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

#include <Metal_HelperBase.hh>

Inheritance diagram for protocols::cyclic_peptide::crosslinker::Metal_HelperBase:

[legend]

Public Member Functions
	Metal_HelperBase (std::string const &metal_name_in="Zn")
	Default constructor. More...

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

	~Metal_HelperBase () override
	Destructor (important for properly forward-declaring smart-pointer members) 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 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 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 exactly three 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 exactly three 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 four 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 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 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...

void	set_metal_type_from_name (std::string const &name_in)
	Given a metal name, set the type. More...

std::string	metal_type_string () const
	Get the current metal type, as a string. 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...

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

Protected Member Functions
virtual void	check_residue_indices_valid (utility::vector1< core::Size > const &indices, core::pose::Pose const &pose) const =0
	Check that the correct number of residues have been selected, that they are within the pose, and that they are allowed residue types. More...

virtual bool	is_allowed_type (core::chemical::ResidueType const &type) const =0
	Given a residue type, check whether it's an allowed residue type for tetrahedrally coordinating metals. More...

virtual void	add_angle_constraints (core::pose::Pose &pose, utility::vector1< core::Size > const &res_indices, core::Size const i, core::Size const j) const =0
	Given a pose, a list of residues, and indices i and j in that list, add angle constraints between the two residues specified. More...

virtual void	add_dihedral_constraints (core::pose::Pose &pose, utility::vector1< core::Size > const &res_indices) const
	Given a pose and a list of residues, add dihedral constraints (e.g. improper dihedrals to enforce planarity). More...

virtual core::Real const &	ideal_bond_length (Metal_HelperBase_Metal const metal_type, Metal_HelperBase_MetalLigand const ligand_type) const =0
	Given a metal type and a metal-liganding atom type, return the ideal bond length. More...

void	set_metal_bond_length (core::pose::Pose &pose, core::Size const res_index) const
	Given a pose and a residue with the VIRTUAL_METAL_CONJUGATION variant type already added, set the metal-metal liganding atom bond length appropriately for the metal in question. More...

Metal_HelperBase_MetalLigand	liganding_atom_from_restype (core::chemical::ResidueType const &restype) const
	Given a ResidueType with the VIRTUAL_METAL_CONJUGATION variant type already added, get the metal-liganding atom enum. More...

std::string	metal_type_string_from_enum (Metal_HelperBase_Metal const metal_type) const
	Given a metal type enum, return the corresponding string. More...

Metal_HelperBase_Metal	metal_type_enum_from_string (std::string const &metal_type_string) const
	Given a metal type string, return the corresponding enum. More...

virtual void	check_compatible_symmetry_type () const =0
	Check that the symmetry type is one of a few compatible types. More...

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...

Private Attributes
Metal_HelperBase_Metal	metal_type_
	The type of metal to add (Zn, Cu, etc.). More...

Detailed Description

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

Constructor & Destructor Documentation

◆ Metal_HelperBase() [1/2]

protocols::cyclic_peptide::crosslinker::Metal_HelperBase::Metal_HelperBase ( std::string const & metal_name_in = "Zn" )

Default constructor.

Constructors ///.

Default constructor

References set_metal_type_from_name().

◆ Metal_HelperBase() [2/2]

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

Copy constructor.

◆ ~Metal_HelperBase()

protocols::cyclic_peptide::crosslinker::Metal_HelperBase::~Metal_HelperBase ( )

override

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

Member Function Documentation

◆ add_angle_constraints()

virtual void protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_angle_constraints	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	res_indices,
		core::Size const	i,
		core::Size const	j
	)		const

protectedpure virtual

Given a pose, a list of residues, and indices i and j in that list, add angle constraints between the two residues specified.

Implemented in protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper, protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper, protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper, protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper, and protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper.

Referenced by add_linker_constraints_asymmetric(), and add_linker_constraints_symmetric().

◆ add_dihedral_constraints()

void protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_dihedral_constraints	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	res_indices
	)		const

protectedvirtual

Given a pose and a list of residues, add dihedral constraints (e.g. improper dihedrals to enforce planarity).

Private Methods ///.

Defaults to a function that does nothing. Can be overridden by derived classes.

Given a pose and a list of residues, add dihedral constraints (e.g. improper dihedrals to enforce planarity).

Defaults to a function that does nothing. Can be overridden by derived classes.

Reimplemented in protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper, protocols::cyclic_peptide::crosslinker::SquarePyramidalMetal_Helper, and protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper.

Referenced by add_linker_constraints_asymmetric(), and add_linker_constraints_symmetric().

◆ add_linker_asymmetric()

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

Public Methods ///.

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

Given a pose and a selection of four 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.

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

References core::pose::add_variant_type_to_pose_residue(), check_residue_indices_valid(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), set_metal_bond_length(), core::pose::Pose::update_residue_neighbors(), and core::chemical::VIRTUAL_METAL_CONJUGATION.

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::re_append_octahedral_metal_residues(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::re_append_square_planar_metal_residues(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::re_append_square_pyramidal_metal_residues(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::re_append_tetrahedral_metal_residues(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::re_append_trigonal_metal_residues().

◆ add_linker_bonds_asymmetric()

void protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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.

◆ add_linker_bonds_symmetric()

void protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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.

◆ add_linker_constraints_asymmetric()

void protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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 crosslinker, add constraints for the crosslinker.

Given a selection of four 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 add_angle_constraints(), add_dihedral_constraints(), protocols::cyclic_peptide::CreateDistanceConstraint::apply(), check_residue_indices_valid(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), protocols::hybridization::r1, protocols::hybridization::r2, and protocols::cyclic_peptide::CreateDistanceConstraint::set().

◆ add_linker_constraints_symmetric()

void protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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 crosslinker, add constraints for the crosslinker.

Given a selection of four residues that have already been connected to a crosslinker, add constraints for the crosslinker.

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

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

References add_angle_constraints(), add_dihedral_constraints(), protocols::cyclic_peptide::CreateDistanceConstraint::apply(), check_compatible_symmetry_type(), check_residue_indices_valid(), core::pose::Pose::conformation_ptr(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), core::pose::symmetry::is_symmetric(), protocols::hybridization::r1, protocols::hybridization::r2, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::selection_is_symmetric(), protocols::cyclic_peptide::CreateDistanceConstraint::set(), and protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected().

◆ add_linker_symmetric()

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

Given a pose and a selection of four 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.

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

References core::pose::add_variant_type_to_pose_residue(), check_compatible_symmetry_type(), check_residue_indices_valid(), core::pose::Pose::conformation_ptr(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), core::pose::symmetry::is_symmetric(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::selection_is_symmetric(), set_metal_bond_length(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected(), core::pose::Pose::update_residue_neighbors(), and core::chemical::VIRTUAL_METAL_CONJUGATION.

◆ check_compatible_symmetry_type()

virtual void protocols::cyclic_peptide::crosslinker::Metal_HelperBase::check_compatible_symmetry_type ( ) const

protectedpure virtual

Check that the symmetry type is one of a few compatible types.

Implemented in protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper, protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper, protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper, protocols::cyclic_peptide::crosslinker::SquarePyramidalMetal_Helper, protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper, and protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper.

Referenced by add_linker_constraints_symmetric(), add_linker_symmetric(), filter_by_constraints_energy_symmetric(), and filter_by_sidechain_distance_symmetric().

◆ check_residue_indices_valid()

virtual void protocols::cyclic_peptide::crosslinker::Metal_HelperBase::check_residue_indices_valid	(	utility::vector1< core::Size > const &	indices,
		core::pose::Pose const &	pose
	)		const

protectedpure virtual

Check that the correct number of residues have been selected, that they are within the pose, and that they are allowed residue types.

Implemented in protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper, protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper, protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper, protocols::cyclic_peptide::crosslinker::SquarePyramidalMetal_Helper, protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper, and protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper.

Referenced by add_linker_asymmetric(), add_linker_constraints_asymmetric(), add_linker_constraints_symmetric(), add_linker_symmetric(), filter_by_sidechain_distance_asymmetric(), and filter_by_sidechain_distance_symmetric().

◆ filter_by_constraints_energy_asymmetric()

bool protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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::Metal_HelperBase::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 check_compatible_symmetry_type(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::filter_by_constraints_energy(), core::pose::symmetry::is_symmetric(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::selection_is_symmetric(), and protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected().

◆ filter_by_sidechain_distance_asymmetric()

bool protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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 check_residue_indices_valid(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), MAX_CB_CB_DIST_SQ, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

◆ filter_by_sidechain_distance_symmetric()

bool protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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 check_compatible_symmetry_type(), check_residue_indices_valid(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices(), core::pose::symmetry::is_symmetric(), MAX_CB_CB_DIST_SQ, core::pose::Pose::residue(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::selection_is_symmetric(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected(), and core::conformation::Residue::xyz().

◆ get_linker_index_asymmetric()

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

overridevirtual

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.

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

◆ get_linker_indices_symmetric()

void protocols::cyclic_peptide::crosslinker::Metal_HelperBase::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.

Given indices of four 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.

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.

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

◆ helper_adds_linker_residue()

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

inlineoverridevirtual

Does this CrosslinkerMoverHelper add a residue for the linker?

No, it does not.

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

◆ ideal_bond_length()

virtual core::Real const& protocols::cyclic_peptide::crosslinker::Metal_HelperBase::ideal_bond_length	(	Metal_HelperBase_Metal const	metal_type,
		Metal_HelperBase_MetalLigand const	ligand_type
	)		const

protectedpure virtual

Given a metal type and a metal-liganding atom type, return the ideal bond length.

This method must be updated if either enum is expanded.

Implemented in protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper, protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper, protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper, protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper, and protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper.

Referenced by set_metal_bond_length().

◆ is_allowed_type()

virtual bool protocols::cyclic_peptide::crosslinker::Metal_HelperBase::is_allowed_type ( core::chemical::ResidueType const & type ) const

protectedpure virtual

Given a residue type, check whether it's an allowed residue type for tetrahedrally coordinating metals.

Returns "true" for pass (allowed type) and "false" for failure (prohibited type). Currently, allowed types are L- and D-histidine, L- or D-aspartate, L- or D-glutamate, L- or D-cysteine, L- or D-homocysteine, and the beta-3-amino acid equivalents.

Implemented in protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper, protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper, protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper, protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper, and protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper.

◆ liganding_atom_from_restype()

Metal_HelperBase_MetalLigand protocols::cyclic_peptide::crosslinker::Metal_HelperBase::liganding_atom_from_restype ( core::chemical::ResidueType const & restype ) const

protected

Given a ResidueType with the VIRTUAL_METAL_CONJUGATION variant type already added, get the metal-liganding atom enum.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_asp, core::chemical::aa_b3d, core::chemical::aa_b3e, core::chemical::aa_b3h, core::chemical::aa_das, core::chemical::aa_dgu, core::chemical::aa_dhi, core::chemical::aa_glu, core::chemical::aa_his, core::chemical::ResidueTypeBase::base_name(), core::chemical::ResidueType::is_sidechain_thiol(), protocols::cyclic_peptide::crosslinker::MHLigand_Nd_histidine, protocols::cyclic_peptide::crosslinker::MHLigand_Ne_histidine, protocols::cyclic_peptide::crosslinker::MHLigand_O_carboxyl, protocols::cyclic_peptide::crosslinker::MHLigand_S_cysteine, and protocols::cyclic_peptide::crosslinker::MHLigand_unknown_ligand.

Referenced by set_metal_bond_length().

◆ metal_type_enum_from_string()

Metal_HelperBase_Metal protocols::cyclic_peptide::crosslinker::Metal_HelperBase::metal_type_enum_from_string ( std::string const & metal_type_string ) const

protected

Given a metal type string, return the corresponding enum.

Returns MH_unknown_metal if the string is unrecognized.

References metal_type_string(), metal_type_string_from_enum(), protocols::cyclic_peptide::crosslinker::MH_end_of_list, and protocols::cyclic_peptide::crosslinker::MH_unknown_metal.

Referenced by set_metal_type_from_name().

◆ metal_type_string()

std::string protocols::cyclic_peptide::crosslinker::Metal_HelperBase::metal_type_string ( ) const

Get the current metal type, as a string.

References metal_type_, and metal_type_string_from_enum().

Referenced by metal_type_enum_from_string().

◆ metal_type_string_from_enum()

std::string protocols::cyclic_peptide::crosslinker::Metal_HelperBase::metal_type_string_from_enum ( Metal_HelperBase_Metal const metal_type ) const

protected

Given a metal type enum, return the corresponding string.

References protocols::cyclic_peptide::crosslinker::MH_Fe2, protocols::cyclic_peptide::crosslinker::MH_Ni2, protocols::cyclic_peptide::crosslinker::MH_unknown_metal, and protocols::cyclic_peptide::crosslinker::MH_Zn.

Referenced by protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper::ideal_bond_length(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::ideal_bond_length(), protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::ideal_bond_length(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::ideal_bond_length(), protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper::ideal_bond_length(), metal_type_enum_from_string(), and metal_type_string().

◆ set_metal_bond_length()

void protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_bond_length	(	core::pose::Pose &	pose,
		core::Size const	res_index
	)		const

protected

Given a pose and a residue with the VIRTUAL_METAL_CONJUGATION variant type already added, set the metal-metal liganding atom bond length appropriately for the metal in question.

Calls ideal_bond_length().

References core::chemical::ResidueType::atom_index(), core::chemical::ICoorAtomID::atomno(), core::chemical::ResidueType::icoor(), ideal_bond_length(), liganding_atom_from_restype(), metal_type_, protocols::cyclic_peptide::crosslinker::MHLigand_unknown_ligand, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::chemical::AtomICoor::stub_atom1(), and core::conformation::Residue::xyz().

Referenced by add_linker_asymmetric(), and add_linker_symmetric().

◆ set_metal_type_from_name()

void protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_type_from_name ( std::string const & name_in )

Given a metal name, set the type.

References metal_type_, metal_type_enum_from_string(), and protocols::cyclic_peptide::crosslinker::MH_unknown_metal.

Referenced by Metal_HelperBase(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::SquarePlanarMetal_Helper(), protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::TetrahedralMetal_Helper(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::TrigonalPlanarMetal_Helper(), and protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper::TrigonalPyramidalMetal_Helper().

Member Data Documentation

◆ metal_type_

Metal_HelperBase_Metal protocols::cyclic_peptide::crosslinker::Metal_HelperBase::metal_type_

private

The type of metal to add (Zn, Cu, etc.).

Determines ideal bond lengths for metal bonds.

Referenced by metal_type_string(), set_metal_bond_length(), and set_metal_type_from_name().

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

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

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Metal_HelperBase() [1/2]

◆ Metal_HelperBase() [2/2]

◆ ~Metal_HelperBase()

Member Function Documentation

◆ add_angle_constraints()

◆ add_dihedral_constraints()

◆ add_linker_asymmetric()

◆ add_linker_bonds_asymmetric()

◆ add_linker_bonds_symmetric()

◆ add_linker_constraints_asymmetric()

◆ add_linker_constraints_symmetric()

◆ add_linker_symmetric()

◆ check_compatible_symmetry_type()

◆ check_residue_indices_valid()

◆ 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()

◆ ideal_bond_length()

◆ is_allowed_type()

◆ liganding_atom_from_restype()

◆ metal_type_enum_from_string()

◆ metal_type_string()

◆ metal_type_string_from_enum()

◆ set_metal_bond_length()

◆ set_metal_type_from_name()

Member Data Documentation

◆ metal_type_