crosslinker

Bindings for protocols::cyclic_peptide::crosslinker namespace

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

Bases: pybind11_object

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

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 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 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 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 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 residues that are already linked to a linker, get the index

of the linker.

Returns zero for this class, since no linker is added.

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

of the indices of the symmetric pieces of the linker.

Returns zero for this class, since no linker is added.

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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::helper_adds_linker_residue() const –> bool

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. Derived classes may override this.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase

Bases: CrosslinkerMoverHelper

A base class for setting up metals. This is a pure virtual class that must be subclassed for specific metal geometries..

add_linker_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase

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

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

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

of the linker.

Not applicable for this particular crosslinker. A “GNDN” function – goes nowhere, does nothing. Only here because the base class has a pure virtual of this name.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

No, it does not.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::helper_adds_linker_residue() const –> bool

metal_type_string(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → str

Get the current metal type, as a string.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::metal_type_string() const –> std::string

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. Derived classes may override this.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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_metal_type_from_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, name_in: str) → None

Given a metal name, set the type.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_type_from_name(const std::string &) –> void

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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_Metal

Bases: pybind11_object

Metal types compatible with this helper.

If you add to this list, you need to add entries to the switch statement in metal_type_string_from_enum(), as well as the map in ideal_bond_length().

Members:

MH_Zn

MH_Fe2

MH_Ni2

MH_unknown_metal

MH_end_of_list

MH_Fe2 = <Metal_HelperBase_Metal.MH_Fe2: 2>

MH_Ni2 = <Metal_HelperBase_Metal.MH_Ni2: 3>

MH_Zn = <Metal_HelperBase_Metal.MH_Zn: 1>

MH_end_of_list = <Metal_HelperBase_Metal.MH_unknown_metal: 4>

MH_unknown_metal = <Metal_HelperBase_Metal.MH_unknown_metal: 4>

property name

property value

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_MetalLigand

Bases: pybind11_object

Metal-liganding atom types compatible with this helper.

If you add to this list, you need to add entries to the map in ideal_bond_length().

Members:

MHLigand_Nd_histidine

MHLigand_Ne_histidine

MHLigand_O_carboxyl

MHLigand_N_pyridine

MHLigand_S_cysteine

MHLigand_unknown_ligand

MHLigand_end_of_list

MHLigand_N_pyridine = <Metal_HelperBase_MetalLigand.MHLigand_N_pyridine: 4>

MHLigand_Nd_histidine = <Metal_HelperBase_MetalLigand.MHLigand_Nd_histidine: 1>

MHLigand_Ne_histidine = <Metal_HelperBase_MetalLigand.MHLigand_Ne_histidine: 2>

MHLigand_O_carboxyl = <Metal_HelperBase_MetalLigand.MHLigand_O_carboxyl: 3>

MHLigand_S_cysteine = <Metal_HelperBase_MetalLigand.MHLigand_S_cysteine: 5>

MHLigand_end_of_list = <Metal_HelperBase_MetalLigand.MHLigand_unknown_ligand: 6>

MHLigand_unknown_ligand = <Metal_HelperBase_MetalLigand.MHLigand_unknown_ligand: 6>

property name

property value

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper

Bases: Metal_HelperBase

A helper class for setting up octahedrally-coordinated metals.

add_linker_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.OctahedralMetal_Helper, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper

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

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

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

of the linker.

Not applicable for this particular crosslinker. A “GNDN” function – goes nowhere, does nothing. Only here because the base class has a pure virtual of this name.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

No, it does not.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::helper_adds_linker_residue() const –> bool

metal_type_string(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → str

Get the current metal type, as a string.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::metal_type_string() const –> std::string

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. This override indicates that this helper was published in Mulligan, Kang, et al. 2021.

C++: protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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_metal_type_from_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, name_in: str) → None

Given a metal name, set the type.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_type_from_name(const std::string &) –> void

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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper

Bases: CrosslinkerMoverHelper

A derived class of the CrosslinkerMoverHelper base class, used to set up the 1,4-bis(bromomethyl)benzene (BBMB) cross-linker.

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

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

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

C++: protocols::cyclic_peptide::crosslinker::One_Four_BBMB_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.One_Four_BBMB_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::One_Four_BBMB_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.One_Four_BBMB_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 BBMB linker and the residues that coordinate the linker.

Called by add_linker_symmetric(). Version for symmetric poses.

C++: protocols::cyclic_peptide::crosslinker::One_Four_BBMB_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.One_Four_BBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

Given a selection of exactly two residues that have already been connected to a 1,4-bis(bromomethyl)benzene crosslinker,

add constraints for the crosslinker.

C++: protocols::cyclic_peptide::crosslinker::One_Four_BBMB_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.One_Four_BBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, linker_was_added: bool) → None

Given a selection of exactly two residues that have already been connected to a 1,4-bis(bromomethyl)benzene crosslinker,

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

C++: protocols::cyclic_peptide::crosslinker::One_Four_BBMB_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.One_Four_BBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

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

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

Version for symmetric poses.

C++: protocols::cyclic_peptide::crosslinker::One_Four_BBMB_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.One_Four_BBMB_Helper, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper

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

filter_by_constraints_energy_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_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::One_Four_BBMB_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.One_Four_BBMB_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::One_Four_BBMB_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.One_Four_BBMB_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 1,4-bis(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::One_Four_BBMB_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.One_Four_BBMB_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 1,4-bis(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::One_Four_BBMB_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.One_Four_BBMB_Helper, pose: pyrosetta.rosetta.core.pose.Pose, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → int

Given indices of two cysteine residues that are already linked to a BBMB, get the index

of the BBMB residue.

Throws an error if the two cysteines are not all linked to the same BBMB residue.

C++: protocols::cyclic_peptide::crosslinker::One_Four_BBMB_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.One_Four_BBMB_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 two 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::One_Four_BBMB_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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

Yes, it does.

C++: protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::helper_adds_linker_residue() const –> bool

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. This override indicates that this helper is unpublished.

C++: protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper

Bases: Metal_HelperBase

A helper class for setting up square planarly-coordinated metals like Ni.

add_linker_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.SquarePlanarMetal_Helper, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper

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

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

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

of the linker.

Not applicable for this particular crosslinker. A “GNDN” function – goes nowhere, does nothing. Only here because the base class has a pure virtual of this name.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

No, it does not.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::helper_adds_linker_residue() const –> bool

metal_type_string(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → str

Get the current metal type, as a string.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::metal_type_string() const –> std::string

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. This override indicates that this helper was published in Mulligan, Kang, et al. 2021.

C++: protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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_metal_type_from_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, name_in: str) → None

Given a metal name, set the type.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_type_from_name(const std::string &) –> void

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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper

Bases: SquarePlanarMetal_Helper

A helper class for setting up square pyramidally-coordinated metals like Ni.

It is convenient to have this inherit from SquarePlanarMetal_Helper.

add_linker_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.SquarePyramidalMetal_Helper, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper

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

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

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

of the linker.

Not applicable for this particular crosslinker. A “GNDN” function – goes nowhere, does nothing. Only here because the base class has a pure virtual of this name.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

No, it does not.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::helper_adds_linker_residue() const –> bool

metal_type_string(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → str

Get the current metal type, as a string.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::metal_type_string() const –> std::string

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. This override indicates that this helper was published in Mulligan, Kang, et al. 2021.

C++: protocols::cyclic_peptide::crosslinker::SquarePyramidalMetal_Helper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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_metal_type_from_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, name_in: str) → None

Given a metal name, set the type.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_type_from_name(const std::string &) –> void

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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

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

Bases: CrosslinkerMoverHelper

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

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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

Yes, it does.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::helper_adds_linker_residue() const –> bool

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. This override indicates that this helper is published in Dang, Wu, Mulligan et al. 2017.

C++: protocols::cyclic_peptide::crosslinker::TBMB_Helper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

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

Bases: CrosslinkerMoverHelper

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

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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

Yes, it does.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::helper_adds_linker_residue() const –> bool

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. This override indicates that this helper is unpublished.

C++: protocols::cyclic_peptide::crosslinker::TMA_Helper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper

Bases: Metal_HelperBase

A helper class for setting up tetrahedrally-coordinated metals like Zn or Cu.

add_linker_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.TetrahedralMetal_Helper, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper

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

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

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

of the linker.

Not applicable for this particular crosslinker. A “GNDN” function – goes nowhere, does nothing. Only here because the base class has a pure virtual of this name.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

No, it does not.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::helper_adds_linker_residue() const –> bool

metal_type_string(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → str

Get the current metal type, as a string.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::metal_type_string() const –> std::string

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. This override indicates that this helper was published in Mulligan, Kang, et al. 2021.

C++: protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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_metal_type_from_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, name_in: str) → None

Given a metal name, set the type.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_type_from_name(const std::string &) –> void

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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper

Bases: CrosslinkerMoverHelper

A CrosslinkerMoverHelper for placing a terminal (or lariat-style) thioether linkage.

Vikram K. Mulligan (vmulligan.org)

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

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

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

Calls add_linker_bonds_asymmetric(). Version for asymmetric poses.

C++: protocols::cyclic_peptide::crosslinker::Thioether_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.Thioether_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.

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

C++: protocols::cyclic_peptide::crosslinker::Thioether_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.Thioether_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 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::Thioether_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.Thioether_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

Given a selection of 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::Thioether_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.Thioether_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, linker_was_added: bool) → None

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

add constraints for the crosslinker.

Version for symmetric poses, but this just calls the asymmetric version.

C++: protocols::cyclic_peptide::crosslinker::Thioether_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.Thioether_Helper, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) → None

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

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

Version for symmetric poses. However, since the linker itself has no symmetry, we can just call the asymmetric version.

C++: protocols::cyclic_peptide::crosslinker::Thioether_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.Thioether_Helper, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper

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

filter_by_constraints_energy_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_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::Thioether_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.Thioether_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::Thioether_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.Thioether_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 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::Thioether_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.Thioether_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 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::Thioether_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.Thioether_Helper, pose: pyrosetta.rosetta.core.pose.Pose, res_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → int

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

of the linker.

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

C++: protocols::cyclic_peptide::crosslinker::Thioether_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.Thioether_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 residues that are already linked to pieces of a linker, get

of the indices of the symmetric pieces of the linker.

Returns an empty vector for linker indices for this class, since no linker is added.

C++: protocols::cyclic_peptide::crosslinker::Thioether_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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

In this case, no: the linker is a patch to the terminal type.

C++: protocols::cyclic_peptide::crosslinker::Thioether_Helper::helper_adds_linker_residue() const –> bool

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. This override indicates that this helper is unpublished.

C++: protocols::cyclic_peptide::crosslinker::Thioether_Helper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper

Bases: Metal_HelperBase

A helper class for setting up trigonal planarly-coordinated metals like Zn or Cu.

add_linker_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.TrigonalPlanarMetal_Helper, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper

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

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

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

of the linker.

Not applicable for this particular crosslinker. A “GNDN” function – goes nowhere, does nothing. Only here because the base class has a pure virtual of this name.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

No, it does not.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::helper_adds_linker_residue() const –> bool

metal_type_string(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → str

Get the current metal type, as a string.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::metal_type_string() const –> std::string

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. This override indicates that this helper was published in Mulligan, Kang, et al. 2021.

C++: protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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_metal_type_from_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, name_in: str) → None

Given a metal name, set the type.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_type_from_name(const std::string &) –> void

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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

class pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper

Bases: Metal_HelperBase

A helper class for setting up trigonal pyramidally-coordinated metals like Zn or Cu.

add_linker_asymmetric(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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.TrigonalPyramidalMetal_Helper, : pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper) → pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper

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

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

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

of the linker.

Not applicable for this particular crosslinker. A “GNDN” function – goes nowhere, does nothing. Only here because the base class has a pure virtual of this name.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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.Metal_HelperBase, 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::Metal_HelperBase::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

helper_adds_linker_residue(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → bool

Does this CrosslinkerMoverHelper add a residue for the linker?

No, it does not.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::helper_adds_linker_residue() const –> bool

metal_type_string(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase) → str

Get the current metal type, as a string.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::metal_type_string() const –> std::string

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

provide_citation_info(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide an opportunity to provide a citation for this crosslinker type.

The base class implementation does nothing. This override indicates that this helper was published in Mulligan, Kang, et al. 2021.

C++: protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper::provide_citation_info(class basic::citation_manager::CitationCollectionList &) 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_metal_type_from_name(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase, name_in: str) → None

Given a metal name, set the type.

C++: protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_type_from_name(const std::string &) –> void

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

symm_subunits_expected(self: pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper) → int

Get the number of expected symmetry subunits, given the symmetry type.

C++: protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected() const –> unsigned long

pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.correct_thioether_virtuals(pose: pyrosetta.rosetta.core.pose.Pose, ntermres: int, sidechainres: int) → None

Correct the bond angles and bond lenghts for virtual atoms at thioether bonds.

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

pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.set_up_thioether_bond_mover(termini: protocols::simple_moves::DeclareBond, pose: pyrosetta.rosetta.core.pose.Pose, ntermres: int, sidechainres: int) → None

Set up the mover that creates thioether lariat bonds.

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

pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.set_up_thioether_constraints(pose: pyrosetta.rosetta.core.pose.Pose, ntermres: int, sidechainres: int) → None

Given a pose and two residues to constrain (the first being the residue with the modified N-terminus,

and the second being the one with the thiol-containing sidechain), add constraints for a thioether linkage.

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

pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.set_up_thioether_variants(pose: pyrosetta.rosetta.core.pose.Pose, ntermres: int, sidechainres: int) → None

Given a pose and two residues, set up the thioether variant types.

Sidechainres gets SIDECHAIN_CONJUGATION; ntermres gets ACETYLATED_NTERMINUS_CONNECTION_VARIANT. The pose is modified by this operation.

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