pure virtual base class More...

#include <RemodelConstraintGenerator.hh>

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

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

Public Types
typedef protocols::forge::components::VarLengthBuildAP	VarLengthBuildAP

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

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)

Mover &	operator= (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 Strings &	info ()
	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
static core::scoring::constraints::ConstraintCOPs const	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, core::scoring::constraints::ConstraintCOPs >	cst_map_

Detailed Description

pure virtual base class

Definition at line 47 of file RemodelConstraintGenerator.hh.

Member Typedef Documentation

typedef protocols::forge::components::VarLengthBuildAP protocols::forge::remodel::RemodelConstraintGenerator::VarLengthBuildAP

Definition at line 64 of file RemodelConstraintGenerator.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 35 of file RemodelConstraintGenerator.cc.

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

Definition at line 39 of file RemodelConstraintGenerator.cc.

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

Definition at line 46 of file RemodelConstraintGenerator.cc.

Member Function Documentation

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

protected

Definition at line 114 of file RemodelConstraintGenerator.cc.

References csts_.

Referenced by add_constraints(), protocols::forge::constraints::NtoC_RCG::generate_remodel_constraints(), protocols::forge::constraints::InvrotTreeRCG::generate_remodel_constraints(), protocols::forge::constraints::InverseRotamersRCG::generate_remodel_constraints(), and protocols::forge::remodel::ResidueVicinityRCG::generate_remodel_constraints().

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

protected

Definition at line 120 of file RemodelConstraintGenerator.cc.

References add_constraint().

Referenced by protocols::forge::constraints::ConstraintFileRCG::generate_remodel_constraints(), and protocols::fldsgn::SheetConstraintsRCG::generate_remodel_constraints().

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

Definition at line 75 of file RemodelConstraintGenerator.cc.

References core::pose::Pose::add_constraints(), clear_constraints(), csts_, generate_remodel_constraints(), and store_constraints().

Referenced by apply(), and protocols::forge::constraints::InvrotTreeRCG::apply().

void protocols::forge::remodel::RemodelConstraintGenerator::apply ( core::pose::Pose & pose)

virtual

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.

Definition at line 55 of file RemodelConstraintGenerator.cc.

References add_remodel_constraints_to_pose(), and init().

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

protected

Definition at line 129 of file RemodelConstraintGenerator.cc.

References clear_stored_constraints(), and csts_.

Referenced by add_remodel_constraints_to_pose(), and protocols::forge::remodel::ResidueVicinityRCG::generate_remodel_constraints().

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

protected

Definition at line 173 of file RemodelConstraintGenerator.cc.

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

Referenced by clear_constraints(), and store_constraints().

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

pure virtual

Implemented in protocols::forge::remodel::ResidueVicinityRCG, protocols::forge::constraints::InverseRotamersRCG, protocols::forge::constraints::InvrotTreeRCG, protocols::fldsgn::SheetConstraintsRCG, protocols::forge::constraints::NtoC_RCG, and protocols::forge::constraints::ConstraintFileRCG.

Referenced by add_remodel_constraints_to_pose().

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

Definition at line 148 of file RemodelConstraintGenerator.cc.

References id_.

Referenced by set_id().

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

inlinevirtual

Pose-specific setup routines go here.

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

Definition at line 95 of file RemodelConstraintGenerator.hh.

Referenced by apply().

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

static

Definition at line 200 of file RemodelConstraintGenerator.cc.

References cst_map_.

Referenced by protocols::forge::constraints::RemoveCsts::apply().

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 &
	)