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- rosetta.core.pack.rotamer_set.RotamerSetOperation(builtins.object)
-
- AddGood2BPairEnergyRotamers
- RigidBodyMoveBaseRSO
-
- RigidBodyMoveRSO
- SpecialRotamerRSO
class AddGood2BPairEnergyRotamers(rosetta.core.pack.rotamer_set.RotamerSetOperation) |
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implementation of rosetta 2.x style rotamer explosion
builds a whole bunch of extra rotamers, but only adds them to the
set if they score better than a cutoff with a given set of target
residues
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- Method resolution order:
- AddGood2BPairEnergyRotamers
- rosetta.core.pack.rotamer_set.RotamerSetOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, seqpos : int, ex_level : int, target_seqpos : rosetta.utility.vector1_unsigned_long, score_cutoff : float, drop_rots_above_cutoff : bool) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- alter_rotamer_set(...) from builtins.PyCapsule
- alter_rotamer_set(self : rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, ptask : rosetta.core.pack.task.PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph, rotamer_set : rosetta.core.pack.rotamer_set.RotamerSet) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, : rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers) -> rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers) -> rosetta.core.pack.rotamer_set.RotamerSetOperation
- get_res_res_score(...) from builtins.PyCapsule
- get_res_res_score(self : rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> float
helper function
- rotamer_set_contains_rotamer(...) from builtins.PyCapsule
- rotamer_set_contains_rotamer(self : rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, rotamer_set : rosetta.core.pack.rotamer_set.RotamerSet, candidte_rot : rosetta.core.conformation.Residue) -> bool
helper function to check if the passed in candi
- set_debug(...) from builtins.PyCapsule
- set_debug(self : rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, setting : bool) -> NoneType
Methods inherited from rosetta.core.pack.rotamer_set.RotamerSetOperation:
- increase_packer_residue_radius(...) from builtins.PyCapsule
- increase_packer_residue_radius(self : rosetta.core.pack.rotamer_set.RotamerSetOperation, pose : rosetta.core.pose.Pose, the_task : rosetta.core.pack.task.PackerTask, residue_in : int) -> float
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class RigidBodyMoveBaseRSO(rosetta.core.pack.rotamer_set.RotamerSetOperation) |
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base class that handles single residue (usually ligand) rigid
body movements in the packer. subclass generates a list of alternative rigid body
placements. when the alter_rotamer_set function is called, this class
superimposes all rotamers in the initial RotamerSet onto every alternative
rigid body conformation in the member data list. these superimposed
conformations then get added to the rotamer set.
this class also handles the increased packer radius necessitated by the
rigid body movements. when the increase_packer_residue_radius function
is called, the biggest distance between the residue in the initial pose
and any of the alternate conformations is returned.
Generating the alternative rigid body positions:
Subclasses must implement get_rigid_body_confs.
Subclasses may implement increase_packer_residue_radius to
optimize this calculation. Default implementation calls get_rigid_body_confs
and calculates the maximum nbr_atom delta.
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- Method resolution order:
- RigidBodyMoveBaseRSO
- rosetta.core.pack.rotamer_set.RotamerSetOperation
- builtins.object
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- alter_rotamer_set(...) from builtins.PyCapsule
- alter_rotamer_set(self : rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, ptask : rosetta.core.pack.task.PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph, rotamer_set : rosetta.core.pack.rotamer_set.RotamerSet) -> NoneType
Adds additional rotamers at each rb conf.
fairly simple: iterate over the rotamers in the rotamer_set, superimpose
each of them onto all the internally stored rigid body confs, and then
add the newly generated rotamers to the rotamer_set
Recalculates chi-angle expansion via call to RotamerSet::extra_chi_samples
and then generate candidate rotamers from each rb conf via
SingleResidueRotamerLibrary::fill_rotamer_vector if rotamer library is
available for the residue type, else just adds the alternate confs.
Does not have full safety checks to make sure all the rotamers in the set are
of the same residue type as the internally stored ones, i.e. that no user sets this
position to designing in the task
- determine_largest_nbr_atom_distance(...) from builtins.PyCapsule
- determine_largest_nbr_atom_distance(target_res : rosetta.core.conformation.Residue, alternate_confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> float
returns the largest observed distance between the nbr atom
in the target res and the nbr atom in any of the candidate rb confs
- get_rigid_body_confs(...) from builtins.PyCapsule
- get_rigid_body_confs(self : rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose : rosetta.core.pose.Pose, ptask : rosetta.core.pack.task.PackerTask, residue_index : int) -> rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t
returns candidate alternate RB conformations
- increase_packer_residue_radius(...) from builtins.PyCapsule
- increase_packer_residue_radius(self : rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask, residue_index : int) -> float
Methods inherited from rosetta.core.pack.rotamer_set.RotamerSetOperation:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.pack.rotamer_set.RotamerSetOperation, : rosetta.core.pack.rotamer_set.RotamerSetOperation) -> rosetta.core.pack.rotamer_set.RotamerSetOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.pack.rotamer_set.RotamerSetOperation) -> rosetta.core.pack.rotamer_set.RotamerSetOperation
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class RigidBodyMoveRSO(RigidBodyMoveBaseRSO) |
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Basic implementation of alternate rb conf set operation.
The alternative positions are set externally before packing.
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- Method resolution order:
- RigidBodyMoveRSO
- RigidBodyMoveBaseRSO
- rosetta.core.pack.rotamer_set.RotamerSetOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, seqpos : int) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO) -> rosetta.core.pack.rotamer_set.RotamerSetOperation
- get_rigid_body_confs(...) from builtins.PyCapsule
- get_rigid_body_confs(self : rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO, pose : rosetta.core.pose.Pose, ptask : rosetta.core.pack.task.PackerTask, residue_index : int) -> rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t
- set_rigid_body_confs(...) from builtins.PyCapsule
- set_rigid_body_confs(self : rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO, rigid_body_confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
Methods inherited from RigidBodyMoveBaseRSO:
- alter_rotamer_set(...) from builtins.PyCapsule
- alter_rotamer_set(self : rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, ptask : rosetta.core.pack.task.PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph, rotamer_set : rosetta.core.pack.rotamer_set.RotamerSet) -> NoneType
Adds additional rotamers at each rb conf.
fairly simple: iterate over the rotamers in the rotamer_set, superimpose
each of them onto all the internally stored rigid body confs, and then
add the newly generated rotamers to the rotamer_set
Recalculates chi-angle expansion via call to RotamerSet::extra_chi_samples
and then generate candidate rotamers from each rb conf via
SingleResidueRotamerLibrary::fill_rotamer_vector if rotamer library is
available for the residue type, else just adds the alternate confs.
Does not have full safety checks to make sure all the rotamers in the set are
of the same residue type as the internally stored ones, i.e. that no user sets this
position to designing in the task
- determine_largest_nbr_atom_distance(...) from builtins.PyCapsule
- determine_largest_nbr_atom_distance(target_res : rosetta.core.conformation.Residue, alternate_confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> float
returns the largest observed distance between the nbr atom
in the target res and the nbr atom in any of the candidate rb confs
- increase_packer_residue_radius(...) from builtins.PyCapsule
- increase_packer_residue_radius(self : rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask, residue_index : int) -> float
Methods inherited from rosetta.core.pack.rotamer_set.RotamerSetOperation:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.pack.rotamer_set.RotamerSetOperation, : rosetta.core.pack.rotamer_set.RotamerSetOperation) -> rosetta.core.pack.rotamer_set.RotamerSetOperation
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class SpecialRotamerRSO(rosetta.core.pack.rotamer_set.RotamerSetOperation) |
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- Method resolution order:
- SpecialRotamerRSO
- rosetta.core.pack.rotamer_set.RotamerSetOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, seqpos : int) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.rotamer_set_operations.SpecialRotamerRSO) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- alter_rotamer_set(...) from builtins.PyCapsule
- alter_rotamer_set(self : rosetta.protocols.toolbox.rotamer_set_operations.SpecialRotamerRSO, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, ptask : rosetta.core.pack.task.PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph, rotamer_set : rosetta.core.pack.rotamer_set.RotamerSet) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.rotamer_set_operations.SpecialRotamerRSO, : rosetta.protocols.toolbox.rotamer_set_operations.SpecialRotamerRSO) -> rosetta.protocols.toolbox.rotamer_set_operations.SpecialRotamerRSO
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.rotamer_set_operations.SpecialRotamerRSO) -> rosetta.core.pack.rotamer_set.RotamerSetOperation
- set_new_rots(...) from builtins.PyCapsule
- set_new_rots(self : rosetta.protocols.toolbox.rotamer_set_operations.SpecialRotamerRSO, new_rots : rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> NoneType
Methods inherited from rosetta.core.pack.rotamer_set.RotamerSetOperation:
- increase_packer_residue_radius(...) from builtins.PyCapsule
- increase_packer_residue_radius(self : rosetta.core.pack.rotamer_set.RotamerSetOperation, pose : rosetta.core.pose.Pose, the_task : rosetta.core.pack.task.PackerTask, residue_in : int) -> float
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