Rosetta
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper Class Referenceabstract

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

#include <CrosslinkerMoverHelper.hh>

Inheritance diagram for protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper:
Inheritance graph
[legend]

Public Member Functions

 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 add_linker_asymmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection) const =0
 Given a pose and a selection of residues, add the linker, align it crudely to the selected residues, and set up covalent bonds. More...
 
virtual void add_linker_bonds_asymmetric (core::pose::Pose &pose, utility::vector1< core::Size > const &res_indices, core::Size const linker_index) const =0
 Given a pose and a linker, add bonds between the linker and the residues that coordinate the linker. More...
 
virtual void add_linker_symmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection) const =0
 Given a pose and a selection of residues, add the linker, align it crudely to the selected residues, and set up covalent bonds. More...
 
virtual void add_linker_bonds_symmetric (core::pose::Pose &pose, core::Size const res1, core::Size const linker_index1, core::Size const linker_index2) const =0
 Given a pose and a linker, add bonds between the linker and the residues that coordinate the linker. More...
 
virtual void add_linker_constraints_asymmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection) const =0
 Given a selection of residues that have already been connected to a crosslinker, add constraints for the crosslinker. More...
 
virtual void add_linker_constraints_symmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, bool const linker_was_added) const =0
 Given a selection of residues that have already been connected to a crosslinker, add constraints for the crosslinker. More...
 
virtual core::Size get_linker_index_asymmetric (core::pose::Pose const &pose, utility::vector1< core::Size > const &res_indices) const =0
 Given indices of residues that are already linked to a linker, get the index of the linker. More...
 
virtual void get_linker_indices_symmetric (core::pose::Pose const &pose, utility::vector1< core::Size > const &res_indices, utility::vector1< core::Size > &linker_indices) const =0
 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...
 
virtual bool filter_by_sidechain_distance_asymmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, core::Real const &filter_multiplier) const =0
 Given a pose with residues selected to be linked by a linker, determine whether the residues are too far apart. More...
 
virtual bool filter_by_sidechain_distance_symmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, core::Real const &filter_multiplier) const =0
 Given a pose with residues selected to be linked by a linker, determine whether the residues are too far apart. More...
 
virtual bool filter_by_constraints_energy_asymmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, core::Real const &filter_multiplier) const =0
 Determine whether the sidechain-crosslinker system has too high a constraints score. More...
 
virtual 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 =0
 Determine whether the sidechain-crosslinker system has too high a constraints score. This version is for symmetric poses. More...
 
virtual bool helper_adds_linker_residue () const =0
 Does this CrosslinkerMoverHelper add a residue for the linker? 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 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

char symm_type_
 The symmetry type. More...
 
core::Size symm_count_
 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 base class for helper objects that the CrosslinkerMover uses to set up specific types of linkers.

Constructor & Destructor Documentation

◆ CrosslinkerMoverHelper() [1/2]

protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::CrosslinkerMoverHelper ( )

Default constructor.

Constructors ///.

Default constructor

◆ CrosslinkerMoverHelper() [2/2]

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

Copy constructor.

◆ ~CrosslinkerMoverHelper()

protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::~CrosslinkerMoverHelper ( )
overridedefault

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

Member Function Documentation

◆ add_linker_asymmetric()

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

Given a pose and a selection of residues, add the linker, align it crudely to the selected residues, and set up covalent bonds.

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

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ add_linker_bonds_asymmetric()

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

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.

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ add_linker_bonds_symmetric()

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

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.

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ add_linker_constraints_asymmetric()

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

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.

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

Referenced by filter_by_constraints_energy().

◆ add_linker_constraints_symmetric()

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

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

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

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

Referenced by filter_by_constraints_energy().

◆ add_linker_symmetric()

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

Given a pose and a selection of residues, add the linker, align it crudely to the selected residues, and set up covalent bonds.

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

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ filter_by_constraints_energy()

bool protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::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
protectedvirtual

Determine whether the sidechain-crosslinker system has too high a constraints score. Both the symmetric and asymmetric versions call this code.

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

References add_linker_constraints_asymmetric(), add_linker_constraints_symmetric(), core::scoring::angle_constraint, protocols::constraint_movers::ClearConstraintsMover::apply(), core::scoring::atom_pair_constraint, core::scoring::dihedral_constraint, core::pose::Pose::energies(), core::scoring::Energies::total_energy(), and protocols::cyclic_peptide::TR().

Referenced by protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::filter_by_constraints_energy_asymmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_constraints_energy_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_constraints_energy_asymmetric(), protocols::cyclic_peptide::crosslinker::Thioether_Helper::filter_by_constraints_energy_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_constraints_energy_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::filter_by_constraints_energy_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_constraints_energy_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_constraints_energy_symmetric(), protocols::cyclic_peptide::crosslinker::Thioether_Helper::filter_by_constraints_energy_symmetric(), and protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_constraints_energy_symmetric().

◆ filter_by_constraints_energy_asymmetric()

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

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.

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ filter_by_constraints_energy_symmetric()

virtual bool protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::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
pure virtual

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.

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ filter_by_sidechain_distance_asymmetric()

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

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.

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ filter_by_sidechain_distance_symmetric()

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

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.

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ get_linker_index_asymmetric()

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

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

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

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ get_linker_indices_symmetric()

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

Given indices of residues that are already linked to pieces of a linker, get of the indices of the symmetric pieces of the linker.

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

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ get_sidechain_indices()

void protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::get_sidechain_indices ( core::select::residue_selector::ResidueSubset const &  selection,
utility::vector1< core::Size > &  res_indices 
) const
virtual

Given a ResidueSubset with N residues selected, pull out the indices into a vector.

Overwrites res_indices.

Referenced by protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_sidechain_distance_symmetric(), selection_is_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_asymmetric(), and protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_symmetric().

◆ helper_adds_linker_residue()

virtual bool protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::helper_adds_linker_residue ( ) const
pure virtual

Does this CrosslinkerMoverHelper add a residue for the linker?

Implemented in protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::Metal_HelperBase, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ post_relax_round_update_steps()

void protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::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
virtual

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

Defaults to doing nothing; can be overriden. (One example is the TMA helper, which uses this to update amide bond-dependent atom positions).

Reimplemented in protocols::cyclic_peptide::crosslinker::TMA_Helper.

◆ pre_relax_round_update_steps()

void protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::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
virtual

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

Defaults to doing nothing; can be overriden. (One example is the TMA helper, which uses this to update amide bond-dependent atom positions).

Reimplemented in protocols::cyclic_peptide::crosslinker::TMA_Helper.

◆ provide_citation_info()

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

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

Public Methods ///.

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

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

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

Reimplemented in protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper, protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper, protocols::cyclic_peptide::crosslinker::TMA_Helper, protocols::cyclic_peptide::crosslinker::Thioether_Helper, protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper, protocols::cyclic_peptide::crosslinker::TBMB_Helper, protocols::cyclic_peptide::crosslinker::SquarePyramidalMetal_Helper, protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper, protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper, and protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper.

◆ selection_is_symmetric()

bool protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::selection_is_symmetric ( core::select::residue_selector::ResidueSubset const &  selection,
core::pose::Pose const &  pose,
core::Size const  expected_subunit_count 
) const
virtual

Determine whether a selection is symmetric.

Returns true if and only if (a) the pose is symmetric, (b) there are the expected number of symmetry copies, and (c) the selected residues are equivalent residues in different symmetry copies. Note that, ideally, I'd like to test for CN or SN symmetry, but this is as close as was feasible.

Note
Can be overriden.

References core::pose::Pose::conformation_ptr(), and get_sidechain_indices().

Referenced by protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_constraints_energy_symmetric(), and protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_sidechain_distance_symmetric().

◆ set_symmetry()

void protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::set_symmetry ( char const  symm_type_in,
core::Size const  symm_count_in 
)

Set the symmetry for this crosslinker helper.

References symm_count_, and symm_type_.

◆ symm_count()

core::Size protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count ( ) const
inlineprotected

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.

References symm_count_.

Referenced by protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_bonds_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_bonds_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper::check_compatible_symmetry_type(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::check_compatible_symmetry_type(), protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::check_compatible_symmetry_type(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::check_compatible_symmetry_type(), protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper::check_compatible_symmetry_type(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::confirm_symmetry(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_constraints_energy_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_constraints_energy_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_indices_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_indices_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_symmetric(), symm_subunits_expected(), and protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_symmetric().

◆ symm_subunits_expected()

core::Size protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_subunits_expected ( ) const

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

References symm_count(), and symm_type().

Referenced by protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_constraints_energy_symmetric(), and protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_sidechain_distance_symmetric().

◆ symm_type()

char protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type ( ) const
inlineprotected

Get the symmetry type.

'C' for cylic, 'S' for mirror cyclic, 'D' for dihedral, 'A' for asymmetric.

Note
'A' (asymmetric) by default.

References symm_type_.

Referenced by protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_bonds_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_bonds_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper::check_compatible_symmetry_type(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::check_compatible_symmetry_type(), protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::check_compatible_symmetry_type(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::check_compatible_symmetry_type(), protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper::check_compatible_symmetry_type(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::confirm_symmetry(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_constraints_energy_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_constraints_energy_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_indices_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_indices_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_symmetric(), symm_subunits_expected(), and protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_symmetric().

Member Data Documentation

◆ symm_count_

core::Size protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_count_
private

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.

Referenced by set_symmetry(), and symm_count().

◆ symm_type_

char protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::symm_type_
private

The symmetry type.

'C' for cylic, 'S' for mirror cyclic, 'D' for dihedral, 'A' for asymmetric.

Note
'A' (asymmetric) by default.

Referenced by set_symmetry(), and symm_type().

The documentation for this class was generated from the following files:
Generated on Mon Sep 4 2023 10:56:42 for Rosetta by doxygen 1.9.1