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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:
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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 ()
 
virtual void parse_my_tag (TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual protocols::moves::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...
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void apply (core::pose::Pose &pose)
 generates constraints and adds them to the pose More...
 
virtual void generate_remodel_constraints (core::pose::Pose const &pose)
 
virtual void init (core::pose::Pose const &pose)
 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...
 
- Public Member Functions inherited from protocols::forge::remodel::RemodelConstraintGenerator
virtual ~RemodelConstraintGenerator ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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
 
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)
 
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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

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
 
- Static Public Member Functions inherited from protocols::forge::remodel::RemodelConstraintGenerator
static
core::scoring::constraints::ConstraintCOPs
const 
lookup_stored_constraints (std::string const &id)
 
- 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 ()
 

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 ( )

Referenced by clone(), and fresh_instance().

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 ( )

Member Function Documentation

void protocols::forge::constraints::InvrotTreeRCG::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

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

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
virtual

clone has to be overridden only if clone invocation is expected.

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.

References InvrotTreeRCG().

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

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).

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.

References InvrotTreeRCG().

void protocols::forge::constraints::InvrotTreeRCG::generate_remodel_constraints ( core::pose::Pose const &  pose)
virtual
std::string protocols::forge::constraints::InvrotTreeRCG::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

References protocols::forge::constraints::InvrotTreeCstGeneratorCreator::mover_name().

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

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().

void protocols::forge::constraints::InvrotTreeRCG::parse_my_tag ( TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

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

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, core::chemical::ChemicalManager::get_instance(), 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: