protein_interface_design

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Bindings for protocols::protein_interface_design namespace

class pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue

Bases: pybind11_builtins.pybind11_object

class FavorNativeResidue changes a pose object so that its residue identities at the initialization of FavorNativeResidue are kept in memory. If the res_type_constraint score term is set to a value other than 0, an energy bonus will be assigned if the residue doesn’t change. This is useful e.g., in design based on a native scaffold where we want a barrier to mutation.

__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.protein_interface_design.FavorNativeResidue, pose: pyrosetta.rosetta.core.pose.Pose, native_residue_bonus: float) -> None
2. __init__(self: pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue, pose: pyrosetta.rosetta.core.pose.Pose, native_residue_bonus: pyrosetta.rosetta.utility.vector1_double) -> None
3. __init__(self: pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue, arg0: pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue, : pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue) → pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue

C++: protocols::protein_interface_design::FavorNativeResidue::operator=(const class protocols::protein_interface_design::FavorNativeResidue &) –> class protocols::protein_interface_design::FavorNativeResidue &

class pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue

Bases: pybind11_builtins.pybind11_object

class FavorNonNativeResidue changes a pose object so that its residue identities at the initialization of FavorNonNativeResidue are kept in memory. If the res_type_constraint score term is set to a value other than 0, an energy bonus will be assigned if the residue changes. This is useful if we want to encourage mutation. A negative score would discourage mutation.

__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.protein_interface_design.FavorNonNativeResidue, pose: pyrosetta.rosetta.core.pose.Pose, native_residue_bonus: float) -> None
2. __init__(self: pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue, pose: pyrosetta.rosetta.core.pose.Pose, native_residue_bonus: pyrosetta.rosetta.utility.vector1_double) -> None
3. __init__(self: pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue, arg0: pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue, : pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue) → pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue

C++: protocols::protein_interface_design::FavorNonNativeResidue::operator=(const class protocols::protein_interface_design::FavorNonNativeResidue &) –> class protocols::protein_interface_design::FavorNonNativeResidue &

pyrosetta.rosetta.protocols.protein_interface_design.MinimizeInterface(*args, **kwargs)

Overloaded function.

1. MinimizeInterface(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_bb: pyrosetta.rosetta.utility.vector1_bool, min_sc: pyrosetta.rosetta.utility.vector1_bool, min_rb: pyrosetta.rosetta.utility.vector1_bool, optimize_foldtree: bool, target_residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
2. MinimizeInterface(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_bb: pyrosetta.rosetta.utility.vector1_bool, min_sc: pyrosetta.rosetta.utility.vector1_bool, min_rb: pyrosetta.rosetta.utility.vector1_bool, optimize_foldtree: bool, target_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, simultaneous_minimization: bool) -> None

utility function for minimizing sidechain in rigid-body dof, the interface sc, and bb in the entire protein.

C++: protocols::protein_interface_design::MinimizeInterface(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

class pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences

Bases: pybind11_builtins.pybind11_object

Class ReportSequenceDifferences takes in two poses and provides information on the sequence changes between them, including the residue energies associated with those changes.

__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.protein_interface_design.ReportSequenceDifferences, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
2. __init__(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences, arg0: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences, : pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences) → pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences

C++: protocols::protein_interface_design::ReportSequenceDifferences::operator=(const class protocols::protein_interface_design::ReportSequenceDifferences &) –> class protocols::protein_interface_design::ReportSequenceDifferences &

calculate(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::protein_interface_design::ReportSequenceDifferences::calculate(const class core::pose::Pose &, const class core::pose::Pose &) –> void

get_res_energy(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences, num: int) → pyrosetta.rosetta.std.map_unsigned_long_double

C++: protocols::protein_interface_design::ReportSequenceDifferences::get_res_energy(const unsigned long) const –> const class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > > *

report(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences, out: pyrosetta.rosetta.std.ostream) → None

C++: protocols::protein_interface_design::ReportSequenceDifferences::report(class std::basic_ostream<char> &) const –> void

res_name1(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences) → pyrosetta.rosetta.std.map_unsigned_long_std_string

C++: protocols::protein_interface_design::ReportSequenceDifferences::res_name1() const –> const class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &

res_name2(self: pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences) → pyrosetta.rosetta.std.map_unsigned_long_std_string

C++: protocols::protein_interface_design::ReportSequenceDifferences::res_name2() const –> const class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &

class pyrosetta.rosetta.protocols.protein_interface_design.Revert

Bases: pybind11_builtins.pybind11_object

class Revert takes in ‘wt’ and ‘designed’ poses and attempts to revert all substitutions in the design to their wt identities. Each substitution is tried separately in the context of the designed protein and reversions that don’t adversely affect ddg are made. If the energy of the residue in the design is higher than 0, but the reversion did not succeed, Revert will attempt an Ala substitution.

__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.protein_interface_design.Revert, arg0: pyrosetta.rosetta.core.scoring.ScoreFunction, arg1: float) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.protein_interface_design.Revert, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ddg_tolerance: float, ddg_cycles: int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.protein_interface_design.Revert, arg0: pyrosetta.rosetta.protocols.protein_interface_design.Revert) -> 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).

apply(self: pyrosetta.rosetta.protocols.protein_interface_design.Revert, pose_wt: pyrosetta.rosetta.core.pose.Pose, pose_des: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::protein_interface_design::Revert::apply(class core::pose::Pose &, class core::pose::Pose &) const –> void

assign(self: pyrosetta.rosetta.protocols.protein_interface_design.Revert, : pyrosetta.rosetta.protocols.protein_interface_design.Revert) → pyrosetta.rosetta.protocols.protein_interface_design.Revert

C++: protocols::protein_interface_design::Revert::operator=(const class protocols::protein_interface_design::Revert &) –> class protocols::protein_interface_design::Revert &

pyrosetta.rosetta.protocols.protein_interface_design.SymMinimizeInterface(*args, **kwargs)

Overloaded function.

1. SymMinimizeInterface(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_bb: pyrosetta.rosetta.utility.vector1_bool, min_sc: pyrosetta.rosetta.utility.vector1_bool, min_rb: pyrosetta.rosetta.utility.vector1_bool) -> None
2. SymMinimizeInterface(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_bb: pyrosetta.rosetta.utility.vector1_bool, min_sc: pyrosetta.rosetta.utility.vector1_bool, min_rb: pyrosetta.rosetta.utility.vector1_bool, simultaneous_minimization: bool) -> None

C++: protocols::protein_interface_design::SymMinimizeInterface(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool) –> void

pyrosetta.rosetta.protocols.protein_interface_design.best_bbcst_residues(pose: pyrosetta.rosetta.core.pose.Pose, chain: int, n_return: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

evaluate backbone_stub_constraints for each residue in a chain and return a vector with the top n_return residue numbers by cst score

note that this function is NOT guaranteed to return n_return residues! It will return the best n<=n_return

C++: protocols::protein_interface_design::best_bbcst_residues(const class core::pose::Pose &, const unsigned long, const unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.protein_interface_design.best_cutpoint(pose: pyrosetta.rosetta.core.pose.Pose, prev_u: int, prev_d: int, u: int, d: int) → int

utility function for stub_based_atom_tree. tries to find an optimal cutpoint in a pose given two different boundaries.

C++: protocols::protein_interface_design::best_cutpoint(class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.protein_interface_design.find_lowest_constraint_energy_residue(pose: pyrosetta.rosetta.core.pose.Pose, chain: int, resi: int, lowest_energy: float) → None

C++: protocols::protein_interface_design::find_lowest_constraint_energy_residue(const class core::pose::Pose &, const unsigned long, unsigned long &, double &) –> void

pyrosetta.rosetta.protocols.protein_interface_design.find_nearest_residue(*args, **kwargs)

Overloaded function.

1. find_nearest_residue(pose: pyrosetta.rosetta.core.pose.Pose, target_chain: int, res: int) -> int
2. find_nearest_residue(pose: pyrosetta.rosetta.core.pose.Pose, target_chain: int, res: int, atom: str) -> int

find nearest residue on target_chain to res

C++: protocols::protein_interface_design::find_nearest_residue(const class core::pose::Pose &, const unsigned long, const unsigned long, const class std::basic_string<char> &) –> unsigned long

pyrosetta.rosetta.protocols.protein_interface_design.get_bbcsts(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::protein_interface_design::get_bbcsts(const class core::pose::Pose &) –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

pyrosetta.rosetta.protocols.protein_interface_design.hbonded(*args, **kwargs)

Overloaded function.

1. hbonded(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float) -> pyrosetta.rosetta.std.list_unsigned_long_t
2. hbonded(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float, bb_bb: bool) -> pyrosetta.rosetta.std.list_unsigned_long_t
3. hbonded(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float, bb_bb: bool, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.std.list_unsigned_long_t

utility function for finding hbonding partners among a list of potential binder residues to a specific target

C++: protocols::protein_interface_design::hbonded(const class core::pose::Pose &, const unsigned long, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const bool, const bool, const double, const bool, class std::shared_ptr<class core::scoring::ScoreFunction>) –> class std::list<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.protein_interface_design.hbonded_atom(*args, **kwargs)

Overloaded function.

1. hbonded_atom(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, target_atom: str, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float) -> pyrosetta.rosetta.std.list_unsigned_long_t
2. hbonded_atom(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, target_atom: str, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float, bb_bb: bool) -> pyrosetta.rosetta.std.list_unsigned_long_t
3. hbonded_atom(pose: pyrosetta.rosetta.core.pose.Pose, target_residue: int, target_atom: str, binders: pyrosetta.rosetta.std.set_unsigned_long_t, bb: bool, sc: bool, energy_thres: float, bb_bb: bool, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.std.list_unsigned_long_t

utility function for finding hbonding partners among a list of potential binder residues to a specific target

C++: protocols::protein_interface_design::hbonded_atom(const class core::pose::Pose &, const unsigned long, const class std::basic_string<char> &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const bool, const bool, const double, const bool, class std::shared_ptr<class core::scoring::ScoreFunction>) –> class std::list<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.protein_interface_design.make_hotspot_foldtree(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::protein_interface_design::make_hotspot_foldtree(const class core::pose::Pose &) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.protein_interface_design.optimal_connection_point(residue_type: str) → str

what is the optimal connection point for an atom tree, given a residue type (puts the connection point

at the beginning of a functional group

C++: protocols::protein_interface_design::optimal_connection_point(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.protocols.protein_interface_design.remove_coordinate_constraints_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

removes ALL coordinate constraints from a pose. returns the constraints that were removed

C++: protocols::protein_interface_design::remove_coordinate_constraints_from_pose(class core::pose::Pose &) –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

pyrosetta.rosetta.protocols.protein_interface_design.star_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::protein_interface_design::star_fold_tree(class core::pose::Pose &) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.protein_interface_design.sum_total_residue_energy(pose: pyrosetta.rosetta.core.pose.Pose, resid: int) → float

C++: protocols::protein_interface_design::sum_total_residue_energy(const class core::pose::Pose &, const unsigned long) –> double