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protocols::cyclic_peptide::crosslinker::TMA_Helper Class Reference

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:
Inheritance graph
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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 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 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...
 
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

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

Default constructor.

Constructors ///.

Default constructor

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

Copy constructor.

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

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

Member Function Documentation

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.

Public Methods ///.

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().

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 get_sidechain_amide_name(), core::pose::Pose::residue_type(), and protocols::cyclic_peptide::DeclareBond::set().

Referenced by add_linker_asymmetric().

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
void protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_constraints_asymmetric ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection 
) const
overridevirtual
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
void protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_symmetric ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection 
) const
overridevirtual
void protocols::cyclic_peptide::crosslinker::TMA_Helper::add_sidechain_conjugation ( core::pose::Pose pose,
core::Size const  position 
) const
private
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().

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().

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().

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().

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().

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().

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().

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().

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().

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

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().

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().

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

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().

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().

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().

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

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