#include <TryDisulfPermutations.hh>

Inheritance diagram for protocols::cyclic_peptide::TryDisulfPermutations:

Public Member Functions
	TryDisulfPermutations ()
	Creator for TryDisulfPermutations mover. More...

	TryDisulfPermutations (TryDisulfPermutations const &src)
	Copy constructor for TryDisulfPermutations mover. More...

	~TryDisulfPermutations () override
	Destructor for TryDisulfPermutations mover. More...

protocols::moves::MoverOP	clone () const override
	Clone operator to create a pointer to a fresh TryDisulfPermutations object that copies this one. More...

protocols::moves::MoverOP	fresh_instance () const override
	Fresh_instance operator to create a pointer to a fresh TryDisulfPermutations object that does NOT copy this one. More...

void	apply (core::pose::Pose &pose) override
	Actually apply the mover to the pose. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &) override
	Returns the name of this mover ("TryDisulfPermutations"). More...

bool	consider_already_bonded () const
	Will this mover consider alternative disulfides involving residues currently in a disulfide bond? More...

void	set_consider_already_bonded (bool const setting)
	Set whether this mover will consider alternative disulfides involving residues currently in a disulfide bond. More...

std::string const &	mintype () const
	Get the minmization flavour. More...

void	set_mintype (std::string const &type)
	Set the minimization flavour. More...

core::Real const &	mintolerance () const
	Get the minimizer tolerance. More...

void	set_mintolerance (core::Real const &val)
	Set the minimizer tolerance. More...

void	set_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Set the residue selector. More...

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

bool	mover_is_unpublished () const override
	Indicate that this mover is unpublished. More...

utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const override
	Provide authorship information for an unpublished Rosetta module. 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 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 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...

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::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	generate_disulf_permutations (utility::vector1< core::Size > const &residues, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &permutations) const
	Given a list of disulfide-forming residues, generate all possible permtutations. More...

void	recursively_generate_permutation (utility::vector1< std::pair< core::Size, core::Size > > &cur_permutation, utility::vector1< core::Size > const &residues, utility::vector1< bool > &placed, utility::vector1< core::Size > const &index, core::Size const &level) const
	Given a permutation index, generate a permutation. More...

void	increment_index (utility::vector1< core::Size > &index, core::Size const index_index, core::Size const max_levels) const
	Increment the perturbation index. More...

void	generate_disulfides (core::pose::PoseOP pose, utility::vector1< std::pair< core::Size, core::Size > > disulf_pairs) const
	Given a set of disulfides to form, make these disulfide bonds. More...

core::Real	repack_minimize_disulfides (core::pose::PoseOP pose, utility::vector1< core::Size > const &disulf_res) const
	Repack and minimize a set of disulfides, using only the fa_dslf and fa_dun score terms. More...

bool	is_in_list (core::Size const val, utility::vector1< core::Size > const &list) const
	Is a value in a list? More...

Private Attributes
bool	consider_already_bonded_
	Should we consider residues that are already disulfide-bonded (i.e. let them form other disulfides), or should we just consider unbonded disulfide-formers? More...

std::string	mintype_
	The minimizer behaviour. More...

core::Real	mintolerance_
	The minimizer tolerance. More...

core::select::residue_selector::ResidueSelectorOP	selector_
	An optional ResidueSelector, for applying this mover to a subset of a pose. 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 protocols::filters::Filters_map	Filters_map

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...

Constructor & Destructor Documentation

protocols::cyclic_peptide::TryDisulfPermutations::TryDisulfPermutations ( )

Creator for TryDisulfPermutations mover.

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

Copy constructor for TryDisulfPermutations mover.

Creator for TryDisulfPermutations mover.

References selector_.

protocols::cyclic_peptide::TryDisulfPermutations::~TryDisulfPermutations ( )

overridedefault

Destructor for TryDisulfPermutations mover.

Member Function Documentation

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

overridevirtual

Actually apply the mover to the pose.

Implements protocols::moves::Mover.

References core::pose::Pose::clone(), consider_already_bonded(), generate_disulf_permutations(), generate_disulfides(), core::chemical::ResidueTypeBase::get_disulfide_atom_name(), core::chemical::ResidueType::is_disulfide_bonded(), repack_minimize_disulfides(), core::pose::Pose::residue(), selector_, core::pose::Pose::size(), protocols::cyclic_peptide::TR(), and core::conformation::Residue::type().

protocols::moves::MoverOP protocols::cyclic_peptide::TryDisulfPermutations::clone ( ) const

overridevirtual

Clone operator to create a pointer to a fresh TryDisulfPermutations object that copies this one.

Reimplemented from protocols::moves::Mover.

bool protocols::cyclic_peptide::TryDisulfPermutations::consider_already_bonded ( ) const

inline

Will this mover consider alternative disulfides involving residues currently in a disulfide bond?

References consider_already_bonded_.

Referenced by apply(), and parse_my_tag().

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

overridevirtual

Fresh_instance operator to create a pointer to a fresh TryDisulfPermutations object that does NOT copy this one.

Reimplemented from protocols::moves::Mover.

void protocols::cyclic_peptide::TryDisulfPermutations::generate_disulf_permutations	(	utility::vector1< core::Size > const &	residues,
		utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &	permutations
	)		const

private

Given a list of disulfide-forming residues, generate all possible permtutations.

Parameters

[in]	residues	The list of disulfide-forming positions.
[out]	permutations	The list of lists of disulfide pairs representing all possible permutations.

Note that this function does NOT clear the permutations vector; it only appends to it.

References increment_index(), recursively_generate_permutation(), and protocols::cyclic_peptide::TR().

Referenced by apply().

void protocols::cyclic_peptide::TryDisulfPermutations::generate_disulfides	(	core::pose::PoseOP	pose,
		utility::vector1< std::pair< core::Size, core::Size > >	disulf_pairs
	)		const

private

Given a set of disulfides to form, make these disulfide bonds.

References core::conformation::form_disulfide().

Referenced by apply().

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::cyclic_peptide::TryDisulfPermutations::increment_index	(	utility::vector1< core::Size > &	index,
		core::Size const	index_index,
		core::Size const	max_levels
	)		const

private

Increment the perturbation index.

Recursively calls itself.

Referenced by generate_disulf_permutations().

bool protocols::cyclic_peptide::TryDisulfPermutations::is_in_list	(	core::Size const	val,
		utility::vector1< core::Size > const &	list
	)		const

inlineprivate

Is a value in a list?

Referenced by repack_minimize_disulfides().

core::Real const& protocols::cyclic_peptide::TryDisulfPermutations::mintolerance ( ) const

inline

Get the minimizer tolerance.

References mintolerance_.

Referenced by parse_my_tag(), and repack_minimize_disulfides().

std::string const& protocols::cyclic_peptide::TryDisulfPermutations::mintype ( ) const

inline

Get the minmization flavour.

References mintype_.

Referenced by parse_my_tag(), and repack_minimize_disulfides().

bool protocols::cyclic_peptide::TryDisulfPermutations::mover_is_unpublished ( ) const

overridevirtual

Indicate that this mover is unpublished.

Reimplemented from protocols::moves::Mover.

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

static

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

void protocols::cyclic_peptide::TryDisulfPermutations::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &
	)

overridevirtual

Returns the name of this mover ("TryDisulfPermutations").

parse XML (specifically in the context of the parser/Rosetta_scripting scheme)

Reimplemented from protocols::moves::Mover.

References consider_already_bonded(), protocols::pack_daemon::error_message, mintolerance(), mintype(), set_consider_already_bonded(), set_mintolerance(), set_mintype(), set_selector(), and protocols::cyclic_peptide::TR().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::cyclic_peptide::TryDisulfPermutations::provide_authorship_info_for_unpublished ( ) const

overridevirtual

Provide authorship information for an unpublished Rosetta module.

Reimplemented from protocols::moves::Mover.

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

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

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

void protocols::cyclic_peptide::TryDisulfPermutations::recursively_generate_permutation	(	utility::vector1< std::pair< core::Size, core::Size > > &	cur_permutation,
		utility::vector1< core::Size > const &	residues,
		utility::vector1< bool > &	placed,
		utility::vector1< core::Size > const &	index,
		core::Size const &	level
	)		const

private

Given a permutation index, generate a permutation.

Assumes that cur_permutation is an empty vector. Recursively calls itself.

Referenced by generate_disulf_permutations().

core::Real protocols::cyclic_peptide::TryDisulfPermutations::repack_minimize_disulfides	(	core::pose::PoseOP	pose,
		utility::vector1< core::Size > const &	disulf_res
	)		const

private

Repack and minimize a set of disulfides, using only the fa_dslf and fa_dun score terms.

Returns the fa_dslf energy after repacking and minimization.

References core::scoring::dslf_fa13, core::scoring::fa_dun, is_in_list(), mintolerance(), and mintype().

Referenced by apply().

void protocols::cyclic_peptide::TryDisulfPermutations::set_consider_already_bonded ( bool const setting )

inline

Set whether this mover will consider alternative disulfides involving residues currently in a disulfide bond.

References consider_already_bonded_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::TryDisulfPermutations::set_mintolerance ( core::Real const & val )

inline

Set the minimizer tolerance.

References mintolerance_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::TryDisulfPermutations::set_mintype ( std::string const & type )

inline

Set the minimization flavour.

References mintype_, and protocols::moves::Mover::type().

Referenced by parse_my_tag().

void protocols::cyclic_peptide::TryDisulfPermutations::set_selector ( core::select::residue_selector::ResidueSelectorCOP selector_in )

Set the residue selector.

CLONES the input.

References selector_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::cyclic_peptide::TryDisulfPermutations::consider_already_bonded_

private

Should we consider residues that are already disulfide-bonded (i.e. let them form other disulfides), or should we just consider unbonded disulfide-formers?

Default true (considers everything).

Referenced by consider_already_bonded(), and set_consider_already_bonded().

core::Real protocols::cyclic_peptide::TryDisulfPermutations::mintolerance_

private

The minimizer tolerance.

Referenced by mintolerance(), and set_mintolerance().

std::string protocols::cyclic_peptide::TryDisulfPermutations::mintype_

private

The minimizer behaviour.

Referenced by mintype(), and set_mintype().

core::select::residue_selector::ResidueSelectorOP protocols::cyclic_peptide::TryDisulfPermutations::selector_

private