Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes | Static Private Attributes | List of all members
protocols::forge::remodel::RemodelConstraintGenerator Class Referenceabstract

pure virtual base class More...

#include <RemodelConstraintGenerator.hh>

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

Public Types

typedef protocols::forge::components::VarLengthBuildAP VarLengthBuildAP
- 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

 ~RemodelConstraintGenerator () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
void apply (core::pose::Pose &pose) override
 generates constraints and adds them to the pose More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 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
core::scoring::constraints::ConstraintCOPs const & constraints () const
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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
virtual std::string get_name () const =0
 Each derived class must specify its name. The class name. More...
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 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 core::scoring::constraints::ConstraintCOPs const lookup_stored_constraints (std::string const &id)
static void attributes_for_remodel_constraint_generator (utility::tag::AttributeList &)
- 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...

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, core::scoring::constraints::ConstraintCOPscst_map_

Detailed Description

pure virtual base class

Member Typedef Documentation

◆ VarLengthBuildAP

Constructor & Destructor Documentation

◆ ~RemodelConstraintGenerator()

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

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

◆ RemodelConstraintGenerator() [1/2]

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

◆ RemodelConstraintGenerator() [2/2]

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

Member Function Documentation

◆ add_constraint()

void protocols::forge::remodel::RemodelConstraintGenerator::add_constraint ( core::scoring::constraints::ConstraintCOP  cst)

◆ add_constraints()

void protocols::forge::remodel::RemodelConstraintGenerator::add_constraints ( core::scoring::constraints::ConstraintCOPs  csts)

◆ add_remodel_constraints_to_pose()

void protocols::forge::remodel::RemodelConstraintGenerator::add_remodel_constraints_to_pose ( core::pose::Pose pose)

◆ apply()

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.

References add_remodel_constraints_to_pose(), and init().

◆ attributes_for_remodel_constraint_generator()

void protocols::forge::remodel::RemodelConstraintGenerator::attributes_for_remodel_constraint_generator ( utility::tag::AttributeList &  attlist)

◆ clear_constraints()

void protocols::forge::remodel::RemodelConstraintGenerator::clear_constraints ( )

◆ clear_stored_constraints()

void protocols::forge::remodel::RemodelConstraintGenerator::clear_stored_constraints ( )

◆ constraints()

core::scoring::constraints::ConstraintCOPs const & protocols::forge::remodel::RemodelConstraintGenerator::constraints ( ) const

References csts_.

◆ generate_remodel_constraints()

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

◆ id()

std::string protocols::forge::remodel::RemodelConstraintGenerator::id ( ) const

References id_.

Referenced by set_id().

◆ init()

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().

◆ lookup_stored_constraints()

core::scoring::constraints::ConstraintCOPs const protocols::forge::remodel::RemodelConstraintGenerator::lookup_stored_constraints ( std::string const &  id)

◆ parse_my_tag()

void protocols::forge::remodel::RemodelConstraintGenerator::parse_my_tag ( utility::tag::TagCOP  tag,

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().

◆ remove_remodel_constraints_from_pose()

void protocols::forge::remodel::RemodelConstraintGenerator::remove_remodel_constraints_from_pose ( core::pose::Pose pose) const

◆ seqmap()

core::id::SequenceMappingCOP protocols::forge::remodel::RemodelConstraintGenerator::seqmap ( ) const

◆ set_id()

void protocols::forge::remodel::RemodelConstraintGenerator::set_id ( std::string const &  id)

◆ set_seqmap()

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

References seqmap(), and seqmap_.

◆ set_vlb()

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

References vlb(), and vlb_.

◆ store_constraints()

void protocols::forge::remodel::RemodelConstraintGenerator::store_constraints ( )

◆ vlb()

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

Member Data Documentation

◆ cst_map_

std::map< std::string, core::scoring::constraints::ConstraintCOPs > protocols::forge::remodel::RemodelConstraintGenerator::cst_map_

◆ csts_

core::scoring::constraints::ConstraintCOPs protocols::forge::remodel::RemodelConstraintGenerator::csts_

◆ id_

std::string protocols::forge::remodel::RemodelConstraintGenerator::id_

◆ seqmap_

core::id::SequenceMappingCOP protocols::forge::remodel::RemodelConstraintGenerator::seqmap_

Referenced by seqmap(), and set_seqmap().

◆ vlb_

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

Referenced by set_vlb(), and vlb().

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