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:

[legend]

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...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override
	Provide the citation. 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 Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor 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
protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperOP	crosslinkermover_helper_from_type () const
	Generate the CrosslinkerMoverHelper based on the setting of linker_. More...

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_ = CrossLinker::no_crosslinker
	The crosslinker to use. More...

bool	add_linker_ = true
	Should we add the linker? More...

bool	constrain_linker_ = true
	Should we set up constraints for the linker? More...

bool	pack_and_minimize_linker_and_sidechains_ = true
	Should we pack and minimize the linker and the side-chains to which it connects? More...

bool	do_final_fastrelax_ = false
	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_ = 3
	The number of rounds of FastRelax to apply when packing and minimizing side-chains and the linker. More...

core::Size	final_frlx_rounds_ = 3
	The number of rounds of FastRelax to apply at the end of the protocol. More...

bool	filter_by_sidechain_distance_ = true
	Should we filter based on initial distance between residues that are to be linked? More...

bool	filter_by_constraints_energy_ = true
	Should we filter based on constraints energy after the initial minimization of the linker? More...

bool	filter_by_total_score_ = false
	Should we filter by total score (including constraints energy) at the end? More...

core::Real	filter_by_total_score_cutoff_energy_ = 0.0
	If we're filtering by total score, this is the cutoff energy. More...

core::Real	sidechain_distance_filter_multiplier_ = 1.0
	Multiplier to affect stringency of sidechain distance filter. Higher values are more permissive. More...

core::Real	constraints_energy_filter_multiplier_ = 1.0
	Multiplier to affect stringency of constraints energy filter. Higher values are more permissive. More...

char	symm_type_ = 'A'
	The symmetry type. More...

core::Size	symm_count_ = 1
	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_ = "Zn"
	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

◆ CrosslinkerMover() [1/2]

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

Constructors ///.

Default constructor

◆ CrosslinkerMover() [2/2]

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

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~CrosslinkerMover()

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

overridedefault

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

Member Function Documentation

◆ add_linker()

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().

◆ add_linker_asymmetric()

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().

◆ add_linker_constraints_asymmetric()

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().

◆ add_linker_constraints_symmetric()

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().

◆ add_linker_symmetric()

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().

◆ apply()

void protocols::cyclic_peptide::CrosslinkerMover::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover

Implements protocols::moves::Mover.

References asymmetric_apply(), core::pose::Pose::conformation(), crosslinkermover_helper_from_type(), core::conformation::symmetry::is_symmetric(), residue_selector(), scorefxn(), symm_count(), symm_type(), and symmetric_apply().

◆ asymmetric_apply()

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

Apply the mover to an asymmetric pose.

Requires and asymmetric pose, and no symmetry.

References add_linker(), add_linker_asymmetric(), add_linker_constraints_asymmetric(), core::pose::Pose::clone(), constrain_linker(), do_final_fastrelax(), protocols::moves::FAIL_RETRY, filter_by_constraints_energy(), filter_by_constraints_energy_asymmetric(), filter_by_sidechain_distance(), filter_by_sidechain_distance_asymmetric(), filter_by_total_score(), protocols::moves::MS_SUCCESS, pack_and_minimize_linker_and_sidechains(), protocols::moves::Mover::set_last_move_status(), symm_count(), symm_type(), and protocols::cyclic_peptide::TR().

Referenced by apply().

◆ class_name()

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().

◆ clone()

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().

◆ constrain_linker()

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().

◆ constraints_energy_filter_multiplier()

core::Real const& protocols::cyclic_peptide::CrosslinkerMover::constraints_energy_filter_multiplier ( ) const

inlineprivate

The constraints energy filter multiplier.

References constraints_energy_filter_multiplier_.

Referenced by filter_by_constraints_energy_asymmetric(), filter_by_constraints_energy_symmetric(), parse_my_tag(), and set_filter_behaviour().

◆ crosslinkermover_helper_from_type()

protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperOP protocols::cyclic_peptide::CrosslinkerMover::crosslinkermover_helper_from_type ( ) const

private

Generate the CrosslinkerMoverHelper based on the setting of linker_.

private methods ///

Generate the CrosslinkerMoverHelper based on the setting of linker_.

References linker_, metal_type(), protocols::cyclic_peptide::octahedral_metal, protocols::cyclic_peptide::One_Four_BBMB, protocols::cyclic_peptide::square_planar_metal, protocols::cyclic_peptide::square_pyramidal_metal, protocols::cyclic_peptide::TBMB, protocols::cyclic_peptide::tetrahedral_metal, protocols::cyclic_peptide::thioether, protocols::cyclic_peptide::TMA, protocols::cyclic_peptide::trigonal_planar_metal, and protocols::cyclic_peptide::trigonal_pyramidal_metal.

Referenced by apply(), and provide_citation_info().

◆ do_final_fastrelax()

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().

◆ filter_by_constraints_energy()

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().

◆ filter_by_constraints_energy_asymmetric()

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().

◆ filter_by_constraints_energy_symmetric()

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().

◆ filter_by_sidechain_distance()

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().

◆ filter_by_sidechain_distance_asymmetric()

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().

◆ filter_by_sidechain_distance_symmetric()

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().

◆ filter_by_total_score() [1/2]

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().

◆ filter_by_total_score() [2/2]

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().

◆ filter_by_total_score_cutoff_energy()

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().

◆ final_frlx_rounds()

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().

◆ fresh_instance()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_crosslinker_enum()

CrossLinker protocols::cyclic_peptide::CrosslinkerMover::get_crosslinker_enum ( std::string const & name )

static

Given a CrossLinker name, get its enum.

References protocols::cyclic_peptide::end_of_crosslinker_list, get_crosslinker_name(), protocols::moves::Mover::name(), and protocols::cyclic_peptide::unknown_crosslinker.

Referenced by set_linker_name().

◆ get_crosslinker_name()

std::string protocols::cyclic_peptide::CrosslinkerMover::get_crosslinker_name ( CrossLinker const crosslinker )

static

Given a CrossLinker enum, get its name.

References protocols::cyclic_peptide::no_crosslinker, protocols::cyclic_peptide::octahedral_metal, protocols::cyclic_peptide::One_Four_BBMB, protocols::cyclic_peptide::square_planar_metal, protocols::cyclic_peptide::square_pyramidal_metal, protocols::cyclic_peptide::TBMB, protocols::cyclic_peptide::tetrahedral_metal, protocols::cyclic_peptide::thioether, protocols::cyclic_peptide::TMA, protocols::cyclic_peptide::trigonal_planar_metal, and protocols::cyclic_peptide::trigonal_pyramidal_metal.

Referenced by get_crosslinker_enum(), and linker_name().

◆ get_jump_index_for_crosslinker()

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(), core::kinematics::FoldTree::is_jump_point(), and core::pose::Pose::total_residue().

Referenced by pack_and_minimize_linker_and_sidechains().

◆ get_jump_indices_for_symmetric_crosslinker()

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(), core::kinematics::FoldTree::get_jump_that_builds_residue(), and core::kinematics::FoldTree::is_jump_point().

Referenced by pack_and_minimize_linker_and_sidechains().

◆ get_name()

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

overridevirtual

Get the name of the Mover.

Implements protocols::moves::Mover.

References class_name().

◆ linker_name()

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

Get the linker name.

References get_crosslinker_name(), and linker_.

◆ metal_type()

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 crosslinkermover_helper_from_type().

◆ mover_name()

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

static

Returns the name of this Mover.

Referenced by provide_xml_schema().

◆ pack_and_minimize_linker_and_sidechains() [1/2]

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().

◆ pack_and_minimize_linker_and_sidechains() [2/2]

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

Repack and minimize the sidechains.

Also repacks and minimzes the linker, letting the jump vary.

Also repacks and minimzes the linker, letting all jumps vary.

References add_linker(), core::scoring::angle_constraint, protocols::relax::FastRelax::apply(), core::scoring::atom_pair_constraint, clone(), core::scoring::dihedral_constraint, final_frlx_rounds(), get_jump_index_for_crosslinker(), get_jump_indices_for_symmetric_crosslinker(), scorefxn(), protocols::relax::RelaxProtocolBase::set_movemap(), protocols::relax::FastRelax::set_movemap_disables_packing_of_fixed_chi_positions(), and sidechain_frlx_rounds().

◆ parse_my_tag()

void protocols::cyclic_peptide::CrosslinkerMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

Rosetta Scripts Support ///.

RosettaScripts Support ///.

Parse XML tag (to use this Mover in Rosetta Scripts).

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References add_linker(), constrain_linker(), constraints_energy_filter_multiplier(), do_final_fastrelax(), filter_by_constraints_energy(), filter_by_sidechain_distance(), filter_by_total_score(), filter_by_total_score_cutoff_energy(), final_frlx_rounds(), pack_and_minimize_linker_and_sidechains(), core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), residue_selector(), set_behaviour(), set_filter_behaviour(), set_final_frlx_rounds(), set_linker_name(), set_metal_type(), set_residue_selector(), set_scorefxn(), set_sidechain_frlx_rounds(), set_symmetry(), sidechain_distance_filter_multiplier(), and sidechain_frlx_rounds().

◆ provide_citation_info()

void protocols::cyclic_peptide::CrosslinkerMover::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References crosslinkermover_helper_from_type(), linker_, and protocols::cyclic_peptide::no_crosslinker.

◆ provide_xml_schema()

void protocols::cyclic_peptide::CrosslinkerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Provide information on what options are available in XML tag.

References core::select::residue_selector::attributes_for_parse_residue_selector_when_required(), core::scoring::attributes_for_parse_score_function_w_description_when_required(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::cyclic_peptide::CrosslinkerMoverCreator::provide_xml_schema().

◆ residue_selector()

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().

◆ scorefxn()

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().

◆ set_behaviour()

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
	)

Set the behaviour of this mover.

References add_linker(), add_linker_, constrain_linker(), constrain_linker_, do_final_fastrelax(), do_final_fastrelax_, pack_and_minimize_linker_and_sidechains(), and pack_and_minimize_linker_and_sidechains_.

Referenced by parse_my_tag().

◆ set_filter_behaviour()

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
	)

Set the filtering behaviour of this mover.

References constraints_energy_filter_multiplier(), constraints_energy_filter_multiplier_, filter_by_constraints_energy(), filter_by_constraints_energy_, filter_by_sidechain_distance(), filter_by_sidechain_distance_, filter_by_total_score(), filter_by_total_score_, filter_by_total_score_cutoff_energy(), filter_by_total_score_cutoff_energy_, sidechain_distance_filter_multiplier(), and sidechain_distance_filter_multiplier_.

Referenced by parse_my_tag().

◆ set_final_frlx_rounds()

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().

◆ set_linker_name()

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

Set the linker name.

References get_crosslinker_enum(), linker_, and protocols::cyclic_peptide::unknown_crosslinker.

Referenced by parse_my_tag().

◆ set_metal_type()

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().

◆ set_residue_selector()

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().

◆ set_scorefxn()

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().

◆ set_sidechain_frlx_rounds()

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().

◆ set_symm_count()

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().

◆ set_symm_type()

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().

◆ 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().

◆ show()

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<<().

◆ sidechain_distance_filter_multiplier()

core::Real const& protocols::cyclic_peptide::CrosslinkerMover::sidechain_distance_filter_multiplier ( ) const

inlineprivate

The distance filter multiplier.

References sidechain_distance_filter_multiplier_.

Referenced by filter_by_sidechain_distance_asymmetric(), filter_by_sidechain_distance_symmetric(), parse_my_tag(), and set_filter_behaviour().

◆ sidechain_frlx_rounds()

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().

◆ symm_count()

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().

◆ symm_type()

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().

◆ 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

Apply the mover to a symmetric pose.

Requires symmetry in the pose matching the expected symmetry.

References add_linker(), add_linker_constraints_symmetric(), add_linker_symmetric(), core::pose::Pose::clone(), constrain_linker(), do_final_fastrelax(), protocols::moves::FAIL_RETRY, filter_by_constraints_energy(), filter_by_constraints_energy_symmetric(), filter_by_sidechain_distance(), filter_by_sidechain_distance_symmetric(), filter_by_total_score(), protocols::moves::MS_SUCCESS, pack_and_minimize_linker_and_sidechains(), protocols::moves::Mover::set_last_move_status(), symm_count(), symm_type(), and protocols::cyclic_peptide::TR().

Referenced by apply().

Member Data Documentation

◆ add_linker_

bool protocols::cyclic_peptide::CrosslinkerMover::add_linker_ = true

private

Should we add the linker?

Default true.

Referenced by add_linker(), and set_behaviour().

◆ constrain_linker_

bool protocols::cyclic_peptide::CrosslinkerMover::constrain_linker_ = true

private

Should we set up constraints for the linker?

Default true.

Referenced by constrain_linker(), and set_behaviour().

◆ constraints_energy_filter_multiplier_

core::Real protocols::cyclic_peptide::CrosslinkerMover::constraints_energy_filter_multiplier_ = 1.0

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().

◆ do_final_fastrelax_

bool protocols::cyclic_peptide::CrosslinkerMover::do_final_fastrelax_ = false

private

Should we FastRelax the whole structure?

Default false.

Referenced by do_final_fastrelax(), and set_behaviour().

◆ filter_by_constraints_energy_

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_constraints_energy_ = true

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().

◆ filter_by_sidechain_distance_

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_sidechain_distance_ = true

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().

◆ filter_by_total_score_

bool protocols::cyclic_peptide::CrosslinkerMover::filter_by_total_score_ = false

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().

◆ filter_by_total_score_cutoff_energy_

core::Real protocols::cyclic_peptide::CrosslinkerMover::filter_by_total_score_cutoff_energy_ = 0.0

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().

◆ final_frlx_rounds_

core::Size protocols::cyclic_peptide::CrosslinkerMover::final_frlx_rounds_ = 3

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().

◆ linker_

CrossLinker protocols::cyclic_peptide::CrosslinkerMover::linker_ = CrossLinker::no_crosslinker

private

The crosslinker to use.

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

Referenced by crosslinkermover_helper_from_type(), linker_name(), provide_citation_info(), and set_linker_name().

◆ metal_type_

std::string protocols::cyclic_peptide::CrosslinkerMover::metal_type_ = "Zn"

private

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

Defaults to "Zn".

Referenced by metal_type(), and set_metal_type().

◆ pack_and_minimize_linker_and_sidechains_

bool protocols::cyclic_peptide::CrosslinkerMover::pack_and_minimize_linker_and_sidechains_ = true

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().

◆ residue_selector_

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().

◆ sfxn_

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().

◆ sidechain_distance_filter_multiplier_

core::Real protocols::cyclic_peptide::CrosslinkerMover::sidechain_distance_filter_multiplier_ = 1.0

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().

◆ sidechain_frlx_rounds_

core::Size protocols::cyclic_peptide::CrosslinkerMover::sidechain_frlx_rounds_ = 3

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().

◆ symm_count_

core::Size protocols::cyclic_peptide::CrosslinkerMover::symm_count_ = 1

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().

◆ symm_type_

char protocols::cyclic_peptide::CrosslinkerMover::symm_type_ = 'A'

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:

src/protocols/cyclic_peptide/CrosslinkerMover.hh
src/protocols/cyclic_peptide/CrosslinkerMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CrosslinkerMover() [1/2]

◆ CrosslinkerMover() [2/2]

◆ ~CrosslinkerMover()

Member Function Documentation

◆ add_linker()

◆ add_linker_asymmetric()

◆ add_linker_constraints_asymmetric()

◆ add_linker_constraints_symmetric()

◆ add_linker_symmetric()

◆ apply()

◆ asymmetric_apply()

◆ class_name()

◆ clone()

◆ constrain_linker()

◆ constraints_energy_filter_multiplier()

◆ crosslinkermover_helper_from_type()

◆ do_final_fastrelax()

◆ filter_by_constraints_energy()

◆ filter_by_constraints_energy_asymmetric()

◆ filter_by_constraints_energy_symmetric()

◆ filter_by_sidechain_distance()

◆ filter_by_sidechain_distance_asymmetric()

◆ filter_by_sidechain_distance_symmetric()

◆ filter_by_total_score() [1/2]

◆ filter_by_total_score() [2/2]

◆ filter_by_total_score_cutoff_energy()

◆ final_frlx_rounds()

◆ fresh_instance()

◆ get_crosslinker_enum()

◆ get_crosslinker_name()

◆ get_jump_index_for_crosslinker()

◆ get_jump_indices_for_symmetric_crosslinker()

◆ get_name()

◆ linker_name()

◆ metal_type()

◆ mover_name()

◆ pack_and_minimize_linker_and_sidechains() [1/2]

◆ pack_and_minimize_linker_and_sidechains() [2/2]

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ residue_selector()

◆ scorefxn()

◆ set_behaviour()

◆ set_filter_behaviour()

◆ set_final_frlx_rounds()

◆ set_linker_name()

◆ set_metal_type()

◆ set_residue_selector()

◆ set_scorefxn()

◆ set_sidechain_frlx_rounds()

◆ set_symm_count()

◆ set_symm_type()

◆ set_symmetry()

◆ show()

◆ sidechain_distance_filter_multiplier()

◆ sidechain_frlx_rounds()

◆ symm_count()

◆ symm_type()

◆ symmetric_apply()

Member Data Documentation

◆ add_linker_

◆ constrain_linker_

◆ constraints_energy_filter_multiplier_

◆ do_final_fastrelax_

◆ filter_by_constraints_energy_

◆ filter_by_sidechain_distance_

◆ filter_by_total_score_

◆ filter_by_total_score_cutoff_energy_

◆ final_frlx_rounds_

◆ linker_

◆ metal_type_

◆ pack_and_minimize_linker_and_sidechains_