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protocols::seeded_abinitio::SeedSetupMover Class Reference

#include <SeedSetupMover.hh>

Inheritance diagram for protocols::seeded_abinitio::SeedSetupMover:
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Collaboration diagram for protocols::seeded_abinitio::SeedSetupMover:
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Public Member Functions

 SeedSetupMover ()
 
virtual ~SeedSetupMover ()
 
void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. 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...
 
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...
 
void clear_task_factory ()
 
void task_factory (core::pack::task::TaskFactoryOP tf)
 
core::pack::task::TaskFactoryOPtask_factory ()
 getters More...
 
- 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 set_packerTasks_target_and_seeds (core::pose::Pose &pose, protocols::loops::Loops &seeds, utility::vector1< core::Size > &designable_residues, utility::vector1< core::Size > &norepack_res, core::pack::task::TaskFactoryOP &tf)
 

Private Attributes

core::pack::task::TaskFactoryOP task_factory_
 
core::pack::task::PackerTaskOP task_
 
core::kinematics::MoveMapOP movemap_
 movemap More...
 
bool repack_target_
 switches for folding and desing behavior: More...
 
bool repack_foldpose_
 
bool allow_all_aas_
 
bool design_target_
 
bool design_foldpose_
 
utility::vector1< std::pair
< std::string, std::string > > 
seed_vector_
 
std::string design_res_
 designable residues More...
 
std::string norepack_res_
 dont repack residues More...
 
protocols::loops::Loops all_seeds_
 
core::scoring::ScoreFunctionOP scorefxn_repack_
 in case someone wanted to instantly design, but really this is only for debugging purposes in there More...
 
core::scoring::ScoreFunctionOP scorefxn_minimize_
 
bool design_
 
bool chi_chain1_
 let chi angles of chain 1 move More...
 
bool chi_chain2_
 let chi angles of chain 2 move More...
 
bool interface_chi1_
 interface chi angles be movable More...
 
bool interface_chi2_
 
core::Real interface_distance_cutoff_
 
bool packtask_
 set helper taskfactory More...
 

Additional Inherited Members

- 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
 
- 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...
 

Constructor & Destructor Documentation

protocols::seeded_abinitio::SeedSetupMover::SeedSetupMover ( )
protocols::seeded_abinitio::SeedSetupMover::~SeedSetupMover ( )
virtual

Member Function Documentation

void protocols::seeded_abinitio::SeedSetupMover::apply ( core::pose::Pose pose)
virtual
void protocols::seeded_abinitio::SeedSetupMover::clear_task_factory ( )

References task_factory_.

Referenced by apply().

protocols::moves::MoverOP protocols::seeded_abinitio::SeedSetupMover::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 SeedSetupMover().

protocols::moves::MoverOP protocols::seeded_abinitio::SeedSetupMover::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.

std::string protocols::seeded_abinitio::SeedSetupMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

References protocols::seeded_abinitio::SeedSetupMoverCreator::mover_name().

void protocols::seeded_abinitio::SeedSetupMover::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 allow_all_aas_, chi_chain1_, chi_chain2_, design_, design_foldpose_, design_res_, design_target_, protocols::moves::DataMap::get(), interface_chi1_, interface_chi2_, interface_distance_cutoff_, movemap_, norepack_res_, packtask_, protocols::rosetta_scripts::parse_movemap(), repack_foldpose_, repack_target_, scorefxn_minimize_, scorefxn_repack_, and seed_vector_.

void protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds ( core::pose::Pose pose,
protocols::loops::Loops seeds,
utility::vector1< core::Size > &  designable_residues,
utility::vector1< core::Size > &  norepack_res,
core::pack::task::TaskFactoryOP tf 
)
private
void protocols::seeded_abinitio::SeedSetupMover::task_factory ( core::pack::task::TaskFactoryOP  tf)

References task_factory_.

core::pack::task::TaskFactoryOP & protocols::seeded_abinitio::SeedSetupMover::task_factory ( )

getters

References task_factory_.

Member Data Documentation

protocols::loops::Loops protocols::seeded_abinitio::SeedSetupMover::all_seeds_
private

Referenced by apply().

bool protocols::seeded_abinitio::SeedSetupMover::allow_all_aas_
private

Referenced by parse_my_tag(), and SeedSetupMover().

bool protocols::seeded_abinitio::SeedSetupMover::chi_chain1_
private

let chi angles of chain 1 move

Referenced by apply(), parse_my_tag(), and SeedSetupMover().

bool protocols::seeded_abinitio::SeedSetupMover::chi_chain2_
private

let chi angles of chain 2 move

Referenced by apply(), parse_my_tag(), and SeedSetupMover().

bool protocols::seeded_abinitio::SeedSetupMover::design_
private

Referenced by apply(), and parse_my_tag().

bool protocols::seeded_abinitio::SeedSetupMover::design_foldpose_
private
std::string protocols::seeded_abinitio::SeedSetupMover::design_res_
private

designable residues

Referenced by apply(), parse_my_tag(), and SeedSetupMover().

bool protocols::seeded_abinitio::SeedSetupMover::design_target_
private
bool protocols::seeded_abinitio::SeedSetupMover::interface_chi1_
private

interface chi angles be movable

Referenced by apply(), and parse_my_tag().

bool protocols::seeded_abinitio::SeedSetupMover::interface_chi2_
private

Referenced by apply(), and parse_my_tag().

core::Real protocols::seeded_abinitio::SeedSetupMover::interface_distance_cutoff_
private

Referenced by apply(), and parse_my_tag().

core::kinematics::MoveMapOP protocols::seeded_abinitio::SeedSetupMover::movemap_
private

movemap

Referenced by apply(), and parse_my_tag().

std::string protocols::seeded_abinitio::SeedSetupMover::norepack_res_
private

dont repack residues

Referenced by apply(), parse_my_tag(), and SeedSetupMover().

bool protocols::seeded_abinitio::SeedSetupMover::packtask_
private

set helper taskfactory

Referenced by apply(), parse_my_tag(), and SeedSetupMover().

bool protocols::seeded_abinitio::SeedSetupMover::repack_foldpose_
private
bool protocols::seeded_abinitio::SeedSetupMover::repack_target_
private

switches for folding and desing behavior:

Referenced by parse_my_tag(), SeedSetupMover(), and set_packerTasks_target_and_seeds().

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::SeedSetupMover::scorefxn_minimize_
private

Referenced by parse_my_tag().

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::SeedSetupMover::scorefxn_repack_
private

in case someone wanted to instantly design, but really this is only for debugging purposes in there

Referenced by apply(), and parse_my_tag().

utility::vector1< std::pair < std::string,std::string > > protocols::seeded_abinitio::SeedSetupMover::seed_vector_
private

Referenced by apply(), and parse_my_tag().

core::pack::task::PackerTaskOP protocols::seeded_abinitio::SeedSetupMover::task_
private
core::pack::task::TaskFactoryOP protocols::seeded_abinitio::SeedSetupMover::task_factory_
private

this taskfactory contains all the information about which residues should be repacked and designed it assumes the fold pose is the last chain. Seeds are parse at runtime and incorporated into this taskfactory

Referenced by apply(), clear_task_factory(), and task_factory().


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