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protocols::forge::remodel::RemodelConstraintGenerator Class Referenceabstract

pure virtual base class More...

#include <RemodelConstraintGenerator.hh>

Inheritance diagram for protocols::forge::remodel::RemodelConstraintGenerator:
Inheritance graph
Collaboration diagram for protocols::forge::remodel::RemodelConstraintGenerator:
Collaboration graph

Public Types

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::string > Strings

Public Member Functions

virtual ~RemodelConstraintGenerator ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
virtual void apply (core::pose::Pose &pose)
 generates constraints and adds them to the pose More...
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 This is called if this mover is instantiated from XML. More...
 RemodelConstraintGenerator ()
 RemodelConstraintGenerator (RemodelConstraintGenerator const &rval)
void add_remodel_constraints_to_pose (core::pose::Pose &pose)
void remove_remodel_constraints_from_pose (core::pose::Pose &pose) const
virtual void generate_remodel_constraints (core::pose::Pose const &pose)=0
virtual void init (core::pose::Pose const &)
 Pose-specific setup routines go here. More...
VarLengthBuildAP vlb () const
void set_vlb (VarLengthBuildAP vlb)
std::string id () const
void set_id (std::string const &id)
void set_seqmap (core::id::SequenceMappingCOP seqmap)
core::id::SequenceMappingCOP seqmap () const
- 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)
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
virtual std::string get_name () const =0
 Each derived class must specify its name. The class name. More...
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...
virtual MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const

Static Public Member Functions

lookup_stored_constraints (std::string const &id)
- 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

void add_constraint (core::scoring::constraints::ConstraintCOP cst)
void add_constraints (core::scoring::constraints::ConstraintCOPs csts)
void clear_constraints ()
void clear_stored_constraints ()
void store_constraints ()
- 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...

Private Attributes

std::string id_
core::scoring::constraints::ConstraintCOPs csts_
core::id::SequenceMappingCOP seqmap_
VarLengthBuildAP vlb_

Static Private Attributes

static std::map< std::string,

Detailed Description

pure virtual base class

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelConstraintGenerator::~RemodelConstraintGenerator ( )

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

protocols::forge::remodel::RemodelConstraintGenerator::RemodelConstraintGenerator ( )
protocols::forge::remodel::RemodelConstraintGenerator::RemodelConstraintGenerator ( RemodelConstraintGenerator const &  rval)

Member Function Documentation

void protocols::forge::remodel::RemodelConstraintGenerator::add_constraint ( core::scoring::constraints::ConstraintCOP  cst)
void protocols::forge::remodel::RemodelConstraintGenerator::add_constraints ( core::scoring::constraints::ConstraintCOPs  csts)
void protocols::forge::remodel::RemodelConstraintGenerator::add_remodel_constraints_to_pose ( core::pose::Pose pose)
void protocols::forge::remodel::RemodelConstraintGenerator::apply ( core::pose::Pose pose)

generates constraints and adds them to the pose

When called, generates constraints for the pose, and adds them to the pose

Implements protocols::moves::Mover.

Reimplemented in protocols::forge::constraints::InvrotTreeRCG.

References add_remodel_constraints_to_pose(), and init().

void protocols::forge::remodel::RemodelConstraintGenerator::clear_constraints ( )
void protocols::forge::remodel::RemodelConstraintGenerator::clear_stored_constraints ( )
virtual void protocols::forge::remodel::RemodelConstraintGenerator::generate_remodel_constraints ( core::pose::Pose const &  pose)
pure virtual
std::string protocols::forge::remodel::RemodelConstraintGenerator::id ( ) const

References id_.

Referenced by set_id().

virtual void protocols::forge::remodel::RemodelConstraintGenerator::init ( core::pose::Pose const &  )

Pose-specific setup routines go here.

Reimplemented in protocols::forge::constraints::InvrotTreeRCG.

Referenced by apply().

core::scoring::constraints::ConstraintCOPs const protocols::forge::remodel::RemodelConstraintGenerator::lookup_stored_constraints ( std::string const &  id)
void protocols::forge::remodel::RemodelConstraintGenerator::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap ,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &   

This is called if this mover is instantiated from XML.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::forge::remodel::ResidueVicinityRCG.

References protocols::moves::Mover::get_name(), id_, and protocols::forge::remodel::TR().

Referenced by protocols::forge::remodel::ResidueVicinityRCG::parse_my_tag().

void protocols::forge::remodel::RemodelConstraintGenerator::remove_remodel_constraints_from_pose ( core::pose::Pose pose) const
core::id::SequenceMappingCOP protocols::forge::remodel::RemodelConstraintGenerator::seqmap ( ) const
void protocols::forge::remodel::RemodelConstraintGenerator::set_id ( std::string const &  id)

References id(), and id_.

void protocols::forge::remodel::RemodelConstraintGenerator::set_seqmap ( core::id::SequenceMappingCOP  seqmap)

References seqmap(), and seqmap_.

void protocols::forge::remodel::RemodelConstraintGenerator::set_vlb ( VarLengthBuildAP  vlb)

References vlb(), and vlb_.

void protocols::forge::remodel::RemodelConstraintGenerator::store_constraints ( )
RemodelConstraintGenerator::VarLengthBuildAP protocols::forge::remodel::RemodelConstraintGenerator::vlb ( ) const

Member Data Documentation

std::map< std::string, core::scoring::constraints::ConstraintCOPs > protocols::forge::remodel::RemodelConstraintGenerator::cst_map_
core::scoring::constraints::ConstraintCOPs protocols::forge::remodel::RemodelConstraintGenerator::csts_
std::string protocols::forge::remodel::RemodelConstraintGenerator::id_
core::id::SequenceMappingCOP protocols::forge::remodel::RemodelConstraintGenerator::seqmap_

Referenced by seqmap(), and set_seqmap().

VarLengthBuildAP protocols::forge::remodel::RemodelConstraintGenerator::vlb_

Referenced by set_vlb(), and vlb().

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