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protocols::pose_creation::MakePolyXMover Class Reference

#include <MakePolyXMover.hh>

Inheritance diagram for protocols::pose_creation::MakePolyXMover:
Inheritance graph
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Public Types

typedef protocols::moves::MoverOP MoverOP
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
typedef
core::select::residue_selector::ResidueSelectorOP 
ResidueSelectorOP
 
typedef
core::select::residue_selector::ResidueSelectorCOP 
ResidueSelectorCOP
 
- 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

 MakePolyXMover ()
 
 MakePolyXMover (std::string const &aa, bool keep_pro, bool keep_gly, bool keep_disulfide_cys)
 
 ~MakePolyXMover () override
 
protocols::moves::MoverOP clone () const override
 clone this object More...
 
protocols::moves::MoverOP fresh_instance () const override
 create this type of object More...
 
void apply (core::pose::Pose &pose) override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 parse xml More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_chis (utility::vector1< core::Real > chis)
 
- 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...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string 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 Attributes

std::string aa_
 using amino acid for converting pose to poly XXX More...
 
bool keep_pro_
 if true, proline, proline are not converted More...
 
bool keep_gly_
 if true, proline, glycine are not converted More...
 
bool keep_disulfide_cys_
 if true, proline, cystein are not converted More...
 
ResidueSelectorCOP selector_
 selects which residues to mutate More...
 
utility::vector1< core::Realchis_
 Use specific chis after mutating. More...
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::pose_creation::MakePolyXMover::DataMap

Constructor & Destructor Documentation

protocols::pose_creation::MakePolyXMover::MakePolyXMover ( )
protocols::pose_creation::MakePolyXMover::MakePolyXMover ( std::string const &  aa,
bool  keep_pro,
bool  keep_gly,
bool  keep_disulfide_cys 
)
protocols::pose_creation::MakePolyXMover::~MakePolyXMover ( )
overridedefault

Member Function Documentation

void protocols::pose_creation::MakePolyXMover::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::pose_creation::MakePolyXMover::clone ( ) const
overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::pose_creation::MakePolyXMover::fresh_instance ( ) const
overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

std::string protocols::pose_creation::MakePolyXMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::pose_creation::MakePolyXMover::mover_name ( )
static
void protocols::pose_creation::MakePolyXMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::pose_creation::MakePolyXMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::pose_creation::MakePolyXMover::set_chis ( utility::vector1< core::Real chis)
inline

References chis_.

Member Data Documentation

std::string protocols::pose_creation::MakePolyXMover::aa_
private

using amino acid for converting pose to poly XXX

Referenced by apply(), and parse_my_tag().

utility::vector1< core::Real > protocols::pose_creation::MakePolyXMover::chis_
private

Use specific chis after mutating.

Referenced by apply(), parse_my_tag(), and set_chis().

bool protocols::pose_creation::MakePolyXMover::keep_disulfide_cys_
private

if true, proline, cystein are not converted

Referenced by apply(), and parse_my_tag().

bool protocols::pose_creation::MakePolyXMover::keep_gly_
private

if true, proline, glycine are not converted

Referenced by apply(), and parse_my_tag().

bool protocols::pose_creation::MakePolyXMover::keep_pro_
private

if true, proline, proline are not converted

Referenced by apply(), and parse_my_tag().

ResidueSelectorCOP protocols::pose_creation::MakePolyXMover::selector_
private

selects which residues to mutate

Referenced by apply(), and parse_my_tag().


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