#include <DisulfidizeMover.hh>

Inheritance diagram for protocols::denovo_design::DisulfidizeMover:

[legend]

Public Types
typedef utility::vector1< std::pair< core::Size, core::Size > >	DisulfideList

typedef utility::vector1< std::pair< core::Real, core::pose::PoseOP > >	PoseList

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

Public Member Functions
	DisulfidizeMover ()
	Default constructor. More...

	DisulfidizeMover (DisulfidizeMover const &src)
	Copy constructor. More...

	~DisulfidizeMover () override
	virtual constructor to allow derivation More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Parses the DisulfidizerMoverTags. More...

protocols::moves::MoverOP	clone () const override
	Return the name of this mover. More...

DisulfideList	find_current_disulfides (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset1, core::select::residue_selector::ResidueSubset const &subset2) const
	finds disulfides within a pose subset More...

void	mutate_disulfides_to_ala (core::pose::Pose &pose, DisulfideList const &current_ds) const
	mutates the given disulfides to ALA More...

utility::vector1< DisulfideList >	recursive_multiple_disulfide_former (DisulfideList const &disulfides_formed, DisulfideList const &disulfides_possible) const
	Function for recursively creating multiple disulfides. More...

void	tag_disulfide (core::pose::Pose &pose, core::Size const res1, core::Size const res2) const
	creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize More...

void	tag_disulfides (core::pose::Pose &pose, DisulfidizeMover::DisulfideList const &disulf) const
	creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize More...

void	make_disulfide (core::pose::Pose &pose, core::Size const res1, core::Size const res2, bool const relax_bb, core::scoring::ScoreFunctionOP sfxn) const
	forms a disulfide between res1 and res2, optionally allowing backbone movement More...

void	make_disulfides (core::pose::Pose &pose, DisulfideList const &disulf, bool const relax_bb, core::scoring::ScoreFunctionOP sfxn) const
	creates disulfides given the list of pairs given More...

core::Real	build_and_score_disulfide (core::pose::Pose &blank_pose, core::scoring::ScoreFunctionOP sfxn_disulfonly, core::scoring::ScoreFunctionOP sfxn_full, const bool relax_bb, core::Size const res1, core::Size const res2) const
	temporarily tries building a disulfide between the given positions, scores, and restores the pose More...

DisulfideList	find_possible_disulfides (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &residueset1, core::select::residue_selector::ResidueSubset const &residueset2, core::scoring::ScoreFunctionOP sfxn) const
	find disulfides in the given neighborhood More...

DisulfideList	find_possible_disulfides (core::pose::Pose const &pose, std::set< core::Size > const &set1, std::set< core::Size > const &set2, core::scoring::ScoreFunctionOP sfxn) const
	find disulfides in the given neighborhood between residues in set 1 and residues in set 2 More...

bool	check_residue_type (core::pose::Pose const &pose, core::Size const res) const
	checks seqpos to ensure that min_loop is satisfied More...

bool	check_disulfide_seqpos (core::Size const res1, core::Size const res2) const
	checks seqpos to ensure that min_loop is satisfied More...

bool	check_disulfide_cb_distance (core::pose::Pose const &pose, core::Size const res1, core::Size const res2) const
	checks disulfide CB-CB distance More...

bool	check_disulfide_score (core::pose::Pose &pose, core::Size const res1, core::Size const res2, core::scoring::ScoreFunctionOP sfxn_disulfonly, core::scoring::ScoreFunctionOP sfxn_full) const
	checks disulfide rosetta score More...

bool	check_disulfide_match_rt (core::pose::Pose const &pose, core::Size const res1, core::Size const res2, core::scoring::disulfides::DisulfideMatchingPotential const &disulfPot, bool const mirror) const
	checks disulfide match rt More...

bool	mixed_disulfide (core::pose::Pose const &pose, core::Size const res1, core::Size const res2) const
	Returns true if this is a mixed D/L disulfide, false otherwise. More...

bool	noncanonical_disulfide (core::pose::Pose const &pose, core::Size const res1, core::Size const res2) const
	Returns true if at least one of the partners in this disulfide is NOT D-cysteine or L-cysteine. Returns false otherwise. More...

void	set_set1_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	sets the selector for set 1 – disulfides will connect residues in set 1 to residues in set 2 More...

void	set_set2_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	sets the selector for set 2 – disulfides will connect residues in set 1 to residues in set 2 More...

void	set_min_loop (core::Size const minloopval)
	sets the min_loop value (number of residues between disulfide-joined residues) (default=8) More...

void	set_min_disulfides (core::Size const min_disulf)
	sets minimum number of disulfides More...

void	set_max_disulfides (core::Size const max_disulf)
	sets maximum number of disulfides More...

void	set_max_dist (core::Real const dist)
	sets the maximum distance to have an allowed disulfide More...

void	set_max_disulf_score (core::Real const maxscoreval)
	sets the maximum allowed per-disulfide dslf_fa13 score (default=0.0) More...

void	set_match_rt_limit (core::Real const matchrtval)
	sets the maximum allowed "match-rt-limit" (default=1.0) More...

void	set_cys_types (bool const lcys, bool const dcys, bool const beta_cys)
	Set the types of cysteines that we design with: More...

void	set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
	Set the scorefunction to use for scoring disulfides, minimizing, and repacking. More...

void	set_sort_scorefxn (core::scoring::ScoreFunctionCOP sort_scorefxn)
	Set the scorefunction to use for sorting the final results. More...

void	set_mutate_gly (bool const mutate_gly)
	If true, GLY --> CYS mutations will be allowed. Default=false. More...

void	set_mutate_pro (bool const mutate_pro)
	If true, PRO --> CYS mutations will be allowed. Default=false. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	set_keep_current_ds (bool const keep_current)
	If set, the current disulfides in the pose will be kept as-is. More...

void	set_include_current_ds (bool const include_current)
	If set, the current disulfides in the pose will be included in the set of possible disulfide configurations that are returned. More...

void	set_score_or_matchrt (bool const score_or_match)
	If true, the disulfide score OR the match_rt score can indicate that a disulfide is reasonable. If false, both the disulfide score AND the match_rt score are needed. More...

Public Member Functions inherited from protocols::rosetta_scripts::MultiplePoseMover
	MultiplePoseMover ()
	No-argument constructor. More...

	~MultiplePoseMover () override=default
	Virtual destructor. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	apply (core::pose::Pose &pose) override
	Process input pose. More...

core::pose::PoseOP	get_additional_output () override
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Parse settings in tag. More...

void	set_previous_mover (protocols::moves::MoverOP const m)
	Used by RosettaScripts to set the previous mover to pull poses from. More...

void	set_rosetta_scripts_tag (utility::tag::TagCOP tag)
	sets rosettascripts tag More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. 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...

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 void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::rosetta_scripts::MultiplePoseMover
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Protected Member Functions
bool	process_pose (core::pose::Pose &pose, utility::vector1< core::pose::PoseOP > &additional_poses) override
	Identifies disulfides for a given input pose. More...

void	prune_symmetric_disulfides (core::pose::Pose const &pose, DisulfideList &disulf_list) const
	Given a list of disulfides and a symmetric pose, prune the list to remove symmetry duplicates. More...

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...

Private Attributes
core::Real	match_rt_limit_

core::Real	max_disulf_score_

core::Real	max_dist_sq_

core::Size	min_loop_

core::Size	min_disulfides_

core::Size	max_disulfides_

bool	include_current_ds_

bool	keep_current_ds_

bool	keep_all_ds_ = false

bool	score_or_matchrt_

bool	allow_l_cys_
	Can disulfides involve L-cystine? More...

bool	allow_d_cys_
	Can disulfides involve D-cystine? More...

bool	allow_beta_cys_
	Can disulfides involve beta-3-cysteine? More...

bool	mutate_gly_
	Can GLY be mutated? More...

bool	mutate_pro_
	Can PRO be mutated? More...

core::select::residue_selector::ResidueSelectorCOP	set1_selector_
	disulfides connect residues from set1 to residues from set2 More...

core::select::residue_selector::ResidueSelectorCOP	set2_selector_

core::scoring::ScoreFunctionOP	sfxn_ = nullptr
	The scorefunction that we will use for: – scoring disulfides – repacking/minimizing disulfides. More...

core::scoring::ScoreFunctionCOP	sort_sfxn_ = nullptr

Member Typedef Documentation

◆ DisulfideList

typedef utility::vector1< std::pair< core::Size, core::Size > > protocols::denovo_design::DisulfidizeMover::DisulfideList

◆ PoseList

typedef utility::vector1< std::pair< core::Real, core::pose::PoseOP > > protocols::denovo_design::DisulfidizeMover::PoseList

Constructor & Destructor Documentation

◆ DisulfidizeMover() [1/2]

protocols::denovo_design::DisulfidizeMover::DisulfidizeMover ( )

Default constructor.

DisulfidizeMover main code:

References protocols::rosetta_scripts::MultiplePoseMover::set_rosetta_scripts_tag().

◆ DisulfidizeMover() [2/2]

protocols::denovo_design::DisulfidizeMover::DisulfidizeMover ( DisulfidizeMover const & src )

Copy constructor.

References sfxn_, and sort_sfxn_.

◆ ~DisulfidizeMover()

protocols::denovo_design::DisulfidizeMover::~DisulfidizeMover ( )

overridedefault

virtual constructor to allow derivation

destructor - this class has no dynamic allocation, so

Member Function Documentation

◆ build_and_score_disulfide()

core::Real protocols::denovo_design::DisulfidizeMover::build_and_score_disulfide	(	core::pose::Pose &	blank_pose,
		core::scoring::ScoreFunctionOP	sfxn_disulfonly,
		core::scoring::ScoreFunctionOP	sfxn_full,
		const bool	relax_bb,
		core::Size const	res1,
		core::Size const	res2
	)		const

temporarily tries building a disulfide between the given positions, scores, and restores the pose

References make_disulfide(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), protocols::hybridization::score, core::pose::Pose::size(), and protocols::TR().

Referenced by check_disulfide_score().

◆ check_disulfide_cb_distance()

bool protocols::denovo_design::DisulfidizeMover::check_disulfide_cb_distance	(	core::pose::Pose const &	pose,
		core::Size const	res1,
		core::Size const	res2
	)		const

checks disulfide CB-CB distance

References max_dist_sq_, core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and protocols::TR().

Referenced by find_possible_disulfides().

◆ check_disulfide_match_rt()

bool protocols::denovo_design::DisulfidizeMover::check_disulfide_match_rt	(	core::pose::Pose const &	pose,
		core::Size const	res1,
		core::Size const	res2,
		core::scoring::disulfides::DisulfideMatchingPotential const &	disulfPot,
		bool const	mirror
	)		const

checks disulfide match rt

References match_rt_limit_, core::pose::Pose::residue(), core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide(), and protocols::TR().

Referenced by find_possible_disulfides().

◆ check_disulfide_score()

bool protocols::denovo_design::DisulfidizeMover::check_disulfide_score	(	core::pose::Pose &	pose,
		core::Size const	res1,
		core::Size const	res2,
		core::scoring::ScoreFunctionOP	sfxn_disulfonly,
		core::scoring::ScoreFunctionOP	sfxn_full
	)		const

checks disulfide rosetta score

References build_and_score_disulfide(), max_disulf_score_, and protocols::TR().

Referenced by find_possible_disulfides().

◆ check_disulfide_seqpos()

bool protocols::denovo_design::DisulfidizeMover::check_disulfide_seqpos	(	core::Size const	res1,
		core::Size const	res2
	)		const

checks seqpos to ensure that min_loop is satisfied

References min_loop_, and protocols::TR().

Referenced by find_possible_disulfides().

◆ check_residue_type()

bool protocols::denovo_design::DisulfidizeMover::check_residue_type	(	core::pose::Pose const &	pose,
		core::Size const	res
	)		const

checks seqpos to ensure that min_loop is satisfied

checks residue type to ensure that we can mutate this to CYD

References core::conformation::Residue::aa(), core::chemical::aa_b3g, core::chemical::aa_b3p, core::chemical::aa_dpr, core::chemical::aa_gly, core::chemical::aa_pro, core::conformation::Residue::is_protein(), mutate_gly_, mutate_pro_, core::conformation::Residue::name(), core::pose::Pose::residue(), and protocols::TR().

Referenced by find_possible_disulfides().

◆ clone()

protocols::moves::MoverOP protocols::denovo_design::DisulfidizeMover::clone ( ) const

overridevirtual

Return the name of this mover.

Return a copy of ourselves.

return a fresh instance of this class in an owning pointer

Reimplemented from protocols::moves::Mover.

◆ find_current_disulfides()

DisulfidizeMover::DisulfideList protocols::denovo_design::DisulfidizeMover::find_current_disulfides	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	subset1,
		core::select::residue_selector::ResidueSubset const &	subset2
	)		const

finds disulfides within a pose subset

References core::chemical::ResidueType::atom_index(), core::pose::Pose::conformation(), core::chemical::ResidueTypeBase::get_disulfide_atom_name(), core::conformation::Conformation::is_bonded(), core::conformation::Residue::is_bonded(), core::chemical::ResidueType::is_disulfide_bonded(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::TR(), and core::conformation::Residue::type().

Referenced by process_pose().

◆ find_possible_disulfides() [1/2]

DisulfidizeMover::DisulfideList protocols::denovo_design::DisulfidizeMover::find_possible_disulfides	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	residueset1,
		core::select::residue_selector::ResidueSubset const &	residueset2,
		core::scoring::ScoreFunctionOP	sfxn
	)		const

find disulfides in the given neighborhood

find disulfides in the given neighborhood between residues in set 1 and residues in set 2

References protocols::TR().

Referenced by process_pose().

◆ find_possible_disulfides() [2/2]

DisulfidizeMover::DisulfideList protocols::denovo_design::DisulfidizeMover::find_possible_disulfides	(	core::pose::Pose const &	pose,
		std::set< core::Size > const &	set1,
		std::set< core::Size > const &	set2,
		core::scoring::ScoreFunctionOP	sfxn
	)		const

find disulfides in the given neighborhood between residues in set 1 and residues in set 2

References protocols::denovo_design::add_to_list(), allow_d_cys_, allow_l_cys_, check_disulfide_cb_distance(), check_disulfide_match_rt(), check_disulfide_score(), check_disulfide_seqpos(), check_residue_type(), protocols::denovo_design::construct_poly_ala_pose(), core::scoring::dslf_fa13, core::chemical::ResidueType::is_disulfide_bonded(), keep_current_ds_, mixed_disulfide(), noncanonical_disulfide(), core::pose::Pose::residue(), score_or_matchrt_, protocols::TR(), and core::conformation::Residue::type().

◆ get_name()

std::string protocols::denovo_design::DisulfidizeMover::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

◆ make_disulfide()

void protocols::denovo_design::DisulfidizeMover::make_disulfide	(	core::pose::Pose &	pose,
		core::Size const	res1,
		core::Size const	res2,
		bool const	relax_bb,
		core::scoring::ScoreFunctionOP	sfxn
	)		const

forms a disulfide between res1 and res2, optionally allowing backbone movement

References allow_d_cys_, allow_l_cys_, core::pose::Pose::conformation(), core::conformation::form_disulfide(), core::util::rebuild_disulfide(), and protocols::TR().

Referenced by build_and_score_disulfide(), and make_disulfides().

◆ make_disulfides()

void protocols::denovo_design::DisulfidizeMover::make_disulfides	(	core::pose::Pose &	pose,
		DisulfidizeMover::DisulfideList const &	disulf,
		bool const	relax_bb,
		core::scoring::ScoreFunctionOP	sfxn
	)		const

creates disulfides given the list of pairs given

References make_disulfide().

Referenced by process_pose().

◆ mixed_disulfide()

bool protocols::denovo_design::DisulfidizeMover::mixed_disulfide	(	core::pose::Pose const &	pose,
		core::Size const	res1,
		core::Size const	res2
	)		const

Returns true if this is a mixed D/L disulfide, false otherwise.

References allow_d_cys_, allow_l_cys_, core::chemical::ResidueTypeBase::is_d_aa(), core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by find_possible_disulfides().

◆ mover_name()

std::string protocols::denovo_design::DisulfidizeMover::mover_name ( )

static

Referenced by get_name(), protocols::denovo_design::DisulfidizeMoverCreator::keyname(), and provide_xml_schema().

◆ mutate_disulfides_to_ala()

void protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala	(	core::pose::Pose &	pose,
		DisulfideList const &	current_ds
	)		const

mutates the given disulfides to ALA

References protocols::simple_moves::MutateResidue::apply(), core::conformation::break_disulfide(), core::pose::Pose::conformation(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueTypeBase::is_d_aa(), core::pose::Pose::residue(), protocols::TR(), and core::conformation::Residue::type().

Referenced by process_pose().

◆ noncanonical_disulfide()

bool protocols::denovo_design::DisulfidizeMover::noncanonical_disulfide	(	core::pose::Pose const &	pose,
		core::Size const	res1,
		core::Size const	res2
	)		const

Returns true if at least one of the partners in this disulfide is NOT D-cysteine or L-cysteine. Returns false otherwise.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_cys, core::chemical::aa_dcs, and core::pose::Pose::residue_type().

Referenced by find_possible_disulfides().

◆ parse_my_tag()

void protocols::denovo_design::DisulfidizeMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

◆ process_pose()

bool protocols::denovo_design::DisulfidizeMover::process_pose	(	core::pose::Pose &	pose,
		utility::vector1< core::pose::PoseOP > &	additional_poses
	)

overrideprotectedvirtual

Identifies disulfides for a given input pose.

does the work – scans pose for disulfides, stores first result in pose, adds others to additional_poses

Reimplemented from protocols::rosetta_scripts::MultiplePoseMover.

References core::pose::Pose::clone(), find_current_disulfides(), find_possible_disulfides(), core::pose::Pose::fold_tree(), core::scoring::get_score_function(), include_current_ds_, core::conformation::symmetry::is_symmetric(), core::pose::symmetry::is_symmetric(), keep_all_ds_, keep_current_ds_, make_disulfides(), max_disulfides_, min_disulfides_, mutate_disulfides_to_ala(), prune_symmetric_disulfides(), recursive_multiple_disulfide_former(), protocols::denovo_design::remove_all_jump_atoms(), core::scoring::rg, protocols::hybridization::score, set1_selector_, set2_selector_, sfxn_, core::pose::Pose::size(), sort_sfxn_, tag_disulfides(), and protocols::TR().

◆ provide_xml_schema()

void protocols::denovo_design::DisulfidizeMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), core::scoring::attributes_for_parse_score_function_w_description(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::denovo_design::DisulfidizeMoverCreator::provide_xml_schema().

◆ prune_symmetric_disulfides()

void protocols::denovo_design::DisulfidizeMover::prune_symmetric_disulfides	(	core::pose::Pose const &	pose,
		DisulfideList &	disulf_list
	)		const

protected

Given a list of disulfides and a symmetric pose, prune the list to remove symmetry duplicates.

Does nothing if the pose is not symmetric.

Author: Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::pose::Pose::conformation_ptr().

Referenced by process_pose().

◆ recursive_multiple_disulfide_former()

utility::vector1< DisulfidizeMover::DisulfideList > protocols::denovo_design::DisulfidizeMover::recursive_multiple_disulfide_former	(	DisulfideList const &	disulfides_formed,
		DisulfideList const &	disulfides_possible
	)		const

Function for recursively creating multiple disulfides.

References core::sequence::end, and max_disulfides_.

Referenced by process_pose().

◆ set_cys_types()

void protocols::denovo_design::DisulfidizeMover::set_cys_types	(	bool const	lcys,
		bool const	dcys,
		bool const	beta_cys
	)

Set the types of cysteines that we design with:

By default, we use only L-cysteine (not D-cysteine or beta-3-cysteine).

By default, we use only L-cysteine (not D-cysteine).

References allow_beta_cys_, allow_d_cys_, and allow_l_cys_.

Referenced by parse_my_tag().

◆ set_include_current_ds()

void protocols::denovo_design::DisulfidizeMover::set_include_current_ds ( bool const include_current )

inline

If set, the current disulfides in the pose will be included in the set of possible disulfide configurations that are returned.

References include_current_ds_.

Referenced by parse_my_tag().

◆ set_keep_current_ds()

void protocols::denovo_design::DisulfidizeMover::set_keep_current_ds ( bool const keep_current )

inline

If set, the current disulfides in the pose will be kept as-is.

References keep_current_ds_.

Referenced by parse_my_tag().

◆ set_match_rt_limit()

void protocols::denovo_design::DisulfidizeMover::set_match_rt_limit ( core::Real const matchrtval )

sets the maximum allowed "match-rt-limit" (default=1.0)

sets the maximum allowed "match-rt-limit" (default=2.0)

Changed from default=2.0 by VKM on 19 Aug 2015 after fixing major bug in DisulfideMatchPotential.

References match_rt_limit_.

Referenced by parse_my_tag().

◆ set_max_dist()

void protocols::denovo_design::DisulfidizeMover::set_max_dist ( core::Real const dist )

sets the maximum distance to have an allowed disulfide

References max_dist_sq_.

Referenced by parse_my_tag().

◆ set_max_disulf_score()

void protocols::denovo_design::DisulfidizeMover::set_max_disulf_score ( core::Real const maxscoreval )

sets the maximum allowed per-disulfide dslf_fa13 score (default=0.0)

References max_disulf_score_.

Referenced by parse_my_tag().

◆ set_max_disulfides()

void protocols::denovo_design::DisulfidizeMover::set_max_disulfides ( core::Size const max_disulf )

inline

sets maximum number of disulfides

References max_disulfides_.

Referenced by parse_my_tag().

◆ set_min_disulfides()

void protocols::denovo_design::DisulfidizeMover::set_min_disulfides ( core::Size const min_disulf )

inline

sets minimum number of disulfides

References min_disulfides_.

Referenced by parse_my_tag().

◆ set_min_loop()

void protocols::denovo_design::DisulfidizeMover::set_min_loop ( core::Size const minloopval )

sets the min_loop value (number of residues between disulfide-joined residues) (default=8)

References min_loop_.

Referenced by parse_my_tag().

◆ set_mutate_gly()

void protocols::denovo_design::DisulfidizeMover::set_mutate_gly ( bool const mutate_gly )

If true, GLY --> CYS mutations will be allowed. Default=false.

References mutate_gly_.

Referenced by parse_my_tag().

◆ set_mutate_pro()

void protocols::denovo_design::DisulfidizeMover::set_mutate_pro ( bool const mutate_pro )

If true, PRO --> CYS mutations will be allowed. Default=false.

References mutate_pro_.

Referenced by parse_my_tag().

◆ set_score_or_matchrt()

void protocols::denovo_design::DisulfidizeMover::set_score_or_matchrt ( bool const score_or_match )

inline

If true, the disulfide score OR the match_rt score can indicate that a disulfide is reasonable. If false, both the disulfide score AND the match_rt score are needed.

References score_or_matchrt_.

Referenced by parse_my_tag().

◆ set_scorefxn()

void protocols::denovo_design::DisulfidizeMover::set_scorefxn ( core::scoring::ScoreFunctionCOP sfxn_in )

Set the scorefunction to use for scoring disulfides, minimizing, and repacking.

Clones the input scorefunction; does not copy it.

References sfxn_.

Referenced by parse_my_tag().

◆ set_set1_selector()

void protocols::denovo_design::DisulfidizeMover::set_set1_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

sets the selector for set 1 – disulfides will connect residues in set 1 to residues in set 2

References set1_selector_.

Referenced by parse_my_tag().

◆ set_set2_selector()

void protocols::denovo_design::DisulfidizeMover::set_set2_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

sets the selector for set 2 – disulfides will connect residues in set 1 to residues in set 2

References set2_selector_.

Referenced by parse_my_tag().

◆ set_sort_scorefxn()

void protocols::denovo_design::DisulfidizeMover::set_sort_scorefxn ( core::scoring::ScoreFunctionCOP sort_scorefxn )

Set the scorefunction to use for sorting the final results.

Clones the input scorefunction; does not copy it.

References sort_sfxn_.

◆ tag_disulfide()

void protocols::denovo_design::DisulfidizeMover::tag_disulfide	(	core::pose::Pose &	pose,
		core::Size const	res1,
		core::Size const	res2
	)		const

creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize

References core::pose::Pose::pdb_info().

Referenced by tag_disulfides().

◆ tag_disulfides()

void protocols::denovo_design::DisulfidizeMover::tag_disulfides	(	core::pose::Pose &	pose,
		DisulfidizeMover::DisulfideList const &	disulf
	)		const

creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize

References core::pose::add_comment(), and tag_disulfide().

Referenced by process_pose().

Member Data Documentation

◆ allow_beta_cys_

bool protocols::denovo_design::DisulfidizeMover::allow_beta_cys_

private

Can disulfides involve beta-3-cysteine?

Default false. If true, beta-3-cysteine is considered only at beta-amino acid positions.

Referenced by parse_my_tag(), and set_cys_types().

◆ allow_d_cys_

bool protocols::denovo_design::DisulfidizeMover::allow_d_cys_

private

Can disulfides involve D-cystine?

Default false

Referenced by find_possible_disulfides(), make_disulfide(), mixed_disulfide(), parse_my_tag(), and set_cys_types().

◆ allow_l_cys_

bool protocols::denovo_design::DisulfidizeMover::allow_l_cys_

private

Can disulfides involve L-cystine?

Default true

Referenced by find_possible_disulfides(), make_disulfide(), mixed_disulfide(), parse_my_tag(), and set_cys_types().

◆ include_current_ds_

bool protocols::denovo_design::DisulfidizeMover::include_current_ds_

private

Referenced by parse_my_tag(), process_pose(), and set_include_current_ds().

◆ keep_all_ds_

bool protocols::denovo_design::DisulfidizeMover::keep_all_ds_ = false

private

Referenced by parse_my_tag(), and process_pose().

◆ keep_current_ds_

bool protocols::denovo_design::DisulfidizeMover::keep_current_ds_

private

Referenced by find_possible_disulfides(), parse_my_tag(), process_pose(), and set_keep_current_ds().

◆ match_rt_limit_

core::Real protocols::denovo_design::DisulfidizeMover::match_rt_limit_

private

Referenced by check_disulfide_match_rt(), parse_my_tag(), and set_match_rt_limit().

◆ max_dist_sq_

core::Real protocols::denovo_design::DisulfidizeMover::max_dist_sq_

private

Referenced by check_disulfide_cb_distance(), and set_max_dist().

◆ max_disulf_score_

core::Real protocols::denovo_design::DisulfidizeMover::max_disulf_score_

private

Referenced by check_disulfide_score(), parse_my_tag(), and set_max_disulf_score().

◆ max_disulfides_

core::Size protocols::denovo_design::DisulfidizeMover::max_disulfides_

private

Referenced by parse_my_tag(), process_pose(), recursive_multiple_disulfide_former(), and set_max_disulfides().

◆ min_disulfides_

core::Size protocols::denovo_design::DisulfidizeMover::min_disulfides_

private

Referenced by parse_my_tag(), process_pose(), and set_min_disulfides().

◆ min_loop_

core::Size protocols::denovo_design::DisulfidizeMover::min_loop_

private

Referenced by check_disulfide_seqpos(), parse_my_tag(), and set_min_loop().

◆ mutate_gly_

bool protocols::denovo_design::DisulfidizeMover::mutate_gly_

private

Can GLY be mutated?

Referenced by check_residue_type(), parse_my_tag(), and set_mutate_gly().

◆ mutate_pro_

bool protocols::denovo_design::DisulfidizeMover::mutate_pro_

private

Can PRO be mutated?

Referenced by check_residue_type(), parse_my_tag(), and set_mutate_pro().

◆ score_or_matchrt_

bool protocols::denovo_design::DisulfidizeMover::score_or_matchrt_

private

Referenced by find_possible_disulfides(), parse_my_tag(), and set_score_or_matchrt().

◆ set1_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::DisulfidizeMover::set1_selector_

private

disulfides connect residues from set1 to residues from set2

Referenced by process_pose(), and set_set1_selector().

◆ set2_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::DisulfidizeMover::set2_selector_

private

Referenced by process_pose(), and set_set2_selector().

◆ sfxn_

core::scoring::ScoreFunctionOP protocols::denovo_design::DisulfidizeMover::sfxn_ = nullptr

private

The scorefunction that we will use for: – scoring disulfides – repacking/minimizing disulfides.

Set by user, or obtained from globals if null.

Referenced by DisulfidizeMover(), process_pose(), and set_scorefxn().

◆ sort_sfxn_

core::scoring::ScoreFunctionCOP protocols::denovo_design::DisulfidizeMover::sort_sfxn_ = nullptr

private

Referenced by DisulfidizeMover(), process_pose(), and set_sort_scorefxn().

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

src/protocols/denovo_design/movers/DisulfidizeMover.hh
src/protocols/denovo_design/movers/DisulfidizeMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Member Typedef Documentation

◆ DisulfideList

◆ PoseList

Constructor & Destructor Documentation

◆ DisulfidizeMover() [1/2]

DisulfidizeMover main code:

◆ DisulfidizeMover() [2/2]

◆ ~DisulfidizeMover()

Member Function Documentation

◆ build_and_score_disulfide()

◆ check_disulfide_cb_distance()

◆ check_disulfide_match_rt()

◆ check_disulfide_score()

◆ check_disulfide_seqpos()

◆ check_residue_type()

◆ clone()

◆ find_current_disulfides()

◆ find_possible_disulfides() [1/2]

◆ find_possible_disulfides() [2/2]

◆ get_name()

◆ make_disulfide()

◆ make_disulfides()

◆ mixed_disulfide()

◆ mover_name()

◆ mutate_disulfides_to_ala()

◆ noncanonical_disulfide()

◆ parse_my_tag()

◆ process_pose()

◆ provide_xml_schema()

◆ prune_symmetric_disulfides()

◆ recursive_multiple_disulfide_former()

◆ set_cys_types()

◆ set_include_current_ds()

◆ set_keep_current_ds()

◆ set_match_rt_limit()

◆ set_max_dist()

◆ set_max_disulf_score()

◆ set_max_disulfides()

◆ set_min_disulfides()

◆ set_min_loop()

◆ set_mutate_gly()

◆ set_mutate_pro()

◆ set_score_or_matchrt()

◆ set_scorefxn()

◆ set_set1_selector()

◆ set_set2_selector()

◆ set_sort_scorefxn()

◆ tag_disulfide()

◆ tag_disulfides()

Member Data Documentation

◆ allow_beta_cys_

◆ allow_d_cys_

◆ allow_l_cys_

◆ include_current_ds_

◆ keep_all_ds_

◆ keep_current_ds_

◆ match_rt_limit_

◆ max_dist_sq_

◆ max_disulf_score_

◆ max_disulfides_

◆ min_disulfides_

◆ min_loop_

◆ mutate_gly_

◆ mutate_pro_

◆ score_or_matchrt_

◆ set1_selector_

◆ set2_selector_

◆ sfxn_

◆ sort_sfxn_