Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::denovo_design::movers::BridgeChainsMover Class Reference

Creates a bridge connection between two chains using remodel. More...

#include <BridgeChainsMover.hh>

Inheritance diagram for protocols::denovo_design::movers::BridgeChainsMover:
Inheritance graph

Public Member Functions

 BridgeChainsMover ()
 BridgeChainsMover (std::string const &class_name)
 subclasses should call this constructor More...
 ~BridgeChainsMover () override
void apply (core::pose::Pose &pose) override
 Main Method. More...
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML tag (to use this Mover in Rosetta Scripts) 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...
connection::ConnectionArchitect const & architect () const
void set_id (std::string const &my_id)
void set_segment1_ids (std::string const &segments)
void set_segment2_ids (std::string const &segments)
void set_motifs (std::string const &motifs_str, std::string const &cut_resis_str)
core::Size overlap () const
void set_overlap (core::Size const overlap_val)
void set_iterations (core::Size const iterations)
core::scoring::ScoreFunction const & scorefxn () const
void set_scorefxn (core::scoring::ScoreFunction const &sfxn)
bool dry_run () const
void set_dry_run (bool const dry_run)
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...
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 Stringsinfo ()
 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 void setup_attlist_for_derived_classes (utility::tag::AttributeList &attlist)
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

connection::ConnectionArchitectOP architect_
core::scoring::ScoreFunctionOP scorefxn_
core::Size overlap_
core::Size iterations_
bool dry_run_

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

Creates a bridge connection between two chains using remodel.

Constructor & Destructor Documentation

◆ BridgeChainsMover() [1/2]

protocols::denovo_design::movers::BridgeChainsMover::BridgeChainsMover ( )

◆ BridgeChainsMover() [2/2]

protocols::denovo_design::movers::BridgeChainsMover::BridgeChainsMover ( std::string const &  class_name)

subclasses should call this constructor

◆ ~BridgeChainsMover()

protocols::denovo_design::movers::BridgeChainsMover::~BridgeChainsMover ( )

Member Function Documentation

◆ apply()

void protocols::denovo_design::movers::BridgeChainsMover::apply ( core::pose::Pose )

◆ architect()

connection::ConnectionArchitect const & protocols::denovo_design::movers::BridgeChainsMover::architect ( ) const

References architect_.

Referenced by apply(), and scorefxn().

◆ clone()

protocols::moves::MoverOP protocols::denovo_design::movers::BridgeChainsMover::clone ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ dry_run()

bool protocols::denovo_design::movers::BridgeChainsMover::dry_run ( ) const

References dry_run_.

Referenced by apply(), and set_dry_run().

◆ fresh_instance()

protocols::moves::MoverOP protocols::denovo_design::movers::BridgeChainsMover::fresh_instance ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::denovo_design::movers::BridgeChainsMover::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::denovo_design::movers::BridgeChainsMover::mover_name ( )

◆ overlap()

core::Size protocols::denovo_design::movers::BridgeChainsMover::overlap ( ) const

References overlap_.

Referenced by apply().

◆ parse_my_tag()

void protocols::denovo_design::movers::BridgeChainsMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

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

Reimplemented from protocols::moves::Mover.

References architect_, dry_run_, iterations_, overlap_, core::scoring::parse_score_function(), set_dry_run(), set_iterations(), set_overlap(), and set_scorefxn().

◆ provide_xml_schema()

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

◆ scorefxn()

core::scoring::ScoreFunction const & protocols::denovo_design::movers::BridgeChainsMover::scorefxn ( ) const

◆ set_dry_run()

void protocols::denovo_design::movers::BridgeChainsMover::set_dry_run ( bool const  dry_run)

References dry_run(), and dry_run_.

Referenced by parse_my_tag().

◆ set_id()

void protocols::denovo_design::movers::BridgeChainsMover::set_id ( std::string const &  my_id)

References architect_.

◆ set_iterations()

void protocols::denovo_design::movers::BridgeChainsMover::set_iterations ( core::Size const  iterations)

References iterations_.

Referenced by parse_my_tag().

◆ set_motifs()

void protocols::denovo_design::movers::BridgeChainsMover::set_motifs ( std::string const &  motifs_str,
std::string const &  cut_resis_str 

References architect_.

◆ set_overlap()

void protocols::denovo_design::movers::BridgeChainsMover::set_overlap ( core::Size const  overlap_val)

References overlap_.

Referenced by parse_my_tag().

◆ set_scorefxn()

void protocols::denovo_design::movers::BridgeChainsMover::set_scorefxn ( core::scoring::ScoreFunction const &  sfxn)

◆ set_segment1_ids()

void protocols::denovo_design::movers::BridgeChainsMover::set_segment1_ids ( std::string const &  segments)

References architect_.

◆ set_segment2_ids()

void protocols::denovo_design::movers::BridgeChainsMover::set_segment2_ids ( std::string const &  segments)

References architect_.

◆ setup_attlist_for_derived_classes()

void protocols::denovo_design::movers::BridgeChainsMover::setup_attlist_for_derived_classes ( utility::tag::AttributeList &  attlist)

◆ show()

void protocols::denovo_design::movers::BridgeChainsMover::show ( std::ostream &  output = std::cout) const

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::denovo_design::movers::operator<<().

Member Data Documentation

◆ architect_

connection::ConnectionArchitectOP protocols::denovo_design::movers::BridgeChainsMover::architect_

◆ dry_run_

bool protocols::denovo_design::movers::BridgeChainsMover::dry_run_

Referenced by dry_run(), parse_my_tag(), and set_dry_run().

◆ iterations_

core::Size protocols::denovo_design::movers::BridgeChainsMover::iterations_

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

◆ overlap_

core::Size protocols::denovo_design::movers::BridgeChainsMover::overlap_

Referenced by overlap(), parse_my_tag(), and set_overlap().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::denovo_design::movers::BridgeChainsMover::scorefxn_

Referenced by apply(), scorefxn(), and set_scorefxn().

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