Public Types | Public Member Functions | Private Types | Private Attributes | List of all members
protocols::forge::remodel::RemodelGlobalFrame Class Reference

#include <RemodelGlobalFrame.hh>

Inheritance diagram for protocols::forge::remodel::RemodelGlobalFrame:
Inheritance graph

Public Types

typedef core::Real Real
typedef core::Size Size
typedef core::kinematics::MoveMap MoveMap
typedef core::pose::Pose Pose
typedef core::scoring::ScoreFunctionOP ScoreFunctionOP
typedef core::scoring::ScoreFunction ScoreFunction
typedef core::pack::task::PackerTaskOP PackerTaskOP
typedef core::pack::task::PackerTask PackerTask
typedef protocols::moves::MoverOP MoverOP
typedef protocols::forge::remodel::RemodelData RemodelData
typedef protocols::forge::remodel::RemodelWorkingSet RemodelWorkingSet
typedef core::scoring::constraints::ConstraintSetOP ConstraintSetOP
typedef core::scoring::constraints::ConstraintSet ConstraintSet
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::string > Strings

Public Member Functions

 RemodelGlobalFrame ()
 RemodelGlobalFrame (RemodelData const &remodel_data, RemodelWorkingSet const &working_model, ScoreFunctionOP const &sfxn)
 value constructor More...
 RemodelGlobalFrame (core::Size segment_size)
 ~RemodelGlobalFrame () override
 copy constructor More...
MoverOP clone () const override
 clone this object More...
MoverOP fresh_instance () const override
 create this type of object More...
void apply (Pose &pose) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void get_helical_params (Pose &pose)
void align_segment (Pose &pose)
void setup_helical_constraint (Pose &pose)
void setup_CM_helical_constraint (Pose &pose)
void matrix3f_to_xyzMatrix (Eigen::Matrix3f const &Re, numeric::xyzMatrix< core::Real > &R)
void identity_matrix (numeric::xyzMatrix< core::Real > &R)
void restore_original_cst (Pose &pose)
void set_native_cst_set (ConstraintSet const &cst_set)
void set_native_cst_set (Pose const &pose)
void set_segment_size (core::Size segment_size)
Real radius ()
Real rise ()
Real omega ()
void scorefunction (ScoreFunctionOP const &sfxn)
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual MoverOP create ()
MoverCOP get_self_ptr () const
MoverOP get_self_ptr ()
MoverCAP get_self_weak_ptr () const
MoverAP get_self_weak_ptr ()
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
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...
virtual bool reinitialize_for_each_job () const
 Inform 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
 Inform 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...
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...
void set_type (std::string const &setting)
 Set the 'type' string. More...
std::string get_type () const
void type (const std::string &type_in)
 Set the 'type' string. More...
std::string const & type () const
 Get the set 'type' string. More...
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 parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void set_current_tag (std::string const &new_tag)
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...
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
virtual core::Real last_proposal_density_ratio ()
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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Types

typedef protocols::moves::Mover Super

Private Attributes

RemodelData remodel_data_
RemodelWorkingSet working_model_
ScoreFunctionOP score_fxn_
Real radius_
Real rise_
Real omega_
core::Size seg_size
int left_handed_
ConstraintSetOP native_cst_set

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. 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...

Member Typedef Documentation

◆ ConstraintSet

◆ ConstraintSetOP

◆ MoveMap

◆ MoverOP

◆ PackerTask

◆ PackerTaskOP

◆ Pose

◆ Real

◆ RemodelData

◆ RemodelWorkingSet

◆ ScoreFunction

◆ ScoreFunctionOP

◆ Size

◆ Super

Constructor & Destructor Documentation

◆ RemodelGlobalFrame() [1/3]

protocols::forge::remodel::RemodelGlobalFrame::RemodelGlobalFrame ( )

◆ RemodelGlobalFrame() [2/3]

protocols::forge::remodel::RemodelGlobalFrame::RemodelGlobalFrame ( RemodelData const &  remodel_data,
RemodelWorkingSet const &  working_model,
ScoreFunctionOP const &  sfxn 

◆ RemodelGlobalFrame() [3/3]

protocols::forge::remodel::RemodelGlobalFrame::RemodelGlobalFrame ( core::Size  segment_size)

◆ ~RemodelGlobalFrame()

protocols::forge::remodel::RemodelGlobalFrame::~RemodelGlobalFrame ( )

copy constructor

default destructor

Member Function Documentation

◆ align_segment()

void protocols::forge::remodel::RemodelGlobalFrame::align_segment ( Pose pose)

◆ apply()

void protocols::forge::remodel::RemodelGlobalFrame::apply ( Pose )

◆ clone()

protocols::moves::MoverOP protocols::forge::remodel::RemodelGlobalFrame::clone ( ) const

clone this object

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::forge::remodel::RemodelGlobalFrame::fresh_instance ( ) const

create this type of object

Reimplemented from protocols::moves::Mover.

◆ get_helical_params()

void protocols::forge::remodel::RemodelGlobalFrame::get_helical_params ( Pose pose)

◆ get_name()

std::string protocols::forge::remodel::RemodelGlobalFrame::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ identity_matrix()

void protocols::forge::remodel::RemodelGlobalFrame::identity_matrix ( numeric::xyzMatrix< core::Real > &  R)

◆ matrix3f_to_xyzMatrix()

void protocols::forge::remodel::RemodelGlobalFrame::matrix3f_to_xyzMatrix ( Eigen::Matrix3f const &  Re,
numeric::xyzMatrix< core::Real > &  R 

◆ omega()

Real protocols::forge::remodel::RemodelGlobalFrame::omega ( )

◆ radius()

Real protocols::forge::remodel::RemodelGlobalFrame::radius ( )

◆ restore_original_cst()

void protocols::forge::remodel::RemodelGlobalFrame::restore_original_cst ( Pose pose)

◆ rise()

Real protocols::forge::remodel::RemodelGlobalFrame::rise ( )

◆ scorefunction()

void protocols::forge::remodel::RemodelGlobalFrame::scorefunction ( ScoreFunctionOP const &  sfxn)

◆ set_native_cst_set() [1/2]

void protocols::forge::remodel::RemodelGlobalFrame::set_native_cst_set ( ConstraintSet const &  cst_set)

◆ set_native_cst_set() [2/2]

void protocols::forge::remodel::RemodelGlobalFrame::set_native_cst_set ( Pose const &  pose)

◆ set_segment_size()

void protocols::forge::remodel::RemodelGlobalFrame::set_segment_size ( core::Size  segment_size)

◆ setup_CM_helical_constraint()

void protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint ( Pose pose)

◆ setup_helical_constraint()

void protocols::forge::remodel::RemodelGlobalFrame::setup_helical_constraint ( Pose pose)

Member Data Documentation

◆ left_handed_

int protocols::forge::remodel::RemodelGlobalFrame::left_handed_

◆ native_cst_set

ConstraintSetOP protocols::forge::remodel::RemodelGlobalFrame::native_cst_set

◆ omega_

Real protocols::forge::remodel::RemodelGlobalFrame::omega_

Referenced by omega().

◆ radius_

Real protocols::forge::remodel::RemodelGlobalFrame::radius_

Referenced by radius().

◆ remodel_data_

RemodelData protocols::forge::remodel::RemodelGlobalFrame::remodel_data_

◆ rise_

Real protocols::forge::remodel::RemodelGlobalFrame::rise_

Referenced by rise().

◆ score_fxn_

ScoreFunctionOP protocols::forge::remodel::RemodelGlobalFrame::score_fxn_

◆ seg_size

core::Size protocols::forge::remodel::RemodelGlobalFrame::seg_size

◆ working_model_

RemodelWorkingSet protocols::forge::remodel::RemodelGlobalFrame::working_model_

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