rotamer_set_operations

Bindings for protocols::toolbox::rotamer_set_operations namespace

class pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers

Bases: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, seqpos: int, ex_level: int, target_seqpos: pyrosetta.rosetta.utility.vector1_unsigned_long, score_cutoff: float, drop_rots_above_cutoff: bool) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, arg0: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

alter_rotamer_set(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

C++: protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSet &) –> void

assign(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, : pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers) → pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers

C++: protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::operator=(const class protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers &) –> class protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers &

clone(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

get_res_res_score(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → float

helper function

C++: protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::get_res_res_score(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> double

increase_packer_residue_radius(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) → float

C++: core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) const –> double

rotamer_set_contains_rotamer(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, candidte_rot: pyrosetta.rosetta.core.conformation.Residue) → bool

helper function to check if the passed in candi

C++: protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer(const class core::pack::rotamer_set::RotamerSet &, const class core::conformation::Residue &) const –> bool

set_debug(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers, setting: bool) → None

C++: protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::set_debug(bool) –> void

class pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO

Bases: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

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.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

alter_rotamer_set(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

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

C++: protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSet &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: core::pack::rotamer_set::RotamerSetOperation::operator=(const class core::pack::rotamer_set::RotamerSetOperation &) –> class core::pack::rotamer_set::RotamerSetOperation &

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: core::pack::rotamer_set::RotamerSetOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

determine_largest_nbr_atom_distance(target_res: pyrosetta.rosetta.core.conformation.Residue, alternate_confs: pyrosetta.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

C++: protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(const class core::conformation::Residue &, class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >) –> double

get_rigid_body_confs(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose: pyrosetta.rosetta.core.pose.Pose, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, residue_index: int) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t

returns candidate alternate RB conformations

C++: protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::get_rigid_body_confs(const class core::pose::Pose &, const class core::pack::task::PackerTask &, unsigned long) –> class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

increase_packer_residue_radius(*args, **kwargs)

Overloaded function.

1. increase_packer_residue_radius(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) -> float
2. increase_packer_residue_radius(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask, residue_index: int) -> float

C++: protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) –> double

class pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO

Bases: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO

Basic implementation of alternate rb conf set operation. The alternative positions are set externally before packing.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO, seqpos: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO, arg0: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

alter_rotamer_set(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

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

C++: protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSet &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: core::pack::rotamer_set::RotamerSetOperation::operator=(const class core::pack::rotamer_set::RotamerSetOperation &) –> class core::pack::rotamer_set::RotamerSetOperation &

clone(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

determine_largest_nbr_atom_distance(target_res: pyrosetta.rosetta.core.conformation.Residue, alternate_confs: pyrosetta.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

C++: protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(const class core::conformation::Residue &, class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >) –> double

get_rigid_body_confs(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO, pose: pyrosetta.rosetta.core.pose.Pose, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, residue_index: int) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t

C++: protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO::get_rigid_body_confs(const class core::pose::Pose &, const class core::pack::task::PackerTask &, unsigned long) –> class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

increase_packer_residue_radius(*args, **kwargs)

Overloaded function.

1. increase_packer_residue_radius(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) -> float
2. increase_packer_residue_radius(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask, residue_index: int) -> float

C++: protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) –> double

set_rigid_body_confs(self: pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO, rigid_body_confs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) → None

C++: protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO::set_rigid_body_confs(const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) –> void