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protocols::cyclic_peptide::TryDisulfPermutations Class Reference

#include <TryDisulfPermutations.hh>

Inheritance diagram for protocols::cyclic_peptide::TryDisulfPermutations:
Inheritance graph
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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) 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 Indicate that this mover is unpublished.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 Provide authorship information for an unpublished Rosetta module.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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 

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 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
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]residuesThe list of disulfide-forming positions.
[out]permutationsThe 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
void protocols::cyclic_peptide::TryDisulfPermutations::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
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, core::select::residue_selector::get_residue_selector(), 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
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

An optional ResidueSelector, for applying this mover to a subset of a pose.

Referenced by apply(), set_selector(), and TryDisulfPermutations().


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