#include <SecretionOptimizationMover.hh>
Classes | |
| struct | mutt |
| struct | tm_region |
Public Types | |
| typedef core::Real | Real |
| typedef core::scoring::ScoreType | ScoreType |
| typedef core::pose::Pose | Pose |
 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 | |
| SecretionOptimizationMover () | |
| SecretionOptimizationMover (core::scoring::ScoreFunctionCOP scorefxn) | |
| void | apply (Pose &) override |
| Main Method. More... | |
| ~SecretionOptimizationMover () override | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| protocols::moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| void | parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | task_factory (core::pack::task::TaskFactoryCOP task_factory) |
| core::pack::task::TaskFactoryCOP | task_factory () const |
| void | set_max_mutations (core::Size const max_mutations) |
| core::Size | get_max_mutations () |
| void | set_aas_allowed (std::string const aas_allowed) |
| std::string | get_aas_allowed () |
| void | set_dG_ins_threshold (core::Real const dG_ins_threshold) |
| core::Real | get_dG_ins_threshold () |
| void | set_score_tolerance (core::Real const score_tolerance) |
| core::Real | get_score_tolerance () |
| void | set_chain_to_degrease (std::string const chain_to_degrease) |
| std::string | get_chain_to_degrease () |
| void | set_dG_tolerance (core::Real const dG_tolerance) |
| core::Real | get_dG_tolerance () |
| void | set_dump_multis (bool dump_multis) |
| bool | get_dump_multis () |
| void | set_dump_singles (bool dump_singles) |
| bool | get_dump_singles () |
| void | set_dump_dir (std::string const dump_dir) |
| std::string | get_dump_dir () |
| void | use_largest_ddg (bool largest_ddg) |
| void | use_smallest_dscore (bool smallest_dscore) |
| bool | largest_ddg () |
| bool | smallest_dscore () |
| void | make_table () |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| Real | dG_term_for_residue_at_position (double &position, std::string &residue) |
| Real | normalize_position_in_helix_given_length (core::Size &position, double &helix_length) |
| Real | dG_ins_for_window (std::string &window) |
| std::string | get_window_at_index (Pose &pose, core::Size &wlen, core::Size &start) |
| virtual void | report_test (std::ostream &out, Pose &pose) |
| utility::vector1< SecretionOptimizationMover::tm_region > | find_tm_regions (std::ostream &out, Pose &pose) |
| Real | repack_shell () const |
| void | repack_shell (Real const repack_shell) |
| void | DesignAroundApply (core::pose::Pose const &pose, utility::vector1< SecretionOptimizationMover::mutt > &targets) const |
| void | packeruser (core::pose::Pose &pose) const |
| void | test_move (core::pose::Pose &pose) override |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying 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 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 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... | |
Private Attributes | |
| utility::vector1< SecretionOptimizationMover::mutt > | resids_ |
| utility::vector1< SecretionOptimizationMover::mutt > | mutids_ |
| std::string | window_ = "AAAAAAAAAAAAAAAAAAA" |
| core::Size | window_size_ = 19 |
| core::pack::task::TaskFactoryCOP | task_factory_ |
| core::Size | max_mutations_ = 3 |
| core::Real | dG_ins_threshold_ = 3.5 |
| core::Real | dG_tolerance_ = 0.27 |
| core::Real | score_tolerance_ = 15 |
| core::Real | repack_shell_ = 8.0 |
| core::Real | repack_shell_squared_ = 64.0 |
| std::string | keep_ = "DEKRQNSTY" |
| std::string | chain_to_degrease_ = "A" |
| bool | dump_multis_ = false |
| bool | dump_singles_ = true |
| std::string | dump_dir_ = "." |
| bool | largest_ddg_ = true |
| bool | smallest_dscore_ = false |
| std::unordered_map< std::string, std::unordered_map< std::string, core::Real > > | coeffs |
| protocols::minimization_packing::PackRotamersMoverOP | pack_it_ |
| core::scoring::ScoreFunctionOP | scorefxn_ |
| utility::vector1< SecretionOptimizationMover::tm_region > | found_regions_ |
| core::pack::task::PackerTaskOP | task_ |
Additional Inherited Members | |
| 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
◆ Pose
| typedef core::pose::Pose protocols::protein_interface_design::movers::SecretionOptimizationMover::Pose |
◆ Real
◆ ScoreType
| typedef core::scoring::ScoreType protocols::protein_interface_design::movers::SecretionOptimizationMover::ScoreType |
Constructor & Destructor Documentation
◆ SecretionOptimizationMover() [1/2]
| protocols::protein_interface_design::movers::SecretionOptimizationMover::SecretionOptimizationMover | ( | ) |
References make_table().
Referenced by clone().
◆ SecretionOptimizationMover() [2/2]
| protocols::protein_interface_design::movers::SecretionOptimizationMover::SecretionOptimizationMover | ( | core::scoring::ScoreFunctionCOP | scorefxn | ) |
References make_table().
◆ ~SecretionOptimizationMover()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References core::pose::motif::a(), protocols::cluster::calibur::aa, protocols::score_filters::ScoreTypeFilter::compute(), protocols::jd2::current_output_name(), DesignAroundApply(), dG_ins_for_window(), dG_tolerance_, dump_dir_, dump_multis_, core::pose::Pose::dump_pdb(), dump_singles_, core::chemical::element::F, found_regions_, get_window_at_index(), largest_ddg_, max_mutations_, mutids_, protocols::moves::Mover::name(), core::conformation::Residue::name1(), packeruser(), report_test(), resids_, core::pose::Pose::residue(), protocols::hybridization::score, score_tolerance_, scorefxn_, core::pose::setPoseExtraScore(), smallest_dscore_, task_, task_factory_, core::id::to_string(), core::scoring::total_score, protocols::protein_interface_design::movers::TR(), and window_size_.
Referenced by test_move().
◆ clone()
|
overridevirtual |
Return a clone of the Mover object.
clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.
Reimplemented from protocols::moves::Mover.
References SecretionOptimizationMover().
◆ DesignAroundApply()
| void protocols::protein_interface_design::movers::SecretionOptimizationMover::DesignAroundApply | ( | core::pose::Pose const & | pose, |
| utility::vector1< SecretionOptimizationMover::mutt > & | targets | ||
| ) | const |
References core::pose::motif::a(), protocols::cluster::calibur::aa, core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), core::pack::task::operation::PreventRepacking::apply(), protocols::match::upstream::b, core::pack::task::operation::PreventRepacking::clear(), core::pack::task::operation::RestrictAbsentCanonicalAAS::include_residue(), core::pack::task::operation::PreventRepacking::include_residue(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), core::conformation::Residue::nbr_atom(), protocols::antibody::design::repack, repack_shell(), core::pose::Pose::residue(), core::pose::symmetry::symmetry_info(), task_, task_factory_, core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().
Referenced by apply().
◆ dG_ins_for_window()
| core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::dG_ins_for_window | ( | std::string & | window | ) |
References dG_term_for_residue_at_position(), and normalize_position_in_helix_given_length().
Referenced by apply(), and find_tm_regions().
◆ dG_term_for_residue_at_position()
| core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::dG_term_for_residue_at_position | ( | double & | position, |
| std::string & | residue | ||
| ) |
References coeffs.
Referenced by dG_ins_for_window().
◆ find_tm_regions()
| utility::vector1< SecretionOptimizationMover::tm_region > protocols::protein_interface_design::movers::SecretionOptimizationMover::find_tm_regions | ( | std::ostream & | out, |
| Pose & | pose | ||
| ) |
References chain_to_degrease_, protocols::protein_interface_design::movers::SecretionOptimizationMover::tm_region::dG_ins, dG_ins_for_window(), dG_ins_threshold_, core::pose::get_resnums_for_chain(), get_window_at_index(), protocols::protein_interface_design::movers::SecretionOptimizationMover::tm_region::index, keep_, core::conformation::membrane::out, protocols::protein_interface_design::movers::SecretionOptimizationMover::tm_region::possible_mutants, core::chemical::rings::q, protocols::protein_interface_design::movers::SecretionOptimizationMover::tm_region::sequence, core::id::to_string(), and window_size_.
Referenced by report_test().
◆ fresh_instance()
|
overridevirtual |
Generates a new Mover object freshly created with the default ctor.
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
◆ get_aas_allowed()
|
inline |
References keep_.
◆ get_chain_to_degrease()
|
inline |
References chain_to_degrease_.
◆ get_dG_ins_threshold()
|
inline |
References dG_ins_threshold_.
◆ get_dG_tolerance()
|
inline |
References dG_tolerance_.
◆ get_dump_dir()
|
inline |
References dump_dir_.
◆ get_dump_multis()
|
inline |
References dump_multis_.
◆ get_dump_singles()
|
inline |
References dump_singles_.
◆ get_max_mutations()
|
inline |
References max_mutations_.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ get_score_tolerance()
|
inline |
References score_tolerance_.
◆ get_window_at_index()
| std::string protocols::protein_interface_design::movers::SecretionOptimizationMover::get_window_at_index | ( | Pose & | pose, |
| core::Size & | wlen, | ||
| core::Size & | start | ||
| ) |
References core::pose::Pose::sequence(), and protocols::loops::start.
Referenced by apply(), and find_tm_regions().
◆ largest_ddg()
|
inline |
References largest_ddg_.
Referenced by use_largest_ddg().
◆ make_table()
| void protocols::protein_interface_design::movers::SecretionOptimizationMover::make_table | ( | ) |
References coeffs.
Referenced by SecretionOptimizationMover().
◆ mover_name()
|
static |
◆ normalize_position_in_helix_given_length()
| core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::normalize_position_in_helix_given_length | ( | core::Size & | position, |
| double & | helix_length | ||
| ) |
Referenced by dG_ins_for_window().
◆ packeruser()
| void protocols::protein_interface_design::movers::SecretionOptimizationMover::packeruser | ( | core::pose::Pose & | pose | ) | const |
◆ 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::scoring::parse_score_function(), core::pack::task::parse_task_operations(), repack_shell(), scorefxn_, set_aas_allowed(), set_chain_to_degrease(), set_dG_ins_threshold(), set_dG_tolerance(), set_dump_dir(), set_dump_multis(), set_dump_singles(), set_max_mutations(), set_score_tolerance(), task_factory(), use_largest_ddg(), and use_smallest_dscore().
◆ provide_xml_schema()
|
static |
References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::protein_interface_design::movers::SecretionOptimizationMoverCreator::provide_xml_schema().
◆ repack_shell() [1/2]
|
inline |
References repack_shell_.
Referenced by DesignAroundApply(), parse_my_tag(), and repack_shell().
◆ repack_shell() [2/2]
|
inline |
References repack_shell(), repack_shell_, and repack_shell_squared_.
◆ report_test()
|
virtual |
◆ set_aas_allowed()
|
inline |
References keep_.
Referenced by parse_my_tag().
◆ set_chain_to_degrease()
|
inline |
References chain_to_degrease_.
Referenced by parse_my_tag().
◆ set_dG_ins_threshold()
|
inline |
References dG_ins_threshold_.
Referenced by parse_my_tag().
◆ set_dG_tolerance()
|
inline |
References dG_tolerance_.
Referenced by parse_my_tag().
◆ set_dump_dir()
|
inline |
References dump_dir_.
Referenced by parse_my_tag().
◆ set_dump_multis()
|
inline |
References dump_multis_.
Referenced by parse_my_tag().
◆ set_dump_singles()
|
inline |
References dump_singles_.
Referenced by parse_my_tag().
◆ set_max_mutations()
|
inline |
References max_mutations_.
Referenced by parse_my_tag().
◆ set_score_tolerance()
|
inline |
References score_tolerance_.
Referenced by parse_my_tag().
◆ smallest_dscore()
|
inline |
References smallest_dscore_.
Referenced by use_smallest_dscore().
◆ task_factory() [1/2]
|
inline |
References task_factory_.
Referenced by parse_my_tag(), and task_factory().
◆ task_factory() [2/2]
|
inline |
References task_factory(), and task_factory_.
◆ test_move()
|
overridevirtual |
: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying
Reimplemented from protocols::moves::Mover.
References apply().
◆ use_largest_ddg()
|
inline |
References largest_ddg(), and largest_ddg_.
Referenced by parse_my_tag().
◆ use_smallest_dscore()
|
inline |
References smallest_dscore(), and smallest_dscore_.
Referenced by parse_my_tag().
Member Data Documentation
◆ chain_to_degrease_
|
private |
Referenced by find_tm_regions(), get_chain_to_degrease(), and set_chain_to_degrease().
◆ coeffs
|
private |
Referenced by dG_term_for_residue_at_position(), and make_table().
◆ dG_ins_threshold_
|
private |
Referenced by find_tm_regions(), get_dG_ins_threshold(), report_test(), and set_dG_ins_threshold().
◆ dG_tolerance_
|
private |
Referenced by apply(), get_dG_tolerance(), and set_dG_tolerance().
◆ dump_dir_
|
private |
Referenced by apply(), get_dump_dir(), and set_dump_dir().
◆ dump_multis_
|
private |
Referenced by apply(), get_dump_multis(), and set_dump_multis().
◆ dump_singles_
|
private |
Referenced by apply(), get_dump_singles(), and set_dump_singles().
◆ found_regions_
|
private |
Referenced by apply(), and report_test().
◆ keep_
|
private |
Referenced by find_tm_regions(), get_aas_allowed(), report_test(), and set_aas_allowed().
◆ largest_ddg_
|
private |
Referenced by apply(), largest_ddg(), and use_largest_ddg().
◆ max_mutations_
|
private |
Referenced by apply(), get_max_mutations(), report_test(), and set_max_mutations().
◆ mutids_
|
private |
Referenced by apply().
◆ pack_it_
|
private |
Referenced by packeruser().
◆ repack_shell_
|
private |
Referenced by repack_shell().
◆ repack_shell_squared_
|
private |
Referenced by repack_shell().
◆ resids_
|
private |
Referenced by apply().
◆ score_tolerance_
|
private |
Referenced by apply(), get_score_tolerance(), report_test(), and set_score_tolerance().
◆ scorefxn_
|
private |
Referenced by apply(), packeruser(), and parse_my_tag().
◆ smallest_dscore_
|
private |
Referenced by apply(), smallest_dscore(), and use_smallest_dscore().
◆ task_
|
private |
Referenced by apply(), DesignAroundApply(), and packeruser().
◆ task_factory_
|
private |
Referenced by apply(), DesignAroundApply(), and task_factory().
◆ window_
|
private |
◆ window_size_
|
private |
Referenced by apply(), and find_tm_regions().
The documentation for this class was generated from the following files:
- src/protocols/protein_interface_design/movers/SecretionOptimizationMover.hh
- src/protocols/protein_interface_design/movers/SecretionOptimizationMover.cc
