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- builtins.object
-
- CCluster
- CClusterSet
- ComparisonGrid
- FingerprintBase
-
- NonPlaidFingerprint
- PlaidFingerprint
- GenPharmacophore
- PCluster
- PClusterSet
- PocketGrid
-
- EggshellGrid
- ElectrostaticpotentialGrid
- TargetPocketGrid
- SmallMol
- UnionEdge
- ray_distance_derivs
- spherical_coor_triplet
- triplet_and_originnum
- rosetta.core.optimization.Multifunc(builtins.object)
-
- FingerprintMultifunc
- PocketExemplarMultifunc
- rosetta.core.optimization.ParticleSwarmMinimizer(builtins.object)
-
- DarcParticleSwarmMinimizer
- rosetta.core.scoring.constraints.Constraint(builtins.object)
-
- PocketConstraint
- rosetta.core.scoring.constraints.ConstraintCreator(builtins.object)
-
- PocketConstraintCreator
class CCluster(builtins.object) |
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@ Cluster of exemplar points
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.pockets.CCluster, int, int, int, str, float) -> NoneType
doc
2. __init__(rosetta.protocols.pockets.CCluster, int, int, int, str, float, float) -> NoneType
doc
3. __init__(rosetta.protocols.pockets.CCluster, int, int, int, str, float, float, float) -> NoneType
doc
4. __init__(self : rosetta.protocols.pockets.CCluster, x : int, y : int, z : int, atype : str, step_ : float, absX : float, absY : float, absZ : float) -> NoneType
5. __init__(self : rosetta.protocols.pockets.CCluster, old : rosetta.protocols.pockets.CCluster) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add(...) from builtins.PyCapsule
- add(*args, **kwargs)
Overloaded function.
1. add(self : rosetta.protocols.pockets.CCluster, x : int, y : int, z : int, atype : str) -> NoneType
2. add(self : rosetta.protocols.pockets.CCluster, x : int, y : int, z : int, atype : str, absX : float) -> NoneType
3. add(self : rosetta.protocols.pockets.CCluster, x : int, y : int, z : int, atype : str, absX : float, absY : float) -> NoneType
4. add(self : rosetta.protocols.pockets.CCluster, x : int, y : int, z : int, atype : str, absX : float, absY : float, absZ : float) -> NoneType
- isClose(...) from builtins.PyCapsule
- isClose(self : rosetta.protocols.pockets.CCluster, c2 : rosetta.protocols.pockets.CCluster) -> bool
- isSolventExposed(...) from builtins.PyCapsule
- isSolventExposed(rosetta.protocols.pockets.CCluster) -> bool
- isTarget(...) from builtins.PyCapsule
- isTarget(*args, **kwargs)
Overloaded function.
1. isTarget(rosetta.protocols.pockets.CCluster) -> bool
2. isTarget(self : rosetta.protocols.pockets.CCluster, numTargets : int) -> bool
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.pockets.CCluster) -> int
- testNeighbor(...) from builtins.PyCapsule
- testNeighbor(self : rosetta.protocols.pockets.CCluster, c2 : rosetta.protocols.pockets.CCluster) -> bool
Data descriptors defined here:
- points_
|
class CClusterSet(builtins.object) |
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@ Set of clusters of exemplar points
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.pockets.CClusterSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add(...) from builtins.PyCapsule
- add(*args, **kwargs)
Overloaded function.
1. add(self : rosetta.protocols.pockets.CClusterSet, x : int, y : int, z : int, aname : str, step : float) -> std::_List_iterator<protocols::pockets::CCluster>
2. add(self : 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 : 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 : 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>
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.CClusterSet, old : rosetta.protocols.pockets.CClusterSet) -> rosetta.protocols.pockets.CClusterSet
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.pockets.CClusterSet) -> NoneType
- findClusters(...) from builtins.PyCapsule
- findClusters(rosetta.protocols.pockets.CClusterSet) -> NoneType
- getLargestClusterSize(...) from builtins.PyCapsule
- getLargestClusterSize(self : rosetta.protocols.pockets.CClusterSet, stepSize : float, minClusterSize : float, numTargets : int, ignoreBuried : bool, ignoreSurface : bool) -> float
- getNetClusterSize(...) from builtins.PyCapsule
- getNetClusterSize(self : rosetta.protocols.pockets.CClusterSet, stepSize : float, minClusterSize : float, numTargets : int, ignoreBuried : bool, ignoreSurface : bool) -> float
- join(...) from builtins.PyCapsule
- join(self : rosetta.protocols.pockets.CClusterSet, c1 : std::_List_iterator<protocols::pockets::CCluster>, c2 : std::_List_iterator<protocols::pockets::CCluster>) -> NoneType
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.pockets.CClusterSet) -> int
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class EggshellGrid(PocketGrid) |
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@
|
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- Method resolution order:
- EggshellGrid
- PocketGrid
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.pockets.EggshellGrid, rhs : rosetta.protocols.pockets.PocketGrid) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, gr : rosetta.protocols.pockets.PocketGrid) -> NoneType
2. __init__(self : handle, grd : rosetta.protocols.pockets.PocketGrid, ligand_pose : rosetta.core.pose.Pose) -> NoneType
3. __init__(self : handle, ext_grd : rosetta.protocols.pockets.PocketGrid, eggshell_coord_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> NoneType
4. __init__(self : handle, protein_pose : rosetta.core.pose.Pose, pocket_grid : rosetta.protocols.pockets.PocketGrid, grid_for_extshell : rosetta.protocols.pockets.PocketGrid) -> NoneType
5. __init__(self : handle, fname : str) -> NoneType
6. __init__(handle, rosetta.protocols.pockets.EggshellGrid) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.EggshellGrid, : rosetta.protocols.pockets.EggshellGrid) -> rosetta.protocols.pockets.EggshellGrid
- calculate_center_xyz(...) from builtins.PyCapsule
- calculate_center_xyz(self : rosetta.protocols.pockets.EggshellGrid, pocketshell_coord_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> rosetta.numeric.xyzVector_double_t
- dump_eggshell(...) from builtins.PyCapsule
- dump_eggshell(*args, **kwargs)
Overloaded function.
1. dump_eggshell(self : rosetta.protocols.pockets.EggshellGrid, fname : str) -> NoneType
2. dump_eggshell(self : rosetta.protocols.pockets.EggshellGrid, fname : str, rot1 : rosetta.numeric.xyzMatrix_double_t, rot2 : rosetta.numeric.xyzMatrix_double_t, rot3 : rosetta.numeric.xyzMatrix_double_t) -> NoneType
- eggshell_coord_list(...) from builtins.PyCapsule
- eggshell_coord_list(rosetta.protocols.pockets.EggshellGrid) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- extra_coord_list(...) from builtins.PyCapsule
- extra_coord_list(rosetta.protocols.pockets.EggshellGrid) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- get_connolly_eggshell(...) from builtins.PyCapsule
- get_connolly_eggshell(self : rosetta.protocols.pockets.EggshellGrid, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, eggGrid : rosetta.protocols.pockets.PocketGrid, extGrid : rosetta.protocols.pockets.PocketGrid) -> NoneType
- get_connolly_eggshell_on_grid(...) from builtins.PyCapsule
- get_connolly_eggshell_on_grid(self : rosetta.protocols.pockets.EggshellGrid, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, eggGrid : rosetta.protocols.pockets.PocketGrid, extGrid : rosetta.protocols.pockets.PocketGrid) -> NoneType
- get_eggshell_distance(...) from builtins.PyCapsule
- get_eggshell_distance(*args, **kwargs)
Overloaded function.
1. get_eggshell_distance(self : rosetta.protocols.pockets.EggshellGrid, template_eggshell : rosetta.protocols.pockets.EggshellGrid) -> float
2. get_eggshell_distance(self : rosetta.protocols.pockets.EggshellGrid, template_eggshell : rosetta.protocols.pockets.EggshellGrid, comparison_pdbname : str) -> float
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.protocols.pockets.EggshellGrid, other : rosetta.protocols.pockets.PocketGrid) -> bool
- write_Grid_to_pdb(...) from builtins.PyCapsule
- write_Grid_to_pdb(self : rosetta.protocols.pockets.EggshellGrid, gr : rosetta.protocols.pockets.PocketGrid, output_pdbname : str) -> NoneType
- write_eggshell_to_pdb(...) from builtins.PyCapsule
- write_eggshell_to_pdb(*args, **kwargs)
Overloaded function.
1. write_eggshell_to_pdb(self : rosetta.protocols.pockets.EggshellGrid, output_pdbname : str) -> NoneType
2. write_eggshell_to_pdb(self : rosetta.protocols.pockets.EggshellGrid, output_pdbname : str, rot1 : rosetta.numeric.xyzMatrix_double_t, rot2 : rosetta.numeric.xyzMatrix_double_t, rot3 : rosetta.numeric.xyzMatrix_double_t) -> NoneType
Methods inherited from PocketGrid:
- alter_espGrid(...) from builtins.PyCapsule
- alter_espGrid(self : rosetta.protocols.pockets.PocketGrid, espGrid_filename : str) -> NoneType
- alter_espGrid_with_bound_ligand(...) from builtins.PyCapsule
- alter_espGrid_with_bound_ligand(self : rosetta.protocols.pockets.PocketGrid, espGrid_filename : str, protein_pose : rosetta.core.pose.Pose) -> NoneType
- autoexpanding_pocket_eval(...) from builtins.PyCapsule
- autoexpanding_pocket_eval(*args, **kwargs)
Overloaded function.
1. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int) -> bool
2. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool) -> bool
3. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float) -> bool
4. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float) -> bool
5. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float, z : float) -> bool
6. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int) -> bool
7. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool) -> bool
8. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float) -> bool
9. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float) -> bool
10. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float, z : float) -> bool
11. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose) -> bool
12. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool) -> bool
13. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float) -> bool
14. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float) -> bool
15. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float, z : float) -> bool
16. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose) -> bool
17. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool) -> bool
18. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float) -> bool
19. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float) -> bool
20. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float, z : float) -> bool
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.pockets.PocketGrid) -> NoneType
- clearSmallPockets(...) from builtins.PyCapsule
- clearSmallPockets(self : rosetta.protocols.pockets.PocketGrid, minsize : int) -> NoneType
- clusterCPockets(...) from builtins.PyCapsule
- clusterCPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- clusterPockets(...) from builtins.PyCapsule
- clusterPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- dim(...) from builtins.PyCapsule
- dim(rosetta.protocols.pockets.PocketGrid) -> rosetta.numeric.xyzVector_double_t
- dumpExemplarToFile(...) from builtins.PyCapsule
- dumpExemplarToFile(*args, **kwargs)
Overloaded function.
1. dumpExemplarToFile(rosetta.protocols.pockets.PocketGrid) -> NoneType
2. dumpExemplarToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- dumpGridToFile(...) from builtins.PyCapsule
- dumpGridToFile(*args, **kwargs)
Overloaded function.
1. dumpGridToFile(rosetta.protocols.pockets.PocketGrid) -> NoneType
2. dumpGridToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- dumpTargetPocketsToFile(...) from builtins.PyCapsule
- dumpTargetPocketsToFile(*args, **kwargs)
Overloaded function.
1. dumpTargetPocketsToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
2. dumpTargetPocketsToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str, rot1 : rosetta.numeric.xyzMatrix_double_t, rot2 : rosetta.numeric.xyzMatrix_double_t, rot3 : rosetta.numeric.xyzMatrix_double_t) -> NoneType
- dumpTargetPocketsToPDB(...) from builtins.PyCapsule
- dumpTargetPocketsToPDB(*args, **kwargs)
Overloaded function.
1. dumpTargetPocketsToPDB(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
2. dumpTargetPocketsToPDB(self : rosetta.protocols.pockets.PocketGrid, output_filename : str, minipock : bool) -> NoneType
3. dumpTargetPocketsToPDB(self : rosetta.protocols.pockets.PocketGrid, output_filename : str, rot1 : rosetta.numeric.xyzMatrix_double_t, rot2 : rosetta.numeric.xyzMatrix_double_t, rot3 : rosetta.numeric.xyzMatrix_double_t) -> NoneType
- fillTargetPockets(...) from builtins.PyCapsule
- fillTargetPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- findClusters(...) from builtins.PyCapsule
- findClusters(rosetta.protocols.pockets.PocketGrid) -> NoneType
- findClustersByExemplars(...) from builtins.PyCapsule
- findClustersByExemplars(rosetta.protocols.pockets.PocketGrid) -> NoneType
- findExemplars(...) from builtins.PyCapsule
- findExemplars(self : rosetta.protocols.pockets.PocketGrid, inPose : rosetta.core.pose.Pose, total_residues : int) -> NoneType
- findPSP(...) from builtins.PyCapsule
- findPSP(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- findPockets(...) from builtins.PyCapsule
- findPockets(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- findSPS(...) from builtins.PyCapsule
- findSPS(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- getBounds(...) from builtins.PyCapsule
- getBounds(rosetta.protocols.pockets.PocketGrid) -> rosetta.utility.vector1_double
- getRelaxResidues(...) from builtins.PyCapsule
- getRelaxResidues(input_pose : rosetta.core.pose.Pose, resids : str) -> rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t
- get_connolly_surfacePoints(...) from builtins.PyCapsule
- get_connolly_surfacePoints(self : rosetta.protocols.pockets.PocketGrid, protein_pose : rosetta.core.pose.Pose) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- get_connolly_surfacePoints_within_grid(...) from builtins.PyCapsule
- get_connolly_surfacePoints_within_grid(self : rosetta.protocols.pockets.PocketGrid, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- get_pocket_distance(...) from builtins.PyCapsule
- get_pocket_distance(*args, **kwargs)
Overloaded function.
1. get_pocket_distance(self : rosetta.protocols.pockets.PocketGrid, template_pocket : rosetta.protocols.pockets.PocketGrid) -> float
2. get_pocket_distance(self : rosetta.protocols.pockets.PocketGrid, template_pocket : rosetta.protocols.pockets.PocketGrid, comparison_pdbname : str) -> float
- initialize(...) from builtins.PyCapsule
- initialize(*args, **kwargs)
Overloaded function.
1. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float) -> NoneType
2. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float, stepSize : float) -> NoneType
3. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float, stepSize : float, psp : bool) -> NoneType
4. initialize(self : 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) -> NoneType
5. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float) -> NoneType
6. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float) -> NoneType
7. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float, psp : bool) -> NoneType
8. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float, psp : bool, sps : bool) -> NoneType
9. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float) -> NoneType
10. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float) -> NoneType
11. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float, psp : bool) -> NoneType
12. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float, psp : bool, sps : bool) -> NoneType
13. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float) -> NoneType
14. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float) -> NoneType
15. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
16. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
17. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float) -> NoneType
18. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float) -> NoneType
19. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
20. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
21. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float) -> NoneType
22. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float) -> NoneType
23. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
24. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
- isTooSmall(...) from builtins.PyCapsule
- isTooSmall(rosetta.protocols.pockets.PocketGrid) -> bool
- largestTargetPocketVolume(...) from builtins.PyCapsule
- largestTargetPocketVolume(rosetta.protocols.pockets.PocketGrid) -> float
- linkExemplarsThroughSolvent(...) from builtins.PyCapsule
- linkExemplarsThroughSolvent(rosetta.protocols.pockets.PocketGrid) -> NoneType
- mark(...) from builtins.PyCapsule
- mark(*args, **kwargs)
Overloaded function.
1. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float) -> NoneType
2. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float, polar : bool) -> NoneType
3. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float, polar : bool, targetResi : int) -> NoneType
4. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float) -> NoneType
5. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float, polar : bool) -> NoneType
6. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float, polar : bool, targetResi : int) -> NoneType
- markDepth(...) from builtins.PyCapsule
- markDepth(self : rosetta.protocols.pockets.PocketGrid, x : int, y : int, z : int, surf_d : float, bur_d : float) -> NoneType
- markEdgeDepth(...) from builtins.PyCapsule
- markEdgeDepth(self : rosetta.protocols.pockets.PocketGrid, surf_d : float, bur_d : float) -> NoneType
- markOneEdgeDepth(...) from builtins.PyCapsule
- markOneEdgeDepth(self : rosetta.protocols.pockets.PocketGrid, x : int, y : int, z : int, surf_d : float, bur_d : float, isTarget : bool) -> bool
- markPocketDepth(...) from builtins.PyCapsule
- markPocketDepth(self : rosetta.protocols.pockets.PocketGrid, surf_d : float, bur_d : float) -> NoneType
- move_pose_to_standard_orie(...) from builtins.PyCapsule
- move_pose_to_standard_orie(self : rosetta.protocols.pockets.PocketGrid, central_seqpos : int, pose : rosetta.core.pose.Pose) -> NoneType
- netTargetPocketVolume(...) from builtins.PyCapsule
- netTargetPocketVolume(rosetta.protocols.pockets.PocketGrid) -> float
- print(...) from builtins.PyCapsule
- print(rosetta.protocols.pockets.PocketGrid) -> NoneType
- randomAngle(...) from builtins.PyCapsule
- randomAngle(rosetta.protocols.pockets.PocketGrid) -> NoneType
- recenter(...) from builtins.PyCapsule
- recenter(*args, **kwargs)
Overloaded function.
1. recenter(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float) -> NoneType
2. recenter(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue) -> NoneType
3. recenter(self : rosetta.protocols.pockets.PocketGrid, central_rsds : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
4. recenter(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t) -> NoneType
- spacing(...) from builtins.PyCapsule
- spacing(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketHeuristicScore(...) from builtins.PyCapsule
- targetPocketHeuristicScore(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketHydrophobicProteinSurface(...) from builtins.PyCapsule
- targetPocketHydrophobicProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketPolarProteinSurface(...) from builtins.PyCapsule
- targetPocketPolarProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketProteinSurface(...) from builtins.PyCapsule
- targetPocketProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketSolventSurface(...) from builtins.PyCapsule
- targetPocketSolventSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketVolume(...) from builtins.PyCapsule
- targetPocketVolume(self : rosetta.protocols.pockets.PocketGrid, surf_sc : float, bur_sc : float) -> float
- whatIsTooSmall(...) from builtins.PyCapsule
- whatIsTooSmall(rosetta.protocols.pockets.PocketGrid) -> rosetta.numeric.xyzVector_double_t
- write_pocketGrid_to_pdb(...) from builtins.PyCapsule
- write_pocketGrid_to_pdb(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- zeroAngle(...) from builtins.PyCapsule
- zeroAngle(rosetta.protocols.pockets.PocketGrid) -> NoneType
|
class ElectrostaticpotentialGrid(PocketGrid) |
| | |
- Method resolution order:
- ElectrostaticpotentialGrid
- PocketGrid
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, other : rosetta.protocols.pockets.PocketGrid) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, str, rosetta.core.pose.Pose, rosetta.protocols.pockets.PocketGrid) -> NoneType
doc
3. __init__(self : handle, input_espGrid_filename : str, protein_pose : rosetta.core.pose.Pose, pocket_grid : rosetta.protocols.pockets.PocketGrid, delphi : bool) -> NoneType
4. __init__(handle, rosetta.protocols.pockets.ElectrostaticpotentialGrid) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, : rosetta.protocols.pockets.ElectrostaticpotentialGrid) -> rosetta.protocols.pockets.ElectrostaticpotentialGrid
- assign_esp_for_atom_grid_points(...) from builtins.PyCapsule
- assign_esp_for_atom_grid_points(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, atom_coord : rosetta.numeric.xyzVector_double_t, inflated_radius : float) -> NoneType
- assign_esp_for_protein_grid_points(...) from builtins.PyCapsule
- assign_esp_for_protein_grid_points(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, protein_pose : rosetta.core.pose.Pose, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> NoneType
- assign_esp_for_surface_grid_points(...) from builtins.PyCapsule
- assign_esp_for_surface_grid_points(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> NoneType
- assign_esp_for_surface_grid_points_by_nn(...) from builtins.PyCapsule
- assign_esp_for_surface_grid_points_by_nn(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> NoneType
- cap_espGrid(...) from builtins.PyCapsule
- cap_espGrid(rosetta.protocols.pockets.ElectrostaticpotentialGrid) -> NoneType
- change_espGrid_for_darc(...) from builtins.PyCapsule
- change_espGrid_for_darc(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, espGrid_filename : str, protein_pose : rosetta.core.pose.Pose, pocket_grid : rosetta.protocols.pockets.PocketGrid) -> NoneType
- espGrid_point_list(...) from builtins.PyCapsule
- espGrid_point_list(rosetta.protocols.pockets.ElectrostaticpotentialGrid) -> rosetta.std.list_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t
- fill_espGrid_values(...) from builtins.PyCapsule
- fill_espGrid_values(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_OEgrid_filename : str) -> NoneType
- fill_espGrid_values_with_type(...) from builtins.PyCapsule
- fill_espGrid_values_with_type(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_OEgrid_filename : str) -> NoneType
- get_DELPHI_espGrid_values(...) from builtins.PyCapsule
- get_DELPHI_espGrid_values(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_espGrid_filename : str) -> NoneType
- get_ZAP_espGrid_values(...) from builtins.PyCapsule
- get_ZAP_espGrid_values(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_espGrid_filename : str) -> NoneType
- get_ZAP_espGrid_values_with_type(...) from builtins.PyCapsule
- get_ZAP_espGrid_values_with_type(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_espGrid_filename : str) -> NoneType
- get_atom_dist_from_connolly_surface(...) from builtins.PyCapsule
- get_atom_dist_from_connolly_surface(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, atom_coord : rosetta.numeric.xyzVector_double_t, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> float
- get_oegrid_dimensions(...) from builtins.PyCapsule
- get_oegrid_dimensions(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, input_OEgrid_filename : str) -> NoneType
- initialize_espGrid(...) from builtins.PyCapsule
- initialize_espGrid(rosetta.protocols.pockets.ElectrostaticpotentialGrid) -> NoneType
- initialize_typGrid(...) from builtins.PyCapsule
- initialize_typGrid(rosetta.protocols.pockets.ElectrostaticpotentialGrid) -> NoneType
- mark_atom_espGrid_points(...) from builtins.PyCapsule
- mark_atom_espGrid_points(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, atom_coord : rosetta.numeric.xyzVector_double_t, vdWd : float) -> NoneType
- mark_buried_solvent_points(...) from builtins.PyCapsule
- mark_buried_solvent_points(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, protein_pose : rosetta.core.pose.Pose, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> NoneType
- mark_protein_espGrid_points(...) from builtins.PyCapsule
- mark_protein_espGrid_points(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, protein_pose : rosetta.core.pose.Pose) -> NoneType
- print_to_oegrid(...) from builtins.PyCapsule
- print_to_oegrid(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, output_OEgrid_filename : str) -> NoneType
- resize_espGrid_to_match_pocketGrid(...) from builtins.PyCapsule
- resize_espGrid_to_match_pocketGrid(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, espGrid_filename : str, pg : rosetta.protocols.pockets.PocketGrid) -> NoneType
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, other : rosetta.protocols.pockets.PocketGrid) -> bool
- set_protein_esp_to_zero(...) from builtins.PyCapsule
- set_protein_esp_to_zero(rosetta.protocols.pockets.ElectrostaticpotentialGrid) -> NoneType
- set_surface_esp_to_zero(...) from builtins.PyCapsule
- set_surface_esp_to_zero(rosetta.protocols.pockets.ElectrostaticpotentialGrid) -> NoneType
- write_connollySurface_to_pdb(...) from builtins.PyCapsule
- write_connollySurface_to_pdb(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, output_pdbname : str) -> NoneType
- write_espGrid_to_pdb(...) from builtins.PyCapsule
- write_espGrid_to_pdb(self : rosetta.protocols.pockets.ElectrostaticpotentialGrid, output_pdbname : str) -> NoneType
Data descriptors defined here:
- espGrid_
- typGrid_
Data and other attributes defined here:
- PROTEIN = PtType.PROTEIN
- PSEUDO_PROTEIN = PtType.PSEUDO_PROTEIN
- PtType = <class 'rosetta.protocols.pockets.ElectrostaticpotentialGrid.PtType'>
- SOLVENT = PtType.SOLVENT
- SURFACE = PtType.SURFACE
Methods inherited from PocketGrid:
- alter_espGrid(...) from builtins.PyCapsule
- alter_espGrid(self : rosetta.protocols.pockets.PocketGrid, espGrid_filename : str) -> NoneType
- alter_espGrid_with_bound_ligand(...) from builtins.PyCapsule
- alter_espGrid_with_bound_ligand(self : rosetta.protocols.pockets.PocketGrid, espGrid_filename : str, protein_pose : rosetta.core.pose.Pose) -> NoneType
- autoexpanding_pocket_eval(...) from builtins.PyCapsule
- autoexpanding_pocket_eval(*args, **kwargs)
Overloaded function.
1. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int) -> bool
2. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool) -> bool
3. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float) -> bool
4. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float) -> bool
5. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float, z : float) -> bool
6. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int) -> bool
7. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool) -> bool
8. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float) -> bool
9. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float) -> bool
10. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float, z : float) -> bool
11. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose) -> bool
12. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool) -> bool
13. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float) -> bool
14. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float) -> bool
15. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float, z : float) -> bool
16. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose) -> bool
17. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool) -> bool
18. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float) -> bool
19. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float) -> bool
20. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float, z : float) -> bool
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.pockets.PocketGrid) -> NoneType
- clearSmallPockets(...) from builtins.PyCapsule
- clearSmallPockets(self : rosetta.protocols.pockets.PocketGrid, minsize : int) -> NoneType
- clusterCPockets(...) from builtins.PyCapsule
- clusterCPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- clusterPockets(...) from builtins.PyCapsule
- clusterPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- dim(...) from builtins.PyCapsule
- dim(rosetta.protocols.pockets.PocketGrid) -> rosetta.numeric.xyzVector_double_t
- dumpExemplarToFile(...) from builtins.PyCapsule
- dumpExemplarToFile(*args, **kwargs)
Overloaded function.
1. dumpExemplarToFile(rosetta.protocols.pockets.PocketGrid) -> NoneType
2. dumpExemplarToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- dumpGridToFile(...) from builtins.PyCapsule
- dumpGridToFile(*args, **kwargs)
Overloaded function.
1. dumpGridToFile(rosetta.protocols.pockets.PocketGrid) -> NoneType
2. dumpGridToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- dumpTargetPocketsToFile(...) from builtins.PyCapsule
- dumpTargetPocketsToFile(*args, **kwargs)
Overloaded function.
1. dumpTargetPocketsToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
2. dumpTargetPocketsToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str, rot1 : rosetta.numeric.xyzMatrix_double_t, rot2 : rosetta.numeric.xyzMatrix_double_t, rot3 : rosetta.numeric.xyzMatrix_double_t) -> NoneType
- dumpTargetPocketsToPDB(...) from builtins.PyCapsule
- dumpTargetPocketsToPDB(*args, **kwargs)
Overloaded function.
1. dumpTargetPocketsToPDB(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
2. dumpTargetPocketsToPDB(self : rosetta.protocols.pockets.PocketGrid, output_filename : str, minipock : bool) -> NoneType
3. dumpTargetPocketsToPDB(self : rosetta.protocols.pockets.PocketGrid, output_filename : str, rot1 : rosetta.numeric.xyzMatrix_double_t, rot2 : rosetta.numeric.xyzMatrix_double_t, rot3 : rosetta.numeric.xyzMatrix_double_t) -> NoneType
- fillTargetPockets(...) from builtins.PyCapsule
- fillTargetPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- findClusters(...) from builtins.PyCapsule
- findClusters(rosetta.protocols.pockets.PocketGrid) -> NoneType
- findClustersByExemplars(...) from builtins.PyCapsule
- findClustersByExemplars(rosetta.protocols.pockets.PocketGrid) -> NoneType
- findExemplars(...) from builtins.PyCapsule
- findExemplars(self : rosetta.protocols.pockets.PocketGrid, inPose : rosetta.core.pose.Pose, total_residues : int) -> NoneType
- findPSP(...) from builtins.PyCapsule
- findPSP(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- findPockets(...) from builtins.PyCapsule
- findPockets(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- findSPS(...) from builtins.PyCapsule
- findSPS(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- getBounds(...) from builtins.PyCapsule
- getBounds(rosetta.protocols.pockets.PocketGrid) -> rosetta.utility.vector1_double
- getRelaxResidues(...) from builtins.PyCapsule
- getRelaxResidues(input_pose : rosetta.core.pose.Pose, resids : str) -> rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t
- get_connolly_surfacePoints(...) from builtins.PyCapsule
- get_connolly_surfacePoints(self : rosetta.protocols.pockets.PocketGrid, protein_pose : rosetta.core.pose.Pose) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- get_connolly_surfacePoints_within_grid(...) from builtins.PyCapsule
- get_connolly_surfacePoints_within_grid(self : rosetta.protocols.pockets.PocketGrid, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- get_pocket_distance(...) from builtins.PyCapsule
- get_pocket_distance(*args, **kwargs)
Overloaded function.
1. get_pocket_distance(self : rosetta.protocols.pockets.PocketGrid, template_pocket : rosetta.protocols.pockets.PocketGrid) -> float
2. get_pocket_distance(self : rosetta.protocols.pockets.PocketGrid, template_pocket : rosetta.protocols.pockets.PocketGrid, comparison_pdbname : str) -> float
- initialize(...) from builtins.PyCapsule
- initialize(*args, **kwargs)
Overloaded function.
1. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float) -> NoneType
2. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float, stepSize : float) -> NoneType
3. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float, stepSize : float, psp : bool) -> NoneType
4. initialize(self : 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) -> NoneType
5. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float) -> NoneType
6. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float) -> NoneType
7. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float, psp : bool) -> NoneType
8. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float, psp : bool, sps : bool) -> NoneType
9. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float) -> NoneType
10. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float) -> NoneType
11. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float, psp : bool) -> NoneType
12. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float, psp : bool, sps : bool) -> NoneType
13. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float) -> NoneType
14. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float) -> NoneType
15. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
16. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
17. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float) -> NoneType
18. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float) -> NoneType
19. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
20. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
21. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float) -> NoneType
22. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float) -> NoneType
23. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
24. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
- isTooSmall(...) from builtins.PyCapsule
- isTooSmall(rosetta.protocols.pockets.PocketGrid) -> bool
- largestTargetPocketVolume(...) from builtins.PyCapsule
- largestTargetPocketVolume(rosetta.protocols.pockets.PocketGrid) -> float
- linkExemplarsThroughSolvent(...) from builtins.PyCapsule
- linkExemplarsThroughSolvent(rosetta.protocols.pockets.PocketGrid) -> NoneType
- mark(...) from builtins.PyCapsule
- mark(*args, **kwargs)
Overloaded function.
1. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float) -> NoneType
2. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float, polar : bool) -> NoneType
3. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float, polar : bool, targetResi : int) -> NoneType
4. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float) -> NoneType
5. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float, polar : bool) -> NoneType
6. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float, polar : bool, targetResi : int) -> NoneType
- markDepth(...) from builtins.PyCapsule
- markDepth(self : rosetta.protocols.pockets.PocketGrid, x : int, y : int, z : int, surf_d : float, bur_d : float) -> NoneType
- markEdgeDepth(...) from builtins.PyCapsule
- markEdgeDepth(self : rosetta.protocols.pockets.PocketGrid, surf_d : float, bur_d : float) -> NoneType
- markOneEdgeDepth(...) from builtins.PyCapsule
- markOneEdgeDepth(self : rosetta.protocols.pockets.PocketGrid, x : int, y : int, z : int, surf_d : float, bur_d : float, isTarget : bool) -> bool
- markPocketDepth(...) from builtins.PyCapsule
- markPocketDepth(self : rosetta.protocols.pockets.PocketGrid, surf_d : float, bur_d : float) -> NoneType
- move_pose_to_standard_orie(...) from builtins.PyCapsule
- move_pose_to_standard_orie(self : rosetta.protocols.pockets.PocketGrid, central_seqpos : int, pose : rosetta.core.pose.Pose) -> NoneType
- netTargetPocketVolume(...) from builtins.PyCapsule
- netTargetPocketVolume(rosetta.protocols.pockets.PocketGrid) -> float
- print(...) from builtins.PyCapsule
- print(rosetta.protocols.pockets.PocketGrid) -> NoneType
- randomAngle(...) from builtins.PyCapsule
- randomAngle(rosetta.protocols.pockets.PocketGrid) -> NoneType
- recenter(...) from builtins.PyCapsule
- recenter(*args, **kwargs)
Overloaded function.
1. recenter(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float) -> NoneType
2. recenter(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue) -> NoneType
3. recenter(self : rosetta.protocols.pockets.PocketGrid, central_rsds : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
4. recenter(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t) -> NoneType
- spacing(...) from builtins.PyCapsule
- spacing(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketHeuristicScore(...) from builtins.PyCapsule
- targetPocketHeuristicScore(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketHydrophobicProteinSurface(...) from builtins.PyCapsule
- targetPocketHydrophobicProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketPolarProteinSurface(...) from builtins.PyCapsule
- targetPocketPolarProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketProteinSurface(...) from builtins.PyCapsule
- targetPocketProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketSolventSurface(...) from builtins.PyCapsule
- targetPocketSolventSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketVolume(...) from builtins.PyCapsule
- targetPocketVolume(self : rosetta.protocols.pockets.PocketGrid, surf_sc : float, bur_sc : float) -> float
- whatIsTooSmall(...) from builtins.PyCapsule
- whatIsTooSmall(rosetta.protocols.pockets.PocketGrid) -> rosetta.numeric.xyzVector_double_t
- write_pocketGrid_to_pdb(...) from builtins.PyCapsule
- write_pocketGrid_to_pdb(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- zeroAngle(...) from builtins.PyCapsule
- zeroAngle(rosetta.protocols.pockets.PocketGrid) -> NoneType
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class FingerprintBase(builtins.object) |
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Methods defined here:
- CHEAT_CoM(...) from builtins.PyCapsule
- CHEAT_CoM(self : rosetta.protocols.pockets.FingerprintBase, inp_CoM : rosetta.numeric.xyzVector_double_t) -> NoneType
- CoM(...) from builtins.PyCapsule
- CoM(rosetta.protocols.pockets.FingerprintBase) -> rosetta.numeric.xyzVector_double_t
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.pockets.FingerprintBase) -> NoneType
2. __init__(self : rosetta.protocols.pockets.FingerprintBase, : rosetta.protocols.pockets.FingerprintBase) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.FingerprintBase, : rosetta.protocols.pockets.FingerprintBase) -> rosetta.protocols.pockets.FingerprintBase
- multi_origin_list(...) from builtins.PyCapsule
- multi_origin_list(rosetta.protocols.pockets.FingerprintBase) -> rosetta.utility.vector1_numeric_xyzVector_double_t
- num_origins(...) from builtins.PyCapsule
- num_origins(rosetta.protocols.pockets.FingerprintBase) -> int
- origin(...) from builtins.PyCapsule
- origin(rosetta.protocols.pockets.FingerprintBase) -> rosetta.numeric.xyzVector_double_t
- print_to_file(...) from builtins.PyCapsule
- print_to_file(self : rosetta.protocols.pockets.FingerprintBase, output_filename : str) -> NoneType
- print_to_pdb(...) from builtins.PyCapsule
- print_to_pdb(*args, **kwargs)
Overloaded function.
1. print_to_pdb(self : rosetta.protocols.pockets.FingerprintBase, output_pdbname : str) -> NoneType
2. print_to_pdb(self : rosetta.protocols.pockets.FingerprintBase, output_pdbname : str, translation : rosetta.numeric.xyzVector_double_t) -> NoneType
- triplet_fingerprint_data(...) from builtins.PyCapsule
- triplet_fingerprint_data(rosetta.protocols.pockets.FingerprintBase) -> rosetta.std.list_protocols_pockets_spherical_coor_triplet_std_allocator_protocols_pockets_spherical_coor_triplet_t
Data descriptors defined here:
- pocketGrid_dim_
- pocketGrid_mid_
- pocketGrid_spacing_
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class FingerprintMultifunc(rosetta.core.optimization.Multifunc) |
| |
Atom tree multifunction class
|
| |
- Method resolution order:
- FingerprintMultifunc
- rosetta.core.optimization.Multifunc
- builtins.object
Methods defined here:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.protocols.pockets.FingerprintMultifunc, vars : rosetta.utility.vector1_double) -> float
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, nfp_in : rosetta.protocols.pockets.NonPlaidFingerprint, pfp_in : rosetta.protocols.pockets.PlaidFingerprint, missing_point_weight : float, steric_weight : float, extra_point_weight : float, nconformers : int) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- dfunc(...) from builtins.PyCapsule
- dfunc(self : rosetta.protocols.pockets.FingerprintMultifunc, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double) -> NoneType
- dump(...) from builtins.PyCapsule
- dump(self : rosetta.protocols.pockets.FingerprintMultifunc, vars : rosetta.utility.vector1_double) -> NoneType
Error state reached; dump out current pdb.
Methods inherited from rosetta.core.optimization.Multifunc:
- abort_min(...) from builtins.PyCapsule
- abort_min(self : rosetta.core.optimization.Multifunc, : 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!
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class GenPharmacophore(builtins.object) |
| | |
Methods defined here:
- ReplaceString(...) from builtins.PyCapsule
- ReplaceString(self : rosetta.protocols.pockets.GenPharmacophore, subject : str, search : str, replace : str) -> str
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.pockets.GenPharmacophore) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.GenPharmacophore, : rosetta.protocols.pockets.GenPharmacophore) -> rosetta.protocols.pockets.GenPharmacophore
- cluster_KeyFeatures(...) from builtins.PyCapsule
- cluster_KeyFeatures(self : rosetta.protocols.pockets.GenPharmacophore, input_filename : str, output_filename : str) -> NoneType
- extract_Hbond_atoms_from_protein_rna_complex(...) from builtins.PyCapsule
- extract_Hbond_atoms_from_protein_rna_complex(self : rosetta.protocols.pockets.GenPharmacophore, protein_pose : rosetta.core.pose.Pose, rna_pose : rosetta.core.pose.Pose) -> str
- extract_rna_rings_from_protein_rna_complex(...) from builtins.PyCapsule
- extract_rna_rings_from_protein_rna_complex(self : rosetta.protocols.pockets.GenPharmacophore, protein_pose : rosetta.core.pose.Pose, rna_pose : rosetta.core.pose.Pose) -> str
- get_RNAring_sasa(...) from builtins.PyCapsule
- get_RNAring_sasa(self : rosetta.protocols.pockets.GenPharmacophore, rsd : rosetta.core.conformation.Residue, rsdno : int, pose_atom_sasa : rosetta.core.id.AtomID_Map_double_t) -> float
- get_ideal_hydrogenBond_atoms(...) from builtins.PyCapsule
- get_ideal_hydrogenBond_atoms(self : rosetta.protocols.pockets.GenPharmacophore, protein_pose : rosetta.core.pose.Pose) -> NoneType
- is_buried_ring(...) from builtins.PyCapsule
- is_buried_ring(self : rosetta.protocols.pockets.GenPharmacophore, rsd : rosetta.core.conformation.Residue, ring_sasa : float, sasa_cutoff : float) -> bool
- make_compatible_with_ROCS_custom_ForceField(...) from builtins.PyCapsule
- make_compatible_with_ROCS_custom_ForceField(self : rosetta.protocols.pockets.GenPharmacophore, input_filename : str) -> str
- print_string_to_PDBfile(...) from builtins.PyCapsule
- print_string_to_PDBfile(self : rosetta.protocols.pockets.GenPharmacophore, input_filename : str, output_filename : str) -> NoneType
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class NonPlaidFingerprint(FingerprintBase) |
| | |
- Method resolution order:
- NonPlaidFingerprint
- FingerprintBase
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.pockets.NonPlaidFingerprint) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.NonPlaidFingerprint, : rosetta.protocols.pockets.NonPlaidFingerprint) -> rosetta.protocols.pockets.NonPlaidFingerprint
- calculate_protein_CoM(...) from builtins.PyCapsule
- calculate_protein_CoM(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose) -> rosetta.numeric.xyzVector_double_t
- change_CoM_to_ligandCoM(...) from builtins.PyCapsule
- change_CoM_to_ligandCoM(self : rosetta.protocols.pockets.NonPlaidFingerprint, ligandCoM : rosetta.numeric.xyzVector_double_t) -> NoneType
- choose_origin_with_lowest_eggshell_ruggedness(...) from builtins.PyCapsule
- choose_origin_with_lowest_eggshell_ruggedness(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose, egg_and_extra_shell : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> NoneType
- combine_xyz_lists(...) from builtins.PyCapsule
- combine_xyz_lists(self : rosetta.protocols.pockets.NonPlaidFingerprint, xyz_list_1 : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, xyz_list_2 : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- convert_cart_to_spherical_and_round(...) from builtins.PyCapsule
- convert_cart_to_spherical_and_round(self : rosetta.protocols.pockets.NonPlaidFingerprint, xyz_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> rosetta.std.list_protocols_pockets_spherical_coor_triplet_std_allocator_protocols_pockets_spherical_coor_triplet_t
- convert_spherical_list_to_cartesian_list(...) from builtins.PyCapsule
- convert_spherical_list_to_cartesian_list(self : rosetta.protocols.pockets.NonPlaidFingerprint, unique_triplet : rosetta.std.list_protocols_pockets_spherical_coor_triplet_std_allocator_protocols_pockets_spherical_coor_triplet_t) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- get_Rvalue(...) from builtins.PyCapsule
- get_Rvalue(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose, egg_and_extra_shell : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, set_origin_option : int) -> float
- get_electrostatics_energy(...) from builtins.PyCapsule
- get_electrostatics_energy(self : rosetta.protocols.pockets.NonPlaidFingerprint, ligand_pose : rosetta.core.pose.Pose) -> float
- get_interpolated_esp_energy(...) from builtins.PyCapsule
- get_interpolated_esp_energy(self : rosetta.protocols.pockets.NonPlaidFingerprint, ligand_atom : rosetta.numeric.xyzVector_double_t, atom_charge : float) -> float
- get_interpolated_esp_energy_with_type(...) from builtins.PyCapsule
- get_interpolated_esp_energy_with_type(self : rosetta.protocols.pockets.NonPlaidFingerprint, ligand_atom : rosetta.numeric.xyzVector_double_t, atom_charge : float) -> float
- get_nearest_neighbour_esp_energy(...) from builtins.PyCapsule
- get_nearest_neighbour_esp_energy(self : rosetta.protocols.pockets.NonPlaidFingerprint, ligand_atom : rosetta.numeric.xyzVector_double_t, atom_charge : float) -> float
- get_pose_resnum(...) from builtins.PyCapsule
- get_pose_resnum(self : rosetta.protocols.pockets.NonPlaidFingerprint, pdbnum : int, pdbchn : str, ps : rosetta.core.pose.Pose) -> int
- get_surface_esp(...) from builtins.PyCapsule
- get_surface_esp(self : rosetta.protocols.pockets.NonPlaidFingerprint, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, inp_espGrid_fname : str) -> float
- include_eggshell_points_based_on_known_ligand(...) from builtins.PyCapsule
- include_eggshell_points_based_on_known_ligand(self : rosetta.protocols.pockets.NonPlaidFingerprint, known_ligand_pose : rosetta.core.pose.Pose, trim_dist : float) -> NoneType
- place_origin_point(...) from builtins.PyCapsule
- place_origin_point(self : rosetta.protocols.pockets.NonPlaidFingerprint, angle : float) -> rosetta.numeric.xyzVector_double_t
- remove_duplicate_phi_psi(...) from builtins.PyCapsule
- remove_duplicate_phi_psi(self : rosetta.protocols.pockets.NonPlaidFingerprint, rounded_triplet : rosetta.std.list_protocols_pockets_spherical_coor_triplet_std_allocator_protocols_pockets_spherical_coor_triplet_t) -> rosetta.std.list_protocols_pockets_spherical_coor_triplet_std_allocator_protocols_pockets_spherical_coor_triplet_t
- set_multiple_origin(...) from builtins.PyCapsule
- set_multiple_origin(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose, egg_and_extra_shell : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> NoneType
- set_origin(...) from builtins.PyCapsule
- set_origin(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose, egg_and_extra_shell : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> NoneType
- set_origin_away_from_eggshell(...) from builtins.PyCapsule
- set_origin_away_from_eggshell(self : rosetta.protocols.pockets.NonPlaidFingerprint, egg_and_extra_shell : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, protein_pose : rosetta.core.pose.Pose) -> NoneType
- set_origin_away_from_eggshell_plane(...) from builtins.PyCapsule
- set_origin_away_from_eggshell_plane(self : rosetta.protocols.pockets.NonPlaidFingerprint, egg_and_extra_shell : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, protein_pose : rosetta.core.pose.Pose, set_origin_option : int) -> NoneType
- set_origin_away_from_protein_center(...) from builtins.PyCapsule
- set_origin_away_from_protein_center(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose) -> NoneType
- set_origin_from_option_(...) from builtins.PyCapsule
- set_origin_from_option_(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose, egg_and_extra_shell : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, set_origin_option : int) -> NoneType
- set_origin_from_residue(...) from builtins.PyCapsule
- set_origin_from_residue(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose) -> NoneType
- set_rho_to_zero(...) from builtins.PyCapsule
- set_rho_to_zero(self : rosetta.protocols.pockets.NonPlaidFingerprint, rounded_triplet : rosetta.std.list_protocols_pockets_spherical_coor_triplet_std_allocator_protocols_pockets_spherical_coor_triplet_t) -> rosetta.std.list_protocols_pockets_spherical_coor_triplet_std_allocator_protocols_pockets_spherical_coor_triplet_t
- setup_from_ConnollySurface(...) from builtins.PyCapsule
- setup_from_ConnollySurface(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose, pocket_grid : rosetta.protocols.pockets.PocketGrid, grid_for_extshell : rosetta.protocols.pockets.PocketGrid) -> NoneType
- setup_from_EggshellGrid(...) from builtins.PyCapsule
- setup_from_EggshellGrid(rosetta.protocols.pockets.NonPlaidFingerprint) -> NoneType
- setup_from_PlaidFingerprint(...) from builtins.PyCapsule
- setup_from_PlaidFingerprint(self : rosetta.protocols.pockets.NonPlaidFingerprint, pfp : protocols::pockets::PlaidFingerprint) -> NoneType
- setup_from_PocketGrid(...) from builtins.PyCapsule
- setup_from_PocketGrid(*args, **kwargs)
Overloaded function.
1. setup_from_PocketGrid(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose, pocket_grid : rosetta.protocols.pockets.PocketGrid) -> NoneType
2. setup_from_PocketGrid(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose, pocket_grid : rosetta.protocols.pockets.PocketGrid, grid_for_extshell : rosetta.protocols.pockets.PocketGrid) -> NoneType
- setup_from_PocketGrid_and_known_ligand(...) from builtins.PyCapsule
- setup_from_PocketGrid_and_known_ligand(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose, pocket_grid : rosetta.protocols.pockets.PocketGrid, grid_for_extshell : rosetta.protocols.pockets.PocketGrid, known_ligand_pose : rosetta.core.pose.Pose, trim_dist : float) -> NoneType
- setup_from_PocketGrid_using_bound_ligand(...) from builtins.PyCapsule
- setup_from_PocketGrid_using_bound_ligand(self : rosetta.protocols.pockets.NonPlaidFingerprint, protein_pose : rosetta.core.pose.Pose, pocket_grid : rosetta.protocols.pockets.PocketGrid, grid_for_extshell : rosetta.protocols.pockets.PocketGrid, known_ligand_pose : rosetta.core.pose.Pose) -> NoneType
- setup_from_eggshell_pdb_file(...) from builtins.PyCapsule
- setup_from_eggshell_pdb_file(self : rosetta.protocols.pockets.NonPlaidFingerprint, input_filename : str) -> NoneType
- setup_from_eggshell_triplet_file(...) from builtins.PyCapsule
- setup_from_eggshell_triplet_file(self : rosetta.protocols.pockets.NonPlaidFingerprint, input_filename : str) -> NoneType
- setup_from_espGrid(...) from builtins.PyCapsule
- setup_from_espGrid(self : rosetta.protocols.pockets.NonPlaidFingerprint, input_filename : str, protein_pose : rosetta.core.pose.Pose, delphi : bool) -> NoneType
- trim_based_on_known_ligand(...) from builtins.PyCapsule
- trim_based_on_known_ligand(self : rosetta.protocols.pockets.NonPlaidFingerprint, known_ligand_pose : rosetta.core.pose.Pose) -> NoneType
- write_eggshell_to_pdb_file(...) from builtins.PyCapsule
- write_eggshell_to_pdb_file(self : rosetta.protocols.pockets.NonPlaidFingerprint, output_eggshell_name : str) -> NoneType
Data descriptors defined here:
- egg_and_ext_list_
- eggshell_list_
- espGrid_
- esp_dim_
- esp_mid_
- esp_spacing_
- extshell_list_
- pocket_CoM_
- typGrid_
Methods inherited from FingerprintBase:
- CHEAT_CoM(...) from builtins.PyCapsule
- CHEAT_CoM(self : rosetta.protocols.pockets.FingerprintBase, inp_CoM : rosetta.numeric.xyzVector_double_t) -> NoneType
- CoM(...) from builtins.PyCapsule
- CoM(rosetta.protocols.pockets.FingerprintBase) -> rosetta.numeric.xyzVector_double_t
- multi_origin_list(...) from builtins.PyCapsule
- multi_origin_list(rosetta.protocols.pockets.FingerprintBase) -> rosetta.utility.vector1_numeric_xyzVector_double_t
- num_origins(...) from builtins.PyCapsule
- num_origins(rosetta.protocols.pockets.FingerprintBase) -> int
- origin(...) from builtins.PyCapsule
- origin(rosetta.protocols.pockets.FingerprintBase) -> rosetta.numeric.xyzVector_double_t
- print_to_file(...) from builtins.PyCapsule
- print_to_file(self : rosetta.protocols.pockets.FingerprintBase, output_filename : str) -> NoneType
- print_to_pdb(...) from builtins.PyCapsule
- print_to_pdb(*args, **kwargs)
Overloaded function.
1. print_to_pdb(self : rosetta.protocols.pockets.FingerprintBase, output_pdbname : str) -> NoneType
2. print_to_pdb(self : rosetta.protocols.pockets.FingerprintBase, output_pdbname : str, translation : rosetta.numeric.xyzVector_double_t) -> NoneType
- triplet_fingerprint_data(...) from builtins.PyCapsule
- triplet_fingerprint_data(rosetta.protocols.pockets.FingerprintBase) -> rosetta.std.list_protocols_pockets_spherical_coor_triplet_std_allocator_protocols_pockets_spherical_coor_triplet_t
Data descriptors inherited from FingerprintBase:
- pocketGrid_dim_
- pocketGrid_mid_
- pocketGrid_spacing_
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class PCluster(builtins.object) |
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@ Cluster of Pocket points
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.pockets.PCluster, x : int, y : int, z : int, step_ : float) -> NoneType
2. __init__(self : rosetta.protocols.pockets.PCluster, old : rosetta.protocols.pockets.PCluster) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add(...) from builtins.PyCapsule
- add(self : rosetta.protocols.pockets.PCluster, x : int, y : int, z : int) -> NoneType
- isClose(...) from builtins.PyCapsule
- isClose(self : rosetta.protocols.pockets.PCluster, c2 : rosetta.protocols.pockets.PCluster) -> bool
- isSolventExposed(...) from builtins.PyCapsule
- isSolventExposed(rosetta.protocols.pockets.PCluster) -> bool
- isTarget(...) from builtins.PyCapsule
- isTarget(*args, **kwargs)
Overloaded function.
1. isTarget(rosetta.protocols.pockets.PCluster) -> bool
2. isTarget(self : rosetta.protocols.pockets.PCluster, numTargets : int) -> bool
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.pockets.PCluster) -> int
- testNeighbor(...) from builtins.PyCapsule
- testNeighbor(self : rosetta.protocols.pockets.PCluster, c2 : rosetta.protocols.pockets.PCluster) -> bool
Data descriptors defined here:
- points_
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class PClusterSet(builtins.object) |
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@ Set of cluster of pocket points
|
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.pockets.PClusterSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add(...) from builtins.PyCapsule
- add(self : rosetta.protocols.pockets.PClusterSet, x : int, y : int, z : int, step : float) -> std::_List_iterator<protocols::pockets::PCluster>
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.PClusterSet, old : rosetta.protocols.pockets.PClusterSet) -> rosetta.protocols.pockets.PClusterSet
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.pockets.PClusterSet) -> NoneType
- findClusters(...) from builtins.PyCapsule
- findClusters(rosetta.protocols.pockets.PClusterSet) -> NoneType
- getLargestClusterSize(...) from builtins.PyCapsule
- getLargestClusterSize(self : rosetta.protocols.pockets.PClusterSet, stepSize : float, minClusterSize : float, numTargets : int, ignoreBuried : bool, ignoreSurface : bool) -> float
- getNetClusterSize(...) from builtins.PyCapsule
- getNetClusterSize(self : rosetta.protocols.pockets.PClusterSet, stepSize : float, minClusterSize : float, numTargets : int, ignoreBuried : bool, ignoreSurface : bool) -> float
- join(...) from builtins.PyCapsule
- join(self : rosetta.protocols.pockets.PClusterSet, c1 : std::_List_iterator<protocols::pockets::PCluster>, c2 : std::_List_iterator<protocols::pockets::PCluster>) -> NoneType
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.pockets.PClusterSet) -> int
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class PlaidFingerprint(FingerprintBase) |
| | |
- Method resolution order:
- PlaidFingerprint
- FingerprintBase
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.pockets.PlaidFingerprint, input_pose : rosetta.core.pose.Pose, fp : rosetta.protocols.pockets.FingerprintBase) -> NoneType
2. __init__(self : rosetta.protocols.pockets.PlaidFingerprint, : rosetta.protocols.pockets.PlaidFingerprint) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.PlaidFingerprint, : rosetta.protocols.pockets.PlaidFingerprint) -> rosetta.protocols.pockets.PlaidFingerprint
- calculate_ligand_CoM(...) from builtins.PyCapsule
- calculate_ligand_CoM(self : rosetta.protocols.pockets.PlaidFingerprint, ligand_pose : rosetta.core.pose.Pose) -> rosetta.numeric.xyzVector_double_t
- compute_ligand_natoms(...) from builtins.PyCapsule
- compute_ligand_natoms(*args, **kwargs)
Overloaded function.
1. compute_ligand_natoms(self : rosetta.protocols.pockets.PlaidFingerprint, pose : rosetta.core.pose.Pose) -> int
2. compute_ligand_natoms(rosetta.protocols.pockets.PlaidFingerprint) -> int
- compute_ligand_natoms_with_hydrogens(...) from builtins.PyCapsule
- compute_ligand_natoms_with_hydrogens(*args, **kwargs)
Overloaded function.
1. compute_ligand_natoms_with_hydrogens(self : rosetta.protocols.pockets.PlaidFingerprint, pose : rosetta.core.pose.Pose) -> int
2. compute_ligand_natoms_with_hydrogens(rosetta.protocols.pockets.PlaidFingerprint) -> int
- compute_ligand_nconformers(...) from builtins.PyCapsule
- compute_ligand_nconformers(*args, **kwargs)
Overloaded function.
1. compute_ligand_nconformers(self : rosetta.protocols.pockets.PlaidFingerprint, pose : rosetta.core.pose.Pose) -> int
2. compute_ligand_nconformers(rosetta.protocols.pockets.PlaidFingerprint) -> int
- compute_ligand_resnum(...) from builtins.PyCapsule
- compute_ligand_resnum(*args, **kwargs)
Overloaded function.
1. compute_ligand_resnum(self : rosetta.protocols.pockets.PlaidFingerprint, pose : rosetta.core.pose.Pose) -> int
2. compute_ligand_resnum(rosetta.protocols.pockets.PlaidFingerprint) -> int
- dump_oriented_pose_and_fp_to_pdb(...) from builtins.PyCapsule
- dump_oriented_pose_and_fp_to_pdb(*args, **kwargs)
Overloaded function.
1. dump_oriented_pose_and_fp_to_pdb(self : rosetta.protocols.pockets.PlaidFingerprint, pose_filename : str, fp_filename : str, fp : rosetta.protocols.pockets.FingerprintBase, angle1_offset : float, angle2_offset : float, angle3_offset : float) -> NoneType
2. dump_oriented_pose_and_fp_to_pdb(self : rosetta.protocols.pockets.PlaidFingerprint, pose_filename : str, fp_filename : str, fp : rosetta.protocols.pockets.FingerprintBase, angle1_offset : float, angle2_offset : float, angle3_offset : float, original_pocket_angle_transform : rosetta.utility.vector1_double) -> NoneType
3. dump_oriented_pose_and_fp_to_pdb(self : rosetta.protocols.pockets.PlaidFingerprint, pose_filename : str, fp_filename : str, fp : rosetta.protocols.pockets.FingerprintBase, angle1_offset : float, angle2_offset : float, angle3_offset : float, CoM_offset : rosetta.numeric.xyzVector_double_t) -> NoneType
4. dump_oriented_pose_and_fp_to_pdb(self : rosetta.protocols.pockets.PlaidFingerprint, pose_filename : str, fp_filename : str, fp : rosetta.protocols.pockets.FingerprintBase, angle1_offset : float, angle2_offset : float, angle3_offset : float, original_pocket_angle_transform : rosetta.utility.vector1_double, CoM_offset : rosetta.numeric.xyzVector_double_t) -> NoneType
- find_optimal_rotation(...) from builtins.PyCapsule
- find_optimal_rotation(*args, **kwargs)
Overloaded function.
1. find_optimal_rotation(self : rosetta.protocols.pockets.PlaidFingerprint, fp : rosetta.protocols.pockets.FingerprintBase, angle_increment : float, optimal_angle1 : float, optimal_angle2 : float, optimal_angle3 : float, missing_point_weight : float, steric_weight : float, extra_point_weight : float) -> float
2. find_optimal_rotation(self : rosetta.protocols.pockets.PlaidFingerprint, fp : rosetta.protocols.pockets.FingerprintBase, angle_increment : float, optimal_angle1 : float, optimal_angle2 : float, optimal_angle3 : float, missing_point_weight : float, steric_weight : float, extra_point_weight : float, no_CoM_offset : rosetta.numeric.xyzVector_double_t) -> float
- fp_compare(...) from builtins.PyCapsule
- fp_compare(self : rosetta.protocols.pockets.PlaidFingerprint, fp : rosetta.protocols.pockets.FingerprintBase, missing_point_weight : float, steric_weight : float, extra_point_weight : float) -> float
- fp_compare_deriv(...) from builtins.PyCapsule
- fp_compare_deriv(self : rosetta.protocols.pockets.PlaidFingerprint, fp : rosetta.protocols.pockets.FingerprintBase, missing_point_weight : float, steric_weight : float, extra_point_weight : float, dE_dx : float, dE_dy : float, dE_dz : float, dE_dv4 : float, dE_dv5 : float, dE_dv6 : float) -> NoneType
- get_oriented_pose(...) from builtins.PyCapsule
- get_oriented_pose(*args, **kwargs)
Overloaded function.
1. get_oriented_pose(self : rosetta.protocols.pockets.PlaidFingerprint, fp : rosetta.protocols.pockets.FingerprintBase, angle1_offset : float, angle2_offset : float, angle3_offset : float, CoM_offset : rosetta.numeric.xyzVector_double_t, conformer : int) -> rosetta.core.pose.Pose
2. get_oriented_pose(self : rosetta.protocols.pockets.PlaidFingerprint, fp : rosetta.protocols.pockets.FingerprintBase, angle1_offset : float, angle2_offset : float, angle3_offset : float, original_pocket_angle_transform : rosetta.utility.vector1_double, CoM_offset : rosetta.numeric.xyzVector_double_t, conformer : int) -> rosetta.core.pose.Pose
- move_ligand_and_update_rhos_(...) from builtins.PyCapsule
- move_ligand_and_update_rhos_(*args, **kwargs)
Overloaded function.
1. move_ligand_and_update_rhos_(self : rosetta.protocols.pockets.PlaidFingerprint, fp : rosetta.protocols.pockets.FingerprintBase, CoM_offset : rosetta.numeric.xyzVector_double_t, angle1_offset : float, angle2_offset : float, angle3_offset : float, conformer : int) -> NoneType
2. move_ligand_and_update_rhos_(self : rosetta.protocols.pockets.PlaidFingerprint, fp : rosetta.protocols.pockets.FingerprintBase, CoM_offset : rosetta.numeric.xyzVector_double_t, angle1_offset : float, angle2_offset : float, angle3_offset : float, conformer : int, update_derivatives : bool) -> NoneType
- pose(...) from builtins.PyCapsule
- pose(rosetta.protocols.pockets.PlaidFingerprint) -> rosetta.core.pose.Pose
- rmsd(...) from builtins.PyCapsule
- rmsd(self : rosetta.protocols.pockets.PlaidFingerprint, original_pose : rosetta.core.pose.Pose, oriented_pose : rosetta.core.pose.Pose) -> float
- search_random_poses(...) from builtins.PyCapsule
- search_random_poses(*args, **kwargs)
Overloaded function.
1. search_random_poses(self : rosetta.protocols.pockets.PlaidFingerprint, fp : rosetta.protocols.pockets.FingerprintBase, num_pose_search : int, optimal_angle1 : float, optimal_angle2 : float, optimal_angle3 : float, missing_point_weight : float, steric_weight : float, extra_point_weight : float) -> float
2. search_random_poses(self : rosetta.protocols.pockets.PlaidFingerprint, fp : rosetta.protocols.pockets.FingerprintBase, num_pose_search : int, optimal_angle1 : float, optimal_angle2 : float, optimal_angle3 : float, missing_point_weight : float, steric_weight : float, extra_point_weight : float, no_CoM_offset : rosetta.numeric.xyzVector_double_t) -> float
Methods inherited from FingerprintBase:
- CHEAT_CoM(...) from builtins.PyCapsule
- CHEAT_CoM(self : rosetta.protocols.pockets.FingerprintBase, inp_CoM : rosetta.numeric.xyzVector_double_t) -> NoneType
- CoM(...) from builtins.PyCapsule
- CoM(rosetta.protocols.pockets.FingerprintBase) -> rosetta.numeric.xyzVector_double_t
- multi_origin_list(...) from builtins.PyCapsule
- multi_origin_list(rosetta.protocols.pockets.FingerprintBase) -> rosetta.utility.vector1_numeric_xyzVector_double_t
- num_origins(...) from builtins.PyCapsule
- num_origins(rosetta.protocols.pockets.FingerprintBase) -> int
- origin(...) from builtins.PyCapsule
- origin(rosetta.protocols.pockets.FingerprintBase) -> rosetta.numeric.xyzVector_double_t
- print_to_file(...) from builtins.PyCapsule
- print_to_file(self : rosetta.protocols.pockets.FingerprintBase, output_filename : str) -> NoneType
- print_to_pdb(...) from builtins.PyCapsule
- print_to_pdb(*args, **kwargs)
Overloaded function.
1. print_to_pdb(self : rosetta.protocols.pockets.FingerprintBase, output_pdbname : str) -> NoneType
2. print_to_pdb(self : rosetta.protocols.pockets.FingerprintBase, output_pdbname : str, translation : rosetta.numeric.xyzVector_double_t) -> NoneType
- triplet_fingerprint_data(...) from builtins.PyCapsule
- triplet_fingerprint_data(rosetta.protocols.pockets.FingerprintBase) -> rosetta.std.list_protocols_pockets_spherical_coor_triplet_std_allocator_protocols_pockets_spherical_coor_triplet_t
Data descriptors inherited from FingerprintBase:
- pocketGrid_dim_
- pocketGrid_mid_
- pocketGrid_spacing_
|
class PocketConstraint(rosetta.core.scoring.constraints.Constraint) |
| |
This constraint favors creating a pocket suitable for a small-molecule
|
| |
- Method resolution order:
- PocketConstraint
- rosetta.core.scoring.constraints.Constraint
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.pockets.PocketConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, pose : rosetta.core.pose.Pose) -> NoneType
3. __init__(handle, rosetta.protocols.pockets.PocketConstraint) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- atom(...) from builtins.PyCapsule
- atom(self : rosetta.protocols.pockets.PocketConstraint, index : int) -> rosetta.core.id.AtomID
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.pockets.PocketConstraint) -> rosetta.core.scoring.constraints.Constraint
- fill_f1_f2(...) from builtins.PyCapsule
- fill_f1_f2(self : rosetta.protocols.pockets.PocketConstraint, : rosetta.core.id.AtomID, : rosetta.core.scoring.func.XYZ_Func, : rosetta.numeric.xyzVector_double_t, : rosetta.numeric.xyzVector_double_t, weights : rosetta.core.scoring.EMapVector) -> NoneType
- init(...) from builtins.PyCapsule
- init(self : rosetta.protocols.pockets.PocketConstraint, pose : rosetta.core.pose.Pose) -> NoneType
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.protocols.pockets.PocketConstraint) -> int
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.protocols.pockets.PocketConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.pockets.PocketConstraint, xyz_func : rosetta.core.scoring.func.XYZ_Func, weights : rosetta.core.scoring.EMapVector, emap : rosetta.core.scoring.EMapVector) -> NoneType
- set_target_res(...) from builtins.PyCapsule
- set_target_res(self : rosetta.protocols.pockets.PocketConstraint, pose : rosetta.core.pose.Pose, new_seqpos : int) -> NoneType
- set_target_res_pdb(...) from builtins.PyCapsule
- set_target_res_pdb(self : rosetta.protocols.pockets.PocketConstraint, pose : rosetta.core.pose.Pose, resid : str) -> NoneType
- target_res(...) from builtins.PyCapsule
- target_res(rosetta.protocols.pockets.PocketConstraint) -> int
- type(...) from builtins.PyCapsule
- type(rosetta.protocols.pockets.PocketConstraint) -> str
Methods inherited from rosetta.core.scoring.constraints.Constraint:
- __ne__(...) from builtins.PyCapsule
- __ne__(self : rosetta.core.scoring.constraints.Constraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
Inequality operator to test whether two constraints are not functionally
identical.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.scoring.constraints.Constraint) -> str
- choose_effective_sequence_separation(...) from builtins.PyCapsule
- choose_effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, sp : rosetta.core.kinematics.ShortestPathInFoldTree, : rosetta.numeric.random.RandomGenerator) -> int
- dist(...) from builtins.PyCapsule
- dist(*args, **kwargs)
Overloaded function.
1. dist(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> float
return the raw "distance" before that distance is handed to the FUNC object
2. dist(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func) -> float
- effective_sequence_separation(...) from builtins.PyCapsule
- effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.kinematics.ShortestPathInFoldTree) -> int
- get_func(...) from builtins.PyCapsule
- get_func(rosetta.core.scoring.constraints.Constraint) -> core::scoring::func::Func
Returns the func::Func object associated with this Constraint object.
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.id.SequenceMapping) -> 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.
- remapped_clone(...) from builtins.PyCapsule
- remapped_clone(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose, : rosetta.core.pose.Pose, map : rosetta.core.id.SequenceMapping) -> 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.
- residues(...) from builtins.PyCapsule
- residues(rosetta.core.scoring.constraints.Constraint) -> 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.
- score_type(...) from builtins.PyCapsule
- score_type(rosetta.core.scoring.constraints.Constraint) -> rosetta.core.scoring.ScoreType
Returns the ScoreType that this Constraint object will use.
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- steal_def(...) from builtins.PyCapsule
- steal_def(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> NoneType
take coordinates, distances, angles, etc from given pose
- to_string(...) from builtins.PyCapsule
- to_string(rosetta.core.scoring.constraints.Constraint) -> str
Convenience function, returns the results of show() as a string.
Not to be overriden by derived classes.
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class PocketExemplarMultifunc(rosetta.core.optimization.Multifunc) |
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Pocket multifunction class, does objective function of optimization
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- Method resolution order:
- PocketExemplarMultifunc
- rosetta.core.optimization.Multifunc
- builtins.object
Methods defined here:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.protocols.pockets.PocketExemplarMultifunc, vars : rosetta.utility.vector1_double) -> float
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, input_pdb_name : str, resid : str, c_rad : float, rep_weight : float, p_min : rosetta.utility.vector1_double, p_max : rosetta.utility.vector1_double) -> NoneType
2. __init__(handle, rosetta.protocols.pockets.PocketExemplarMultifunc) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.PocketExemplarMultifunc, : rosetta.protocols.pockets.PocketExemplarMultifunc) -> rosetta.protocols.pockets.PocketExemplarMultifunc
- dfunc(...) from builtins.PyCapsule
- dfunc(self : rosetta.protocols.pockets.PocketExemplarMultifunc, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double) -> NoneType
- dump(...) from builtins.PyCapsule
- dump(self : rosetta.protocols.pockets.PocketExemplarMultifunc, vars : rosetta.utility.vector1_double, : rosetta.utility.vector1_double) -> NoneType
Error state reached; dump out current pdb.
Methods inherited from rosetta.core.optimization.Multifunc:
- abort_min(...) from builtins.PyCapsule
- abort_min(self : rosetta.core.optimization.Multifunc, : 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!
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class PocketGrid(builtins.object) |
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@
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Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.pockets.PocketGrid, other : rosetta.protocols.pockets.PocketGrid) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.pockets.PocketGrid) -> NoneType
3. __init__(self : handle, central_rsd : rosetta.core.conformation.Residue) -> NoneType
4. __init__(self : handle, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
5. __init__(self : handle, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float) -> NoneType
6. __init__(self : handle, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float) -> NoneType
7. __init__(self : handle, xc : float, yc : float, zc : float, x : float, y : float, z : float, stepSize : float) -> NoneType
8. __init__(self : handle, xc : float, yc : float, zc : float, x : float, y : float, z : float) -> NoneType
9. __init__(self : handle, xc : float, yc : float, zc : float, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
10. __init__(handle, float, float, float, float) -> NoneType
doc
11. __init__(handle, float, float, float, float, float) -> NoneType
doc
12. __init__(handle, float, float, float, float, float, bool) -> NoneType
doc
13. __init__(self : handle, xc : float, yc : float, zc : float, x : float, stepSize : float, psp : bool, sps : bool) -> NoneType
14. __init__(handle, rosetta.numeric.xyzVector_double_t, float) -> NoneType
doc
15. __init__(handle, rosetta.numeric.xyzVector_double_t, float, float) -> NoneType
doc
16. __init__(handle, rosetta.numeric.xyzVector_double_t, float, float, bool) -> NoneType
doc
17. __init__(self : handle, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float, psp : bool, sps : bool) -> NoneType
18. __init__(handle, rosetta.numeric.xyzVector_double_t, float, float, float) -> NoneType
doc
19. __init__(handle, rosetta.numeric.xyzVector_double_t, float, float, float, float) -> NoneType
doc
20. __init__(handle, rosetta.numeric.xyzVector_double_t, float, float, float, float, bool) -> NoneType
doc
21. __init__(self : handle, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- alter_espGrid(...) from builtins.PyCapsule
- alter_espGrid(self : rosetta.protocols.pockets.PocketGrid, espGrid_filename : str) -> NoneType
- alter_espGrid_with_bound_ligand(...) from builtins.PyCapsule
- alter_espGrid_with_bound_ligand(self : rosetta.protocols.pockets.PocketGrid, espGrid_filename : str, protein_pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.PocketGrid, gr : rosetta.protocols.pockets.PocketGrid) -> rosetta.protocols.pockets.PocketGrid
- autoexpanding_pocket_eval(...) from builtins.PyCapsule
- autoexpanding_pocket_eval(*args, **kwargs)
Overloaded function.
1. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int) -> bool
2. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool) -> bool
3. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float) -> bool
4. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float) -> bool
5. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float, z : float) -> bool
6. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int) -> bool
7. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool) -> bool
8. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float) -> bool
9. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float) -> bool
10. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float, z : float) -> bool
11. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose) -> bool
12. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool) -> bool
13. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float) -> bool
14. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float) -> bool
15. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float, z : float) -> bool
16. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose) -> bool
17. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool) -> bool
18. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float) -> bool
19. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float) -> bool
20. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float, z : float) -> bool
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.pockets.PocketGrid) -> NoneType
- clearSmallPockets(...) from builtins.PyCapsule
- clearSmallPockets(self : rosetta.protocols.pockets.PocketGrid, minsize : int) -> NoneType
- clusterCPockets(...) from builtins.PyCapsule
- clusterCPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- clusterPockets(...) from builtins.PyCapsule
- clusterPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- dim(...) from builtins.PyCapsule
- dim(rosetta.protocols.pockets.PocketGrid) -> rosetta.numeric.xyzVector_double_t
- dumpExemplarToFile(...) from builtins.PyCapsule
- dumpExemplarToFile(*args, **kwargs)
Overloaded function.
1. dumpExemplarToFile(rosetta.protocols.pockets.PocketGrid) -> NoneType
2. dumpExemplarToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- dumpGridToFile(...) from builtins.PyCapsule
- dumpGridToFile(*args, **kwargs)
Overloaded function.
1. dumpGridToFile(rosetta.protocols.pockets.PocketGrid) -> NoneType
2. dumpGridToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- dumpTargetPocketsToFile(...) from builtins.PyCapsule
- dumpTargetPocketsToFile(*args, **kwargs)
Overloaded function.
1. dumpTargetPocketsToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
2. dumpTargetPocketsToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str, rot1 : rosetta.numeric.xyzMatrix_double_t, rot2 : rosetta.numeric.xyzMatrix_double_t, rot3 : rosetta.numeric.xyzMatrix_double_t) -> NoneType
- dumpTargetPocketsToPDB(...) from builtins.PyCapsule
- dumpTargetPocketsToPDB(*args, **kwargs)
Overloaded function.
1. dumpTargetPocketsToPDB(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
2. dumpTargetPocketsToPDB(self : rosetta.protocols.pockets.PocketGrid, output_filename : str, minipock : bool) -> NoneType
3. dumpTargetPocketsToPDB(self : rosetta.protocols.pockets.PocketGrid, output_filename : str, rot1 : rosetta.numeric.xyzMatrix_double_t, rot2 : rosetta.numeric.xyzMatrix_double_t, rot3 : rosetta.numeric.xyzMatrix_double_t) -> NoneType
- fillTargetPockets(...) from builtins.PyCapsule
- fillTargetPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- findClusters(...) from builtins.PyCapsule
- findClusters(rosetta.protocols.pockets.PocketGrid) -> NoneType
- findClustersByExemplars(...) from builtins.PyCapsule
- findClustersByExemplars(rosetta.protocols.pockets.PocketGrid) -> NoneType
- findExemplars(...) from builtins.PyCapsule
- findExemplars(self : rosetta.protocols.pockets.PocketGrid, inPose : rosetta.core.pose.Pose, total_residues : int) -> NoneType
- findPSP(...) from builtins.PyCapsule
- findPSP(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- findPockets(...) from builtins.PyCapsule
- findPockets(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- findSPS(...) from builtins.PyCapsule
- findSPS(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- getBounds(...) from builtins.PyCapsule
- getBounds(rosetta.protocols.pockets.PocketGrid) -> rosetta.utility.vector1_double
- getRelaxResidues(...) from builtins.PyCapsule
- getRelaxResidues(input_pose : rosetta.core.pose.Pose, resids : str) -> rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t
- get_connolly_surfacePoints(...) from builtins.PyCapsule
- get_connolly_surfacePoints(self : rosetta.protocols.pockets.PocketGrid, protein_pose : rosetta.core.pose.Pose) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- get_connolly_surfacePoints_within_grid(...) from builtins.PyCapsule
- get_connolly_surfacePoints_within_grid(self : rosetta.protocols.pockets.PocketGrid, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- get_pocket_distance(...) from builtins.PyCapsule
- get_pocket_distance(*args, **kwargs)
Overloaded function.
1. get_pocket_distance(self : rosetta.protocols.pockets.PocketGrid, template_pocket : rosetta.protocols.pockets.PocketGrid) -> float
2. get_pocket_distance(self : rosetta.protocols.pockets.PocketGrid, template_pocket : rosetta.protocols.pockets.PocketGrid, comparison_pdbname : str) -> float
- initialize(...) from builtins.PyCapsule
- initialize(*args, **kwargs)
Overloaded function.
1. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float) -> NoneType
2. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float, stepSize : float) -> NoneType
3. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float, stepSize : float, psp : bool) -> NoneType
4. initialize(self : 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) -> NoneType
5. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float) -> NoneType
6. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float) -> NoneType
7. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float, psp : bool) -> NoneType
8. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float, psp : bool, sps : bool) -> NoneType
9. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float) -> NoneType
10. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float) -> NoneType
11. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float, psp : bool) -> NoneType
12. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float, psp : bool, sps : bool) -> NoneType
13. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float) -> NoneType
14. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float) -> NoneType
15. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
16. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
17. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float) -> NoneType
18. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float) -> NoneType
19. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
20. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
21. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float) -> NoneType
22. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float) -> NoneType
23. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
24. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
- isTooSmall(...) from builtins.PyCapsule
- isTooSmall(rosetta.protocols.pockets.PocketGrid) -> bool
- largestTargetPocketVolume(...) from builtins.PyCapsule
- largestTargetPocketVolume(rosetta.protocols.pockets.PocketGrid) -> float
- linkExemplarsThroughSolvent(...) from builtins.PyCapsule
- linkExemplarsThroughSolvent(rosetta.protocols.pockets.PocketGrid) -> NoneType
- mark(...) from builtins.PyCapsule
- mark(*args, **kwargs)
Overloaded function.
1. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float) -> NoneType
2. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float, polar : bool) -> NoneType
3. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float, polar : bool, targetResi : int) -> NoneType
4. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float) -> NoneType
5. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float, polar : bool) -> NoneType
6. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float, polar : bool, targetResi : int) -> NoneType
- markDepth(...) from builtins.PyCapsule
- markDepth(self : rosetta.protocols.pockets.PocketGrid, x : int, y : int, z : int, surf_d : float, bur_d : float) -> NoneType
- markEdgeDepth(...) from builtins.PyCapsule
- markEdgeDepth(self : rosetta.protocols.pockets.PocketGrid, surf_d : float, bur_d : float) -> NoneType
- markOneEdgeDepth(...) from builtins.PyCapsule
- markOneEdgeDepth(self : rosetta.protocols.pockets.PocketGrid, x : int, y : int, z : int, surf_d : float, bur_d : float, isTarget : bool) -> bool
- markPocketDepth(...) from builtins.PyCapsule
- markPocketDepth(self : rosetta.protocols.pockets.PocketGrid, surf_d : float, bur_d : float) -> NoneType
- move_pose_to_standard_orie(...) from builtins.PyCapsule
- move_pose_to_standard_orie(self : rosetta.protocols.pockets.PocketGrid, central_seqpos : int, pose : rosetta.core.pose.Pose) -> NoneType
- netTargetPocketVolume(...) from builtins.PyCapsule
- netTargetPocketVolume(rosetta.protocols.pockets.PocketGrid) -> float
- print(...) from builtins.PyCapsule
- print(rosetta.protocols.pockets.PocketGrid) -> NoneType
- randomAngle(...) from builtins.PyCapsule
- randomAngle(rosetta.protocols.pockets.PocketGrid) -> NoneType
- recenter(...) from builtins.PyCapsule
- recenter(*args, **kwargs)
Overloaded function.
1. recenter(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float) -> NoneType
2. recenter(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue) -> NoneType
3. recenter(self : rosetta.protocols.pockets.PocketGrid, central_rsds : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
4. recenter(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t) -> NoneType
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.protocols.pockets.PocketGrid, other : rosetta.protocols.pockets.PocketGrid) -> bool
- spacing(...) from builtins.PyCapsule
- spacing(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketHeuristicScore(...) from builtins.PyCapsule
- targetPocketHeuristicScore(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketHydrophobicProteinSurface(...) from builtins.PyCapsule
- targetPocketHydrophobicProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketPolarProteinSurface(...) from builtins.PyCapsule
- targetPocketPolarProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketProteinSurface(...) from builtins.PyCapsule
- targetPocketProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketSolventSurface(...) from builtins.PyCapsule
- targetPocketSolventSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketVolume(...) from builtins.PyCapsule
- targetPocketVolume(self : rosetta.protocols.pockets.PocketGrid, surf_sc : float, bur_sc : float) -> float
- whatIsTooSmall(...) from builtins.PyCapsule
- whatIsTooSmall(rosetta.protocols.pockets.PocketGrid) -> rosetta.numeric.xyzVector_double_t
- write_pocketGrid_to_pdb(...) from builtins.PyCapsule
- write_pocketGrid_to_pdb(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- zeroAngle(...) from builtins.PyCapsule
- zeroAngle(rosetta.protocols.pockets.PocketGrid) -> NoneType
|
class SmallMol(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.pockets.SmallMol) -> NoneType
2. __init__(self : rosetta.protocols.pockets.SmallMol, other : rosetta.protocols.pockets.SmallMol) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_atom(...) from builtins.PyCapsule
- add_atom(self : rosetta.protocols.pockets.SmallMol, line : str) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.SmallMol, : rosetta.protocols.pockets.SmallMol) -> rosetta.protocols.pockets.SmallMol
- calRMSD(...) from builtins.PyCapsule
- calRMSD(mol1 : rosetta.protocols.pockets.SmallMol, mol2 : rosetta.protocols.pockets.SmallMol) -> float
- cal_distance(...) from builtins.PyCapsule
- cal_distance(self : rosetta.protocols.pockets.SmallMol, other : rosetta.protocols.pockets.SmallMol) -> float
- cal_min_dist(...) from builtins.PyCapsule
- cal_min_dist(self : rosetta.protocols.pockets.SmallMol, other : rosetta.protocols.pockets.SmallMol) -> float
- connect(...) from builtins.PyCapsule
- connect(self : rosetta.protocols.pockets.SmallMol, m : rosetta.protocols.pockets.SmallMol) -> NoneType
- connected(...) from builtins.PyCapsule
- connected(self : rosetta.protocols.pockets.SmallMol, m : rosetta.protocols.pockets.SmallMol) -> bool
- findRoot(...) from builtins.PyCapsule
- findRoot(rosetta.protocols.pockets.SmallMol) -> rosetta.protocols.pockets.SmallMol
- getContent(...) from builtins.PyCapsule
- getContent(rosetta.protocols.pockets.SmallMol) -> str
- get_center(...) from builtins.PyCapsule
- get_center(self : rosetta.protocols.pockets.SmallMol, c : int) -> float
- get_coordinates(...) from builtins.PyCapsule
- get_coordinates(rosetta.protocols.pockets.SmallMol) -> rosetta.std.vector_std_vector_double_std_allocator_double_t
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.pockets.SmallMol) -> str
- get_parent(...) from builtins.PyCapsule
- get_parent(rosetta.protocols.pockets.SmallMol) -> rosetta.protocols.pockets.SmallMol
- get_rmsd(...) from builtins.PyCapsule
- get_rmsd(rosetta.protocols.pockets.SmallMol) -> float
- get_root(...) from builtins.PyCapsule
- get_root(rosetta.protocols.pockets.SmallMol) -> rosetta.protocols.pockets.SmallMol
- get_size(...) from builtins.PyCapsule
- get_size(rosetta.protocols.pockets.SmallMol) -> int
- get_visited(...) from builtins.PyCapsule
- get_visited(rosetta.protocols.pockets.SmallMol) -> bool
- numberOfAtoms(...) from builtins.PyCapsule
- numberOfAtoms(rosetta.protocols.pockets.SmallMol) -> int
- printContent(...) from builtins.PyCapsule
- printContent(rosetta.protocols.pockets.SmallMol) -> NoneType
- printCoordinates(...) from builtins.PyCapsule
- printCoordinates(rosetta.protocols.pockets.SmallMol) -> NoneType
- set_name(...) from builtins.PyCapsule
- set_name(self : rosetta.protocols.pockets.SmallMol, name : str) -> NoneType
- set_parent(...) from builtins.PyCapsule
- set_parent(self : rosetta.protocols.pockets.SmallMol, p : rosetta.protocols.pockets.SmallMol) -> NoneType
- set_size(...) from builtins.PyCapsule
- set_size(self : rosetta.protocols.pockets.SmallMol, t : int) -> NoneType
- set_visited(...) from builtins.PyCapsule
- set_visited(self : rosetta.protocols.pockets.SmallMol, v : bool) -> NoneType
- update_center(...) from builtins.PyCapsule
- update_center(rosetta.protocols.pockets.SmallMol) -> NoneType
|
class TargetPocketGrid(PocketGrid) |
| |
@
|
| |
- Method resolution order:
- TargetPocketGrid
- PocketGrid
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, gr : rosetta.protocols.pockets.PocketGrid) -> NoneType
2. __init__(self : handle, fname : str) -> NoneType
3. __init__(handle, rosetta.protocols.pockets.TargetPocketGrid) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.pockets.TargetPocketGrid, : rosetta.protocols.pockets.TargetPocketGrid) -> rosetta.protocols.pockets.TargetPocketGrid
- dumpTargetPocketsToPDB(...) from builtins.PyCapsule
- dumpTargetPocketsToPDB(*args, **kwargs)
Overloaded function.
1. dumpTargetPocketsToPDB(self : rosetta.protocols.pockets.TargetPocketGrid, output_filename : str) -> NoneType
2. dumpTargetPocketsToPDB(self : rosetta.protocols.pockets.TargetPocketGrid, output_filename : str, minipock : bool) -> NoneType
- findClusters(...) from builtins.PyCapsule
- findClusters(rosetta.protocols.pockets.TargetPocketGrid) -> NoneType
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.protocols.pockets.TargetPocketGrid, other : rosetta.protocols.pockets.PocketGrid) -> bool
Methods inherited from PocketGrid:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.pockets.PocketGrid, other : rosetta.protocols.pockets.PocketGrid) -> bool
- alter_espGrid(...) from builtins.PyCapsule
- alter_espGrid(self : rosetta.protocols.pockets.PocketGrid, espGrid_filename : str) -> NoneType
- alter_espGrid_with_bound_ligand(...) from builtins.PyCapsule
- alter_espGrid_with_bound_ligand(self : rosetta.protocols.pockets.PocketGrid, espGrid_filename : str, protein_pose : rosetta.core.pose.Pose) -> NoneType
- autoexpanding_pocket_eval(...) from builtins.PyCapsule
- autoexpanding_pocket_eval(*args, **kwargs)
Overloaded function.
1. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int) -> bool
2. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool) -> bool
3. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float) -> bool
4. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float) -> bool
5. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float, z : float) -> bool
6. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int) -> bool
7. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool) -> bool
8. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float) -> bool
9. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float) -> bool
10. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, xyz_func : rosetta.core.scoring.func.XYZ_Func, total_residues : int, center_target : bool, x : float, y : float, z : float) -> bool
11. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose) -> bool
12. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool) -> bool
13. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float) -> bool
14. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float) -> bool
15. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float, z : float) -> bool
16. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose) -> bool
17. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool) -> bool
18. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float) -> bool
19. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float) -> bool
20. autoexpanding_pocket_eval(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, inPose : rosetta.core.pose.Pose, center_target : bool, x : float, y : float, z : float) -> bool
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.pockets.PocketGrid) -> NoneType
- clearSmallPockets(...) from builtins.PyCapsule
- clearSmallPockets(self : rosetta.protocols.pockets.PocketGrid, minsize : int) -> NoneType
- clusterCPockets(...) from builtins.PyCapsule
- clusterCPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- clusterPockets(...) from builtins.PyCapsule
- clusterPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- dim(...) from builtins.PyCapsule
- dim(rosetta.protocols.pockets.PocketGrid) -> rosetta.numeric.xyzVector_double_t
- dumpExemplarToFile(...) from builtins.PyCapsule
- dumpExemplarToFile(*args, **kwargs)
Overloaded function.
1. dumpExemplarToFile(rosetta.protocols.pockets.PocketGrid) -> NoneType
2. dumpExemplarToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- dumpGridToFile(...) from builtins.PyCapsule
- dumpGridToFile(*args, **kwargs)
Overloaded function.
1. dumpGridToFile(rosetta.protocols.pockets.PocketGrid) -> NoneType
2. dumpGridToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- dumpTargetPocketsToFile(...) from builtins.PyCapsule
- dumpTargetPocketsToFile(*args, **kwargs)
Overloaded function.
1. dumpTargetPocketsToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
2. dumpTargetPocketsToFile(self : rosetta.protocols.pockets.PocketGrid, output_filename : str, rot1 : rosetta.numeric.xyzMatrix_double_t, rot2 : rosetta.numeric.xyzMatrix_double_t, rot3 : rosetta.numeric.xyzMatrix_double_t) -> NoneType
- fillTargetPockets(...) from builtins.PyCapsule
- fillTargetPockets(rosetta.protocols.pockets.PocketGrid) -> NoneType
- findClustersByExemplars(...) from builtins.PyCapsule
- findClustersByExemplars(rosetta.protocols.pockets.PocketGrid) -> NoneType
- findExemplars(...) from builtins.PyCapsule
- findExemplars(self : rosetta.protocols.pockets.PocketGrid, inPose : rosetta.core.pose.Pose, total_residues : int) -> NoneType
- findPSP(...) from builtins.PyCapsule
- findPSP(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- findPockets(...) from builtins.PyCapsule
- findPockets(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- findSPS(...) from builtins.PyCapsule
- findSPS(self : rosetta.protocols.pockets.PocketGrid, thr : int, max : float) -> NoneType
- getBounds(...) from builtins.PyCapsule
- getBounds(rosetta.protocols.pockets.PocketGrid) -> rosetta.utility.vector1_double
- getRelaxResidues(...) from builtins.PyCapsule
- getRelaxResidues(input_pose : rosetta.core.pose.Pose, resids : str) -> rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t
- get_connolly_surfacePoints(...) from builtins.PyCapsule
- get_connolly_surfacePoints(self : rosetta.protocols.pockets.PocketGrid, protein_pose : rosetta.core.pose.Pose) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- get_connolly_surfacePoints_within_grid(...) from builtins.PyCapsule
- get_connolly_surfacePoints_within_grid(self : rosetta.protocols.pockets.PocketGrid, surfacePoints_list : rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) -> rosetta.std.list_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t
- get_pocket_distance(...) from builtins.PyCapsule
- get_pocket_distance(*args, **kwargs)
Overloaded function.
1. get_pocket_distance(self : rosetta.protocols.pockets.PocketGrid, template_pocket : rosetta.protocols.pockets.PocketGrid) -> float
2. get_pocket_distance(self : rosetta.protocols.pockets.PocketGrid, template_pocket : rosetta.protocols.pockets.PocketGrid, comparison_pdbname : str) -> float
- initialize(...) from builtins.PyCapsule
- initialize(*args, **kwargs)
Overloaded function.
1. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float) -> NoneType
2. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float, stepSize : float) -> NoneType
3. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, size_x : float, size_y : float, size_z : float, stepSize : float, psp : bool) -> NoneType
4. initialize(self : 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) -> NoneType
5. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float) -> NoneType
6. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float) -> NoneType
7. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float, psp : bool) -> NoneType
8. initialize(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float, x : float, stepSize : float, psp : bool, sps : bool) -> NoneType
9. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float) -> NoneType
10. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float) -> NoneType
11. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float, psp : bool) -> NoneType
12. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, stepSize : float, psp : bool, sps : bool) -> NoneType
13. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float) -> NoneType
14. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float) -> NoneType
15. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
16. initialize(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
17. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float) -> NoneType
18. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float) -> NoneType
19. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
20. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
21. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float) -> NoneType
22. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float) -> NoneType
23. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float, psp : bool) -> NoneType
24. initialize(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t, x : float, y : float, z : float, stepSize : float, psp : bool, sps : bool) -> NoneType
- isTooSmall(...) from builtins.PyCapsule
- isTooSmall(rosetta.protocols.pockets.PocketGrid) -> bool
- largestTargetPocketVolume(...) from builtins.PyCapsule
- largestTargetPocketVolume(rosetta.protocols.pockets.PocketGrid) -> float
- linkExemplarsThroughSolvent(...) from builtins.PyCapsule
- linkExemplarsThroughSolvent(rosetta.protocols.pockets.PocketGrid) -> NoneType
- mark(...) from builtins.PyCapsule
- mark(*args, **kwargs)
Overloaded function.
1. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float) -> NoneType
2. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float, polar : bool) -> NoneType
3. mark(self : rosetta.protocols.pockets.PocketGrid, x : float, y : float, z : float, vdWd : float, buffer : float, polar : bool, targetResi : int) -> NoneType
4. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float) -> NoneType
5. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float, polar : bool) -> NoneType
6. mark(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t, vdWd : float, buffer : float, polar : bool, targetResi : int) -> NoneType
- markDepth(...) from builtins.PyCapsule
- markDepth(self : rosetta.protocols.pockets.PocketGrid, x : int, y : int, z : int, surf_d : float, bur_d : float) -> NoneType
- markEdgeDepth(...) from builtins.PyCapsule
- markEdgeDepth(self : rosetta.protocols.pockets.PocketGrid, surf_d : float, bur_d : float) -> NoneType
- markOneEdgeDepth(...) from builtins.PyCapsule
- markOneEdgeDepth(self : rosetta.protocols.pockets.PocketGrid, x : int, y : int, z : int, surf_d : float, bur_d : float, isTarget : bool) -> bool
- markPocketDepth(...) from builtins.PyCapsule
- markPocketDepth(self : rosetta.protocols.pockets.PocketGrid, surf_d : float, bur_d : float) -> NoneType
- move_pose_to_standard_orie(...) from builtins.PyCapsule
- move_pose_to_standard_orie(self : rosetta.protocols.pockets.PocketGrid, central_seqpos : int, pose : rosetta.core.pose.Pose) -> NoneType
- netTargetPocketVolume(...) from builtins.PyCapsule
- netTargetPocketVolume(rosetta.protocols.pockets.PocketGrid) -> float
- print(...) from builtins.PyCapsule
- print(rosetta.protocols.pockets.PocketGrid) -> NoneType
- randomAngle(...) from builtins.PyCapsule
- randomAngle(rosetta.protocols.pockets.PocketGrid) -> NoneType
- recenter(...) from builtins.PyCapsule
- recenter(*args, **kwargs)
Overloaded function.
1. recenter(self : rosetta.protocols.pockets.PocketGrid, xc : float, yc : float, zc : float) -> NoneType
2. recenter(self : rosetta.protocols.pockets.PocketGrid, central_rsd : rosetta.core.conformation.Residue) -> NoneType
3. recenter(self : rosetta.protocols.pockets.PocketGrid, central_rsds : rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
4. recenter(self : rosetta.protocols.pockets.PocketGrid, center : rosetta.numeric.xyzVector_double_t) -> NoneType
- spacing(...) from builtins.PyCapsule
- spacing(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketHeuristicScore(...) from builtins.PyCapsule
- targetPocketHeuristicScore(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketHydrophobicProteinSurface(...) from builtins.PyCapsule
- targetPocketHydrophobicProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketPolarProteinSurface(...) from builtins.PyCapsule
- targetPocketPolarProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketProteinSurface(...) from builtins.PyCapsule
- targetPocketProteinSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketSolventSurface(...) from builtins.PyCapsule
- targetPocketSolventSurface(rosetta.protocols.pockets.PocketGrid) -> float
- targetPocketVolume(...) from builtins.PyCapsule
- targetPocketVolume(self : rosetta.protocols.pockets.PocketGrid, surf_sc : float, bur_sc : float) -> float
- whatIsTooSmall(...) from builtins.PyCapsule
- whatIsTooSmall(rosetta.protocols.pockets.PocketGrid) -> rosetta.numeric.xyzVector_double_t
- write_pocketGrid_to_pdb(...) from builtins.PyCapsule
- write_pocketGrid_to_pdb(self : rosetta.protocols.pockets.PocketGrid, output_filename : str) -> NoneType
- zeroAngle(...) from builtins.PyCapsule
- zeroAngle(rosetta.protocols.pockets.PocketGrid) -> NoneType
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