string &, const std::string &, class protocols::pockets::FingerprintBase &, const double &, const double &, const double &, const class numeric::xyzVector<double> &) –> void

4. dump_oriented_pose_and_fp_to_pdb(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, pose_filename: str, fp_filename: str, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, angle1_offset: float, angle2_offset: float, angle3_offset: float, original_pocket_angle_transform: pyrosetta.rosetta.utility.vector1_double, CoM_offset: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(const std::string &, const std::string &, class protocols::pockets::FingerprintBase &, const double &, const double &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const class numeric::xyzVector<double> &) –> void

find_optimal_rotation(*args, **kwargs)

Overloaded function.

1. find_optimal_rotation(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, angle_increment: float, optimal_angle1: float, optimal_angle2: float, optimal_angle3: float, missing_point_weight: float, steric_weight: float, extra_point_weight: float) -> float

C++: protocols::pockets::PlaidFingerprint::find_optimal_rotation(class protocols::pockets::FingerprintBase &, const double &, double &, double &, double &, const double &, const double &, const double &) –> double

2. find_optimal_rotation(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, angle_increment: float, optimal_angle1: float, optimal_angle2: float, optimal_angle3: float, missing_point_weight: float, steric_weight: float, extra_point_weight: float, no_CoM_offset: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

C++: protocols::pockets::PlaidFingerprint::find_optimal_rotation(class protocols::pockets::FingerprintBase &, const double &, double &, double &, double &, const double &, const double &, const double &, const class numeric::xyzVector<double> &) –> double

fp_compare(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, missing_point_weight: float, steric_weight: float, extra_point_weight: float) → float

C++: protocols::pockets::PlaidFingerprint::fp_compare(class protocols::pockets::FingerprintBase &, const double &, const double &, const double &) const –> double

fp_compare_deriv(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, missing_point_weight: float, steric_weight: float, extra_point_weight: float, dE_dx: float, dE_dy: float, dE_dz: float, dE_dv4: float, dE_dv5: float, dE_dv6: float) → None

C++: protocols::pockets::PlaidFingerprint::fp_compare_deriv(class protocols::pockets::FingerprintBase &, const double &, const double &, const double &, double &, double &, double &, double &, double &, double &) const –> void

get_oriented_pose(*args, **kwargs)

Overloaded function.

1. get_oriented_pose(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, angle1_offset: float, angle2_offset: float, angle3_offset: float, CoM_offset: pyrosetta.rosetta.numeric.xyzVector_double_t, conformer: int) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::pockets::PlaidFingerprint::get_oriented_pose(class protocols::pockets::FingerprintBase &, const double &, const double &, const double &, const class numeric::xyzVector<double> &, const unsigned long) –> class core::pose::Pose

2. get_oriented_pose(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, angle1_offset: float, angle2_offset: float, angle3_offset: float, original_pocket_angle_transform: pyrosetta.rosetta.utility.vector1_double, CoM_offset: pyrosetta.rosetta.numeric.xyzVector_double_t, conformer: int) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::pockets::PlaidFingerprint::get_oriented_pose(class protocols::pockets::FingerprintBase &, const double &, const double &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const class numeric::xyzVector<double> &, const unsigned long) –> class core::pose::Pose

move_ligand_and_update_rhos_(*args, **kwargs)

Overloaded function.

1. move_ligand_and_update_rhos_(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, CoM_offset: pyrosetta.rosetta.numeric.xyzVector_double_t, angle1_offset: float, angle2_offset: float, angle3_offset: float, conformer: int) -> None

2. move_ligand_and_update_rhos_(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, CoM_offset: pyrosetta.rosetta.numeric.xyzVector_double_t, angle1_offset: float, angle2_offset: float, angle3_offset: float, conformer: int, update_derivatives: bool) -> None

C++: protocols::pockets::PlaidFingerprint::move_ligand_and_update_rhos_(class protocols::pockets::FingerprintBase &, const class numeric::xyzVector<double> &, const double &, const double &, const double &, const unsigned long &, const bool) –> void

multi_origin_list(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: protocols::pockets::FingerprintBase::multi_origin_list() const –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

num_origins(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → int

C++: protocols::pockets::FingerprintBase::num_origins() const –> unsigned long

origin(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::FingerprintBase::origin() const –> class numeric::xyzVector<double>

property pocketGrid_dim_

property pocketGrid_mid_

property pocketGrid_spacing_

pose(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::pockets::PlaidFingerprint::pose() –> class core::pose::Pose &

print_to_file(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, output_filename: str) → None

C++: protocols::pockets::FingerprintBase::print_to_file(const std::string &) const –> void

print_to_pdb(*args, **kwargs)

Overloaded function.

1. print_to_pdb(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, output_pdbname: str) -> None

C++: protocols::pockets::FingerprintBase::print_to_pdb(const std::string &) const –> void

2. print_to_pdb(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase, output_pdbname: str, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::FingerprintBase::print_to_pdb(const std::string &, const class numeric::xyzVector<double> &) const –> void

rmsd(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, original_pose: pyrosetta.rosetta.core.pose.Pose, oriented_pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::pockets::PlaidFingerprint::rmsd(const class core::pose::Pose &, const class core::pose::Pose &) –> double

search_random_poses(*args, **kwargs)

Overloaded function.

1. search_random_poses(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, num_pose_search: int, optimal_angle1: float, optimal_angle2: float, optimal_angle3: float, missing_point_weight: float, steric_weight: float, extra_point_weight: float) -> float

C++: protocols::pockets::PlaidFingerprint::search_random_poses(class protocols::pockets::FingerprintBase &, const unsigned long &, double &, double &, double &, const double &, const double &, const double &) –> double

2. search_random_poses(self: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, fp: pyrosetta.rosetta.protocols.pockets.FingerprintBase, num_pose_search: int, optimal_angle1: float, optimal_angle2: float, optimal_angle3: float, missing_point_weight: float, steric_weight: float, extra_point_weight: float, no_CoM_offset: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

C++: protocols::pockets::PlaidFingerprint::search_random_poses(class protocols::pockets::FingerprintBase &, const unsigned long &, double &, double &, double &, const double &, const double &, const double &, const class numeric::xyzVector<double> &) –> double

triplet_fingerprint_data(self: pyrosetta.rosetta.protocols.pockets.FingerprintBase) → pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t

C++: protocols::pockets::FingerprintBase::triplet_fingerprint_data() const –> const class std::list<struct protocols::pockets::spherical_coor_triplet, class std::allocator<struct protocols::pockets::spherical_coor_triplet> > &

class pyrosetta.rosetta.protocols.pockets.PocketConstraint

Bases: Constraint

This constraint favors creating a pocket suitable for a small-molecule

atom(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, index: int) → pyrosetta.rosetta.core.id.AtomID

C++: protocols::pockets::PocketConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : numeric::random::RandomGenerator) → int

C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::pockets::PocketConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)

Overloaded function.

1. dist(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float

2. dist(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, : pyrosetta.rosetta.core.scoring.func.XYZ_Func) -> float

PocketConstraints don’t have a single distance

C++: protocols::pockets::PocketConstraint::dist(const class core::scoring::func::XYZ_Func &) const –> double

effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) → int

C++: core::scoring::constraints::Constraint::effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &) const –> unsigned long

fill_f1_f2(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, : pyrosetta.rosetta.core.id.AtomID, : pyrosetta.rosetta.core.scoring.func.XYZ_Func, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.numeric.xyzVector_double_t, weights: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: protocols::pockets::PocketConstraint::fill_f1_f2(const class core::id::AtomID &, const class core::scoring::func::XYZ_Func &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::scoring::EMapVector &) const –> void

get_func(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → core::scoring::func::Func

Returns the func::Func object associated with this Constraint object.

C++: core::scoring::constraints::Constraint::get_func() const –> const class core::scoring::func::Func &

init(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::PocketConstraint::init(const class core::pose::Pose &) –> void

natoms(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint) → int

C++: protocols::pockets::PocketConstraint::natoms() const –> unsigned long

read_constraint(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose) → None

This method is totally redundant with read_def YAY

DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

C++: core::scoring::constraints::Constraint::read_constraint(std::istream &, const class core::pose::Pose &) –> void

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) → None

initialize this Constraint from the given std::istream. It’s amazing

that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

C++: core::scoring::constraints::Constraint::read_data(std::istream &) –> void

read_def(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, in: pyrosetta.rosetta.std.istream, pose: pyrosetta.rosetta.core.pose.Pose, func_factory: pyrosetta.rosetta.core.scoring.func.FuncFactory) → None

C++: protocols::pockets::PocketConstraint::read_def(std::istream &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint

apply a resid remapping to this constraint, returns the remapped

constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice.

C++: core::scoring::constraints::Constraint::remap_resid(const class core::id::SequenceMapping &) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pose.Pose, map: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint

Copies the data from this Constraint into a new object and returns

an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.

C++: core::scoring::constraints::Constraint::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

residues(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

C++: core::scoring::constraints::Constraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool

C++: protocols::pockets::PocketConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float

2. score(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float

3. score(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: protocols::pockets::PocketConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score_type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → pyrosetta.rosetta.core.scoring.ScoreType

Returns the ScoreType that this Constraint object will use.

C++: core::scoring::constraints::Constraint::score_type() const –> const enum core::scoring::ScoreType &

set_target_res(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, pose: pyrosetta.rosetta.core.pose.Pose, new_seqpos: int) → None

C++: protocols::pockets::PocketConstraint::set_target_res(const class core::pose::Pose &, unsigned long) –> void

set_target_res_pdb(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, pose: pyrosetta.rosetta.core.pose.Pose, resid: str) → None

C++: protocols::pockets::PocketConstraint::set_target_res_pdb(const class core::pose::Pose &, std::string) –> void

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::constraints::Constraint::setup_for_derivatives(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::constraints::Constraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.ostream) → None

This method is intended to show the value of the Constraint function

evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms.

C++: core::scoring::constraints::Constraint::show(std::ostream &) const –> void

show_def(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::PocketConstraint::show_def(std::ostream &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int) -> int

2. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int, threshold: float) -> int

Prints the violations of this constraint to the given

std::ostream. What are violations? It’s not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don’t know which definition is the right one. Documentation would be nice …

C++: core::scoring::constraints::Constraint::show_violations(std::ostream &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose) → None

take coordinates, distances, angles, etc from given pose

C++: core::scoring::constraints::Constraint::steal_def(const class core::pose::Pose &) –> void

target_res(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint) → int

C++: protocols::pockets::PocketConstraint::target_res() const –> unsigned long

to_string(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str

Convenience function, returns the results of show() as a string.

Not to be overriden by derived classes.

C++: core::scoring::constraints::Constraint::to_string() const –> std::string

type(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint) → str

C++: protocols::pockets::PocketConstraint::type() const –> std::string

class pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator

Bases: ConstraintCreator

Mover creator for the PocketConstraint constraint

assign(self: pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator, : pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator) → pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator

C++: protocols::pockets::PocketConstraintCreator::operator=(const class protocols::pockets::PocketConstraintCreator &) –> class protocols::pockets::PocketConstraintCreator &

create_constraint(self: pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::pockets::PocketConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator) → str

C++: protocols::pockets::PocketConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc

Bases: Multifunc

Pocket multifunction class, does objective function of optimization

abort_min(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double) → bool

Christophe added the following to allow premature end of minimization

If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!

C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

assign(self: pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc, : pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc) → pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc

C++: protocols::pockets::PocketExemplarMultifunc::operator=(const class protocols::pockets::PocketExemplarMultifunc &) –> class protocols::pockets::PocketExemplarMultifunc &

dfunc(self: pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::pockets::PocketExemplarMultifunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dump(self: pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.utility.vector1_double) → None

Error state reached; dump out current pdb.

C++: protocols::pockets::PocketExemplarMultifunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

class pyrosetta.rosetta.protocols.pockets.PocketGrid

Bases: pybind11_object

@

GetExemplarNumAtoms(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumAtoms() const –> unsigned long

GetExemplarNumClusters(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumClusters() const –> unsigned long

GetExemplarNumPolarAtoms(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumPolarAtoms() const –> unsigned long

alter_espGrid(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, espGrid_filename: str) → None

C++: protocols::pockets::PocketGrid::alter_espGrid(const std::string &) –> void

alter_espGrid_with_bound_ligand(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, espGrid_filename: str, protein_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(const std::string &, const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, gr: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.protocols.pockets.PocketGrid

C++: protocols::pockets::PocketGrid::operator=(const class protocols::pockets::PocketGrid &) –> class protocols::pockets::PocketGrid &

autoexpanding_pocket_eval(*args, **kwargs)

Overloaded function.

1. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int) -> bool

2. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool) -> bool

3. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float) -> bool

4. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float) -> bool

5. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class core::conformation::Residue &, const class core::scoring::func::XYZ_Func &, const unsigned long, bool, double, double, double) –> bool

6. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int) -> bool

7. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool) -> bool

8. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float) -> bool

9. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float) -> bool

10. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::scoring::func::XYZ_Func &, const unsigned long, bool, double, double, double) –> bool

11. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose) -> bool

12. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool) -> bool

13. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float) -> bool

14. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float) -> bool

15. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class core::conformation::Residue &, const class core::pose::Pose &, bool, double, double, double) –> bool

16. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose) -> bool

17. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool) -> bool

18. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float) -> bool

19. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float) -> bool

20. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::pose::Pose &, bool, double, double, double) –> bool

clear(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clear() –> void

clusterCPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clusterCPockets() –> void

clusterPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clusterPockets() –> void

dim(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::PocketGrid::dim() const –> class numeric::xyzVector<double>

dumpExemplarToFile(*args, **kwargs)

Overloaded function.

1. dumpExemplarToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None

C++: protocols::pockets::PocketGrid::dumpExemplarToFile() –> void

2. dumpExemplarToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpExemplarToFile(const std::string &) –> void

dumpGridToFile(*args, **kwargs)

Overloaded function.

1. dumpGridToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None

C++: protocols::pockets::PocketGrid::dumpGridToFile() –> void

2. dumpGridToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpGridToFile(const std::string &) –> void

dumpTargetPocketsToFile(*args, **kwargs)

Overloaded function.

1. dumpTargetPocketsToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToFile(const std::string &) –> void

2. dumpTargetPocketsToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str, rot1: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot2: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot3: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToFile(const std::string &, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>) –> void

dumpTargetPocketsToPDB(*args, **kwargs)

Overloaded function.

1. dumpTargetPocketsToPDB(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

2. dumpTargetPocketsToPDB(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str, minipock: bool) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToPDB(const std::string &, bool) –> void

3. dumpTargetPocketsToPDB(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str, rot1: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot2: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot3: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToPDB(const std::string &, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>) –> void

fillTargetPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::fillTargetPockets() –> void

findClusters(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::findClusters() –> void

findClustersByExemplars(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::findClustersByExemplars() –> void

findExemplars(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, inPose: pyrosetta.rosetta.core.pose.Pose, total_residues: int) → None

C++: protocols::pockets::PocketGrid::findExemplars(const class core::pose::Pose &, const unsigned long) –> void

findPSP(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findPSP(unsigned long, double) –> void

findPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findPockets(unsigned long, double) –> void

findSPS(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findSPS(unsigned long, double) –> void

getBounds(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::pockets::PocketGrid::getBounds() –> class utility::vector1<double, class std::allocator<double> >

static getRelaxResidues(input_pose: pyrosetta.rosetta.core.pose.Pose, resids: str) → pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t

C++: protocols::pockets::PocketGrid::getRelaxResidues(const class core::pose::Pose &, const std::string &) –> class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

get_connolly_surfacePoints(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, protein_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::PocketGrid::get_connolly_surfacePoints(const class core::pose::Pose &) const –> class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

get_connolly_surfacePoints_within_grid(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::PocketGrid::get_connolly_surfacePoints_within_grid(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

get_pocket_distance(*args, **kwargs)

Overloaded function.

1. get_pocket_distance(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, template_pocket: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> float

C++: protocols::pockets::PocketGrid::get_pocket_distance(const class protocols::pockets::PocketGrid &) const –> double

2. get_pocket_distance(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, template_pocket: pyrosetta.rosetta.protocols.pockets.PocketGrid, comparison_pdbname: str) -> float

C++: protocols::pockets::PocketGrid::get_pocket_distance(const class protocols::pockets::PocketGrid &, const std::string &) const –> double

initialize(*args, **kwargs)

Overloaded function.

1. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float) -> None

2. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float) -> None

3. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float, psp: bool) -> None

4. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const double &, const double &, const double &, const double, const double, const double, const double &, bool, bool) –> void

5. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float) -> None

6. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float) -> None

7. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float, psp: bool) -> None

8. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const double &, const double &, const double &, double, const double &, bool, bool) –> void

9. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float) -> None

10. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float) -> None

11. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float, psp: bool) -> None

12. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class numeric::xyzVector<double> &, double, const double &, bool, bool) –> void

13. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float) -> None

14. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float) -> None

15. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

16. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class numeric::xyzVector<double> &, const double &, const double &, const double &, const double &, bool, bool) –> void

17. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float) -> None

18. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float) -> None

19. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

20. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class core::conformation::Residue &, const double &, const double &, const double &, const double &, bool, bool) –> void

21. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float) -> None

22. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float) -> None

23. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

24. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const double &, const double &, const double &, const double &, bool, bool) –> void

isTooSmall(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → bool

C++: protocols::pockets::PocketGrid::isTooSmall() const –> bool

largestTargetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::largestTargetPocketVolume() –> double

linkExemplarsThroughSolvent(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::linkExemplarsThroughSolvent() –> void

mark(*args, **kwargs)

Overloaded function.

1. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float) -> None

2. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float, polar: bool) -> None

3. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float, polar: bool, targetResi: int) -> None

C++: protocols::pockets::PocketGrid::mark(double, double, double, const double &, const double &, bool, int) –> void

4. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float) -> None

5. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float, polar: bool) -> None

6. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float, polar: bool, targetResi: int) -> None

C++: protocols::pockets::PocketGrid::mark(const class numeric::xyzVector<double> &, const double &, const double &, bool, int) –> void

markDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: int, y: int, z: int, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markDepth(unsigned long, unsigned long, unsigned long, const double &, const double &) –> void

markEdgeDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markEdgeDepth(const double &, const double &) –> void

markOneEdgeDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: int, y: int, z: int, surf_d: float, bur_d: float, isTarget: bool) → bool

C++: protocols::pockets::PocketGrid::markOneEdgeDepth(unsigned long, unsigned long, unsigned long, const double &, const double &, bool) –> bool

markPocketDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markPocketDepth(const double &, const double &) –> void

move_pose_to_standard_orie(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_seqpos: int, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::PocketGrid::move_pose_to_standard_orie(const unsigned long &, class core::pose::Pose &) –> void

netTargetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::netTargetPocketVolume() –> double

print(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::print() const –> void

randomAngle(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::randomAngle() –> void

recenter(*args, **kwargs)

Overloaded function.

1. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float) -> None

C++: protocols::pockets::PocketGrid::recenter(const double &, const double &, const double &) –> void

2. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

C++: protocols::pockets::PocketGrid::recenter(const class core::conformation::Residue &) –> void

3. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsds: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t) -> None

C++: protocols::pockets::PocketGrid::recenter(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) –> void

4. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::PocketGrid::recenter(const class numeric::xyzVector<double> &) –> void

same_type_as_me(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, other: pyrosetta.rosetta.protocols.pockets.PocketGrid) → bool

C++: protocols::pockets::PocketGrid::same_type_as_me(const class protocols::pockets::PocketGrid &) const –> bool

spacing(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::spacing() const –> double

targetPocketHeuristicScore(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketHeuristicScore() const –> double

targetPocketHydrophobicProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketHydrophobicProteinSurface() const –> double

targetPocketPolarProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketPolarProteinSurface() const –> double

targetPocketProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketProteinSurface() const –> double

targetPocketSolventSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketSolventSurface() const –> double

targetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_sc: float, bur_sc: float) → float

C++: protocols::pockets::PocketGrid::targetPocketVolume(const double &, const double &) const –> double

whatIsTooSmall(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::PocketGrid::whatIsTooSmall() const –> class numeric::xyzVector<double>

write_pocketGrid_to_pdb(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) → None

C++: protocols::pockets::PocketGrid::write_pocketGrid_to_pdb(const std::string &) –> void

zeroAngle(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::zeroAngle() –> void

class pyrosetta.rosetta.protocols.pockets.SmallMol

Bases: pybind11_object

add_atom(self: pyrosetta.rosetta.protocols.pockets.SmallMol, line: str) → None

C++: protocols::pockets::SmallMol::add_atom(std::string) –> void

assign(self: pyrosetta.rosetta.protocols.pockets.SmallMol, rhs: pyrosetta.rosetta.protocols.pockets.SmallMol) → pyrosetta.rosetta.protocols.pockets.SmallMol

C++: protocols::pockets::SmallMol::operator=(const class protocols::pockets::SmallMol &) –> class protocols::pockets::SmallMol &

static calRMSD(mol1: pyrosetta.rosetta.protocols.pockets.SmallMol, mol2: pyrosetta.rosetta.protocols.pockets.SmallMol) → float

C++: protocols::pockets::SmallMol::calRMSD(class protocols::pockets::SmallMol &, class protocols::pockets::SmallMol &) –> double

cal_distance(self: pyrosetta.rosetta.protocols.pockets.SmallMol, other: pyrosetta.rosetta.protocols.pockets.SmallMol) → float

C++: protocols::pockets::SmallMol::cal_distance(class protocols::pockets::SmallMol *) –> double

cal_min_dist(self: pyrosetta.rosetta.protocols.pockets.SmallMol, other: pyrosetta.rosetta.protocols.pockets.SmallMol) → float

C++: protocols::pockets::SmallMol::cal_min_dist(class protocols::pockets::SmallMol *) –> double

connect(self: pyrosetta.rosetta.protocols.pockets.SmallMol, m: pyrosetta.rosetta.protocols.pockets.SmallMol) → None

C++: protocols::pockets::SmallMol::connect(class protocols::pockets::SmallMol *) –> void

connected(self: pyrosetta.rosetta.protocols.pockets.SmallMol, m: pyrosetta.rosetta.protocols.pockets.SmallMol) → bool

C++: protocols::pockets::SmallMol::connected(class protocols::pockets::SmallMol *) –> bool

findRoot(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → pyrosetta.rosetta.protocols.pockets.SmallMol

C++: protocols::pockets::SmallMol::findRoot() –> class protocols::pockets::SmallMol *

getContent(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → str

C++: protocols::pockets::SmallMol::getContent() const –> std::string

get_center(self: pyrosetta.rosetta.protocols.pockets.SmallMol, c: int) → float

C++: protocols::pockets::SmallMol::get_center(int) –> double

get_coordinates(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → pyrosetta.rosetta.std.vector_std_vector_double_t

C++: protocols::pockets::SmallMol::get_coordinates() –> const class std::vector<class std::vector<double, class std::allocator<double> >, class std::allocator<class std::vector<double, class std::allocator<double> > > > &

get_name(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → str

C++: protocols::pockets::SmallMol::get_name() –> std::string

get_parent(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → pyrosetta.rosetta.protocols.pockets.SmallMol

C++: protocols::pockets::SmallMol::get_parent() –> class protocols::pockets::SmallMol *

get_rmsd(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → float

C++: protocols::pockets::SmallMol::get_rmsd() –> double

get_root(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → pyrosetta.rosetta.protocols.pockets.SmallMol

C++: protocols::pockets::SmallMol::get_root() –> class protocols::pockets::SmallMol *

get_size(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → int

C++: protocols::pockets::SmallMol::get_size() –> int

get_visited(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → bool

C++: protocols::pockets::SmallMol::get_visited() –> bool

numberOfAtoms(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → int

C++: protocols::pockets::SmallMol::numberOfAtoms() const –> int

printContent(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → None

C++: protocols::pockets::SmallMol::printContent() const –> void

printCoordinates(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → None

C++: protocols::pockets::SmallMol::printCoordinates() const –> void

set_name(self: pyrosetta.rosetta.protocols.pockets.SmallMol, name: str) → None

C++: protocols::pockets::SmallMol::set_name(std::string) –> void

set_parent(self: pyrosetta.rosetta.protocols.pockets.SmallMol, p: pyrosetta.rosetta.protocols.pockets.SmallMol) → None

C++: protocols::pockets::SmallMol::set_parent(class protocols::pockets::SmallMol *) –> void

set_size(self: pyrosetta.rosetta.protocols.pockets.SmallMol, t: int) → None

C++: protocols::pockets::SmallMol::set_size(int) –> void

set_visited(self: pyrosetta.rosetta.protocols.pockets.SmallMol, v: bool) → None

C++: protocols::pockets::SmallMol::set_visited(bool) –> void

update_center(self: pyrosetta.rosetta.protocols.pockets.SmallMol) → None

C++: protocols::pockets::SmallMol::update_center() –> void

class pyrosetta.rosetta.protocols.pockets.TargetPocketGrid

Bases: PocketGrid

@

GetExemplarNumAtoms(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumAtoms() const –> unsigned long

GetExemplarNumClusters(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumClusters() const –> unsigned long

GetExemplarNumPolarAtoms(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → int

C++: protocols::pockets::PocketGrid::GetExemplarNumPolarAtoms() const –> unsigned long

alter_espGrid(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, espGrid_filename: str) → None

C++: protocols::pockets::PocketGrid::alter_espGrid(const std::string &) –> void

alter_espGrid_with_bound_ligand(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, espGrid_filename: str, protein_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(const std::string &, const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pockets.TargetPocketGrid, : pyrosetta.rosetta.protocols.pockets.TargetPocketGrid) → pyrosetta.rosetta.protocols.pockets.TargetPocketGrid

C++: protocols::pockets::TargetPocketGrid::operator=(const class protocols::pockets::TargetPocketGrid &) –> class protocols::pockets::TargetPocketGrid &

autoexpanding_pocket_eval(*args, **kwargs)

Overloaded function.

1. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int) -> bool

2. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool) -> bool

3. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float) -> bool

4. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float) -> bool

5. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class core::conformation::Residue &, const class core::scoring::func::XYZ_Func &, const unsigned long, bool, double, double, double) –> bool

6. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int) -> bool

7. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool) -> bool

8. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float) -> bool

9. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float) -> bool

10. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func: pyrosetta.rosetta.core.scoring.func.XYZ_Func, total_residues: int, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::scoring::func::XYZ_Func &, const unsigned long, bool, double, double, double) –> bool

11. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose) -> bool

12. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool) -> bool

13. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float) -> bool

14. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float) -> bool

15. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class core::conformation::Residue &, const class core::pose::Pose &, bool, double, double, double) –> bool

16. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose) -> bool

17. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool) -> bool

18. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float) -> bool

19. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float) -> bool

20. autoexpanding_pocket_eval(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose: pyrosetta.rosetta.core.pose.Pose, center_target: bool, x: float, y: float, z: float) -> bool

C++: protocols::pockets::PocketGrid::autoexpanding_pocket_eval(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::pose::Pose &, bool, double, double, double) –> bool

clear(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clear() –> void

clusterCPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clusterCPockets() –> void

clusterPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::clusterPockets() –> void

dim(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::PocketGrid::dim() const –> class numeric::xyzVector<double>

dumpExemplarToFile(*args, **kwargs)

Overloaded function.

1. dumpExemplarToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None

C++: protocols::pockets::PocketGrid::dumpExemplarToFile() –> void

2. dumpExemplarToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpExemplarToFile(const std::string &) –> void

dumpGridToFile(*args, **kwargs)

Overloaded function.

1. dumpGridToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None

C++: protocols::pockets::PocketGrid::dumpGridToFile() –> void

2. dumpGridToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpGridToFile(const std::string &) –> void

dumpTargetPocketsToFile(*args, **kwargs)

Overloaded function.

1. dumpTargetPocketsToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToFile(const std::string &) –> void

2. dumpTargetPocketsToFile(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str, rot1: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot2: pyrosetta.rosetta.numeric.xyzMatrix_double_t, rot3: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> None

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToFile(const std::string &, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>, class numeric::xyzMatrix<double>) –> void

dumpTargetPocketsToPDB(*args, **kwargs)

Overloaded function.

1. dumpTargetPocketsToPDB(self: pyrosetta.rosetta.protocols.pockets.TargetPocketGrid, output_filename: str) -> None

2. dumpTargetPocketsToPDB(self: pyrosetta.rosetta.protocols.pockets.TargetPocketGrid, output_filename: str, minipock: bool) -> None

C++: protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(const std::string &, bool) –> void

fillTargetPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::fillTargetPockets() –> void

findClusters(self: pyrosetta.rosetta.protocols.pockets.TargetPocketGrid) → None

C++: protocols::pockets::TargetPocketGrid::findClusters() –> void

findClustersByExemplars(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::findClustersByExemplars() –> void

findExemplars(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, inPose: pyrosetta.rosetta.core.pose.Pose, total_residues: int) → None

C++: protocols::pockets::PocketGrid::findExemplars(const class core::pose::Pose &, const unsigned long) –> void

findPSP(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findPSP(unsigned long, double) –> void

findPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findPockets(unsigned long, double) –> void

findSPS(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, thr: int, max: float) → None

C++: protocols::pockets::PocketGrid::findSPS(unsigned long, double) –> void

getBounds(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::pockets::PocketGrid::getBounds() –> class utility::vector1<double, class std::allocator<double> >

static getRelaxResidues(input_pose: pyrosetta.rosetta.core.pose.Pose, resids: str) → pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t

C++: protocols::pockets::PocketGrid::getRelaxResidues(const class core::pose::Pose &, const std::string &) –> class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

get_connolly_surfacePoints(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, protein_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::PocketGrid::get_connolly_surfacePoints(const class core::pose::Pose &) const –> class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

get_connolly_surfacePoints_within_grid(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surfacePoints_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_t) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_t

C++: protocols::pockets::PocketGrid::get_connolly_surfacePoints_within_grid(const class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> class std::list<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

get_pocket_distance(*args, **kwargs)

Overloaded function.

1. get_pocket_distance(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, template_pocket: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> float

C++: protocols::pockets::PocketGrid::get_pocket_distance(const class protocols::pockets::PocketGrid &) const –> double

2. get_pocket_distance(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, template_pocket: pyrosetta.rosetta.protocols.pockets.PocketGrid, comparison_pdbname: str) -> float

C++: protocols::pockets::PocketGrid::get_pocket_distance(const class protocols::pockets::PocketGrid &, const std::string &) const –> double

initialize(*args, **kwargs)

Overloaded function.

1. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float) -> None

2. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float) -> None

3. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float, psp: bool) -> None

4. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, size_x: float, size_y: float, size_z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const double &, const double &, const double &, const double, const double, const double, const double &, bool, bool) –> void

5. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float) -> None

6. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float) -> None

7. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float, psp: bool) -> None

8. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const double &, const double &, const double &, double, const double &, bool, bool) –> void

9. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float) -> None

10. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float) -> None

11. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float, psp: bool) -> None

12. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class numeric::xyzVector<double> &, double, const double &, bool, bool) –> void

13. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float) -> None

14. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float) -> None

15. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

16. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class numeric::xyzVector<double> &, const double &, const double &, const double &, const double &, bool, bool) –> void

17. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float) -> None

18. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float) -> None

19. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

20. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class core::conformation::Residue &, const double &, const double &, const double &, const double &, bool, bool) –> void

21. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float) -> None

22. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float) -> None

23. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float, psp: bool) -> None

24. initialize(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None

C++: protocols::pockets::PocketGrid::initialize(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const double &, const double &, const double &, const double &, bool, bool) –> void

isTooSmall(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → bool

C++: protocols::pockets::PocketGrid::isTooSmall() const –> bool

largestTargetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::largestTargetPocketVolume() –> double

linkExemplarsThroughSolvent(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::linkExemplarsThroughSolvent() –> void

mark(*args, **kwargs)

Overloaded function.

1. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float) -> None

2. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float, polar: bool) -> None

3. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: float, y: float, z: float, vdWd: float, buffer: float, polar: bool, targetResi: int) -> None

C++: protocols::pockets::PocketGrid::mark(double, double, double, const double &, const double &, bool, int) –> void

4. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float) -> None

5. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float, polar: bool) -> None

6. mark(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, vdWd: float, buffer: float, polar: bool, targetResi: int) -> None

C++: protocols::pockets::PocketGrid::mark(const class numeric::xyzVector<double> &, const double &, const double &, bool, int) –> void

markDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: int, y: int, z: int, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markDepth(unsigned long, unsigned long, unsigned long, const double &, const double &) –> void

markEdgeDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markEdgeDepth(const double &, const double &) –> void

markOneEdgeDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, x: int, y: int, z: int, surf_d: float, bur_d: float, isTarget: bool) → bool

C++: protocols::pockets::PocketGrid::markOneEdgeDepth(unsigned long, unsigned long, unsigned long, const double &, const double &, bool) –> bool

markPocketDepth(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_d: float, bur_d: float) → None

C++: protocols::pockets::PocketGrid::markPocketDepth(const double &, const double &) –> void

move_pose_to_standard_orie(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_seqpos: int, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pockets::PocketGrid::move_pose_to_standard_orie(const unsigned long &, class core::pose::Pose &) –> void

netTargetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::netTargetPocketVolume() –> double

print(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::print() const –> void

randomAngle(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::randomAngle() –> void

recenter(*args, **kwargs)

Overloaded function.

1. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float) -> None

C++: protocols::pockets::PocketGrid::recenter(const double &, const double &, const double &) –> void

2. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

C++: protocols::pockets::PocketGrid::recenter(const class core::conformation::Residue &) –> void

3. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsds: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t) -> None

C++: protocols::pockets::PocketGrid::recenter(const class std::vector<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) –> void

4. recenter(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::PocketGrid::recenter(const class numeric::xyzVector<double> &) –> void

same_type_as_me(self: pyrosetta.rosetta.protocols.pockets.TargetPocketGrid, other: pyrosetta.rosetta.protocols.pockets.PocketGrid) → bool

C++: protocols::pockets::TargetPocketGrid::same_type_as_me(const class protocols::pockets::PocketGrid &) const –> bool

spacing(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::spacing() const –> double

targetPocketHeuristicScore(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketHeuristicScore() const –> double

targetPocketHydrophobicProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketHydrophobicProteinSurface() const –> double

targetPocketPolarProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketPolarProteinSurface() const –> double

targetPocketProteinSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketProteinSurface() const –> double

targetPocketSolventSurface(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → float

C++: protocols::pockets::PocketGrid::targetPocketSolventSurface() const –> double

targetPocketVolume(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, surf_sc: float, bur_sc: float) → float

C++: protocols::pockets::PocketGrid::targetPocketVolume(const double &, const double &) const –> double

whatIsTooSmall(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::pockets::PocketGrid::whatIsTooSmall() const –> class numeric::xyzVector<double>

write_pocketGrid_to_pdb(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, output_filename: str) → None

C++: protocols::pockets::PocketGrid::write_pocketGrid_to_pdb(const std::string &) –> void

zeroAngle(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

C++: protocols::pockets::PocketGrid::zeroAngle() –> void

class pyrosetta.rosetta.protocols.pockets.UnionEdge

Bases: pybind11_object

get_a(self: pyrosetta.rosetta.protocols.pockets.UnionEdge) → pyrosetta.rosetta.protocols.pockets.SmallMol

C++: protocols::pockets::UnionEdge::get_a() –> class protocols::pockets::SmallMol *

get_b(self: pyrosetta.rosetta.protocols.pockets.UnionEdge) → pyrosetta.rosetta.protocols.pockets.SmallMol

C++: protocols::pockets::UnionEdge::get_b() –> class protocols::pockets::SmallMol *

get_dist(self: pyrosetta.rosetta.protocols.pockets.UnionEdge) → float

C++: protocols::pockets::UnionEdge::get_dist() const –> double

pyrosetta.rosetta.protocols.pockets.convert_cartesian_to_grid(*args, **kwargs)

Overloaded function.

1. convert_cartesian_to_grid(cart_coord: pyrosetta.rosetta.numeric.xyzVector_double_t, mid: pyrosetta.rosetta.numeric.xyzVector_double_t, dim: pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t, spacing: float, grid_coord: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::convert_cartesian_to_grid(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<unsigned long> &, const double &, class numeric::xyzVector<double> &) –> void

2. convert_cartesian_to_grid(cart_coord: pyrosetta.rosetta.numeric.xyzVector_double_t, mid: pyrosetta.rosetta.numeric.xyzVector_double_t, dim: pyrosetta.rosetta.numeric.xyzVector_double_t, spacing: float, grid_coord: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::convert_cartesian_to_grid(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const double &, class numeric::xyzVector<double> &) –> void

pyrosetta.rosetta.protocols.pockets.convert_cartesian_to_spherical_coor_triplet(coord: pyrosetta.rosetta.numeric.xyzVector_double_t, triplet: pyrosetta.rosetta.protocols.pockets.spherical_coor_triplet) → None

C++: protocols::pockets::convert_cartesian_to_spherical_coor_triplet(const class numeric::xyzVector<double> &, struct protocols::pockets::spherical_coor_triplet &) –> void

pyrosetta.rosetta.protocols.pockets.convert_grid_to_cartesian(*args, **kwargs)

Overloaded function.

1. convert_grid_to_cartesian(grid_coord: pyrosetta.rosetta.numeric.xyzVector_double_t, mid: pyrosetta.rosetta.numeric.xyzVector_double_t, dim: pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t, spacing: float, cart_coord: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::convert_grid_to_cartesian(class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<unsigned long> &, const double &, class numeric::xyzVector<double> &) –> void

2. convert_grid_to_cartesian(grid_coord: pyrosetta.rosetta.numeric.xyzVector_double_t, mid: pyrosetta.rosetta.numeric.xyzVector_double_t, dim: pyrosetta.rosetta.numeric.xyzVector_double_t, spacing: float, cart_coord: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::pockets::convert_grid_to_cartesian(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const double &, class numeric::xyzVector<double> &) –> void

pyrosetta.rosetta.protocols.pockets.convert_spherical_coor_triplet_to_cartesian(triplet: pyrosetta.rosetta.protocols.pockets.spherical_coor_triplet, coord: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::pockets::convert_spherical_coor_triplet_to_cartesian(const struct protocols::pockets::spherical_coor_triplet &, class numeric::xyzVector<double> &) –> void

pyrosetta.rosetta.protocols.pockets.dD_dv1(: float, : float, : float, : float, : float, : float, : float, : float, : float, : float) → float

C++: protocols::pockets::dD_dv1(const double, const double, const double, const double, const double, const double, const double, const double, const double, const double) –> double

pyrosetta.rosetta.protocols.pockets.dD_dv2(: float, : float, : float, : float, : float, : float, : float, : float, : float, : float) → float

C++: protocols::pockets::dD_dv2(const double, const double, const double, const double, const double, const double, const double, const double, const double, const double) –> double

pyrosetta.rosetta.protocols.pockets.dD_dv3(: float, : float, : float, : float, : float, : float, : float, : float, : float, : float) → float

C++: protocols::pockets::dD_dv3(const double, const double, const double, const double, const double, const double, const double, const double, const double, const double) –> double

pyrosetta.rosetta.protocols.pockets.dD_dv4(: float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float) → float

C++: protocols::pockets::dD_dv4(const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double) –> double

pyrosetta.rosetta.protocols.pockets.dD_dv5(: float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float) → float

C++: protocols::pockets::dD_dv5(const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double) –> double

pyrosetta.rosetta.protocols.pockets.dD_dv6(: float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float, : float) → float

C++: protocols::pockets::dD_dv6(const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double, const double) –> double

class pyrosetta.rosetta.protocols.pockets.ray_distance_derivs

Bases: pybind11_object

property dDist_dv1

property dDist_dv2

property dDist_dv3

property dDist_dv4

property dDist_dv5

property dDist_dv6

class pyrosetta.rosetta.protocols.pockets.spherical_coor_triplet

Bases: pybind11_object

property ori

property phi

property psi

property rho

class pyrosetta.rosetta.protocols.pockets.triplet_and_originnum

Bases: pybind11_object

property originnum

property phi

property psi

property rho