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protocols::cyclic_peptide::CrosslinkerMover Class Reference

This mover links two or more residues with a (possibly symmetric) cross-linker. It adds the crosslinker, sets up constraints, optionally packs and energy-mimizes it into place (packing/minimizing only the crosslinker and the side-chains to which it connects), and then optionally relaxes the whole structure. More...

#include <CrosslinkerMover.hh>

Inheritance diagram for protocols::cyclic_peptide::CrosslinkerMover:
Inheritance graph
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Public Member Functions

 CrosslinkerMover ()
 Constructors ///. More...
 
 CrosslinkerMover (CrosslinkerMover const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~CrosslinkerMover () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
 
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
 
std::string get_name () const override
 Get the name of the Mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Rosetta Scripts Support ///. More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
 Set the residue selector to use. More...
 
core::select::residue_selector::ResidueSelectorCOP residue_selector () const
 Get the residue selector that this mover uses. More...
 
void set_linker_name (std::string const &name_in)
 Set the linker name. More...
 
std::string linker_name () const
 Get the linker name. More...
 
void set_behaviour (bool const add_linker, bool const constrain_linker, bool const pack_and_minimize_linker_and_sidechains, bool const do_final_fastrelax)
 Set the behaviour of this mover. More...
 
void set_filter_behaviour (bool const filter_by_sidechain_distance, bool const filter_by_constraints_energy, bool const filter_by_total_score, core::Real const &filter_by_total_score_cutoff_energy, core::Real const &sidechain_distance_filter_multiplier, core::Real const &constraints_energy_filter_multiplier)
 Set the filtering behaviour of this mover. More...
 
bool add_linker () const
 Get whether we're adding the linker. More...
 
bool constrain_linker () const
 Get whether we're adding the linker constraints. More...
 
bool pack_and_minimize_linker_and_sidechains () const
 Get whether we're packing and minimizing the linker and the side-chains to which it is connected. More...
 
bool do_final_fastrelax () const
 Get whether we're doing a final FastRelax on the whole structure. More...
 
void set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
 Set the scorefunction to use for packing and minimization. More...
 
core::scoring::ScoreFunctionCOP scorefxn () const
 Get the scorefunction to use for packing and minimization. More...
 
void set_sidechain_frlx_rounds (core::Size const rounds_in)
 Set the number of rounds of FastRelax to apply when minimizing the linker and the side-chains that connect to it. More...
 
void set_final_frlx_rounds (core::Size const rounds_in)
 Set the number of rounds of FastRelax to apply at the end. More...
 
core::Size sidechain_frlx_rounds () const
 Get the number of rounds of FastRelax to apply when minimizing the linker and the side-chains that connect to it. More...
 
core::Size final_frlx_rounds () const
 Get the number of rounds of FastRelax to apply at the end. More...
 
void set_symmetry (std::string const &symmetry_in)
 Parse a string with a symmetry type (e.g. "C3") and set the symmetry accordingly. More...
 
void set_symm_type (char const type_in)
 Set the symmety type. More...
 
void set_symm_count (signed int const count_in)
 Set the symmetry copy count. More...
 
char symm_type () const
 Get the symmetry type. More...
 
core::Size symm_count () const
 Get the symmetry copy count. More...
 
void set_metal_type (std::string const &metal_in)
 For metal-mediated crosslinkers, set what metal mediates the crosslink. More...
 
std::string const & metal_type () const
 For metal-mediated crosslinkers, what metal mediates the crosslink? More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string get_crosslinker_name (CrossLinker const crosslinker)
 Given a CrossLinker enum, get its name. More...
 
static CrossLinker get_crosslinker_enum (std::string const &name)
 Given a CrossLinker name, get its enum. More...
 
static std::string class_name ()
 Show the contents of the Mover. More...
 
static std::string mover_name ()
 Returns the name of this Mover. More...
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 Provide information on what options are available in XML tag. More...
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Member Functions

void symmetric_apply (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP helper)
 Apply the mover to a symmetric pose. More...
 
bool filter_by_sidechain_distance_symmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP helper) const
 Determine whether the residues to be crosslinked are too far apart. This version is for symmetric poses. More...
 
bool filter_by_constraints_energy_symmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP helper, bool const linker_was_added) const
 Determine whether the sidechain-crosslinker system has too high a constraints score. This version is for symmetric poses. More...
 
void add_linker_symmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP helper) const
 Given a selection of residues, add a crosslinker, align it crudely to the selected residues, and set up covalent bonds. This version is for symmetric poses. More...
 
void add_linker_constraints_symmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP helper, bool const linker_was_added) const
 Given a selection of residues that have already been connected to a crosslinker, add constraints for the crosslinker. This version is for symmetric poses. More...
 
void asymmetric_apply (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP helper)
 Apply the mover to an asymmetric pose. More...
 
bool filter_by_sidechain_distance_asymmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP helper) const
 Determine whether the residues to be crosslinked are too far apart. More...
 
bool filter_by_constraints_energy_asymmetric (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &selection, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP helper) const
 Determine whether the sidechain-crosslinker system has too high a constraints score. More...
 
bool filter_by_total_score (core::pose::Pose const &pose) const
 Determine whether the overall system has too high an overall score (including constraints) at the end of the protocol. More...
 
void add_linker_asymmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP helper) const
 Given a selection of residues, add a crosslinker, align it crudely to the selected residues, and set up covalent bonds. More...
 
void add_linker_constraints_asymmetric (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP helper) const
 Given a selection of residues that have already been connected to a crosslinker, add constraints for the crosslinker. More...
 
void pack_and_minimize_linker_and_sidechains (core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &selection, protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP helper, bool const whole_structure, bool const symmetric) const
 Repack and minimize the sidechains. More...
 
bool filter_by_sidechain_distance () const
 Are we filtering by sidechain distance before placing the linker? More...
 
bool filter_by_constraints_energy () const
 Are we filtering by constraints energy after placing and minimizing the linker? More...
 
bool filter_by_total_score () const
 Are we filtering by total score plus constraints energy at the end of the protocol? More...
 
core::Real const & filter_by_total_score_cutoff_energy () const
 The cutoff energy to use, if we're filtering by the total score plus constraints energy at the end of the protocol. More...
 
core::Real const & sidechain_distance_filter_multiplier () const
 The distance filter multiplier. More...
 
core::Real const & constraints_energy_filter_multiplier () const
 The constraints energy filter multiplier. More...
 
core::Size get_jump_index_for_crosslinker (core::pose::Pose const &pose, core::Size const linker_index) const
 Given a pose and the index of a crosslinker, figure out the jump in the foldtree that moves the crosslinker. More...
 
void get_jump_indices_for_symmetric_crosslinker (core::pose::Pose const &pose, utility::vector1< core::Size > const &linker_indices_in, utility::vector1< core::Size > &jump_indices_out) const
 Given a pose and the indices of the pieces of a symmetric crosslinker, figure out the jumps in the foldtree that move the crosslinker. More...
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP residue_selector_
 A residue selector to select residues to cross-link. More...
 
CrossLinker linker_
 The crosslinker to use. More...
 
bool add_linker_
 Should we add the linker? More...
 
bool constrain_linker_
 Should we set up constraints for the linker? More...
 
bool pack_and_minimize_linker_and_sidechains_
 Should we pack and minimize the linker and the side-chains to which it connects? More...
 
bool do_final_fastrelax_
 Should we FastRelax the whole structure? More...
 
core::scoring::ScoreFunctionCOP sfxn_
 The scorefunction to use for packing and minimization. More...
 
core::Size sidechain_frlx_rounds_
 The number of rounds of FastRelax to apply when packing and minimizing side-chains and the linker. More...
 
core::Size final_frlx_rounds_
 The number of rounds of FastRelax to apply at the end of the protocol. More...
 
bool filter_by_sidechain_distance_
 Should we filter based on initial distance between residues that are to be linked? More...
 
bool filter_by_constraints_energy_
 Should we filter based on constraints energy after the initial minimization of the linker? More...
 
bool filter_by_total_score_
 Should we filter by total score (including constraints energy) at the end? More...
 
core::Real filter_by_total_score_cutoff_energy_
 If we're filtering by total score, this is the cutoff energy. More...
 
core::Real sidechain_distance_filter_multiplier_
 Multiplier to affect stringency of sidechain distance filter. Higher values are more permissive. More...
 
core::Real constraints_energy_filter_multiplier_
 Multiplier to affect stringency of constraints energy filter. Higher values are more permissive. More...
 
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...
 
std::string metal_type_
 For metal-mediated crosslinkers, what metal mediates the crosslink? More...
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Detailed Description

This mover links two or more residues with a (possibly symmetric) cross-linker. It adds the crosslinker, sets up constraints, optionally packs and energy-mimizes it into place (packing/minimizing only the crosslinker and the side-chains to which it connects), and then optionally relaxes the whole structure.

Constructor & Destructor Documentation

protocols::cyclic_peptide::CrosslinkerMover::CrosslinkerMover ( )

Constructors ///.

Default constructor

protocols::cyclic_peptide::CrosslinkerMover::CrosslinkerMover ( CrosslinkerMover const &  src)
default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::cyclic_peptide::CrosslinkerMover::~CrosslinkerMover ( )
overridedefault

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

Member Function Documentation

bool protocols::cyclic_peptide::CrosslinkerMover::add_linker ( ) const
inline

Get whether we're adding the linker.

References add_linker_.

Referenced by asymmetric_apply(), pack_and_minimize_linker_and_sidechains(), parse_my_tag(), set_behaviour(), and symmetric_apply().

void protocols::cyclic_peptide::CrosslinkerMover::add_linker_asymmetric ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection,
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP  helper 
) const
private

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

Referenced by asymmetric_apply().

void protocols::cyclic_peptide::CrosslinkerMover::add_linker_constraints_asymmetric ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection,
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP  helper 
) const
private

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

Referenced by asymmetric_apply().

void protocols::cyclic_peptide::CrosslinkerMover::add_linker_constraints_symmetric ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection,
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP  helper,
bool const  linker_was_added 
) const
private

Given a selection of residues that have already been connected to a crosslinker, add constraints for the crosslinker. This version is for symmetric poses.

Referenced by symmetric_apply().

void protocols::cyclic_peptide::CrosslinkerMover::add_linker_symmetric ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection,
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP  helper 
) const
private

Given a selection of residues, add a crosslinker, align it crudely to the selected residues, and set up covalent bonds. This version is for symmetric poses.

Referenced by symmetric_apply().

void protocols::cyclic_peptide::CrosslinkerMover::apply ( core::pose::Pose pose)
overridevirtual
void protocols::cyclic_peptide::CrosslinkerMover::asymmetric_apply ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection,
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP  helper 
)
private
std::string protocols::cyclic_peptide::CrosslinkerMover::class_name ( )
static

Show the contents of the Mover.

Referenced by get_name(), and protocols::cyclic_peptide::CrosslinkerMoverCreator::keyname().

protocols::moves::MoverOP protocols::cyclic_peptide::CrosslinkerMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Referenced by filter_by_total_score(), and pack_and_minimize_linker_and_sidechains().

bool protocols::cyclic_peptide::CrosslinkerMover::constrain_linker ( ) const
inline

Get whether we're adding the linker constraints.

References constrain_linker_.

Referenced by asymmetric_apply(), parse_my_tag(), set_behaviour(), and symmetric_apply().

core::Real const& protocols::cyclic_peptide::CrosslinkerMover::constraints_energy_filter_multiplier ( ) const
inlineprivate
bool protocols::cyclic_peptide::CrosslinkerMover::do_final_fastrelax ( ) const
inline

Get whether we're doing a final FastRelax on the whole structure.

References do_final_fastrelax_.

Referenced by asymmetric_apply(), parse_my_tag(), set_behaviour(), and symmetric_apply().

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_constraints_energy ( ) const
inlineprivate

Are we filtering by constraints energy after placing and minimizing the linker?

References filter_by_constraints_energy_.

Referenced by asymmetric_apply(), parse_my_tag(), set_filter_behaviour(), and symmetric_apply().

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_constraints_energy_asymmetric ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  selection,
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP  helper 
) const
private

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.

References constraints_energy_filter_multiplier().

Referenced by asymmetric_apply().

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_constraints_energy_symmetric ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  selection,
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP  helper,
bool const  linker_was_added 
) const
private

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.

References constraints_energy_filter_multiplier().

Referenced by symmetric_apply().

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_sidechain_distance ( ) const
inlineprivate

Are we filtering by sidechain distance before placing the linker?

References filter_by_sidechain_distance_.

Referenced by asymmetric_apply(), parse_my_tag(), set_filter_behaviour(), and symmetric_apply().

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_sidechain_distance_asymmetric ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  selection,
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP  helper 
) const
private

Determine whether the residues to be crosslinked are too far apart.

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

References sidechain_distance_filter_multiplier().

Referenced by asymmetric_apply().

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_sidechain_distance_symmetric ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  selection,
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP  helper 
) const
private

Determine whether the residues to be crosslinked are too far apart. This version is for symmetric poses.

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

References sidechain_distance_filter_multiplier().

Referenced by symmetric_apply().

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_total_score ( core::pose::Pose const &  pose) const
private

Determine whether the overall system has too high an overall score (including constraints) at the end of the protocol.

Returns TRUE for failure (too high an overall score) and FALSE for success.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, clone(), core::scoring::dihedral_constraint, core::pose::Pose::energies(), filter_by_total_score_cutoff_energy(), scorefxn(), core::scoring::Energies::total_energy(), and protocols::cyclic_peptide::TR().

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_total_score ( ) const
inlineprivate

Are we filtering by total score plus constraints energy at the end of the protocol?

References filter_by_total_score_.

Referenced by asymmetric_apply(), parse_my_tag(), set_filter_behaviour(), and symmetric_apply().

core::Real const& protocols::cyclic_peptide::CrosslinkerMover::filter_by_total_score_cutoff_energy ( ) const
inlineprivate

The cutoff energy to use, if we're filtering by the total score plus constraints energy at the end of the protocol.

References filter_by_total_score_cutoff_energy_.

Referenced by filter_by_total_score(), parse_my_tag(), and set_filter_behaviour().

core::Size protocols::cyclic_peptide::CrosslinkerMover::final_frlx_rounds ( ) const
inline

Get the number of rounds of FastRelax to apply at the end.

References final_frlx_rounds_.

Referenced by pack_and_minimize_linker_and_sidechains(), and parse_my_tag().

moves::MoverOP protocols::cyclic_peptide::CrosslinkerMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

CrossLinker protocols::cyclic_peptide::CrosslinkerMover::get_crosslinker_enum ( std::string const &  name)
static
std::string protocols::cyclic_peptide::CrosslinkerMover::get_crosslinker_name ( CrossLinker const  crosslinker)
static
core::Size protocols::cyclic_peptide::CrosslinkerMover::get_jump_index_for_crosslinker ( core::pose::Pose const &  pose,
core::Size const  linker_index 
) const
private

Given a pose and the index of a crosslinker, figure out the jump in the foldtree that moves the crosslinker.

Throws an error if the foldtree isn't set up so that a unique jump moves the crosslinker.

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), and core::pose::Pose::total_residue().

Referenced by pack_and_minimize_linker_and_sidechains().

void protocols::cyclic_peptide::CrosslinkerMover::get_jump_indices_for_symmetric_crosslinker ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  linker_indices_in,
utility::vector1< core::Size > &  jump_indices_out 
) const
private

Given a pose and the indices of the pieces of a symmetric crosslinker, figure out the jumps in the foldtree that move the crosslinker.

Throws an error if the foldtree isn't set up so that a unique jump moves the crosslinker.

References core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::get_jump_that_builds_residue().

Referenced by pack_and_minimize_linker_and_sidechains().

std::string protocols::cyclic_peptide::CrosslinkerMover::get_name ( ) const
overridevirtual

Get the name of the Mover.

Implements protocols::moves::Mover.

References class_name().

std::string protocols::cyclic_peptide::CrosslinkerMover::linker_name ( ) const

Get the linker name.

References get_crosslinker_name(), and linker_.

std::string const& protocols::cyclic_peptide::CrosslinkerMover::metal_type ( ) const
inline

For metal-mediated crosslinkers, what metal mediates the crosslink?

References metal_type_.

Referenced by apply().

std::string protocols::cyclic_peptide::CrosslinkerMover::mover_name ( )
static

Returns the name of this Mover.

Referenced by provide_xml_schema().

bool protocols::cyclic_peptide::CrosslinkerMover::pack_and_minimize_linker_and_sidechains ( ) const
inline

Get whether we're packing and minimizing the linker and the side-chains to which it is connected.

References pack_and_minimize_linker_and_sidechains_.

Referenced by asymmetric_apply(), parse_my_tag(), set_behaviour(), and symmetric_apply().

void protocols::cyclic_peptide::CrosslinkerMover::pack_and_minimize_linker_and_sidechains ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection,
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP  helper,
bool const  whole_structure,
bool const  symmetric 
) const
private
void protocols::cyclic_peptide::CrosslinkerMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
void protocols::cyclic_peptide::CrosslinkerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::CrosslinkerMover::residue_selector ( ) const
inline

Get the residue selector that this mover uses.

References residue_selector_.

Referenced by apply(), and parse_my_tag().

core::scoring::ScoreFunctionCOP protocols::cyclic_peptide::CrosslinkerMover::scorefxn ( ) const

Get the scorefunction to use for packing and minimization.

References sfxn_.

Referenced by apply(), filter_by_total_score(), and pack_and_minimize_linker_and_sidechains().

void protocols::cyclic_peptide::CrosslinkerMover::set_behaviour ( bool const  add_linker,
bool const  constrain_linker,
bool const  pack_and_minimize_linker_and_sidechains,
bool const  do_final_fastrelax 
)
void protocols::cyclic_peptide::CrosslinkerMover::set_filter_behaviour ( bool const  filter_by_sidechain_distance,
bool const  filter_by_constraints_energy,
bool const  filter_by_total_score,
core::Real const &  filter_by_total_score_cutoff_energy,
core::Real const &  sidechain_distance_filter_multiplier,
core::Real const &  constraints_energy_filter_multiplier 
)
void protocols::cyclic_peptide::CrosslinkerMover::set_final_frlx_rounds ( core::Size const  rounds_in)

Set the number of rounds of FastRelax to apply at the end.

References final_frlx_rounds_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::CrosslinkerMover::set_linker_name ( std::string const &  name_in)
void protocols::cyclic_peptide::CrosslinkerMover::set_metal_type ( std::string const &  metal_in)

For metal-mediated crosslinkers, set what metal mediates the crosslink.

References metal_type_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::CrosslinkerMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP  selector_in)

Set the residue selector to use.

References residue_selector_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::CrosslinkerMover::set_scorefxn ( core::scoring::ScoreFunctionCOP  sfxn_in)

Set the scorefunction to use for packing and minimization.

Cloned at apply time. (That is, the scorefunction is shared until apply time).

References sfxn_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::CrosslinkerMover::set_sidechain_frlx_rounds ( core::Size const  rounds_in)

Set the number of rounds of FastRelax to apply when minimizing the linker and the side-chains that connect to it.

References sidechain_frlx_rounds_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::CrosslinkerMover::set_symm_count ( signed int const  count_in)

Set 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.

Note
Deliberately a signed int.

For example, symm_type_='C' and symm_count_=3 would specify C3 symmetry. A value of 1 means asymmetry. 1 by default.

Note
Deliberately an int.

References symm_count_, and symm_type().

Referenced by set_symmetry().

void protocols::cyclic_peptide::CrosslinkerMover::set_symm_type ( char const  type_in)

Set the symmety type.

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

Note
'A' (asymmetric) by default.

References symm_type_.

Referenced by set_symmetry().

void protocols::cyclic_peptide::CrosslinkerMover::set_symmetry ( std::string const &  symmetry_in)

Parse a string with a symmetry type (e.g. "C3") and set the symmetry accordingly.

References set_symm_count(), and set_symm_type().

Referenced by parse_my_tag().

void protocols::cyclic_peptide::CrosslinkerMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::cyclic_peptide::operator<<().

core::Real const& protocols::cyclic_peptide::CrosslinkerMover::sidechain_distance_filter_multiplier ( ) const
inlineprivate
core::Size protocols::cyclic_peptide::CrosslinkerMover::sidechain_frlx_rounds ( ) const
inline

Get the number of rounds of FastRelax to apply when minimizing the linker and the side-chains that connect to it.

References sidechain_frlx_rounds_.

Referenced by pack_and_minimize_linker_and_sidechains(), and parse_my_tag().

core::Size protocols::cyclic_peptide::CrosslinkerMover::symm_count ( ) const
inline

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 apply(), asymmetric_apply(), and symmetric_apply().

char protocols::cyclic_peptide::CrosslinkerMover::symm_type ( ) const
inline

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 apply(), asymmetric_apply(), set_symm_count(), and symmetric_apply().

void protocols::cyclic_peptide::CrosslinkerMover::symmetric_apply ( core::pose::Pose pose,
core::select::residue_selector::ResidueSubset const &  selection,
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP  helper 
)
private

Member Data Documentation

bool protocols::cyclic_peptide::CrosslinkerMover::add_linker_
private

Should we add the linker?

Default true.

Referenced by add_linker(), and set_behaviour().

bool protocols::cyclic_peptide::CrosslinkerMover::constrain_linker_
private

Should we set up constraints for the linker?

Default true.

Referenced by constrain_linker(), and set_behaviour().

core::Real protocols::cyclic_peptide::CrosslinkerMover::constraints_energy_filter_multiplier_
private

Multiplier to affect stringency of constraints energy filter. Higher values are more permissive.

Default 1.0.

Referenced by constraints_energy_filter_multiplier(), and set_filter_behaviour().

bool protocols::cyclic_peptide::CrosslinkerMover::do_final_fastrelax_
private

Should we FastRelax the whole structure?

Default false.

Referenced by do_final_fastrelax(), and set_behaviour().

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_constraints_energy_
private

Should we filter based on constraints energy after the initial minimization of the linker?

Default true. Each linker helper has its own evaluator for this.

Referenced by filter_by_constraints_energy(), and set_filter_behaviour().

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_sidechain_distance_
private

Should we filter based on initial distance between residues that are to be linked?

Default true. Each linker helper has its own evaluator to decide whether or not to discard poses.

Referenced by filter_by_sidechain_distance(), and set_filter_behaviour().

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_total_score_
private

Should we filter by total score (including constraints energy) at the end?

Default false.

Referenced by filter_by_total_score(), and set_filter_behaviour().

core::Real protocols::cyclic_peptide::CrosslinkerMover::filter_by_total_score_cutoff_energy_
private

If we're filtering by total score, this is the cutoff energy.

Defaults to 0.

Referenced by filter_by_total_score_cutoff_energy(), and set_filter_behaviour().

core::Size protocols::cyclic_peptide::CrosslinkerMover::final_frlx_rounds_
private

The number of rounds of FastRelax to apply at the end of the protocol.

Default 3.

Referenced by final_frlx_rounds(), and set_final_frlx_rounds().

CrossLinker protocols::cyclic_peptide::CrosslinkerMover::linker_
private

The crosslinker to use.

Must be set. See definition of CrossLinker enum in CrosslinkerMover.hh.

Referenced by apply(), linker_name(), and set_linker_name().

std::string protocols::cyclic_peptide::CrosslinkerMover::metal_type_
private

For metal-mediated crosslinkers, what metal mediates the crosslink?

Defaults to "Zn".

Referenced by metal_type(), and set_metal_type().

bool protocols::cyclic_peptide::CrosslinkerMover::pack_and_minimize_linker_and_sidechains_
private

Should we pack and minimize the linker and the side-chains to which it connects?

Default true.

Referenced by pack_and_minimize_linker_and_sidechains(), and set_behaviour().

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::CrosslinkerMover::residue_selector_
private

A residue selector to select residues to cross-link.

Referenced by residue_selector(), and set_residue_selector().

core::scoring::ScoreFunctionCOP protocols::cyclic_peptide::CrosslinkerMover::sfxn_
private

The scorefunction to use for packing and minimization.

Cloned at apply time.

Referenced by scorefxn(), and set_scorefxn().

core::Real protocols::cyclic_peptide::CrosslinkerMover::sidechain_distance_filter_multiplier_
private

Multiplier to affect stringency of sidechain distance filter. Higher values are more permissive.

Default 1.0.

Referenced by set_filter_behaviour(), and sidechain_distance_filter_multiplier().

core::Size protocols::cyclic_peptide::CrosslinkerMover::sidechain_frlx_rounds_
private

The number of rounds of FastRelax to apply when packing and minimizing side-chains and the linker.

Default 3.

Referenced by set_sidechain_frlx_rounds(), and sidechain_frlx_rounds().

core::Size protocols::cyclic_peptide::CrosslinkerMover::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_symm_count(), and symm_count().

char protocols::cyclic_peptide::CrosslinkerMover::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_symm_type(), and symm_type().


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