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

#include <TBMB_Helper.hh>

Inheritance diagram for protocols::cyclic_peptide::crosslinker::TBMB_Helper:

[legend]

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

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

	~TBMB_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 exactly three residues, add the TBMB 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 exactly three residues, add the TBMB 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 TBMB 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 exactly three residues that have already been connected to a 1,3,5-tris(bromomethyl)benzene 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 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. More...

core::Size	get_linker_index_asymmetric (core::pose::Pose const &pose, utility::vector1< core::Size > const &res_indices) const override
	Given indices of three cysteine residues that are already linked to a TBMB, get the index of the TBMB residue. 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 three cysteine 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 1,3,5-tris(bromomethyl)benzene crosslinker, 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 1,3,5-tris(bromomethyl)benzene crosslinker, determine whether the residues are too far apart. This version is for symmetric poses. 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...

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

Constructor & Destructor Documentation

◆ TBMB_Helper() [1/2]

protocols::cyclic_peptide::crosslinker::TBMB_Helper::TBMB_Helper ( )

default

Default constructor.

Constructors ///.

Default constructor

◆ TBMB_Helper() [2/2]

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

default

Copy constructor.

◆ ~TBMB_Helper()

protocols::cyclic_peptide::crosslinker::TBMB_Helper::~TBMB_Helper ( )

overridedefault

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

Member Function Documentation

◆ add_linker_asymmetric()

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

overridevirtual

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.

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

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_cys, core::chemical::aa_dcs, add_linker_bonds_asymmetric(), core::pose::Pose::append_residue_by_jump(), protocols::simple_moves::ModifyVariantTypeMover::apply(), core::chemical::ResidueType::atom_index(), core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::simple_moves::ModifyVariantTypeMover::set_additional_type_to_add(), protocols::simple_moves::ModifyVariantTypeMover::set_residue_selector(), core::scoring::superimpose_pose(), and core::pose::Pose::total_residue().

◆ add_linker_bonds_asymmetric()

void protocols::cyclic_peptide::crosslinker::TBMB_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.

Called by add_linker_asymmetric(). Version for asymmetric poses.

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

References protocols::simple_moves::DeclareBond::apply(), and protocols::simple_moves::DeclareBond::set().

Referenced by add_linker_asymmetric().

◆ add_linker_bonds_symmetric()

void protocols::cyclic_peptide::crosslinker::TBMB_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 TBMB linker and the residues that coordinate the linker.

Called by add_linker_symmetric(). Version for symmetric poses.

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

References protocols::simple_moves::DeclareBond::apply(), protocols::simple_moves::DeclareBond::set(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count(), and protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type().

Referenced by add_linker_symmetric().

◆ add_linker_constraints_asymmetric()

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

overridevirtual

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.

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

References protocols::cyclic_peptide::CreateDistanceConstraint::apply(), protocols::cyclic_peptide::CreateTorsionConstraint::apply(), get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), protocols::cyclic_peptide::CreateTorsionConstraint::set(), protocols::cyclic_peptide::CreateDistanceConstraint::set(), and protocols::cyclic_peptide::TR().

◆ add_linker_constraints_symmetric()

void protocols::cyclic_peptide::crosslinker::TBMB_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 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.

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

◆ add_linker_symmetric()

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

overridevirtual

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.

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

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_cys, core::chemical::aa_dcs, add_linker_bonds_symmetric(), core::pose::Pose::append_residue_by_jump(), protocols::simple_moves::ModifyVariantTypeMover::apply(), core::chemical::ResidueType::atom_index(), core::pose::Pose::conformation_ptr(), core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::simple_moves::ModifyVariantTypeMover::set_additional_type_to_add(), protocols::simple_moves::ModifyVariantTypeMover::set_residue_selector(), core::scoring::superimpose_pose(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count(), and protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type().

◆ filter_by_constraints_energy_asymmetric()

bool protocols::cyclic_peptide::crosslinker::TBMB_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.

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

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::TBMB_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.

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

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

References protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::filter_by_constraints_energy(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count(), and protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type().

◆ filter_by_sidechain_distance_asymmetric()

bool protocols::cyclic_peptide::crosslinker::TBMB_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 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.

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

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

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

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_cys, core::chemical::aa_dcs, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::cyclic_peptide::TR(), and core::conformation::Residue::xyz().

◆ filter_by_sidechain_distance_symmetric()

bool protocols::cyclic_peptide::crosslinker::TBMB_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 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.

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

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

Note: This version is faster since it only considers the cys1->cys2 distance, and assumes that, due to symmetry, the cys2->cys3 and cys3->cys1 distances must be identical.

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

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_cys, core::chemical::aa_dcs, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type(), protocols::cyclic_peptide::TR(), and core::conformation::Residue::xyz().

◆ get_linker_index_asymmetric()

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

overridevirtual

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.

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

References core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::name3(), core::pose::Pose::residue(), and core::conformation::Residue::residue_connection_partner().

Referenced by add_linker_constraints_asymmetric().

◆ get_linker_indices_symmetric()

void protocols::cyclic_peptide::crosslinker::TBMB_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 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.

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

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

References core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::name3(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count(), and protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type().

Referenced by add_linker_constraints_symmetric().

◆ helper_adds_linker_residue()

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

inlineoverridevirtual

Does this CrosslinkerMoverHelper add a residue for the linker?

Yes, it does.

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

◆ provide_citation_info()

void protocols::cyclic_peptide::crosslinker::TBMB_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 published in Dang, Wu, Mulligan et al. 2017.

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.

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

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TBMB_Helper() [1/2]

◆ TBMB_Helper() [2/2]

◆ ~TBMB_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()

◆ helper_adds_linker_residue()

◆ provide_citation_info()