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

#include <Thioether_Helper.hh>

Inheritance diagram for protocols::cyclic_peptide::crosslinker::Thioether_Helper:

Public Member Functions
	Thioether_Helper ()
	Default constructor. More...

	Thioether_Helper (Thioether_Helper const &src)
	Copy constructor. More...

	~Thioether_Helper () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override
	Provide an opportunity to provide a citation for this crosslinker type. More...

void	add_linker_asymmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection) const override
	Given a pose and a selection of residues, add the linker, align it crudely to the selected residues, and set up covalent bonds. More...

void	add_linker_bonds_asymmetric (core::pose::Pose &pose, utility::vector1< core::Size > const &res_indices, core::Size const linker_index) const override
	Given a pose and a linker, add bonds between the linker and the residues that coordinate the linker. More...

void	add_linker_symmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection) const override
	Given a pose and a selection of residues, add the linker, align it crudely to the selected residues, and set up covalent bonds. More...

void	add_linker_bonds_symmetric (core::pose::Pose &pose, core::Size const res1, core::Size const linker_index1, core::Size const linker_index2) const override
	Given a pose and a linker, add bonds between the linker and the residues that coordinate the linker. More...

void	add_linker_constraints_asymmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection) const override
	Given a selection of residues that have already been connected to a crosslinker, add constraints for the crosslinker. More...

void	add_linker_constraints_symmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, bool const linker_was_added) const override
	Given a selection of residues that have already been connected to a crosslinker, add constraints for the crosslinker. More...

core::Size	get_linker_index_asymmetric (core::pose::Pose const &pose, utility::vector1< core::Size > const &res_indices) const override
	Given indices of residues that are already linked to a linker, get the index of the linker. More...

void	get_linker_indices_symmetric (core::pose::Pose const &pose, utility::vector1< core::Size > const &res_indices, utility::vector1< core::Size > &linker_indices) const override
	Given indices of residues that are already linked to pieces of a linker, get of the indices of the symmetric pieces of the linker. More...

bool	filter_by_sidechain_distance_asymmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, core::Real const &filter_multiplier) const override
	Given a pose with residues selected to be linked by a linker, determine whether the residues are too far apart. More...

bool	filter_by_sidechain_distance_symmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, core::Real const &filter_multiplier) const override
	Given a pose with residues selected to be linked by a linker, determine whether the residues are too far apart. More...

bool	filter_by_constraints_energy_asymmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, core::Real const &filter_multiplier) const override
	Determine whether the sidechain-crosslinker system has too high a constraints score. More...

bool	filter_by_constraints_energy_symmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, bool const linker_was_added, core::Real const &filter_multiplier) const override
	Determine whether the sidechain-crosslinker system has too high a constraints score. This version is for symmetric poses. More...

bool	helper_adds_linker_residue () const override
	Does this CrosslinkerMoverHelper add a residue for the linker? More...

Public Member Functions inherited from protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper
	CrosslinkerMoverHelper ()
	Default constructor. More...

	CrosslinkerMoverHelper (CrosslinkerMoverHelper const &src)
	Copy constructor. More...

	~CrosslinkerMoverHelper () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	set_symmetry (char const symm_type_in, core::Size const symm_count_in)
	Set the symmetry for this crosslinker helper. More...

virtual void	get_sidechain_indices (core::select::residue_selector::ResidueSubset const &selection, utility::vector1< core::Size > &res_indices) const
	Given a ResidueSubset with N residues selected, pull out the indices into a vector. More...

virtual bool	selection_is_symmetric (core::select::residue_selector::ResidueSubset const &selection, core::pose::Pose const &pose, core::Size const expected_subunit_count) const
	Determine whether a selection is symmetric. More...

virtual void	pre_relax_round_update_steps (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, bool const whole_structure, bool const symmetric, bool const linker_was_added) const
	Optional steps that the helper can apply before every relaxation round. More...

virtual void	post_relax_round_update_steps (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, bool const whole_structure, bool const symmetric, bool const linker_was_added) const
	Optional steps that the helper can apply after every relaxation round. More...

core::Size	symm_subunits_expected () const
	Get the number of expected symmetry subunits, given the symmetry type. More...

Private Member Functions
void	get_thioether_residues_from_selection (core::select::residue_selector::ResidueSubset const &selection, core::pose::Pose const &pose, core::Size &ntermres, core::Size &cysres) const
	Given a selection of exactly two residues and a pose, return the two thioether residues. Ensures that the residue that can make an N-terminal connection is ntermres, and that the residue that has a side-chain thiol and can make a side-chain connection is cysres. More...

Additional Inherited Members
Protected Member Functions inherited from protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper
virtual bool	filter_by_constraints_energy (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, bool const symmetric, bool const linker_was_added, core::Real const &filter_multiplier) const
	Determine whether the sidechain-crosslinker system has too high a constraints score. Both the symmetric and asymmetric versions call this code. More...

char	symm_type () const
	Get the symmetry type. More...

core::Size	symm_count () const
	Get the symmetry copy count. For example, symm_type_='C' and symm_count_=3 would specify C3 symmetry. A value of 1 means asymmetry. 1 by default. More...

Detailed Description

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

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Constructor & Destructor Documentation

◆ Thioether_Helper() [1/2]

protocols::cyclic_peptide::crosslinker::Thioether_Helper::Thioether_Helper ( )

default

Default constructor.

Constructors ///.

Default constructor

◆ Thioether_Helper() [2/2]

protocols::cyclic_peptide::crosslinker::Thioether_Helper::Thioether_Helper ( Thioether_Helper const & src )

default

Copy constructor.

◆ ~Thioether_Helper()

protocols::cyclic_peptide::crosslinker::Thioether_Helper::~Thioether_Helper ( )

overridedefault

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

◆ add_linker_asymmetric()

void protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_asymmetric	(	core::pose::Pose &	pose,
		core::select::residue_selector::ResidueSubset const &	selection
	)		const

overridevirtual

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.

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

References add_linker_bonds_asymmetric(), get_thioether_residues_from_selection(), protocols::cyclic_peptide::crosslinker::set_up_thioether_variants(), and protocols::cyclic_peptide::TR().

Referenced by add_linker_symmetric().

◆ add_linker_bonds_asymmetric()

void protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_bonds_asymmetric	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	res_indices,
		core::Size const	linker_index
	)		const

overridevirtual

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.

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

References protocols::simple_moves::DeclareBond::apply(), protocols::cyclic_peptide::crosslinker::correct_thioether_virtuals(), protocols::cyclic_peptide::crosslinker::set_up_thioether_bond_mover(), core::id::to_string(), core::pose::Pose::total_residue(), and protocols::cyclic_peptide::TR().

Referenced by add_linker_asymmetric(), and add_linker_bonds_symmetric().

◆ add_linker_bonds_symmetric()

void protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_bonds_symmetric	(	core::pose::Pose &	pose,
		core::Size const	res1,
		core::Size const	linker_index1,
		core::Size const	linker_index2
	)		const

overridevirtual

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.

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

References add_linker_bonds_asymmetric().

◆ add_linker_constraints_asymmetric()

void protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_constraints_asymmetric	(	core::pose::Pose &	pose,
		core::select::residue_selector::ResidueSubset const &	selection
	)		const

overridevirtual

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.

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

References get_thioether_residues_from_selection(), and protocols::cyclic_peptide::crosslinker::set_up_thioether_constraints().

Referenced by add_linker_constraints_symmetric().

◆ add_linker_constraints_symmetric()

void protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_constraints_symmetric	(	core::pose::Pose &	pose,
		core::select::residue_selector::ResidueSubset const &	selection,
		bool const	linker_was_added
	)		const

overridevirtual

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.

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

References add_linker_constraints_asymmetric().

◆ add_linker_symmetric()

void protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_symmetric	(	core::pose::Pose &	pose,
		core::select::residue_selector::ResidueSubset const &	selection
	)		const

overridevirtual

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.

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

References add_linker_asymmetric().

◆ filter_by_constraints_energy_asymmetric()

bool protocols::cyclic_peptide::crosslinker::Thioether_Helper::filter_by_constraints_energy_asymmetric	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	selection,
		core::Real const &	filter_multiplier
	)		const

overridevirtual

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.

Note: Higher values of the filter multiplier make it more permissive.

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

References protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::filter_by_constraints_energy().

◆ filter_by_constraints_energy_symmetric()

bool protocols::cyclic_peptide::crosslinker::Thioether_Helper::filter_by_constraints_energy_symmetric	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	selection,
		bool const	linker_was_added,
		core::Real const &	filter_multiplier
	)		const

overridevirtual

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.

Note: Higher values of the filter multiplier make it more permissive.

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

References protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::filter_by_constraints_energy().

◆ filter_by_sidechain_distance_asymmetric()

bool protocols::cyclic_peptide::crosslinker::Thioether_Helper::filter_by_sidechain_distance_asymmetric	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	selection,
		core::Real const &	filter_multiplier
	)		const

overridevirtual

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.

Note: Higher values of the filter multiplier make it more permissive.

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

References get_thioether_residues_from_selection(), MAX_CA_CB_DIST_MINUS_NBR, core::chemical::ResidueType::nbr_radius(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().

Referenced by filter_by_sidechain_distance_symmetric().

◆ filter_by_sidechain_distance_symmetric()

bool protocols::cyclic_peptide::crosslinker::Thioether_Helper::filter_by_sidechain_distance_symmetric	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	selection,
		core::Real const &	filter_multiplier
	)		const

overridevirtual

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.

Note: Higher values of the filter multiplier make it more permissive.

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

References filter_by_sidechain_distance_asymmetric().

◆ get_linker_index_asymmetric()

core::Size protocols::cyclic_peptide::crosslinker::Thioether_Helper::get_linker_index_asymmetric	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	res_indices
	)		const

overridevirtual

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.

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

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

◆ get_linker_indices_symmetric()

void protocols::cyclic_peptide::crosslinker::Thioether_Helper::get_linker_indices_symmetric	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	res_indices,
		utility::vector1< core::Size > &	linker_indices
	)		const

overridevirtual

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.

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

◆ get_thioether_residues_from_selection()

void protocols::cyclic_peptide::crosslinker::Thioether_Helper::get_thioether_residues_from_selection	(	core::select::residue_selector::ResidueSubset const &	selection,
		core::pose::Pose const &	pose,
		core::Size &	ntermres,
		core::Size &	cysres
	)		const

private

Given a selection of exactly two residues and a pose, return the two thioether residues. Ensures that the residue that can make an N-terminal connection is ntermres, and that the residue that has a side-chain thiol and can make a side-chain connection is cysres.

References core::conformation::Residue::connected_residue_at_lower(), core::chemical::ResidueType::is_sidechain_thiol(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::id::swap(), and core::pose::Pose::total_residue().

Referenced by add_linker_asymmetric(), add_linker_constraints_asymmetric(), and filter_by_sidechain_distance_asymmetric().

◆ helper_adds_linker_residue()

bool protocols::cyclic_peptide::crosslinker::Thioether_Helper::helper_adds_linker_residue ( ) const

inlineoverridevirtual

Does this CrosslinkerMoverHelper add a residue for the linker?

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

Implements protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

◆ provide_citation_info()

void protocols::cyclic_peptide::crosslinker::Thioether_Helper::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

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

Public Methods ///.

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

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.

Reimplemented from protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper.

The documentation for this class was generated from the following files:

src/protocols/cyclic_peptide/crosslinker/Thioether_Helper.hh
src/protocols/cyclic_peptide/crosslinker/Thioether_Helper.cc

Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Thioether_Helper() [1/2]

◆ Thioether_Helper() [2/2]

◆ ~Thioether_Helper()

Member Function Documentation

◆ add_linker_asymmetric()

◆ add_linker_bonds_asymmetric()

◆ add_linker_bonds_symmetric()

◆ add_linker_constraints_asymmetric()

◆ add_linker_constraints_symmetric()

◆ add_linker_symmetric()

◆ filter_by_constraints_energy_asymmetric()

◆ filter_by_constraints_energy_symmetric()

◆ filter_by_sidechain_distance_asymmetric()

◆ filter_by_sidechain_distance_symmetric()

◆ get_linker_index_asymmetric()

◆ get_linker_indices_symmetric()

◆ get_thioether_residues_from_selection()

◆ helper_adds_linker_residue()

◆ provide_citation_info()