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protocols::chemically_conjugated_docking::UBQ_GTPaseMover Class Reference

A mover typically used for binding ubiquitin to a substrate protein. More...

#include <UBQ_GTPaseMover.hh>

Inheritance diagram for protocols::chemically_conjugated_docking::UBQ_GTPaseMover:
Inheritance graph
[legend]

Public Member Functions

 UBQ_GTPaseMover ()
 Constructors ///. More...
 
 UBQ_GTPaseMover (UBQ_GTPaseMover const &)=default
 Copy constructor (not needed unless you need deep copies) More...
 
 ~UBQ_GTPaseMover () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
 
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Rosetta Scripts Support ///. More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void initialize (core::pose::Pose &GTPase)
 sets up the pose with UBQ and GTPase More...
 
void analyze_and_filter (core::pose::Pose &pose)
 applies filters and stores torsion angles near LYX bond More...
 
void make_index_selector (core::Size index)
 makes an internal ResidueIndexSelector given a residue index on the substrate. More...
 
core::scoring::ScoreFunctionOP get_fullatom_scorefunction () const
 
void set_fullatom_scorefunction (core::scoring::ScoreFunctionOP const &sfxn)
 
core::pack::task::TaskFactoryOP get_task_factory () const
 
void set_task_factory (core::pack::task::TaskFactoryOP const &tasks)
 
core::kinematics::MoveMapOP get_amide_mm () const
 
void set_amide_mm (core::kinematics::MoveMapOP const &mm)
 
protocols::loops::Loop const & get_loop () const
 
void set_loop (protocols::loops::Loop const &loop)
 
utility::vector1
< core::id::AtomID > const & 
get_atom_IDs () const
 
void set_atom_IDs (utility::vector1< core::id::AtomID > const &ids)
 
core::pose::Pose const & get_starting_pose () const
 
std::string const & get_InterfaceSasaDefinition () const
 
protocols::analysis::InterfaceAnalyzerMoverOP get_IAM () const
 
void set_IAM (protocols::analysis::InterfaceAnalyzerMoverOP const &iam)
 
utility::vector1< core::Size >
const & 
get_extra_bodies_chains () const
 
void set_extra_bodies_chains (utility::vector1< core::Size > const &chains)
 
bool get_extra_bodies () const
 
void set_extra_bodies (bool const hasExtra)
 
core::Size get_n_tail_res () const
 
void set_n_tail_res (core::Size const numTails)
 
core::Size get_GTPase_lys () const
 
void set_GTPase_lys (core::Size const lys)
 
core::Real get_scorefilter () const
 
void set_scorefilter (core::Real const maxScore)
 
core::Real get_SASAfilter () const
 
void set_SASAfilter (core::Real const minSASA)
 
std::string const & get_UBQpdb () const
 
void set_UBQpdb (std::string const &ubqFile)
 
core::select::residue_selector::ResidueSelectorCOP get_selector () const
 
void set_selector (core::select::residue_selector::ResidueSelectorCOP const &select)
 
- 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 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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

core::scoring::ScoreFunctionOP fullatom_scorefunction_
 
core::pack::task::TaskFactoryOP task_factory_
 
core::kinematics::MoveMapOP amide_mm_
 
protocols::loops::Loop loop_
 
utility::vector1
< core::id::AtomID
atomIDs
 vector contains atomIDs for isopeptide bond and atoms before/after bond to determine various torsions More...
 
core::pose::Pose starting_pose_
 
std::string const InterfaceSasaDefinition_
 
protocols::analysis::InterfaceAnalyzerMoverOP IAM_
 
core::Size GTPase_lys_ = 0
 
utility::vector1< core::Sizeextra_bodies_chains_
 used to track which chains are "extra" nonmoving bodies in extra bodies mode More...
 
bool extra_bodies_
 
core::Size n_tail_res_
 
core::Real scorefilter_
 
core::Real SASAfilter_
 
std::string UBQpdb_
 
core::select::residue_selector::ResidueSelectorCOP selector_
 
protocols::jd2::JobOP job_me_
 

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...
 

Detailed Description

A mover typically used for binding ubiquitin to a substrate protein.

Constructor & Destructor Documentation

protocols::chemically_conjugated_docking::UBQ_GTPaseMover::UBQ_GTPaseMover ( )
protocols::chemically_conjugated_docking::UBQ_GTPaseMover::UBQ_GTPaseMover ( UBQ_GTPaseMover const &  )
default

Copy constructor (not needed unless you need deep copies)

protocols::chemically_conjugated_docking::UBQ_GTPaseMover::~UBQ_GTPaseMover ( )
override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter ( core::pose::Pose pose)
void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

core::kinematics::MoveMapOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_amide_mm ( ) const

References amide_mm_.

utility::vector1< core::id::AtomID > const & protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_atom_IDs ( ) const

References atomIDs.

bool protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_extra_bodies ( ) const

References extra_bodies_.

utility::vector1< core::Size > const & protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_extra_bodies_chains ( ) const

References extra_bodies_chains_.

core::scoring::ScoreFunctionOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_fullatom_scorefunction ( ) const
core::Size protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_GTPase_lys ( ) const

References GTPase_lys_.

protocols::analysis::InterfaceAnalyzerMoverOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_IAM ( ) const

References IAM_.

std::string const & protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_InterfaceSasaDefinition ( ) const
protocols::loops::Loop const & protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_loop ( ) const

References loop_.

core::Size protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_n_tail_res ( ) const

References n_tail_res_.

std::string protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Real protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_SASAfilter ( ) const

References SASAfilter_.

core::Real protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_scorefilter ( ) const

References scorefilter_.

core::select::residue_selector::ResidueSelectorCOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_selector ( ) const

References selector_.

Referenced by parse_my_tag().

core::pose::Pose const & protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_starting_pose ( ) const

References starting_pose_.

core::pack::task::TaskFactoryOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_task_factory ( ) const

References task_factory_.

std::string const & protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_UBQpdb ( ) const

References UBQpdb_.

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize ( core::pose::Pose GTPase)

sets up the pose with UBQ and GTPase

Mover Methods ///.

init_on_new_input system allows for initializing these details the first time apply() is called. the job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply().

References core::scoring::constraints::add_constraints_from_cmdline_to_pose(), protocols::chemically_conjugated_docking::add_extra_bodies(), amide_mm_, core::pose::Pose::append_residue_by_bond(), apply(), atomIDs, core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), protocols::jd2::JobDistributor::current_job(), core::conformation::Conformation::delete_residue_slow(), core::sequence::end, extra_bodies_, extra_bodies_chains_, core::chemical::FA_STANDARD, protocols::jd2::JobDistributor::get_instance(), core::select::get_residues_from_subset(), GTPase_lys_, core::pose::metrics::CalculatorFactory::Instance(), loop_, n_tail_res_, core::conformation::Conformation::num_chains(), core::scoring::other_pose, protocols::chemically_conjugated_docking::pack_extra_bodies(), core::import_pose::PDB_file, core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), core::pose::metrics::CalculatorFactory::register_calculator(), core::pose::metrics::CalculatorFactory::remove_calculator(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), selector_, core::pose::Pose::size(), protocols::loops::Loop::start(), starting_pose_, protocols::loops::Loop::stop(), task_factory_, protocols::TR(), and UBQpdb_.

Referenced by apply().

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::make_index_selector ( core::Size  index)

makes an internal ResidueIndexSelector given a residue index on the substrate.

References selector_.

Referenced by parse_my_tag().

std::string protocols::chemically_conjugated_docking::UBQ_GTPaseMover::mover_name ( )
static
void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_amide_mm ( core::kinematics::MoveMapOP const &  mm)

References amide_mm_.

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_atom_IDs ( utility::vector1< core::id::AtomID > const &  ids)

References atomIDs.

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_extra_bodies ( bool const  hasExtra)

References extra_bodies_.

Referenced by parse_my_tag().

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_extra_bodies_chains ( utility::vector1< core::Size > const &  chains)

References extra_bodies_chains_.

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_fullatom_scorefunction ( core::scoring::ScoreFunctionOP const &  sfxn)
void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_GTPase_lys ( core::Size const  lys)

References GTPase_lys_.

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_IAM ( protocols::analysis::InterfaceAnalyzerMoverOP const &  iam)

References IAM_.

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_loop ( protocols::loops::Loop const &  loop)

References loop_.

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_n_tail_res ( core::Size const  numTails)

References n_tail_res_.

Referenced by parse_my_tag().

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_SASAfilter ( core::Real const  minSASA)

References SASAfilter_.

Referenced by parse_my_tag().

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_scorefilter ( core::Real const  maxScore)

References scorefilter_.

Referenced by parse_my_tag().

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_selector ( core::select::residue_selector::ResidueSelectorCOP const &  select)

References selector_.

Referenced by parse_my_tag().

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_task_factory ( core::pack::task::TaskFactoryOP const &  tasks)

References task_factory_.

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_UBQpdb ( std::string const &  ubqFile)

References UBQpdb_.

Referenced by parse_my_tag().

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::chemically_conjugated_docking::operator<<().

Member Data Documentation

core::kinematics::MoveMapOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::amide_mm_
private
utility::vector1< core::id::AtomID > protocols::chemically_conjugated_docking::UBQ_GTPaseMover::atomIDs
private

vector contains atomIDs for isopeptide bond and atoms before/after bond to determine various torsions

Referenced by analyze_and_filter(), apply(), get_atom_IDs(), initialize(), and set_atom_IDs().

bool protocols::chemically_conjugated_docking::UBQ_GTPaseMover::extra_bodies_
private
utility::vector1< core::Size > protocols::chemically_conjugated_docking::UBQ_GTPaseMover::extra_bodies_chains_
private

used to track which chains are "extra" nonmoving bodies in extra bodies mode

Referenced by get_extra_bodies_chains(), initialize(), and set_extra_bodies_chains().

core::scoring::ScoreFunctionOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::fullatom_scorefunction_
private
core::Size protocols::chemically_conjugated_docking::UBQ_GTPaseMover::GTPase_lys_ = 0
private
protocols::analysis::InterfaceAnalyzerMoverOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::IAM_
private
std::string const protocols::chemically_conjugated_docking::UBQ_GTPaseMover::InterfaceSasaDefinition_
private
protocols::jd2::JobOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::job_me_
private
protocols::loops::Loop protocols::chemically_conjugated_docking::UBQ_GTPaseMover::loop_
private

Referenced by apply(), get_loop(), initialize(), and set_loop().

core::Size protocols::chemically_conjugated_docking::UBQ_GTPaseMover::n_tail_res_
private
core::Real protocols::chemically_conjugated_docking::UBQ_GTPaseMover::SASAfilter_
private
core::Real protocols::chemically_conjugated_docking::UBQ_GTPaseMover::scorefilter_
private
core::select::residue_selector::ResidueSelectorCOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::selector_
private
core::pose::Pose protocols::chemically_conjugated_docking::UBQ_GTPaseMover::starting_pose_
private
core::pack::task::TaskFactoryOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::task_factory_
private
std::string protocols::chemically_conjugated_docking::UBQ_GTPaseMover::UBQpdb_
private

Referenced by get_UBQpdb(), initialize(), and set_UBQpdb().


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