#include <MatcherMover.hh>
Public Types | |
| typedef core::Real | Real |
| typedef core::Size | Size |
| typedef protocols::moves::MoverOP | MoverOP |
| typedef utility::tag::TagCOP | TagCOP |
| typedef basic::datacache::DataMap | DataMap |
 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 | |
| MatcherMover (bool incorporate_matches_into_pose=true) | |
| Construction and Destruction. More... | |
| ~MatcherMover () override | |
| MatcherMover (MatcherMover const &rval) | |
| copy constructor More... | |
| MoverOP | clone () const override |
| clone this object More... | |
| MoverOP | fresh_instance () const override |
| create this type of object More... | |
| void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | apply (core::pose::Pose &pose) override |
| Main Method. More... | |
| void | set_ligres (core::conformation::ResidueCOP ligres) |
| void | set_match_positions (utility::vector1< core::Size > const &match_positions) |
| void | set_return_single_random_match (bool const single_random) |
| if set to true, a single random match will be returned. More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| Public Member Functions inherited from protocols::rosetta_scripts::MultiplePoseMover | |
| MultiplePoseMover () | |
| No-argument constructor. More... | |
| ~MultiplePoseMover () override=default | |
| Virtual destructor. More... | |
| protocols::moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| void | apply (core::pose::Pose &pose) override |
| Process input pose. More... | |
| core::pose::PoseOP | get_additional_output () override |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override |
| Parse settings in tag. More... | |
| void | set_previous_mover (protocols::moves::MoverOP const m) |
| Used by RosettaScripts to set the previous mover to pull poses from. More... | |
| void | set_rosetta_scripts_tag (utility::tag::TagCOP tag) |
| sets rosettascripts tag More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. 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... | |
| 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 std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| Static Public Member Functions inherited from protocols::rosetta_scripts::MultiplePoseMover | |
| static std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| 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 | |
| bool | process_pose (core::pose::Pose &, utility::vector1< core::pose::PoseOP > &) override |
| Process a single input pose by the RosettaScripts mover. More... | |
| void | setup_seqpos_from_selectors (protocols::match::MatcherTask &mtask, core::pose::Pose const &pose) const |
| 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... | |
Private Attributes | |
| bool | incorporate_matches_into_pose_ |
| bool | return_single_random_match_ |
| core::conformation::ResidueCOP | ligres_ |
| utility::vector1< core::Size > | match_positions_ |
| utility::vector1< core::select::residue_selector::ResidueSelectorCOP > | selectors_ |
| utility::vector1< toolbox::match_enzdes_util::MatchConstraintFileInfoListOP > | mcfi_list_vec_ |
Member Typedef Documentation
◆ DataMap
◆ MoverOP
◆ Real
◆ Size
◆ TagCOP
| typedef utility::tag::TagCOP protocols::match::MatcherMover::TagCOP |
Constructor & Destructor Documentation
◆ MatcherMover() [1/2]
| protocols::match::MatcherMover::MatcherMover | ( | bool | incorporate_matches_into_pose = true | ) |
Construction and Destruction.
◆ ~MatcherMover()
|
overridedefault |
◆ MatcherMover() [2/2]
|
default |
copy constructor
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References protocols::rosetta_scripts::MultiplePoseMover::apply(), and core::pose::Pose::pdb_info().
◆ clone()
|
overridevirtual |
clone this object
Reimplemented from protocols::moves::Mover.
◆ fresh_instance()
|
overridevirtual |
create this type of object
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ mover_name()
|
static |
Referenced by get_name(), protocols::match::MatcherMoverCreator::keyname(), and provide_xml_schema().
◆ parse_my_tag()
|
overridevirtual |
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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References core::chemical::FA_STANDARD, core::select::residue_selector::get_residue_selector(), incorporate_matches_into_pose_, mcfi_list_vec_, selectors_, and protocols::match::tr().
◆ process_pose()
|
overrideprotectedvirtual |
Process a single input pose by the RosettaScripts mover.
Reimplemented from protocols::rosetta_scripts::MultiplePoseMover.
References core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clone(), core::pose::Pose::conformation(), protocols::match::output::ProcessorFactory::create_processor(), core::conformation::ResidueFactory::create_residue(), core::conformation::Conformation::delete_residue_slow(), protocols::moves::FAIL_DO_NOT_RETRY, core::chemical::FULL_ATOM_t, core::scoring::get_score_function(), incorporate_matches_into_pose_, ligres_, match_positions_, mcfi_list_vec_, protocols::moves::MS_SUCCESS, core::chemical::ResidueTypeBase::name3(), protocols::sic_dock::scores::nbr1(), protocols::sic_dock::scores::nbr2(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), return_single_random_match_, selectors_, protocols::moves::Mover::set_last_move_status(), protocols::match::set_ligpose_rotamer(), setup_seqpos_from_selectors(), core::pose::Pose::size(), and protocols::match::tr().
◆ provide_xml_schema()
|
static |
References core::select::residue_selector::attributes_for_parse_residue_selector(), mover_name(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::return_complex_type_for_MatcherConstraint(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().
Referenced by protocols::match::MatcherMoverCreator::provide_xml_schema().
◆ set_ligres()
| void protocols::match::MatcherMover::set_ligres | ( | core::conformation::ResidueCOP | ligres | ) |
References ligres_.
◆ set_match_positions()
| void protocols::match::MatcherMover::set_match_positions | ( | utility::vector1< core::Size > const & | match_positions | ) |
References match_positions_.
◆ set_return_single_random_match()
| void protocols::match::MatcherMover::set_return_single_random_match | ( | bool const | single_random | ) |
if set to true, a single random match will be returned.
The default behavior is to use the MultiplePoseMover framework to return all matches
References return_single_random_match_.
◆ setup_seqpos_from_selectors()
|
protected |
References selectors_, protocols::match::MatcherTask::set_ignore_cmdline_for_build_points(), protocols::match::MatcherTask::set_original_scaffold_build_points_for_geometric_constraint(), protocols::match::tr(), and protocols::match::MatcherTask::use_different_build_points_for_each_geometric_constraint().
Referenced by process_pose().
Member Data Documentation
◆ incorporate_matches_into_pose_
|
private |
Referenced by parse_my_tag(), and process_pose().
◆ ligres_
|
private |
Referenced by process_pose(), and set_ligres().
◆ match_positions_
|
private |
Referenced by process_pose(), and set_match_positions().
◆ mcfi_list_vec_
|
private |
Referenced by parse_my_tag(), and process_pose().
◆ return_single_random_match_
|
private |
Referenced by process_pose(), and set_return_single_random_match().
◆ selectors_
|
private |
Referenced by parse_my_tag(), process_pose(), and setup_seqpos_from_selectors().
The documentation for this class was generated from the following files:
- src/protocols/match/MatcherMover.hh
- src/protocols/match/MatcherMover.cc
