pockets

Bindings for protocols::pockets namespace

class pyrosetta.rosetta.protocols.pockets.CCluster

Bases: pybind11_builtins.pybind11_object

@ Cluster of exemplar points

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.pockets.CCluster, arg0: int, arg1: int, arg2: int, arg3: str, arg4: float) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.pockets.CCluster, arg0: int, arg1: int, arg2: int, arg3: str, arg4: float, arg5: float) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.pockets.CCluster, arg0: int, arg1: int, arg2: int, arg3: str, arg4: float, arg5: float, arg6: float) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.pockets.CCluster, x: int, y: int, z: int, atype: str, step_: float, absX: float, absY: float, absZ: float) -> None
5. __init__(self: pyrosetta.rosetta.protocols.pockets.CCluster, arg0: pyrosetta.rosetta.protocols.pockets.CCluster) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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, class std::basic_string<char>, double, double, double) –> void

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

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_builtins.pybind11_object

@ Set of clusters of exemplar points

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add(*args, **kwargs)

Overloaded function.

1. add(self: pyrosetta.rosetta.protocols.pockets.CClusterSet, x: int, y: int, z: int, aname: str, step: float) -> std::_List_iterator<protocols::pockets::CCluster>
2. add(self: pyrosetta.rosetta.protocols.pockets.CClusterSet, x: int, y: int, z: int, aname: str, step: float, absX: float) -> std::_List_iterator<protocols::pockets::CCluster>
3. add(self: pyrosetta.rosetta.protocols.pockets.CClusterSet, x: int, y: int, z: int, aname: str, step: float, absX: float, absY: float) -> std::_List_iterator<protocols::pockets::CCluster>
4. add(self: pyrosetta.rosetta.protocols.pockets.CClusterSet, x: int, y: int, z: int, aname: str, step: float, absX: float, absY: float, absZ: float) -> std::_List_iterator<protocols::pockets::CCluster>

C++: protocols::pockets::CClusterSet::add(unsigned long, unsigned long, unsigned long, class std::basic_string<char>, double, double, double, double) –> struct std::_List_iterator<class protocols::pockets::CCluster>

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

join(self: pyrosetta.rosetta.protocols.pockets.CClusterSet, c1: std::_List_iterator<protocols::pockets::CCluster>, c2: std::_List_iterator<protocols::pockets::CCluster>) → None

C++: protocols::pockets::CClusterSet::join(struct std::_List_iterator<class protocols::pockets::CCluster>, struct std::_List_iterator<class protocols::pockets::CCluster>) –> void

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

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

class pyrosetta.rosetta.protocols.pockets.ComparisonGrid

Bases: pybind11_builtins.pybind11_object

@

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.pockets.ComparisonGrid, gr: pyrosetta.rosetta.protocols.pockets.PocketGrid) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.EggshellGrid

Bases: pyrosetta.rosetta.protocols.pockets.PocketGrid

@

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, rhs: pyrosetta.rosetta.protocols.pockets.PocketGrid) → bool

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

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, gr: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None
2. __init__(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, grd: pyrosetta.rosetta.protocols.pockets.PocketGrid, ligand_pose: pyrosetta.rosetta.core.pose.Pose) -> None
3. __init__(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, ext_grd: pyrosetta.rosetta.protocols.pockets.PocketGrid, eggshell_coord_list: pyrosetta.rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> None
4. __init__(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, protein_pose: pyrosetta.rosetta.core.pose.Pose, pocket_grid: pyrosetta.rosetta.protocols.pockets.PocketGrid, grid_for_extshell: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None
5. __init__(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, fname: str) -> None
6. __init__(self: pyrosetta.rosetta.protocols.pockets.EggshellGrid, arg0: pyrosetta.rosetta.protocols.pockets.EggshellGrid) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

C++: protocols::pockets::PocketGrid::alter_espGrid(const class std::basic_string<char> &) –> 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 class std::basic_string<char> &, 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_std_allocator_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

clearSmallPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, minsize: int) → None

C++: protocols::pockets::PocketGrid::clearSmallPockets(unsigned long) –> 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> void

dumpTargetPocketsToFile(*args, **kwargs)

Overloaded function.

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

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToFile(const class std::basic_string<char> &) –> 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 class std::basic_string<char> &, 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 class std::basic_string<char> &, 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 class std::basic_string<char> &, 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 class std::basic_string<char> &) 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 class std::basic_string<char> &, 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_std_allocator_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_std_allocator_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> >

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 class std::basic_string<char> &) –> 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_std_allocator_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_std_allocator_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_std_allocator_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_std_allocator_numeric_xyzVector_double_t) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_std_allocator_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 class std::basic_string<char> &) 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 class std::basic_string<char> &) 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 class std::basic_string<char> &) 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 class std::basic_string<char> &) 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 class std::basic_string<char> &, 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 class std::basic_string<char> &) –> 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.FingerprintMultifunc

Bases: pyrosetta.rosetta.core.optimization.Multifunc

Atom tree multifunction class

__call__(self: pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc, vars: pyrosetta.rosetta.utility.vector1_double) → float

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc, nfp_in: pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint, pfp_in: pyrosetta.rosetta.protocols.pockets.PlaidFingerprint, missing_point_weight: float, steric_weight: float, extra_point_weight: float, nconformers: int) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.PCluster

Bases: pybind11_builtins.pybind11_object

@ Cluster of Pocket points

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.pockets.PCluster, x: int, y: int, z: int, step_: float) -> None
2. __init__(self: pyrosetta.rosetta.protocols.pockets.PCluster, arg0: pyrosetta.rosetta.protocols.pockets.PCluster) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

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_builtins.pybind11_object

@ Set of cluster of pocket points

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add(self: pyrosetta.rosetta.protocols.pockets.PClusterSet, x: int, y: int, z: int, step: float) → std::_List_iterator<protocols::pockets::PCluster>

C++: protocols::pockets::PClusterSet::add(unsigned long, unsigned long, unsigned long, double) –> struct std::_List_iterator<class protocols::pockets::PCluster>

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

join(self: pyrosetta.rosetta.protocols.pockets.PClusterSet, c1: std::_List_iterator<protocols::pockets::PCluster>, c2: std::_List_iterator<protocols::pockets::PCluster>) → None

C++: protocols::pockets::PClusterSet::join(struct std::_List_iterator<class protocols::pockets::PCluster>, struct std::_List_iterator<class protocols::pockets::PCluster>) –> void

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

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

class pyrosetta.rosetta.protocols.pockets.PocketConstraint

Bases: pyrosetta.rosetta.core.scoring.constraints.Constraint

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

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

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

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint) -> None
2. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> None
3. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketConstraint, arg0: pyrosetta.rosetta.protocols.pockets.PocketConstraint) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool

Inequality operator to test whether two constraints are not functionally

identical.

C++: core::scoring::constraints::Constraint::operator!=(const class core::scoring::constraints::Constraint &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

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

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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, : pyrosetta.rosetta.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(class std::basic_istream<char> &, 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(class std::basic_istream<char> &) –> 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(class std::basic_istream<char> &, 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 &, class std::basic_string<char>) –> 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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &, 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(class std::basic_ostream<char> &, 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: pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator

Mover creator for the PocketConstraint constraint

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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: pyrosetta.rosetta.core.optimization.Multifunc

Pocket multifunction class, does objective function of optimization

__call__(self: pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc, vars: pyrosetta.rosetta.utility.vector1_double) → float

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc, input_pdb_name: str, resid: str, c_rad: float, rep_weight: float, p_min: pyrosetta.rosetta.utility.vector1_double, p_max: pyrosetta.rosetta.utility.vector1_double) -> None
2. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc, arg0: pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_builtins.pybind11_object

@

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

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

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

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None
2. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, arg0: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None
3. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue) -> None
4. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t) -> None
5. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, central_rsd: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, z: float) -> None
6. __init__(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
7. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, y: float, z: float, stepSize: float) -> None
8. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, y: float, z: float) -> None
9. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, y: float, z: float, stepSize: float, psp: bool, sps: bool) -> None
10. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, arg0: float, arg1: float, arg2: float, arg3: float) -> None

doc

11. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, arg0: float, arg1: float, arg2: float, arg3: float, arg4: float) -> None

doc

12. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, arg0: float, arg1: float, arg2: float, arg3: float, arg4: float, arg5: bool) -> None

doc

13. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, xc: float, yc: float, zc: float, x: float, stepSize: float, psp: bool, sps: bool) -> None
14. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, arg0: pyrosetta.rosetta.numeric.xyzVector_double_t, arg1: float) -> None

doc

15. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, arg0: pyrosetta.rosetta.numeric.xyzVector_double_t, arg1: float, arg2: float) -> None

doc

16. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, arg0: pyrosetta.rosetta.numeric.xyzVector_double_t, arg1: float, arg2: float, arg3: bool) -> None

doc

17. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, center: pyrosetta.rosetta.numeric.xyzVector_double_t, x: float, stepSize: float, psp: bool, sps: bool) -> None
18. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, arg0: pyrosetta.rosetta.numeric.xyzVector_double_t, arg1: float, arg2: float, arg3: float) -> None

doc

19. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, arg0: pyrosetta.rosetta.numeric.xyzVector_double_t, arg1: float, arg2: float, arg3: float, arg4: float) -> None

doc

20. __init__(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, arg0: pyrosetta.rosetta.numeric.xyzVector_double_t, arg1: float, arg2: float, arg3: float, arg4: float, arg5: bool) -> None

doc

21. __init__(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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

C++: protocols::pockets::PocketGrid::alter_espGrid(const class std::basic_string<char> &) –> 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 class std::basic_string<char> &, 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

clearSmallPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, minsize: int) → None

C++: protocols::pockets::PocketGrid::clearSmallPockets(unsigned long) –> 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> void

dumpTargetPocketsToFile(*args, **kwargs)

Overloaded function.

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

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToFile(const class std::basic_string<char> &) –> 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 class std::basic_string<char> &, 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 class std::basic_string<char> &, 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 class std::basic_string<char> &, 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> >

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 class std::basic_string<char> &) –> 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_std_allocator_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_std_allocator_numeric_xyzVector_double_t) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_std_allocator_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 class std::basic_string<char> &) 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 class std::basic_string<char> &) –> void

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

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

class pyrosetta.rosetta.protocols.pockets.TargetPocketGrid

Bases: pyrosetta.rosetta.protocols.pockets.PocketGrid

@

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

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

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

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.pockets.TargetPocketGrid, gr: pyrosetta.rosetta.protocols.pockets.PocketGrid) -> None
2. __init__(self: pyrosetta.rosetta.protocols.pockets.TargetPocketGrid, fname: str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.pockets.TargetPocketGrid, arg0: pyrosetta.rosetta.protocols.pockets.TargetPocketGrid) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

C++: protocols::pockets::PocketGrid::alter_espGrid(const class std::basic_string<char> &) –> 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 class std::basic_string<char> &, 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

clearSmallPockets(self: pyrosetta.rosetta.protocols.pockets.PocketGrid, minsize: int) → None

C++: protocols::pockets::PocketGrid::clearSmallPockets(unsigned long) –> 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> void

dumpTargetPocketsToFile(*args, **kwargs)

Overloaded function.

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

C++: protocols::pockets::PocketGrid::dumpTargetPocketsToFile(const class std::basic_string<char> &) –> 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 class std::basic_string<char> &, 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 class std::basic_string<char> &, 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> >

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 class std::basic_string<char> &) –> 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_std_allocator_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_std_allocator_numeric_xyzVector_double_t) → pyrosetta.rosetta.std.list_numeric_xyzVector_double_std_allocator_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 class std::basic_string<char> &) 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 class std::basic_string<char> &) –> void

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

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

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