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protocols::dna::SeparateDnaFromNonDna Class Reference

#include <SeparateDnaFromNonDna.hh>

Inheritance diagram for protocols::dna::SeparateDnaFromNonDna:
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Collaboration diagram for protocols::dna::SeparateDnaFromNonDna:
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Public Member Functions

 SeparateDnaFromNonDna ()
 
 SeparateDnaFromNonDna (core::Real x, core::Real y, core::Real z)
 
 SeparateDnaFromNonDna (numeric::xyzVector< core::Real > const &xyz)
 
 SeparateDnaFromNonDna (SeparateDnaFromNonDna const &other)
 
virtual ~SeparateDnaFromNonDna ()
 
virtual void apply (core::pose::Pose &pose)
 set up an appropriate fold tree for a non-DNA/DNA interface, and simply pull apart non-DNA and DNA More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
numeric::xyzVector< core::Realtranslation () const
 
virtual void parse_my_tag (TagPtr const, moves::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, Pose const &)
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
virtual moves::MoverOP fresh_instance () const
 required in the context of the parser/scripting scheme More...
 
virtual moves::MoverOP clone () const
 required in the context of the parser/scripting scheme More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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
 
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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Attributes

numeric::xyzVector< core::Realtranslation_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...
 

Constructor & Destructor Documentation

protocols::dna::SeparateDnaFromNonDna::SeparateDnaFromNonDna ( )

Referenced by clone(), and fresh_instance().

protocols::dna::SeparateDnaFromNonDna::SeparateDnaFromNonDna ( core::Real  x,
core::Real  y,
core::Real  z 
)
protocols::dna::SeparateDnaFromNonDna::SeparateDnaFromNonDna ( numeric::xyzVector< core::Real > const &  xyz)
protocols::dna::SeparateDnaFromNonDna::SeparateDnaFromNonDna ( SeparateDnaFromNonDna const &  other)
protocols::dna::SeparateDnaFromNonDna::~SeparateDnaFromNonDna ( )
virtual

Member Function Documentation

void protocols::dna::SeparateDnaFromNonDna::apply ( core::pose::Pose pose)
virtual

set up an appropriate fold tree for a non-DNA/DNA interface, and simply pull apart non-DNA and DNA

addition fold-tree considerations will have to be made if there are any 'non-DNA' chains that should stick to the DNA instead of to the non-DNA group

Implements protocols::moves::Mover.

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::pose::Pose::num_jump(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), core::pose::Pose::set_jump(), core::pose::Pose::total_residue(), protocols::dna::TR(), and translation_.

Referenced by protocols::dna::DnaInterfacePacker::unbound_score().

moves::MoverOP protocols::dna::SeparateDnaFromNonDna::clone ( ) const
virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

References SeparateDnaFromNonDna().

moves::MoverOP protocols::dna::SeparateDnaFromNonDna::fresh_instance ( ) const
virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

References SeparateDnaFromNonDna().

std::string protocols::dna::SeparateDnaFromNonDna::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

References protocols::dna::SeparateDnaFromNonDnaCreator::mover_name().

void protocols::dna::SeparateDnaFromNonDna::parse_my_tag ( TagPtr const  ,
moves::DataMap ,
protocols::filters::Filters_map const &  ,
moves::Movers_map const &  ,
Pose const &   
)
virtual

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

Reimplemented from protocols::moves::Mover.

numeric::xyzVector< core::Real > protocols::dna::SeparateDnaFromNonDna::translation ( ) const
inline

References translation_.

Member Data Documentation

numeric::xyzVector< core::Real > protocols::dna::SeparateDnaFromNonDna::translation_
private

Referenced by apply(), and translation().


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