crosslinker

Bindings for protocols::cyclic_peptide::crosslinker namespace

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper

Bases: pybind11_builtins.pybind11_object

A base class for helper objects that the CrosslinkerMover uses to set up specific types of threefold linkers.

__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.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) -> None
2. __init__(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, arg0: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

add_linker_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

Given a pose and a selection of exactly three residues, add the linker,

align it crudely to the selected residues, and set up covalent bonds.

Must be defined by derived classes. Version for asymmetric poses.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::add_linker_asymmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

add_linker_bonds_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, linker_index: int) → None

Given a pose and a linker, add bonds between the linker and the residues that coordinate the linker.

Can be called by add_linker_asymmetric(). Must be defined by derived classes (pure virtual). Version for asymmetric poses.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::add_linker_bonds_asymmetric(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long) const –> void

add_linker_bonds_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, res1: int, linker_index1: int, linker_index2: int) → None

Given a pose and a linker, add bonds between the linker and the residues that coordinate the linker.

Can be called by add_linker_symmetric(). Must be defined by derived classes (pure virtual). Version for symmetric poses.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::add_linker_bonds_symmetric(class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long) const –> void

add_linker_constraints_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

Given a selection of exactly three residues that have already been connected to a crosslinker,

add constraints for the crosslinker.

Must be defined by derived classes. Version for asymmetric poses.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::add_linker_constraints_asymmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

add_linker_constraints_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, linker_was_added: bool) → None

Given a selection of exactly three residues that have already been connected to a crosslinker,

add constraints for the crosslinker.

Must be defined by derived classes. Version for symmetric poses.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::add_linker_constraints_symmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool) const –> void

add_linker_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

Given a pose and a selection of exactly three residues, add the linker,

align it crudely to the selected residues, and set up covalent bonds.

Must be defined by derived classes. Version for symmetric poses.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::add_linker_symmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::operator=(const class protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper &) –> class protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper &

filter_by_constraints_energy_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, filter_multiplier: float) → bool

Determine whether the sidechain-crosslinker system has too high a constraints score.

Returns TRUE for failure (too high a constraints score) and FALSE for success.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::filter_by_constraints_energy_asymmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const double &) const –> bool

filter_by_constraints_energy_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, linker_was_added: bool, filter_multiplier: float) → bool

Determine whether the sidechain-crosslinker system has too high a constraints score. This version is for symmetric poses.

Returns TRUE for failure (too high a constraints score) and FALSE for success.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::filter_by_constraints_energy_symmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const double &) const –> bool

filter_by_sidechain_distance_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, filter_multiplier: float) → bool

Given a pose with residues selected to be linked by a linker, determine whether the residues are too far apart.

Returns TRUE for failure (residues too far apart) and FALSE for success.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::filter_by_sidechain_distance_asymmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const double &) const –> bool

filter_by_sidechain_distance_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, filter_multiplier: float) → bool

Given a pose with residues selected to be linked by a linker, determine whether the residues are too far apart.

Returns TRUE for failure (residues too far apart) and FALSE for success. This version is for symmetric poses.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::filter_by_sidechain_distance_symmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const double &) const –> bool

get_linker_index_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → int

Given indices of three residues that are already linked to a linker, get the index

of the linker.

Throws an error if the three residues are not all linked to the same linker residue. Must be defined by derived classes.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_linker_index_asymmetric(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

get_linker_indices_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, linker_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Given indices of three cysteine residues that are already linked to pieces of a linker, get

of the indices of the symmetric pieces of the linker.

Throws an error if a residue is not linked to something. Must be defined by derived classes.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_linker_indices_symmetric(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_sidechain_indices(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, selection: pyrosetta.rosetta.utility.vector1_bool, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Given a ResidueSubset with N residues selected, pull out the indices into a vector.

Overwrites res_indices.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(const class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

post_relax_round_update_steps(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, whole_structure: bool, symmetric: bool, linker_was_added: bool) → None

Optional steps that the helper can apply after every relaxation round.

Defaults to doing nothing; can be overriden. (One example is the TMA helper, which uses this to update amide bond-dependent atom positions).

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::post_relax_round_update_steps(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const bool, const bool) const –> void

pre_relax_round_update_steps(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, whole_structure: bool, symmetric: bool, linker_was_added: bool) → None

Optional steps that the helper can apply before every relaxation round.

Defaults to doing nothing; can be overriden. (One example is the TMA helper, which uses this to update amide bond-dependent atom positions).

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::pre_relax_round_update_steps(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const bool, const bool) const –> void

selection_is_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, selection: pyrosetta.rosetta.utility.vector1_bool, pose: pyrosetta.rosetta.core.pose.Pose, expected_subunit_count: int) → bool

Determine whether a selection is symmetric.

Returns true if and only if (a) the pose is symmetric, (b) there are the expected number of symmetry copies, and (c) the selected residues are equivalent residues in different symmetry copies. Note that, ideally, I’d like to test for CN or SN symmetry, but this is as close as was feasible.

Can be overriden.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::selection_is_symmetric(const class utility::vector1<bool, class std::allocator<bool> > &, const class core::pose::Pose &, const unsigned long) const –> bool

set_symmetry(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, symm_type_in: str, symm_count_in: int) → None

Set the symmetry for this crosslinker helper.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::set_symmetry(const char, const unsigned long) –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper

Bases: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper

A derived class of the CrosslinkerMoverHelper base class, used to set up the 1,3,5-tris(bromomethyl)benzene (TBMB) cross-linker.

__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.cyclic_peptide.crosslinker.TBMB_Helper) -> None
2. __init__(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, arg0: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

add_linker_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

Given a pose and a selection of exactly three residues, add the TBMB linker,

align it crudely to the selected residues, and set up covalent bonds.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

add_linker_bonds_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, linker_index: int) → None

Given a pose and a linker, add bonds between the linker and the residues that coordinate the linker.

Called by add_linker_asymmetric(). Version for asymmetric poses.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_bonds_asymmetric(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long) const –> void

add_linker_bonds_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, res1: int, linker_index1: int, linker_index2: int) → None

Given a pose and a linker, add bonds between the TBMB linker and the residues that coordinate the linker.

Called by add_linker_symmetric(). Version for symmetric poses.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_bonds_symmetric(class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long) const –> void

add_linker_constraints_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

Given a selection of exactly three residues that have already been connected to a 1,3,5-tris(bromomethyl)benzene crosslinker,

add constraints for the crosslinker.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_asymmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

add_linker_constraints_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, linker_was_added: bool) → None

Given a selection of exactly three residues that have already been connected to a 1,3,5-tris(bromomethyl)benzene crosslinker,

add constraints for the crosslinker. This version is for symmetric poses.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_symmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool) const –> void

add_linker_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

Given a pose and a selection of exactly three residues, add the TBMB linker,

align it crudely to the selected residues, and set up covalent bonds.

Version for symmetric poses.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::operator=(const class protocols::cyclic_peptide::crosslinker::TBMB_Helper &) –> class protocols::cyclic_peptide::crosslinker::TBMB_Helper &

filter_by_constraints_energy_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, filter_multiplier: float) → bool

Determine whether the sidechain-crosslinker system has too high a constraints score.

Returns TRUE for failure (too high a constraints score) and FALSE for success.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_constraints_energy_asymmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const double &) const –> bool

filter_by_constraints_energy_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, linker_was_added: bool, filter_multiplier: float) → bool

Determine whether the sidechain-crosslinker system has too high a constraints score. This version is for symmetric poses.

Returns TRUE for failure (too high a constraints score) and FALSE for success.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_constraints_energy_symmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const double &) const –> bool

filter_by_sidechain_distance_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, filter_multiplier: float) → bool

Given a pose with residues selected to be linked by a 1,3,5-tris(bromomethyl)benzene crosslinker,

determine whether the residues are too far apart.

Returns TRUE for failure (residues too far apart) and FALSE for success.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_asymmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const double &) const –> bool

filter_by_sidechain_distance_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, filter_multiplier: float) → bool

Given a pose with residues selected to be linked by a 1,3,5-tris(bromomethyl)benzene crosslinker,

determine whether the residues are too far apart. This version is for symmetric poses.

Returns TRUE for failure (residues too far apart) and FALSE for success.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_symmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const double &) const –> bool

get_linker_index_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → int

Given indices of three cysteine residues that are already linked to a TBMB, get the index

of the TBMB residue.

Throws an error if the three cysteines are not all linked to the same TBMB residue.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_index_asymmetric(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

get_linker_indices_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, linker_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Given indices of three cysteine residues that are already linked to pieces of a linker, get

of the indices of the symmetric pieces of the linker.

Throws an error if a residue is not linked to something.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_indices_symmetric(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_sidechain_indices(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, selection: pyrosetta.rosetta.utility.vector1_bool, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Given a ResidueSubset with N residues selected, pull out the indices into a vector.

Overwrites res_indices.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(const class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

post_relax_round_update_steps(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, whole_structure: bool, symmetric: bool, linker_was_added: bool) → None

Optional steps that the helper can apply after every relaxation round.

Defaults to doing nothing; can be overriden. (One example is the TMA helper, which uses this to update amide bond-dependent atom positions).

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::post_relax_round_update_steps(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const bool, const bool) const –> void

pre_relax_round_update_steps(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, whole_structure: bool, symmetric: bool, linker_was_added: bool) → None

Optional steps that the helper can apply before every relaxation round.

Defaults to doing nothing; can be overriden. (One example is the TMA helper, which uses this to update amide bond-dependent atom positions).

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::pre_relax_round_update_steps(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const bool, const bool) const –> void

selection_is_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, selection: pyrosetta.rosetta.utility.vector1_bool, pose: pyrosetta.rosetta.core.pose.Pose, expected_subunit_count: int) → bool

Determine whether a selection is symmetric.

Returns true if and only if (a) the pose is symmetric, (b) there are the expected number of symmetry copies, and (c) the selected residues are equivalent residues in different symmetry copies. Note that, ideally, I’d like to test for CN or SN symmetry, but this is as close as was feasible.

Can be overriden.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::selection_is_symmetric(const class utility::vector1<bool, class std::allocator<bool> > &, const class core::pose::Pose &, const unsigned long) const –> bool

set_symmetry(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, symm_type_in: str, symm_count_in: int) → None

Set the symmetry for this crosslinker helper.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::set_symmetry(const char, const unsigned long) –> void

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper

Bases: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper

A derived class of the CrosslinkerMoverHelper base class, used to set up the trimesic acid (TMA) cross-linker.

__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.cyclic_peptide.crosslinker.TMA_Helper) -> None
2. __init__(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, arg0: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

add_linker_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

Given a pose and a selection of exactly three residues, add the TMA linker,

align it crudely to the selected residues, and set up covalent bonds.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_asymmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

add_linker_bonds_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, linker_index: int) → None

Given a pose and a linker, add bonds between the linker and the residues that coordinate the linker.

Called by add_linker_asymmetric(). Version for asymmetric poses.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_bonds_asymmetric(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long) const –> void

add_linker_bonds_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, res1: int, linker_index1: int, linker_index2: int) → None

Given a pose and a TMA linker, add bonds between the TMA and the residues that coordinate the linker.

Called by add_linker_symmetric(). Version for symmetric poses.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_bonds_symmetric(class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long) const –> void

add_linker_constraints_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

Given a selection of exactly three residues that have already been connected to a trimesic acid crosslinker,

add constraints for the crosslinker.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_asymmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

add_linker_constraints_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, linker_was_added: bool) → None

Given a selection of exactly three residues that have already been connected to a trimesic acid crosslinker,

add constraints for the crosslinker. This version is for symmetric poses.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_symmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool) const –> void

add_linker_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

Given a pose and a selection of exactly three residues, add the TMA linker,

align it crudely to the selected residues, and set up covalent bonds.

Version for symmetric poses.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_symmetric(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

assign(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::operator=(const class protocols::cyclic_peptide::crosslinker::TMA_Helper &) –> class protocols::cyclic_peptide::crosslinker::TMA_Helper &

filter_by_constraints_energy_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, filter_multiplier: float) → bool

Determine whether the sidechain-crosslinker system has too high a constraints score.

Returns TRUE for failure (too high a constraints score) and FALSE for success.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_constraints_energy_asymmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const double &) const –> bool

filter_by_constraints_energy_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, linker_was_added: bool, filter_multiplier: float) → bool

Determine whether the sidechain-crosslinker system has too high a constraints score. This version is for symmetric poses.

Returns TRUE for failure (too high a constraints score) and FALSE for success.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_constraints_energy_symmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const double &) const –> bool

filter_by_sidechain_distance_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, filter_multiplier: float) → bool

Given a pose with residues selected to be linked by a trimesic acid crosslinker,

determine whether the residues are too far apart.

Returns TRUE for failure (residues too far apart) and FALSE for success.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_sidechain_distance_asymmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const double &) const –> bool

filter_by_sidechain_distance_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, filter_multiplier: float) → bool

Given a pose with residues selected to be linked by a trimesic acid crosslinker,

determine whether the residues are too far apart. This version is for symmetric poses.

Returns TRUE for failure (residues too far apart) and FALSE for success.

Higher values of the filter multiplier make it more permissive.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_sidechain_distance_symmetric(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const double &) const –> bool

get_linker_index_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → int

Given indices of three residues that are already linked to a TMA, get the index

of the TMA residue.

Throws an error if the three residues are not all linked to the same TMA residue.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_index_asymmetric(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> unsigned long

get_linker_indices_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, linker_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Given indices of three residues that are already linked to pieces of a linker, get

of the indices of the symmetric pieces of the linker.

Throws an error if a residue is not linked to something.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_indices_symmetric(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_sidechain_indices(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, selection: pyrosetta.rosetta.utility.vector1_bool, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Given a ResidueSubset with N residues selected, pull out the indices into a vector.

Overwrites res_indices.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(const class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

post_relax_round_update_steps(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, whole_structure: bool, symmetric: bool, linker_was_added: bool) → None

Optional steps that the helper can apply after every relaxation round.

overrides default (doing nothing) to update positions of amide bond dependent atoms.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::post_relax_round_update_steps(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const bool, const bool) const –> void

pre_relax_round_update_steps(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, whole_structure: bool, symmetric: bool, linker_was_added: bool) → None

Optional steps that the helper can apply before every relaxation round.

overrides default (doing nothing) to update positions of amide bond dependent atoms.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::pre_relax_round_update_steps(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool, const bool, const bool) const –> void

selection_is_symmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, selection: pyrosetta.rosetta.utility.vector1_bool, pose: pyrosetta.rosetta.core.pose.Pose, expected_subunit_count: int) → bool

Determine whether a selection is symmetric.

Returns true if and only if (a) the pose is symmetric, (b) there are the expected number of symmetry copies, and (c) the selected residues are equivalent residues in different symmetry copies. Note that, ideally, I’d like to test for CN or SN symmetry, but this is as close as was feasible.

Can be overriden.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::selection_is_symmetric(const class utility::vector1<bool, class std::allocator<bool> > &, const class core::pose::Pose &, const unsigned long) const –> bool

set_symmetry(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, symm_type_in: str, symm_count_in: int) → None

Set the symmetry for this crosslinker helper.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::set_symmetry(const char, const unsigned long) –> void