#include <DrugPolishMover.hh>
Inheritance diagram for protocols::drug_design::DrugPolishMover:
Public Member Functions | |
| DrugPolishMover () | |
| default constructor More... | |
| ~DrugPolishMover () override | |
| destructor More... | |
| protocols::moves::MoverOP | clone () const override |
| create copy constructor More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| create this type of objectt More... | |
| void | apply (core::pose::Pose &pose) override |
| apply DrugPolishMover More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| core::Real | bonus () const |
| The bonus given to scoring for applying (another) reaction. More... | |
| void | bonus (core::Real setting) |
| The bonus given to scoring for applying (another) reaction. More... | |
| void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override |
| parse xml file More... | |
 Public Member Functions inherited from protocols::drug_design::DrugDesignMover | |
| DrugDesignMover () | |
| default constructor More... | |
| ~DrugDesignMover () override | |
| destructor More... | |
| protocols::moves::MoverCOP | redocker () const |
| Return the redocker being used. More... | |
| protocols::filters::FilterCOP | scorer () const |
| Return the scoring filter. More... | |
| core::Real | temperature () const |
| Return the scoring temperature. More... | |
| core::Size | maxtrials () const |
| Returns maximum number of trials. More... | |
| char | chain () const |
| What chain is the ligand supposed to be? More... | |
| std::string | debug_prefix () const |
| What's the prefix of the filename to which intermediate debug structures are dumped? More... | |
| void | add_chemistry (protocols::chemistries::ChemistryOP chemistry, core::Real weight=1.0) |
| Add a chemistry to use. More... | |
| void | add_before_chemistry (protocols::chemistries::ChemistryOP chemistry) |
| Add a chemistry to use. More... | |
| void | add_after_chemistry (protocols::chemistries::ChemistryOP chemistry) |
| Add a chemistry to use. More... | |
| void | redocker (protocols::moves::MoverOP const &mover) |
| set redocking mover More... | |
| void | scorer (protocols::filters::FilterOP const &scorer) |
| Set the scoring filter in use. More... | |
| void | prefilter (protocols::filters::FilterOP const &setting) |
| Set the filter to use before redocking. More... | |
| void | postfilter (protocols::filters::FilterOP const &setting) |
| Set the filter to use after redocking. More... | |
| void | temperature (core::Real const temp) |
| set temperature More... | |
| void | maxtrials (core::Size const ntrial) |
| set max trials of MC trials More... | |
| void | chain (char chain) |
| set the ligand chain to use for design More... | |
| void | debug_prefix (std::string const &setting) |
| What's the prefix of the filename to which intermediate debug structures are dumped? More... | |
| bool | check_design_position (core::pose::Pose const &pose, core::Size n) |
| Is position n a valid designable residue according to the settings. More... | |
| core::Size | find_design_position (core::pose::Pose const &pose) |
| Determine which residue on this pose should be designed. 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... | |
Private Attributes | |
| core::Real | bonus_ |
| The bonus given to scoring for applying (another) reaction. 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 |
| Static Public Member Functions inherited from protocols::drug_design::DrugDesignMover | |
| 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 inherited from protocols::drug_design::DrugDesignMover | |
| std::string | get_jobname () const |
| Return a unique string representing which job this is. More... | |
| utility::vector1< protocols::chemistries::ChemistryOP > & | chemistries () |
| Subclass access to the chemistries. More... | |
| bool | pre_process_restype (core::chemical::MutableResidueTypeOP restype, core::chemical::IndexVDMapping &index_vd_mapping, core::pose::Pose const &pose) |
| Pre-process the ResidueType. More... | |
| bool | post_process_restype (core::chemical::MutableResidueTypeOP restype, core::chemical::IndexVDMapping &index_vd_mapping, std::string const &new_name, core::pose::Pose const &pose) |
| Post-process the residuetype. More... | |
| bool | emplace_residue_type (core::pose::Pose &pose, core::chemical::MutableResidueTypeOP restype, core::chemical::IndexVDMapping const &index_VD_mapping) |
| Take a new residuetype, place it on the pose, and see if it passes filters. More... | |
| void | compute_scores_for_logfile (core::Real score, core::chemical::MutableResidueTypeOP restype, core::Real &raw_score, core::Real &LE_score) const |
| Helper function for calculating raw -> LE or LE -> raw score. More... | |
| std::string | find_new_res_name (std::string original_name, core::Size iteration, core::Size subiteration=0) const |
| Find a new residue name, if the name already exists in the residue type set. More... | |
| void | dump_molecule (core::chemical::MutableResidueType const &restype, std::string const &stage) const |
| Dump the ligand to the given file (appending) More... | |
| void | dump_molecule (core::conformation::Residue const &residue, std::string const &stage) const |
| Dump the ligand to the given file (appending) More... | |
| protocols::chemistries::ChemistryOP | chemistry_from_subtag (utility::tag::TagCOP const subtag, basic::datacache::DataMap &data) 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... | |
Constructor & Destructor Documentation
◆ DrugPolishMover()
| protocols::drug_design::DrugPolishMover::DrugPolishMover | ( | ) |
default constructor
◆ ~DrugPolishMover()
|
override |
destructor
Member Function Documentation
◆ apply()
|
overridevirtual |
apply DrugPolishMover
Reimplemented from protocols::drug_design::DrugDesignMover.
References protocols::chemistries::Chemistry::apply(), core::pose::Pose::clone(), core::chemical::combine(), core::chemical::modifications::ChemistryBase::get_additional_output(), core::chemical::modifications::ChemistryBase::get_last_status(), core::chemical::modifications::ChemistryBase::get_mapping(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::hybridization::score, core::chemical::modifications::SUCCESS, and protocols::drug_design::TR().
◆ bonus() [1/2]
|
inline |
The bonus given to scoring for applying (another) reaction.
References bonus_.
◆ bonus() [2/2]
|
inline |
The bonus given to scoring for applying (another) reaction.
References bonus_.
◆ clone()
|
overridevirtual |
create copy constructor
clone this object
Reimplemented from protocols::drug_design::DrugDesignMover.
◆ fresh_instance()
|
overridevirtual |
create this type of objectt
create this type of object
Reimplemented from protocols::drug_design::DrugDesignMover.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Reimplemented from protocols::drug_design::DrugDesignMover.
References protocols::drug_design::DrugPolishMoverCreator::mover_name().
◆ parse_my_tag()
|
overridevirtual |
parse xml file
Reimplemented from protocols::drug_design::DrugDesignMover.
References protocols::rosetta_scripts::parse_filter(), and protocols::rosetta_scripts::parse_mover().
Member Data Documentation
◆ bonus_
|
private |
The bonus given to scoring for applying (another) reaction.
Referenced by bonus().
The documentation for this class was generated from the following files:
- src/protocols/drug_design/DrugPolishMover.hh
- src/protocols/drug_design/DrugPolishMover.cc
