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protocols::forge::constraints::InvrotTreeRCG Class Reference

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:
Inheritance graph
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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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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
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
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
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
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
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
toolbox::match_enzdes_util::InvrotTreeOP protocols::forge::constraints::InvrotTreeRCG::invrot_tree_
private
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: