a RemodelConstraintGenerator wrapper that makes the constraints generated by an InvrotTree available in VLB or XML More...

#include <InvrotTreeRCG.hh>

Inheritance diagram for protocols::forge::constraints::InvrotTreeRCG:

[legend]

Public Member Functions
	InvrotTreeRCG ()

	InvrotTreeRCG (InvrotTreeRCG const &rval)

	InvrotTreeRCG (toolbox::match_enzdes_util::InvrotTreeOP invrot_tree, toolbox::match_enzdes_util::AllowedSeqposForGeomCstOP geomcst_seqpos)

	~InvrotTreeRCG () override

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	generate_remodel_constraints (core::pose::Pose const &pose) override

void	init (core::pose::Pose const &pose) override
	sets up the allowed sequence positions for enzdes geometric constraints More...

void	set_add_ligand_to_pose (bool const add_lig)
	tells the mover whether it should add the ligand to the pose More...

void	set_cstfile (std::string const &cstfilename)
	sets up the invrot_tree_ and enzcst_io_ from an enzdes constraint filename. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

Public Member Functions inherited from protocols::forge::remodel::RemodelConstraintGenerator
	~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

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 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 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 Strings &	info ()
	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 std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::forge::remodel::RemodelConstraintGenerator
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...

Private Attributes
bool	add_ligand_to_pose_

toolbox::match_enzdes_util::InvrotTreeOP	invrot_tree_

toolbox::match_enzdes_util::EnzConstraintIOCOP	enzcst_io_

toolbox::match_enzdes_util::AllowedSeqposForGeomCstOP	geomcst_seqpos_

toolbox::match_enzdes_util::AlignPoseToInvrotTreeMoverOP	setup_align_pose_

toolbox::match_enzdes_util::AlignPoseToInvrotTreeMoverOP	run_align_pose_

Additional Inherited Members
Public Types inherited from protocols::forge::remodel::RemodelConstraintGenerator
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

Protected Member Functions inherited from protocols::forge::remodel::RemodelConstraintGenerator
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...

Detailed Description

a RemodelConstraintGenerator wrapper that makes the constraints generated by an InvrotTree available in VLB or XML

Constructor & Destructor Documentation

protocols::forge::constraints::InvrotTreeRCG::InvrotTreeRCG ( )

protocols::forge::constraints::InvrotTreeRCG::InvrotTreeRCG ( InvrotTreeRCG const & rval )

protocols::forge::constraints::InvrotTreeRCG::InvrotTreeRCG	(	toolbox::match_enzdes_util::InvrotTreeOP	invrot_tree,
		toolbox::match_enzdes_util::AllowedSeqposForGeomCstOP	geomcst_seqpos
	)

protocols::forge::constraints::InvrotTreeRCG::~InvrotTreeRCG ( )

overridedefault

Member Function Documentation

void protocols::forge::constraints::InvrotTreeRCG::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::forge::remodel::RemodelConstraintGenerator::add_remodel_constraints_to_pose(), geomcst_seqpos_, init(), invrot_tree_, and setup_align_pose_.

protocols::moves::MoverOP protocols::forge::constraints::InvrotTreeRCG::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::forge::constraints::InvrotTreeRCG::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

void protocols::forge::constraints::InvrotTreeRCG::generate_remodel_constraints ( core::pose::Pose const & pose )

overridevirtual

Implements protocols::forge::remodel::RemodelConstraintGenerator.

References protocols::forge::remodel::RemodelConstraintGenerator::add_constraint(), geomcst_seqpos_, invrot_tree_, and tr().

std::string protocols::forge::constraints::InvrotTreeRCG::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::forge::constraints::InvrotTreeRCG::init ( core::pose::Pose const & pose )

overridevirtual

sets up the allowed sequence positions for enzdes geometric constraints

initializes the rcg object

Reimplemented from protocols::forge::remodel::RemodelConstraintGenerator.

References add_ligand_to_pose_, enzcst_io_, geomcst_seqpos_, invrot_tree_, run_align_pose_, setup_align_pose_, and protocols::forge::remodel::RemodelConstraintGenerator::vlb().

Referenced by apply().

std::string protocols::forge::constraints::InvrotTreeRCG::mover_name ( )

static

Referenced by get_name(), protocols::forge::constraints::InvrotTreeCstGeneratorCreator::keyname(), and provide_xml_schema().

void protocols::forge::constraints::InvrotTreeRCG::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References add_ligand_to_pose_, set_add_ligand_to_pose(), and set_cstfile().

void protocols::forge::constraints::InvrotTreeRCG::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::forge::constraints::InvrotTreeCstGeneratorCreator::provide_xml_schema().

void protocols::forge::constraints::InvrotTreeRCG::set_add_ligand_to_pose ( bool const add_lig )

tells the mover whether it should add the ligand to the pose

References add_ligand_to_pose_.

Referenced by parse_my_tag().

void protocols::forge::constraints::InvrotTreeRCG::set_cstfile ( std::string const & cstfilename )

sets up the invrot_tree_ and enzcst_io_ from an enzdes constraint filename.

References enzcst_io_, core::chemical::FA_STANDARD, and invrot_tree_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::forge::constraints::InvrotTreeRCG::add_ligand_to_pose_

private

Referenced by init(), parse_my_tag(), and set_add_ligand_to_pose().

toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::forge::constraints::InvrotTreeRCG::enzcst_io_

private

Referenced by init(), and set_cstfile().

toolbox::match_enzdes_util::AllowedSeqposForGeomCstOP protocols::forge::constraints::InvrotTreeRCG::geomcst_seqpos_

private

Referenced by apply(), generate_remodel_constraints(), and init().

toolbox::match_enzdes_util::InvrotTreeOP protocols::forge::constraints::InvrotTreeRCG::invrot_tree_

private

Referenced by apply(), generate_remodel_constraints(), init(), and set_cstfile().

toolbox::match_enzdes_util::AlignPoseToInvrotTreeMoverOP protocols::forge::constraints::InvrotTreeRCG::run_align_pose_

private

Referenced by init().

toolbox::match_enzdes_util::AlignPoseToInvrotTreeMoverOP protocols::forge::constraints::InvrotTreeRCG::setup_align_pose_

private

Referenced by apply(), and init().

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

src/protocols/forge/constraints/InvrotTreeRCG.hh
src/protocols/forge/constraints/InvrotTreeRCG.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation