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protocols::idealize::IdealizeMover Class Reference

Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points. More...

#include <IdealizeMover.hh>

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Public Types

typedef core::Real Real
 
typedef core::pose::Pose Pose
 
- 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

 IdealizeMover ()
 
virtual moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual 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...
 
IdealizeMoveratom_pair_constraint_weight (core::Real const setting)
 
IdealizeMovercoordinate_constraint_weight (core::Real const setting)
 
IdealizeMoverfast (bool const setting)
 
IdealizeMoverchainbreaks (bool const setting)
 
IdealizeMoverreport_CA_rmsd (bool const setting)
 
void apply (Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_pos_list (utility::vector1< Size > pos_list)
 Sets the list of residue positions to idealize. 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 &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
utility::vector1< core::Sizeignore_residues_in_csts () const
 
void ignore_residues_in_csts (utility::vector1< core::Size > const i)
 
void impose_constraints (bool const i)
 
bool impose_constraints () const
 
bool constraints_only () const
 
void constraints_only (bool const c)
 
- 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 Member Functions

void setup_idealize_constraints (Pose &pose)
 Add the idealize constraints to the pose's constraint set. More...
 

Private Attributes

utility::vector1< Sizepos_list_
 
Real atom_pair_constraint_weight_
 
Real coordinate_constraint_weight_
 
utility::vector1< core::Sizeignore_residues_in_csts_
 
bool fast_
 
bool chainbreaks_
 
bool report_CA_rmsd_
 
bool impose_constraints_
 
bool constraints_only_
 

Additional Inherited Members

- 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 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

Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::idealize::IdealizeMover::IdealizeMover ( )
inline

References ignore_residues_in_csts_.

Referenced by clone(), and fresh_instance().

Member Function Documentation

void protocols::idealize::IdealizeMover::apply ( pose::Pose pose)
virtual

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::all_atom_rmsd(), core::pose::Pose::append_residue_by_jump(), core::scoring::atom_pair_constraint, protocols::idealize::basic_idealize(), core::scoring::CA_rmsd(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::conformation::ResidueFactory::create_residue(), core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dst, core::pose::Pose::fold_tree(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), core::chemical::ResidueTypeSet::name_map(), core::scoring::pro_close, core::kinematics::FoldTree::reorder(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and protocols::idealize::TR().

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::abinitio::AbrelaxApplication::fold(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::cluster::ClusterBase::print_clusters_silentfile(), and protocols::jobdist::universal_main().

IdealizeMover& protocols::idealize::IdealizeMover::atom_pair_constraint_weight ( core::Real const  setting)
inline
IdealizeMover& protocols::idealize::IdealizeMover::chainbreaks ( bool const  setting)
inline
virtual moves::MoverOP protocols::idealize::IdealizeMover::clone ( ) const
inlinevirtual

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

Reimplemented from protocols::moves::Mover.

References IdealizeMover().

bool protocols::idealize::IdealizeMover::constraints_only ( ) const
inline

References constraints_only_.

void protocols::idealize::IdealizeMover::constraints_only ( bool const  c)
inline
IdealizeMover& protocols::idealize::IdealizeMover::coordinate_constraint_weight ( core::Real const  setting)
inline
IdealizeMover& protocols::idealize::IdealizeMover::fast ( bool const  setting)
inline
virtual moves::MoverOP protocols::idealize::IdealizeMover::fresh_instance ( ) const
inlinevirtual

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 IdealizeMover().

std::string protocols::idealize::IdealizeMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

utility::vector1< core::Size > protocols::idealize::IdealizeMover::ignore_residues_in_csts ( ) const
void protocols::idealize::IdealizeMover::ignore_residues_in_csts ( utility::vector1< core::Size > const  i)
void protocols::idealize::IdealizeMover::impose_constraints ( bool const  i)
inline

References impose_constraints_.

bool protocols::idealize::IdealizeMover::impose_constraints ( ) const
inline

References impose_constraints_.

void protocols::idealize::IdealizeMover::parse_my_tag ( utility::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 core::pose::get_resnum_list(), and protocols::idealize::TR().

IdealizeMover& protocols::idealize::IdealizeMover::report_CA_rmsd ( bool const  setting)
inline
void protocols::idealize::IdealizeMover::set_pos_list ( utility::vector1< Size pos_list)
inline

Sets the list of residue positions to idealize.

References pos_list_.

void protocols::idealize::IdealizeMover::setup_idealize_constraints ( Pose pose)
private

Member Data Documentation

Real protocols::idealize::IdealizeMover::atom_pair_constraint_weight_
private
bool protocols::idealize::IdealizeMover::chainbreaks_
private

Referenced by chainbreaks().

bool protocols::idealize::IdealizeMover::constraints_only_
private

Referenced by constraints_only().

Real protocols::idealize::IdealizeMover::coordinate_constraint_weight_
private
bool protocols::idealize::IdealizeMover::fast_
private

Referenced by fast().

utility::vector1< core::Size > protocols::idealize::IdealizeMover::ignore_residues_in_csts_
private

Referenced by IdealizeMover().

bool protocols::idealize::IdealizeMover::impose_constraints_
private

Referenced by impose_constraints().

utility::vector1< Size > protocols::idealize::IdealizeMover::pos_list_
private

Referenced by set_pos_list().

bool protocols::idealize::IdealizeMover::report_CA_rmsd_
private

Referenced by report_CA_rmsd().


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