#include <MPRangeRelaxMover.hh>
Public Member Functions | |
| MPRangeRelaxMover () | |
| Constructors ///. More... | |
| MPRangeRelaxMover (MPRangeRelaxMover const &src) | |
| Copy Constructor. More... | |
| MPRangeRelaxMover & | operator= (MPRangeRelaxMover const &src) |
| Assignment Operator. More... | |
| ~MPRangeRelaxMover () override | |
| Destructor. More... | |
| protocols::moves::MoverOP | clone () const override |
| Rosetta Scripts Methods ///. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Create a Fresh Instance of this Mover. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override |
| Parse Rosetta Scripts Options for this Mover. More... | |
| std::string | get_name () const override |
| Mover Methods ///. More... | |
| void | apply (Pose &pose) override |
| Do a RangeRelax of a membrane protein. More... | |
| void | optimize_membrane (bool yesno) |
| Optimize membrane. More... | |
| core::pose::PoseOP | get_native () const |
| Get Methods ///. More... | |
| core::scoring::ScoreFunctionOP | get_sfxn () const |
| Get scorefxn. More... | |
| core::Size | get_center_resnumber () const |
| Get center residue number. More... | |
| bool | get_set_tm_helical () const |
| Get yes/no for set helical secondary structure in TM region. More... | |
| bool | get_optmem () const |
| Get yes/no for optimize membrane option. More... | |
 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 |
| 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... | |
Static Public Member Functions | |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| Provide xml schema for RosettaScripts compatibility. More... | |
| 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... | |
Private Member Functions | |
| void | register_options () |
| Setup Methods ///. More... | |
| void | set_defaults () |
| Set default values. More... | |
| void | init_from_cmd () |
| Init from commandline. More... | |
Private Attributes | |
| core::pose::PoseOP | native_ |
| Native. More... | |
| core::scoring::ScoreFunctionOP | sfxn_ |
| Scorefxn. More... | |
| core::Size | center_resnumber_ |
| Center residue number. More... | |
| bool | set_tm_helical_ |
| Set helical secondary structure in TM region. More... | |
| bool | optmem_ |
| optimize membrane? More... | |
Additional Inherited Members | |
| 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 |
| 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
◆ MPRangeRelaxMover() [1/2]
| protocols::relax::membrane::MPRangeRelaxMover::MPRangeRelaxMover | ( | ) |
Constructors ///.
Default Constructor
References init_from_cmd(), register_options(), and set_defaults().
Referenced by operator=().
◆ MPRangeRelaxMover() [2/2]
|
default |
Copy Constructor.
Create a deep copy of this mover
◆ ~MPRangeRelaxMover()
|
overridedefault |
Destructor.
Member Function Documentation
◆ apply()
|
overridevirtual |
Do a RangeRelax of a membrane protein.
Implements protocols::moves::Mover.
References core::pose::Pose::clone(), core::pose::Pose::conformation(), protocols::membrane::create_membrane_foldtree_anchor_pose_tmcom(), core::pose::Pose::fold_tree(), core::conformation::Conformation::is_membrane(), protocols::membrane::is_membrane_fixed(), core::pose::Pose::membrane_info(), native_, core::pose::nres_protein(), protocols::membrane::pose_tm_com(), protocols::antibody::design::relax, core::kinematics::FoldTree::reorder(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), set_tm_helical_, sfxn_, core::kinematics::FoldTree::show(), and protocols::relax::TR().
◆ clone()
|
overridevirtual |
Rosetta Scripts Methods ///.
Create a Clone of this mover
Reimplemented from protocols::moves::Mover.
◆ fresh_instance()
|
overridevirtual |
Create a Fresh Instance of this Mover.
Reimplemented from protocols::moves::Mover.
◆ get_center_resnumber()
| core::Size protocols::relax::membrane::MPRangeRelaxMover::get_center_resnumber | ( | ) | const |
Get center residue number.
References center_resnumber_.
◆ get_name()
|
overridevirtual |
Mover Methods ///.
Create a new copy of this mover.
Get the name of this Mover (MPRangeRelaxMover)
Mover Methods ///
Get the name of this Mover (MPRangeRelaxMover)
Implements protocols::moves::Mover.
◆ get_native()
| core::pose::PoseOP protocols::relax::membrane::MPRangeRelaxMover::get_native | ( | ) | const |
◆ get_optmem()
| bool protocols::relax::membrane::MPRangeRelaxMover::get_optmem | ( | ) | const |
Get yes/no for optimize membrane option.
References optmem_.
◆ get_set_tm_helical()
| bool protocols::relax::membrane::MPRangeRelaxMover::get_set_tm_helical | ( | ) | const |
Get yes/no for set helical secondary structure in TM region.
References set_tm_helical_.
◆ get_sfxn()
| core::scoring::ScoreFunctionOP protocols::relax::membrane::MPRangeRelaxMover::get_sfxn | ( | ) | const |
Get scorefxn.
References sfxn_.
◆ init_from_cmd()
|
private |
Init from commandline.
Set default values.
References native_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), and set_tm_helical_.
Referenced by MPRangeRelaxMover().
◆ operator=()
| MPRangeRelaxMover & protocols::relax::membrane::MPRangeRelaxMover::operator= | ( | MPRangeRelaxMover const & | src | ) |
Assignment Operator.
References MPRangeRelaxMover().
◆ optimize_membrane()
| void protocols::relax::membrane::MPRangeRelaxMover::optimize_membrane | ( | bool | yesno | ) |
Optimize membrane.
References optmem_.
◆ parse_my_tag()
|
overridevirtual |
Parse Rosetta Scripts Options for this Mover.
Reimplemented from protocols::moves::Mover.
References center_resnumber_, core::scoring::ScoreFunctionFactory::create_score_function(), native_, optmem_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), set_tm_helical_, and sfxn_.
◆ provide_xml_schema()
|
static |
Provide xml schema for RosettaScripts compatibility.
References protocols::moves::xsd_type_definition_w_attributes().
◆ register_options()
|
private |
Setup Methods ///.
Register Options from Command Line.
Register Options from Command Line
Referenced by MPRangeRelaxMover().
◆ set_defaults()
|
private |
Set default values.
Setup Methods ///.
Set default values
References center_resnumber_, core::scoring::ScoreFunctionFactory::create_score_function(), native_, optmem_, set_tm_helical_, and sfxn_.
Referenced by MPRangeRelaxMover().
Member Data Documentation
◆ center_resnumber_
|
private |
Center residue number.
Referenced by get_center_resnumber(), parse_my_tag(), and set_defaults().
◆ native_
|
private |
Native.
Referenced by apply(), get_native(), init_from_cmd(), parse_my_tag(), and set_defaults().
◆ optmem_
|
private |
optimize membrane?
Referenced by get_optmem(), optimize_membrane(), parse_my_tag(), and set_defaults().
◆ set_tm_helical_
|
private |
Set helical secondary structure in TM region.
Referenced by apply(), get_set_tm_helical(), init_from_cmd(), parse_my_tag(), and set_defaults().
◆ sfxn_
|
private |
Scorefxn.
Referenced by apply(), get_sfxn(), parse_my_tag(), and set_defaults().
The documentation for this class was generated from the following files:
- src/protocols/relax/membrane/MPRangeRelaxMover.hh
- src/protocols/relax/membrane/MPRangeRelaxMover.cc
