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protocols::swa::protein::StepWiseProteinPoseMinimizer Class Reference

#include <StepWiseProteinPoseMinimizer.hh>

Inheritance diagram for protocols::swa::protein::StepWiseProteinPoseMinimizer:
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Collaboration diagram for protocols::swa::protein::StepWiseProteinPoseMinimizer:
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Public Member Functions

 StepWiseProteinPoseMinimizer (core::io::silent::SilentFileDataOP sfd, utility::vector1< Size > const &moving_residues)
 
 StepWiseProteinPoseMinimizer (PoseList &pose_list, utility::vector1< Size > const &moving_residues)
 
 ~StepWiseProteinPoseMinimizer ()
 
virtual void apply (core::pose::Pose &pose_to_visualize)
 Apply the minimizer to one pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_silent_file (std::string const &setting)
 
void set_min_tolerance (core::Real const &setting)
 
void set_min_type (std::string const &setting)
 
void set_fixed_res (utility::vector1< core::Size > const &fixed_res)
 
void set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)
 
void set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
 
void set_move_takeoff_torsions (bool const value)
 
void set_rescore_only (bool const &setting)
 
void set_move_jumps_between_chains (bool const &setting)
 
core::io::silent::SilentFileDataOPsilent_file_data ()
 
- 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)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 
virtual 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 set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

void initialize_parameters ()
 
void initialize_protein_input_silent_file_data_from_pose_list (PoseList &pose_list)
 
void let_neighboring_chis_minimize (core::kinematics::MoveMap &mm, core::pose::Pose &pose)
 
bool pose_has_chainbreak (core::pose::Pose const &pose)
 

Private Attributes

PoseList pose_list_
 
utility::vector1< core::Size >
const & 
moving_residues_
 
utility::vector1< core::Sizefixed_res_
 
utility::vector1< core::Sizecalc_rms_res_
 
bool move_takeoff_torsions_
 
bool rescore_only_
 
bool move_jumps_between_chains_
 
std::string silent_file_
 
core::scoring::ScoreFunctionOP fa_scorefxn_
 
core::io::silent::SilentFileDataOP sfd_
 
core::io::silent::SilentFileDataOP input_silent_file_data_
 
std::string min_type_
 
core::Real min_tolerance_
 

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::swa::protein::StepWiseProteinPoseMinimizer::StepWiseProteinPoseMinimizer ( core::io::silent::SilentFileDataOP  sfd,
utility::vector1< Size > const &  moving_residues 
)
protocols::swa::protein::StepWiseProteinPoseMinimizer::StepWiseProteinPoseMinimizer ( PoseList pose_list,
utility::vector1< Size > const &  moving_residues 
)
protocols::swa::protein::StepWiseProteinPoseMinimizer::~StepWiseProteinPoseMinimizer ( )

Member Function Documentation

void protocols::swa::protein::StepWiseProteinPoseMinimizer::apply ( core::pose::Pose pose_to_visualize)
virtual
std::string protocols::swa::protein::StepWiseProteinPoseMinimizer::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::swa::protein::StepWiseProteinPoseMinimizer::initialize_parameters ( )
private
void protocols::swa::protein::StepWiseProteinPoseMinimizer::initialize_protein_input_silent_file_data_from_pose_list ( PoseList pose_list)
private
void protocols::swa::protein::StepWiseProteinPoseMinimizer::let_neighboring_chis_minimize ( core::kinematics::MoveMap mm,
core::pose::Pose pose 
)
private
bool protocols::swa::protein::StepWiseProteinPoseMinimizer::pose_has_chainbreak ( core::pose::Pose const &  pose)
private
void protocols::swa::protein::StepWiseProteinPoseMinimizer::set_calc_rms_res ( utility::vector1< core::Size > const &  calc_rms_res)

References calc_rms_res_.

void protocols::swa::protein::StepWiseProteinPoseMinimizer::set_fixed_res ( utility::vector1< core::Size > const &  fixed_res)

References fixed_res_.

void protocols::swa::protein::StepWiseProteinPoseMinimizer::set_min_tolerance ( core::Real const &  setting)

References min_tolerance_.

void protocols::swa::protein::StepWiseProteinPoseMinimizer::set_min_type ( std::string const &  setting)

References min_type_.

void protocols::swa::protein::StepWiseProteinPoseMinimizer::set_move_jumps_between_chains ( bool const &  setting)
inline
void protocols::swa::protein::StepWiseProteinPoseMinimizer::set_move_takeoff_torsions ( bool const  value)
inline
void protocols::swa::protein::StepWiseProteinPoseMinimizer::set_rescore_only ( bool const &  setting)
inline

References rescore_only_.

void protocols::swa::protein::StepWiseProteinPoseMinimizer::set_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References fa_scorefxn_.

void protocols::swa::protein::StepWiseProteinPoseMinimizer::set_silent_file ( std::string const &  setting)

References silent_file_.

core::io::silent::SilentFileDataOP & protocols::swa::protein::StepWiseProteinPoseMinimizer::silent_file_data ( )

References sfd_.

Member Data Documentation

utility::vector1< core::Size > protocols::swa::protein::StepWiseProteinPoseMinimizer::calc_rms_res_
private

Referenced by apply(), and set_calc_rms_res().

core::scoring::ScoreFunctionOP protocols::swa::protein::StepWiseProteinPoseMinimizer::fa_scorefxn_
private
utility::vector1< core::Size > protocols::swa::protein::StepWiseProteinPoseMinimizer::fixed_res_
private

Referenced by apply(), and set_fixed_res().

core::io::silent::SilentFileDataOP protocols::swa::protein::StepWiseProteinPoseMinimizer::input_silent_file_data_
private
core::Real protocols::swa::protein::StepWiseProteinPoseMinimizer::min_tolerance_
private
std::string protocols::swa::protein::StepWiseProteinPoseMinimizer::min_type_
private
bool protocols::swa::protein::StepWiseProteinPoseMinimizer::move_jumps_between_chains_
private
bool protocols::swa::protein::StepWiseProteinPoseMinimizer::move_takeoff_torsions_
private
utility::vector1< core::Size > const& protocols::swa::protein::StepWiseProteinPoseMinimizer::moving_residues_
private
PoseList protocols::swa::protein::StepWiseProteinPoseMinimizer::pose_list_
private
bool protocols::swa::protein::StepWiseProteinPoseMinimizer::rescore_only_
private
core::io::silent::SilentFileDataOP protocols::swa::protein::StepWiseProteinPoseMinimizer::sfd_
private

Referenced by apply(), and silent_file_data().

std::string protocols::swa::protein::StepWiseProteinPoseMinimizer::silent_file_
private

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