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protocols::protein_interface_design::movers::SecretionOptimizationMover Class Reference

#include <SecretionOptimizationMover.hh>

Inheritance diagram for protocols::protein_interface_design::movers::SecretionOptimizationMover:
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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_regionfind_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 Stringsinfo ()
 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::muttresids_
 
utility::vector1< SecretionOptimizationMover::muttmutids_
 
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_regionfound_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

◆ Real

◆ 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()

protocols::protein_interface_design::movers::SecretionOptimizationMover::~SecretionOptimizationMover ( )
overridedefault

Member Function Documentation

◆ apply()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::apply ( Pose )
overridevirtual

◆ clone()

protocols::moves::MoverOP protocols::protein_interface_design::movers::SecretionOptimizationMover::clone ( ) const
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

◆ dG_ins_for_window()

core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::dG_ins_for_window ( std::string &  window)

◆ 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 
)

◆ fresh_instance()

protocols::moves::MoverOP protocols::protein_interface_design::movers::SecretionOptimizationMover::fresh_instance ( ) const
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()

std::string protocols::protein_interface_design::movers::SecretionOptimizationMover::get_aas_allowed ( )
inline

References keep_.

◆ get_chain_to_degrease()

std::string protocols::protein_interface_design::movers::SecretionOptimizationMover::get_chain_to_degrease ( )
inline

References chain_to_degrease_.

◆ get_dG_ins_threshold()

core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::get_dG_ins_threshold ( )
inline

References dG_ins_threshold_.

◆ get_dG_tolerance()

core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::get_dG_tolerance ( )
inline

References dG_tolerance_.

◆ get_dump_dir()

std::string protocols::protein_interface_design::movers::SecretionOptimizationMover::get_dump_dir ( )
inline

References dump_dir_.

◆ get_dump_multis()

bool protocols::protein_interface_design::movers::SecretionOptimizationMover::get_dump_multis ( )
inline

References dump_multis_.

◆ get_dump_singles()

bool protocols::protein_interface_design::movers::SecretionOptimizationMover::get_dump_singles ( )
inline

References dump_singles_.

◆ get_max_mutations()

core::Size protocols::protein_interface_design::movers::SecretionOptimizationMover::get_max_mutations ( )
inline

References max_mutations_.

◆ get_name()

std::string protocols::protein_interface_design::movers::SecretionOptimizationMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

◆ get_score_tolerance()

core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::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 
)

◆ largest_ddg()

bool protocols::protein_interface_design::movers::SecretionOptimizationMover::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()

std::string protocols::protein_interface_design::movers::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

References pack_it_, scorefxn_, and task_.

Referenced by apply().

◆ parse_my_tag()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 
)
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()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

◆ repack_shell() [1/2]

Real protocols::protein_interface_design::movers::SecretionOptimizationMover::repack_shell ( ) const
inline

◆ repack_shell() [2/2]

void protocols::protein_interface_design::movers::SecretionOptimizationMover::repack_shell ( Real const  repack_shell)
inline

◆ report_test()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::report_test ( std::ostream &  out,
Pose pose 
)
virtual

◆ set_aas_allowed()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::set_aas_allowed ( std::string const  aas_allowed)
inline

References keep_.

Referenced by parse_my_tag().

◆ set_chain_to_degrease()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::set_chain_to_degrease ( std::string const  chain_to_degrease)
inline

References chain_to_degrease_.

Referenced by parse_my_tag().

◆ set_dG_ins_threshold()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::set_dG_ins_threshold ( core::Real const  dG_ins_threshold)
inline

References dG_ins_threshold_.

Referenced by parse_my_tag().

◆ set_dG_tolerance()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::set_dG_tolerance ( core::Real const  dG_tolerance)
inline

References dG_tolerance_.

Referenced by parse_my_tag().

◆ set_dump_dir()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::set_dump_dir ( std::string const  dump_dir)
inline

References dump_dir_.

Referenced by parse_my_tag().

◆ set_dump_multis()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::set_dump_multis ( bool  dump_multis)
inline

References dump_multis_.

Referenced by parse_my_tag().

◆ set_dump_singles()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::set_dump_singles ( bool  dump_singles)
inline

References dump_singles_.

Referenced by parse_my_tag().

◆ set_max_mutations()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::set_max_mutations ( core::Size const  max_mutations)
inline

References max_mutations_.

Referenced by parse_my_tag().

◆ set_score_tolerance()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::set_score_tolerance ( core::Real const  score_tolerance)
inline

References score_tolerance_.

Referenced by parse_my_tag().

◆ smallest_dscore()

bool protocols::protein_interface_design::movers::SecretionOptimizationMover::smallest_dscore ( )
inline

References smallest_dscore_.

Referenced by use_smallest_dscore().

◆ task_factory() [1/2]

core::pack::task::TaskFactoryCOP protocols::protein_interface_design::movers::SecretionOptimizationMover::task_factory ( ) const
inline

References task_factory_.

Referenced by parse_my_tag(), and task_factory().

◆ task_factory() [2/2]

void protocols::protein_interface_design::movers::SecretionOptimizationMover::task_factory ( core::pack::task::TaskFactoryCOP  task_factory)
inline

References task_factory(), and task_factory_.

◆ test_move()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::test_move ( core::pose::Pose pose)
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()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::use_largest_ddg ( bool  largest_ddg)
inline

References largest_ddg(), and largest_ddg_.

Referenced by parse_my_tag().

◆ use_smallest_dscore()

void protocols::protein_interface_design::movers::SecretionOptimizationMover::use_smallest_dscore ( bool  smallest_dscore)
inline

References smallest_dscore(), and smallest_dscore_.

Referenced by parse_my_tag().

Member Data Documentation

◆ chain_to_degrease_

std::string protocols::protein_interface_design::movers::SecretionOptimizationMover::chain_to_degrease_ = "A"
private

◆ coeffs

std::unordered_map<std::string, std::unordered_map<std::string, core::Real> > protocols::protein_interface_design::movers::SecretionOptimizationMover::coeffs
private

◆ dG_ins_threshold_

core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::dG_ins_threshold_ = 3.5
private

◆ dG_tolerance_

core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::dG_tolerance_ = 0.27
private

◆ dump_dir_

std::string protocols::protein_interface_design::movers::SecretionOptimizationMover::dump_dir_ = "."
private

Referenced by apply(), get_dump_dir(), and set_dump_dir().

◆ dump_multis_

bool protocols::protein_interface_design::movers::SecretionOptimizationMover::dump_multis_ = false
private

◆ dump_singles_

bool protocols::protein_interface_design::movers::SecretionOptimizationMover::dump_singles_ = true
private

◆ found_regions_

utility::vector1<SecretionOptimizationMover::tm_region> protocols::protein_interface_design::movers::SecretionOptimizationMover::found_regions_
private

Referenced by apply(), and report_test().

◆ keep_

std::string protocols::protein_interface_design::movers::SecretionOptimizationMover::keep_ = "DEKRQNSTY"
private

◆ largest_ddg_

bool protocols::protein_interface_design::movers::SecretionOptimizationMover::largest_ddg_ = true
private

Referenced by apply(), largest_ddg(), and use_largest_ddg().

◆ max_mutations_

core::Size protocols::protein_interface_design::movers::SecretionOptimizationMover::max_mutations_ = 3
private

◆ mutids_

utility::vector1<SecretionOptimizationMover::mutt> protocols::protein_interface_design::movers::SecretionOptimizationMover::mutids_
private

Referenced by apply().

◆ pack_it_

protocols::minimization_packing::PackRotamersMoverOP protocols::protein_interface_design::movers::SecretionOptimizationMover::pack_it_
private

Referenced by packeruser().

◆ repack_shell_

core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::repack_shell_ = 8.0
private

Referenced by repack_shell().

◆ repack_shell_squared_

core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::repack_shell_squared_ = 64.0
private

Referenced by repack_shell().

◆ resids_

utility::vector1<SecretionOptimizationMover::mutt> protocols::protein_interface_design::movers::SecretionOptimizationMover::resids_
private

Referenced by apply().

◆ score_tolerance_

core::Real protocols::protein_interface_design::movers::SecretionOptimizationMover::score_tolerance_ = 15
private

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::SecretionOptimizationMover::scorefxn_
private

Referenced by apply(), packeruser(), and parse_my_tag().

◆ smallest_dscore_

bool protocols::protein_interface_design::movers::SecretionOptimizationMover::smallest_dscore_ = false
private

◆ task_

core::pack::task::PackerTaskOP protocols::protein_interface_design::movers::SecretionOptimizationMover::task_
private

◆ task_factory_

core::pack::task::TaskFactoryCOP protocols::protein_interface_design::movers::SecretionOptimizationMover::task_factory_
private

◆ window_

std::string protocols::protein_interface_design::movers::SecretionOptimizationMover::window_ = "AAAAAAAAAAAAAAAAAAA"
private

◆ window_size_

core::Size protocols::protein_interface_design::movers::SecretionOptimizationMover::window_size_ = 19
private

Referenced by apply(), and find_tm_regions().


The documentation for this class was generated from the following files: