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protocols::cyclic_peptide::crosslinker::TBMB_Helper Class Reference

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

#include <TBMB_Helper.hh>

Inheritance diagram for protocols::cyclic_peptide::crosslinker::TBMB_Helper:
Inheritance graph
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Public Member Functions

 TBMB_Helper ()
 Default constructor. More...
 
 TBMB_Helper (TBMB_Helper const &src)
 Copy constructor. More...
 
 ~TBMB_Helper () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
void add_linker_asymmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection) const override
 Given a pose and a selection of exactly three residues, add the TBMB linker, align it crudely to the selected residues, and set up covalent bonds. More...
 
void add_linker_bonds_asymmetric (core::pose::Pose &pose, utility::vector1< core::Size > const &res_indices, core::Size const linker_index) const override
 Given a pose and a linker, add bonds between the linker and the residues that coordinate the linker. More...
 
void add_linker_symmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection) const override
 Given a pose and a selection of exactly three residues, add the TBMB linker, align it crudely to the selected residues, and set up covalent bonds. More...
 
void add_linker_bonds_symmetric (core::pose::Pose &pose, core::Size const res1, core::Size const linker_index1, core::Size const linker_index2) const override
 Given a pose and a linker, add bonds between the TBMB linker and the residues that coordinate the linker. More...
 
void add_linker_constraints_asymmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection) const override
 Given a selection of exactly three residues that have already been connected to a 1,3,5-tris(bromomethyl)benzene crosslinker, add constraints for the crosslinker. More...
 
void add_linker_constraints_symmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, bool const linker_was_added) const override
 Given a selection of exactly three residues that have already been connected to a 1,3,5-tris(bromomethyl)benzene crosslinker, add constraints for the crosslinker. This version is for symmetric poses. More...
 
core::Size get_linker_index_asymmetric (core::pose::Pose const &pose, utility::vector1< core::Size > const &res_indices) const override
 Given indices of three cysteine residues that are already linked to a TBMB, get the index of the TBMB residue. More...
 
void get_linker_indices_symmetric (core::pose::Pose const &pose, utility::vector1< core::Size > const &res_indices, utility::vector1< core::Size > &linker_indices) const override
 Given indices of three cysteine residues that are already linked to pieces of a linker, get of the indices of the symmetric pieces of the linker. More...
 
bool filter_by_sidechain_distance_asymmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, core::Real const &filter_multiplier) const override
 Given a pose with residues selected to be linked by a 1,3,5-tris(bromomethyl)benzene crosslinker, determine whether the residues are too far apart. More...
 
bool filter_by_sidechain_distance_symmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, core::Real const &filter_multiplier) const override
 Given a pose with residues selected to be linked by a 1,3,5-tris(bromomethyl)benzene crosslinker, determine whether the residues are too far apart. This version is for symmetric poses. More...
 
bool filter_by_constraints_energy_asymmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, core::Real const &filter_multiplier) const override
 Determine whether the sidechain-crosslinker system has too high a constraints score. More...
 
bool filter_by_constraints_energy_symmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, bool const linker_was_added, core::Real const &filter_multiplier) const override
 Determine whether the sidechain-crosslinker system has too high a constraints score. This version is for symmetric poses. More...
 
bool helper_adds_linker_residue () const override
 Does this CrosslinkerMoverHelper add a residue for the linker? More...
 
- Public Member Functions inherited from protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper
 CrosslinkerMoverHelper ()
 Default constructor. More...
 
 CrosslinkerMoverHelper (CrosslinkerMoverHelper const &src)
 Copy constructor. More...
 
 ~CrosslinkerMoverHelper () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
void set_symmetry (char const symm_type_in, core::Size const symm_count_in)
 Set the symmetry for this crosslinker helper. More...
 
virtual bool adds_crosslinker_residue () const
 Does this helper add a residue to the pose? More...
 
virtual void get_sidechain_indices (core::select::residue_selector::ResidueSubset const &selection, utility::vector1< core::Size > &res_indices) const
 Given a ResidueSubset with N residues selected, pull out the indices into a vector. More...
 
virtual bool selection_is_symmetric (core::select::residue_selector::ResidueSubset const &selection, core::pose::Pose const &pose, core::Size const expected_subunit_count) const
 Determine whether a selection is symmetric. More...
 
virtual void pre_relax_round_update_steps (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, bool const whole_structure, bool const symmetric, bool const linker_was_added) const
 Optional steps that the helper can apply before every relaxation round. More...
 
virtual void post_relax_round_update_steps (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, bool const whole_structure, bool const symmetric, bool const linker_was_added) const
 Optional steps that the helper can apply after every relaxation round. More...
 
core::Size symm_subunits_expected () const
 Get the number of expected symmetry subunits, given the symmetry type. More...
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper
virtual bool filter_by_constraints_energy (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, bool const symmetric, bool const linker_was_added, core::Real const &filter_multiplier) const
 Determine whether the sidechain-crosslinker system has too high a constraints score. Both the symmetric and asymmetric versions call this code. More...
 
char symm_type () const
 Get the symmetry type. More...
 
core::Size symm_count () const
 Get the symmetry copy count. For example, symm_type_='C' and symm_count_=3 would specify C3 symmetry. A value of 1 means asymmetry. 1 by default. More...
 

Detailed Description

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

Constructor & Destructor Documentation

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

Default constructor.

Constructors ///.

Default constructor

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

Copy constructor.

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

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

Member Function Documentation

void protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection 
) const
overridevirtual
void protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_bonds_asymmetric ( core::pose::Pose pose,
utility::vector1< core::Size > const &  res_indices,
core::Size const  linker_index 
) const
overridevirtual

Given a pose and a linker, add bonds between the linker and the residues that coordinate the linker.

Called by add_linker_asymmetric(). Version for asymmetric poses.

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

References protocols::cyclic_peptide::DeclareBond::set().

Referenced by add_linker_asymmetric().

void protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_bonds_symmetric ( core::pose::Pose pose,
core::Size const  res1,
core::Size const  linker_index1,
core::Size const  linker_index2 
) const
overridevirtual
void protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_asymmetric ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection 
) const
overridevirtual
void protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_constraints_symmetric ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection,
bool const  linker_was_added 
) const
overridevirtual
void protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection 
) const
overridevirtual
bool protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_constraints_energy_asymmetric ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  selection,
core::Real const &  filter_multiplier 
) const
overridevirtual

Determine whether the sidechain-crosslinker system has too high a constraints score.

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

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

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

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

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

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

Determine whether the sidechain-crosslinker system has too high a constraints score. This version is for symmetric poses.

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

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

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

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

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

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

Given a pose with residues selected to be linked by a 1,3,5-tris(bromomethyl)benzene crosslinker, determine whether the residues are too far apart.

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

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

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

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

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

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

Given a pose with residues selected to be linked by a 1,3,5-tris(bromomethyl)benzene crosslinker, determine whether the residues are too far apart. This version is for symmetric poses.

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

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

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

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

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

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

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

Given indices of three cysteine residues that are already linked to a TBMB, get the index of the TBMB residue.

Throws an error if the three cysteines are not all linked to the same TBMB residue.

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

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

Referenced by add_linker_constraints_asymmetric().

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

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

Throws an error if a residue is not linked to something.

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

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

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

Referenced by add_linker_constraints_symmetric().

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

Does this CrosslinkerMoverHelper add a residue for the linker?

Yes, it does.

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


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