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protocols::protein_interface_design::movers::LoopMoverFromCommandLine Class Reference

#include <LoopMoverFromCommandLine.hh>

Inheritance diagram for protocols::protein_interface_design::movers::LoopMoverFromCommandLine:
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Collaboration diagram for protocols::protein_interface_design::movers::LoopMoverFromCommandLine:
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Public Member Functions

 LoopMoverFromCommandLine ()
 
 LoopMoverFromCommandLine (std::string const protocol, bool const perturb, bool const refine, core::scoring::ScoreFunctionOP &hires_score, core::scoring::ScoreFunctionOP &lores_score, std::string const loop_file_name, protocols::loops::LoopsCOP loops)
 
bool perturb () const
 
void perturb (bool const setting)
 
bool refine () const
 
void refine (bool const setting)
 
void refine (std::string const setting)
 
std::string string_refine () const
 
void intermedrelax (std::string const setting)
 
std::string intermedrelax () const
 
void relax (std::string const setting)
 
std::string relax () const
 
void remodel (std::string const setting)
 
std::string remodel () const
 
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
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 apply (core::pose::Pose &pose)
 a dummy apply so that instantiation of this baseclass would be possible. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, 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...
 
virtual ~LoopMoverFromCommandLine ()
 
- Public Member Functions inherited from protocols::simple_moves::DesignRepackMover
 DesignRepackMover ()
 
 DesignRepackMover (std::string const name)
 
void setup_packer_and_movemap (core::pose::Pose const &pose)
 
void min_rb (utility::vector1< bool > const min_rb)
 
void min_rb (bool const min_rb)
 in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code. More...
 
utility::vector1< bool > const & min_rb () const
 
bool min_rb_set () const
 
void min_sc (utility::vector1< bool > const &min_sc)
 
utility::vector1< bool > const & min_sc () const
 
bool min_sc_set () const
 
void min_bb (utility::vector1< bool > const &min_bb)
 
utility::vector1< bool > const & min_bb () const
 
bool min_bb_set () const
 
bool optimize_foldtree () const
 
void optimize_foldtree (bool const opt)
 
void prevent_repacking (utility::vector1< core::Size > const p)
 
utility::vector1< core::Size >
const & 
prevent_repacking () const
 
void restrict_to_repacking (utility::vector1< core::Size > const p)
 
utility::vector1< core::Size >
const & 
restrict_to_repacking () const
 
void design (bool const des)
 
bool design () const
 
void set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn)
 
core::scoring::ScoreFunctionOP scorefxn_repack () const
 
core::scoring::ScoreFunctionOP scorefxn_minimize () const
 
core::pack::task::PackerTaskCOP task () const
 
core::pack::task::PackerTaskOPtask ()
 
void clear_task ()
 after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered More...
 
void clear_task_factory ()
 
void use_preset_task (bool const bt)
 
bool use_preset_task () const
 
void task_factory (core::pack::task::TaskFactoryOP p)
 
core::pack::task::TaskFactoryOPtask_factory ()
 
core::pack::task::TaskFactoryOP task_factory () const
 
virtual ~DesignRepackMover ()
 
- 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

std::string protocol_
 
core::scoring::ScoreFunctionOP hires_score_
 
core::scoring::ScoreFunctionOP lores_score_
 
bool perturb_
 
bool refine_
 
std::string loop_file_name_
 
protocols::loops::LoopsOP loops_
 
std::string intermedrelax_
 
std::string remodel_
 
std::string relax_
 
std::string string_refine_
 

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...
 
- Protected Attributes inherited from protocols::simple_moves::DesignRepackMover
core::scoring::ScoreFunctionOP scorefxn_repack_
 
core::scoring::ScoreFunctionOP scorefxn_minimize_
 
bool repack_partner1_
 
bool repack_partner2_
 
bool design_partner1_
 
bool design_partner2_
 
utility::vector1< boolmin_sc_
 
utility::vector1< boolcurr_min_sc_
 
utility::vector1< boolmin_rb_
 
utility::vector1< boolmin_bb_
 
utility::vector1< boolcurr_min_bb_
 
utility::vector1< boolcurr_min_rb_
 
bool min_rb_set_
 
bool min_sc_set_
 
bool min_bb_set_
 
utility::vector1< core::Sizetarget_residues_
 
core::Real interface_distance_cutoff_
 
bool repack_non_ala_
 
bool optimize_foldtree_
 
bool automatic_repacking_definition_
 
core::pack::task::PackerTaskOP task_
 
bool use_preset_task_
 
utility::vector1< boolallowed_aas_
 
utility::vector1< core::Sizeprevent_repacking_
 
utility::vector1< core::Sizerestrict_to_repacking_
 
core::pack::task::TaskFactoryOP task_factory_
 
bool symmetry_
 

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::LoopMoverFromCommandLine::LoopMoverFromCommandLine ( )
protocols::protein_interface_design::movers::LoopMoverFromCommandLine::LoopMoverFromCommandLine ( std::string const  protocol,
bool const  perturb,
bool const  refine,
core::scoring::ScoreFunctionOP hires_score,
core::scoring::ScoreFunctionOP lores_score,
std::string const  loop_file_name,
protocols::loops::LoopsCOP  loops 
)
protocols::protein_interface_design::movers::LoopMoverFromCommandLine::~LoopMoverFromCommandLine ( )
virtual

Member Function Documentation

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply ( core::pose::Pose )
virtual

a dummy apply so that instantiation of this baseclass would be possible.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References core::util::add_cutpoint_variants(), protocols::loops::loop_mover::LoopMover::add_fragments(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::allsc(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), core::chemical::CENTROID, core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::comparative_modeling::LoopRelaxMover::frag_libs(), hires_score_, core::scoring::dssp::Dssp::insert_ss_into_pose(), intermedrelax(), protocols::comparative_modeling::LoopRelaxMover::intermedrelax(), loop_file_name_, protocols::comparative_modeling::LoopRelaxMover::loops(), lores_score_, perturb(), perturb_, protocol_, protocols::loops::read_loop_fragments(), refine(), protocols::comparative_modeling::LoopRelaxMover::refine(), refine_, relax(), protocols::comparative_modeling::LoopRelaxMover::relax(), remodel(), protocols::comparative_modeling::LoopRelaxMover::remodel(), protocols::comparative_modeling::LoopRelaxMover::scorefxns(), core::pose::Pose::secstruct(), core::pose::Pose::sequence(), protocols::moves::Mover::set_native_pose(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_redesign_loop(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_redesign_loop(), protocols::loops::set_secstruct_from_psipred_ss2(), protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops(), string_refine(), core::util::switch_to_residue_type_set(), protocols::simple_moves::DesignRepackMover::task_factory(), protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopMoverFromCommandLine::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.

Implements protocols::simple_moves::DesignRepackMover.

References LoopMoverFromCommandLine().

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopMoverFromCommandLine::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.

Implements protocols::simple_moves::DesignRepackMover.

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::get_name ( ) const
virtual

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::protein_interface_design::movers::LoopMoverFromCommandLineCreator::mover_name().

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::intermedrelax ( std::string const  setting)
inline

References intermedrelax_.

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::intermedrelax ( ) const
inline

References intermedrelax_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::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::simple_moves::DesignRepackMover.

References protocols::moves::DataMap::get(), hires_score_, intermedrelax(), loop_file_name_, lores_score_, perturb_, protocol_, refine(), relax(), and remodel().

bool protocols::protein_interface_design::movers::LoopMoverFromCommandLine::perturb ( ) const
inline

References perturb_.

Referenced by apply().

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::perturb ( bool const  setting)
inline

References perturb_.

bool protocols::protein_interface_design::movers::LoopMoverFromCommandLine::refine ( ) const
inline

References refine_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::refine ( bool const  setting)
inline

References refine_.

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::refine ( std::string const  setting)
inline

References string_refine_.

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::relax ( std::string const  setting)
inline

References relax_.

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::relax ( ) const
inline

References relax_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::remodel ( std::string const  setting)
inline

References remodel_.

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::remodel ( ) const
inline

References remodel_.

Referenced by apply(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::string_refine ( ) const
inline

References string_refine_.

Referenced by apply().

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::LoopMoverFromCommandLine::hires_score_
private
std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::intermedrelax_
private

Referenced by intermedrelax().

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::loop_file_name_
private
protocols::loops::LoopsOP protocols::protein_interface_design::movers::LoopMoverFromCommandLine::loops_
private
core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::LoopMoverFromCommandLine::lores_score_
private

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::LoopMoverFromCommandLine::perturb_
private

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

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::protocol_
private

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::LoopMoverFromCommandLine::refine_
private

Referenced by apply(), and refine().

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::relax_
private

Referenced by relax().

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::remodel_
private

Referenced by remodel().

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::string_refine_
private

Referenced by refine(), and string_refine().


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