#include <RemodelGlobalFrame.hh>
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 Strings & | info () |
| 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 |
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
| typedef core::scoring::constraints::ConstraintSet protocols::forge::remodel::RemodelGlobalFrame::ConstraintSet |
◆ ConstraintSetOP
| typedef core::scoring::constraints::ConstraintSetOP protocols::forge::remodel::RemodelGlobalFrame::ConstraintSetOP |
◆ MoveMap
◆ MoverOP
◆ PackerTask
◆ PackerTaskOP
◆ Pose
◆ Real
◆ RemodelData
| typedef protocols::forge::remodel::RemodelData protocols::forge::remodel::RemodelGlobalFrame::RemodelData |
◆ RemodelWorkingSet
| typedef protocols::forge::remodel::RemodelWorkingSet protocols::forge::remodel::RemodelGlobalFrame::RemodelWorkingSet |
◆ ScoreFunction
◆ ScoreFunctionOP
| typedef core::scoring::ScoreFunctionOP protocols::forge::remodel::RemodelGlobalFrame::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 | ||
| ) |
value constructor
References protocols::forge::remodel::RemodelData::blueprint.
◆ RemodelGlobalFrame() [3/3]
| protocols::forge::remodel::RemodelGlobalFrame::RemodelGlobalFrame | ( | core::Size | segment_size | ) |
◆ ~RemodelGlobalFrame()
|
overridedefault |
copy constructor
default destructor
Member Function Documentation
◆ align_segment()
| void protocols::forge::remodel::RemodelGlobalFrame::align_segment | ( | Pose & | pose | ) |
References core::pose::motif::a(), protocols::comparative_modeling::features::A, protocols::symmetry::SetupForSymmetryMover::apply(), protocols::forge::methods::apply_transformation(), core::chemical::element::B, protocols::match::upstream::b, core::pose::Pose::constraint_set(), core::pose::symmetry::extract_asymmetric_unit(), core::chemical::element::H, core::chemical::element::I, core::conformation::Residue::is_protein(), core::conformation::symmetry::is_symmetric(), protocols::features::L, core::chemical::element::N, core::scoring::omega, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::hybridization::t, protocols::forge::remodel::TR(), protocols::hybridization::u, and core::conformation::Residue::xyz().
Referenced by protocols::forge::remodel::RemodelMover::apply().
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
Referenced by protocols::forge::remodel::RemodelMover::apply().
◆ clone()
|
overridevirtual |
clone this object
Reimplemented from protocols::moves::Mover.
◆ fresh_instance()
|
overridevirtual |
create this type of object
Reimplemented from protocols::moves::Mover.
◆ get_helical_params()
| void protocols::forge::remodel::RemodelGlobalFrame::get_helical_params | ( | Pose & | pose | ) |
References protocols::comparative_modeling::features::A, core::chemical::element::B, core::chemical::element::H, core::chemical::element::I, protocols::features::L, core::chemical::element::N, core::scoring::omega, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::hybridization::t, protocols::forge::remodel::TR(), core::io::RemarkInfo::value, and core::conformation::Residue::xyz().
◆ get_name()
|
overridevirtual |
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 | ||
| ) |
References core::chemical::element::Re.
◆ omega()
|
inline |
References omega_.
Referenced by protocols::forge::remodel::RemodelMover::apply().
◆ radius()
|
inline |
References radius_.
Referenced by protocols::forge::remodel::RemodelMover::apply().
◆ restore_original_cst()
| void protocols::forge::remodel::RemodelGlobalFrame::restore_original_cst | ( | Pose & | pose | ) |
◆ rise()
|
inline |
References rise_.
Referenced by protocols::forge::remodel::RemodelMover::apply().
◆ 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 | ) |
Referenced by protocols::forge::remodel::RemodelLoopMover::apply().
◆ set_native_cst_set() [2/2]
| void protocols::forge::remodel::RemodelGlobalFrame::set_native_cst_set | ( | Pose const & | pose | ) |
References core::pose::Pose::constraint_set().
◆ set_segment_size()
| void protocols::forge::remodel::RemodelGlobalFrame::set_segment_size | ( | core::Size | segment_size | ) |
Referenced by protocols::forge::remodel::RemodelLoopMover::apply().
◆ setup_CM_helical_constraint()
| void protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint | ( | Pose & | pose | ) |
References protocols::forge::methods::apply_transformation(), protocols::forge::remodel::compute_center_of_mass(), core::pose::Pose::constraint_set(), core::chemical::element::H, protocols::forge::remodel::ideal_COMs(), core::conformation::Residue::is_protein(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), protocols::forge::remodel::rot_mat(), and protocols::forge::remodel::TR().
Referenced by protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), and protocols::forge::remodel::RemodelLoopMover::repeat_sync().
◆ setup_helical_constraint()
| void protocols::forge::remodel::RemodelGlobalFrame::setup_helical_constraint | ( | Pose & | pose | ) |
References protocols::forge::methods::apply_transformation(), core::pose::Pose::constraint_set(), core::conformation::Residue::is_protein(), core::io::pose_from_pose(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::size(), and protocols::forge::remodel::TR().
Member Data Documentation
◆ left_handed_
|
private |
◆ native_cst_set
|
private |
◆ omega_
◆ radius_
◆ remodel_data_
|
private |
◆ rise_
◆ score_fxn_
|
private |
◆ seg_size
|
private |
◆ working_model_
|
private |
The documentation for this class was generated from the following files:
- src/protocols/forge/remodel/RemodelGlobalFrame.hh
- src/protocols/forge/remodel/RemodelGlobalFrame.cc
