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

#include <TMA_Helper.hh>

Inheritance diagram for protocols::cyclic_peptide::crosslinker::TMA_Helper:

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

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

	~TMA_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 TMA 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 TMA 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 TMA linker, add bonds between the TMA 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 trimesic acid 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 trimesic acid 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 residues that are already linked to a TMA, get the index of the TMA 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 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 trimesic acid 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 trimesic acid 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...

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

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

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

Private Member Functions
bool	is_allowed_residue_type (core::chemical::ResidueType const &type) const
	Given a residue type, return true for D- or L-Lys, Orn, DAB, or DAP/DPP, and false otherwise. More...

std::string	list_allowed_residue_types () const
	Returns a string listing the allowed residue types that can connect to TMA. More...

void	add_sidechain_conjugation (core::pose::Pose &pose, core::Size const position) const
	Given a pose and a position that is one of the allowed types, add the sidechain-conjugation type or patch to the position. More...

std::string	get_sidechain_amide_name (core::chemical::ResidueType const &type) const
	Given a residue type, get the name of the sidechain amide atom. More...

std::string	get_last_sidechain_carbon_name (core::chemical::ResidueType const &type) const
	Given a residue type, get the name of the last carbon in the side chain. More...

core::Size	get_sidechain_connect_index (core::conformation::Residue const &res) const
	Given a residue in a pose, get the index of its first sidechain connection. More...

core::Real	get_max_sidechain_length (core::chemical::ResidueType const &restype) const
	Given one of the residue types that TMA can connect to, return the max distance between the CA and the NZ. (Slightly padded). More...

void	place_tma_asymmetric (core::pose::Pose &tma_pose, core::pose::Pose const &pose, core::Size const res1, core::Size const res2, core::Size const res3) const
	Given a pose and three connector residue indices, create a new pose with TMA placed somewhere in space that crudely aligns it to the connector residues. More...

void	place_tma_symmetric (core::pose::Pose &symm_pose, core::pose::Pose const &asymm_pose) const
	Given a pose containing only an asymmetric TMA molecule, align a symmetric TMA to the first third of the asymmetric TMA, place that in symm_pose. More...

void	update_tma_amide_bond_dependent_atoms (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, bool const symmetric, bool const tma_was_added) const
	Given a pose and a selection of three residues that connect to a TMA residue, update the positions of carbonyl oxygen and amide hydrogen atoms in the amide bonds connecting the TMA to the sidechains. More...

void	update_tma_amide_bond_dependent_atoms_asymmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection) const
	Given a pose and a selection of three residues that connect to a TMA residue, update the positions of carbonyl oxygen and amide hydrogen atoms in the amide bonds connecting the TMA to the sidechains. More...

void	update_tma_amide_bond_dependent_atoms_symmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, bool const tma_was_added) const
	Given a pose and a selection of three residues that connect to a TMA residue, update the positions of carbonyl oxygen and amide hydrogen atoms in the amide bonds connecting the TMA to the sidechains. 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 trimesic acid (TMA) cross-linker.

Constructor & Destructor Documentation

◆ TMA_Helper() [1/2]

protocols::cyclic_peptide::crosslinker::TMA_Helper::TMA_Helper ( )

default

Default constructor.

Constructors ///.

Default constructor

◆ TMA_Helper() [2/2]

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

default

Copy constructor.

◆ ~TMA_Helper()

protocols::cyclic_peptide::crosslinker::TMA_Helper::~TMA_Helper ( )

overridedefault

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

Member Function Documentation

◆ add_linker_asymmetric()

void protocols::cyclic_peptide::crosslinker::TMA_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 TMA linker, align it crudely to the selected residues, and set up covalent bonds.

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

References add_linker_bonds_asymmetric(), add_sidechain_conjugation(), core::pose::Pose::append_residue_by_jump(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), is_allowed_residue_type(), list_allowed_residue_types(), place_tma_asymmetric(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

◆ add_linker_bonds_asymmetric()

void protocols::cyclic_peptide::crosslinker::TMA_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(), get_sidechain_amide_name(), core::pose::Pose::residue_type(), and protocols::simple_moves::DeclareBond::set().

Referenced by add_linker_asymmetric().

◆ add_linker_bonds_symmetric()

void protocols::cyclic_peptide::crosslinker::TMA_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 TMA linker, add bonds between the TMA 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(), get_sidechain_amide_name(), core::pose::Pose::residue_type(), 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::TMA_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 trimesic acid crosslinker, add constraints for the crosslinker.

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

References protocols::cyclic_peptide::CreateDistanceConstraint::apply(), protocols::cyclic_peptide::CreateTorsionConstraint::apply(), get_last_sidechain_carbon_name(), get_linker_index_asymmetric(), get_sidechain_amide_name(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), protocols::hybridization::r1, protocols::hybridization::r2, core::pose::Pose::residue_type(), protocols::cyclic_peptide::CreateTorsionConstraint::set(), protocols::cyclic_peptide::CreateDistanceConstraint::set(), and protocols::cyclic_peptide::TR().

◆ add_linker_constraints_symmetric()

void protocols::cyclic_peptide::crosslinker::TMA_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 trimesic acid crosslinker, add constraints for the crosslinker. This version is for symmetric poses.

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

References protocols::cyclic_peptide::CreateDistanceConstraint::apply(), protocols::cyclic_peptide::CreateTorsionConstraint::apply(), get_last_sidechain_carbon_name(), get_linker_indices_symmetric(), get_sidechain_amide_name(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), protocols::hybridization::r1, protocols::hybridization::r2, core::pose::Pose::residue_type(), protocols::cyclic_peptide::CreateTorsionConstraint::set(), protocols::cyclic_peptide::CreateDistanceConstraint::set(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count(), and protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type().

◆ add_linker_symmetric()

void protocols::cyclic_peptide::crosslinker::TMA_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 TMA linker, align it crudely to the selected residues, and set up covalent bonds.

Version for symmetric poses.

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

References add_linker_bonds_symmetric(), add_sidechain_conjugation(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::conformation_ptr(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), is_allowed_residue_type(), list_allowed_residue_types(), place_tma_asymmetric(), place_tma_symmetric(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count(), and protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type().

◆ add_sidechain_conjugation()

void protocols::cyclic_peptide::crosslinker::TMA_Helper::add_sidechain_conjugation	(	core::pose::Pose &	pose,
		core::Size const	position
	)		const

private

Given a pose and a position that is one of the allowed types, add the sidechain-conjugation type or patch to the position.

References protocols::simple_moves::ModifyVariantTypeMover::apply(), is_allowed_residue_type(), core::pose::Pose::residue_type(), protocols::simple_moves::ModifyVariantTypeMover::set_additional_type_to_add(), and protocols::simple_moves::ModifyVariantTypeMover::set_residue_selector().

Referenced by add_linker_asymmetric(), and add_linker_symmetric().

◆ filter_by_constraints_energy_asymmetric()

bool protocols::cyclic_peptide::crosslinker::TMA_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::TMA_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::TMA_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 trimesic acid 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 get_max_sidechain_length(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().

◆ filter_by_sidechain_distance_symmetric()

bool protocols::cyclic_peptide::crosslinker::TMA_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 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.

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 get_max_sidechain_length(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type(), and core::conformation::Residue::xyz().

◆ get_last_sidechain_carbon_name()

std::string protocols::cyclic_peptide::crosslinker::TMA_Helper::get_last_sidechain_carbon_name ( core::chemical::ResidueType const & type ) const

private

Given a residue type, get the name of the last carbon in the side chain.

Only works for the types allowed to connect to TMA (LYS, ORN, DAP/DPP, DAB and their D-versions).

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_dly, core::chemical::aa_lys, core::chemical::ResidueTypeBase::base_name(), and is_allowed_residue_type().

Referenced by add_linker_constraints_asymmetric(), and add_linker_constraints_symmetric().

◆ get_linker_index_asymmetric()

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

overridevirtual

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.

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

References core::conformation::Residue::connected_residue_at_resconn(), get_sidechain_connect_index(), and core::pose::Pose::residue().

Referenced by add_linker_constraints_asymmetric(), and update_tma_amide_bond_dependent_atoms_asymmetric().

◆ get_linker_indices_symmetric()

void protocols::cyclic_peptide::crosslinker::TMA_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 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::connected_residue_at_resconn(), get_sidechain_connect_index(), core::pose::Pose::residue(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count(), and protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type().

Referenced by add_linker_constraints_symmetric(), and update_tma_amide_bond_dependent_atoms_symmetric().

◆ get_max_sidechain_length()

core::Real protocols::cyclic_peptide::crosslinker::TMA_Helper::get_max_sidechain_length ( core::chemical::ResidueType const & restype ) const

private

Given one of the residue types that TMA can connect to, return the max distance between the CA and the NZ. (Slightly padded).

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_dly, core::chemical::aa_lys, and core::chemical::ResidueTypeBase::base_name().

Referenced by filter_by_sidechain_distance_asymmetric(), filter_by_sidechain_distance_symmetric(), and place_tma_asymmetric().

◆ get_sidechain_amide_name()

std::string protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_amide_name ( core::chemical::ResidueType const & type ) const

private

Given a residue type, get the name of the sidechain amide atom.

Only works for the types allowed to connect to TMA (LYS, ORN, DAP/DPP, DAB and their D-versions).

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_dly, core::chemical::aa_lys, core::chemical::ResidueTypeBase::base_name(), and is_allowed_residue_type().

Referenced by add_linker_bonds_asymmetric(), add_linker_bonds_symmetric(), add_linker_constraints_asymmetric(), add_linker_constraints_symmetric(), and place_tma_asymmetric().

◆ get_sidechain_connect_index()

core::Size protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_connect_index ( core::conformation::Residue const & res ) const

private

Given a residue in a pose, get the index of its first sidechain connection.

References core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), and core::conformation::Residue::n_possible_residue_connections().

Referenced by get_linker_index_asymmetric(), and get_linker_indices_symmetric().

◆ helper_adds_linker_residue()

bool protocols::cyclic_peptide::crosslinker::TMA_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.

◆ is_allowed_residue_type()

bool protocols::cyclic_peptide::crosslinker::TMA_Helper::is_allowed_residue_type ( core::chemical::ResidueType const & type ) const

private

Given a residue type, return true for D- or L-Lys, Orn, DAB, or DAP/DPP, and false otherwise.

Given a residue type, return true for D or L Lys, Orn, DAB, or DAP/DPP, and false otherwise.

Returns true only for the residue types that I can connect to TMA.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_dly, core::chemical::aa_lys, and core::chemical::ResidueTypeBase::base_name().

Referenced by add_linker_asymmetric(), add_linker_symmetric(), add_sidechain_conjugation(), get_last_sidechain_carbon_name(), and get_sidechain_amide_name().

◆ list_allowed_residue_types()

std::string protocols::cyclic_peptide::crosslinker::TMA_Helper::list_allowed_residue_types ( ) const

private

Returns a string listing the allowed residue types that can connect to TMA.

Intended to be human-readable. Used for error messages.

Referenced by add_linker_asymmetric(), and add_linker_symmetric().

◆ place_tma_asymmetric()

void protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric	(	core::pose::Pose &	tma_pose,
		core::pose::Pose const &	pose,
		core::Size const	res1,
		core::Size const	res2,
		core::Size const	res3
	)		const

private

Given a pose and three connector residue indices, create a new pose with TMA placed somewhere in space that crudely aligns it to the connector residues.

References core::pose::Pose::append_residue_by_jump(), core::chemical::ResidueType::atom_index(), core::pose::Pose::clear(), core::conformation::Residue::clone(), core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, get_max_sidechain_length(), get_sidechain_amide_name(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::superimpose_pose(), and core::conformation::Residue::xyz().

Referenced by add_linker_asymmetric(), and add_linker_symmetric().

◆ place_tma_symmetric()

void protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_symmetric	(	core::pose::Pose &	symm_pose,
		core::pose::Pose const &	asymm_pose
	)		const

private

Given a pose containing only an asymmetric TMA molecule, align a symmetric TMA to the first third of the asymmetric TMA, place that in symm_pose.

References core::pose::Pose::append_residue_by_jump(), core::chemical::ResidueType::atom_index(), core::pose::Pose::clear(), core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, core::pose::Pose::residue_type(), core::scoring::superimpose_pose(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count(), and protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type().

Referenced by add_linker_symmetric().

◆ post_relax_round_update_steps()

void protocols::cyclic_peptide::crosslinker::TMA_Helper::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

overridevirtual

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

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

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

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

References update_tma_amide_bond_dependent_atoms().

◆ pre_relax_round_update_steps()

void protocols::cyclic_peptide::crosslinker::TMA_Helper::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

overridevirtual

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

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

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

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

References update_tma_amide_bond_dependent_atoms().

◆ provide_citation_info()

void protocols::cyclic_peptide::crosslinker::TMA_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.

◆ update_tma_amide_bond_dependent_atoms()

void protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms	(	core::pose::Pose &	pose,
		core::select::residue_selector::ResidueSubset const &	selection,
		bool const	symmetric,
		bool const	tma_was_added
	)		const

private

Given a pose and a selection of three residues that connect to a TMA residue, update the positions of carbonyl oxygen and amide hydrogen atoms in the amide bonds connecting the TMA to the sidechains.

References update_tma_amide_bond_dependent_atoms_asymmetric(), and update_tma_amide_bond_dependent_atoms_symmetric().

Referenced by post_relax_round_update_steps(), and pre_relax_round_update_steps().

◆ update_tma_amide_bond_dependent_atoms_asymmetric()

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

private

Given a pose and a selection of three residues that connect to a TMA residue, update the positions of carbonyl oxygen and amide hydrogen atoms in the amide bonds connecting the TMA to the sidechains.

Version for asymmetric poses.

References core::pose::Pose::conformation(), get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), core::pose::symmetry::is_symmetric(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), core::pose::Pose::residue(), and core::conformation::Residue::residue_connection_conn_id().

Referenced by update_tma_amide_bond_dependent_atoms().

◆ update_tma_amide_bond_dependent_atoms_symmetric()

void protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_symmetric	(	core::pose::Pose &	pose,
		core::select::residue_selector::ResidueSubset const &	selection,
		bool const	tma_was_added
	)		const

private

Given a pose and a selection of three residues that connect to a TMA residue, update the positions of carbonyl oxygen and amide hydrogen atoms in the amide bonds connecting the TMA to the sidechains.

Version for symmetric poses.

References core::pose::Pose::conformation(), get_linker_indices_symmetric(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), core::pose::symmetry::is_symmetric(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_conn_id(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count(), and protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type().

Referenced by update_tma_amide_bond_dependent_atoms().

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

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

Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TMA_Helper() [1/2]

◆ TMA_Helper() [2/2]

◆ ~TMA_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()

◆ add_sidechain_conjugation()

◆ filter_by_constraints_energy_asymmetric()

◆ filter_by_constraints_energy_symmetric()

◆ filter_by_sidechain_distance_asymmetric()

◆ filter_by_sidechain_distance_symmetric()

◆ get_last_sidechain_carbon_name()

◆ get_linker_index_asymmetric()

◆ get_linker_indices_symmetric()

◆ get_max_sidechain_length()

◆ get_sidechain_amide_name()

◆ get_sidechain_connect_index()

◆ helper_adds_linker_residue()

◆ is_allowed_residue_type()

◆ list_allowed_residue_types()

◆ place_tma_asymmetric()

◆ place_tma_symmetric()

◆ post_relax_round_update_steps()

◆ pre_relax_round_update_steps()

◆ provide_citation_info()

◆ update_tma_amide_bond_dependent_atoms()

◆ update_tma_amide_bond_dependent_atoms_asymmetric()

◆ update_tma_amide_bond_dependent_atoms_symmetric()