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:

[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 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
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::Size >	extra_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

◆ UBQ_GTPaseMover() [1/2]

protocols::chemically_conjugated_docking::UBQ_GTPaseMover::UBQ_GTPaseMover ( )

Constructors ///.

Default constructor

References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), fullatom_scorefunction_, core::scoring::get_score_function(), IAM_, InterfaceSasaDefinition_, and protocols::TR().

◆ UBQ_GTPaseMover() [2/2]

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

default

Copy constructor (not needed unless you need deep copies)

◆ ~UBQ_GTPaseMover()

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

override

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

Member Function Documentation

◆ analyze_and_filter()

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter ( core::pose::Pose & pose )

applies filters and stores torsion angles near LYX bond

References core::kinematics::FoldTree::add_edge(), core::pose::Pose::atom_tree(), atomIDs, core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), protocols::chemically_conjugated_docking::create_extra_output(), protocols::jd2::JobDistributor::current_job(), extra_bodies_, protocols::moves::FAIL_RETRY, core::pose::Pose::fold_tree(), fullatom_scorefunction_, protocols::jd2::JobDistributor::get_instance(), GTPase_lys_, IAM_, InterfaceSasaDefinition_, core::pose::Pose::metric(), protocols::moves::MS_SUCCESS, core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), SASAfilter_, protocols::hybridization::score, scorefilter_, protocols::moves::Mover::set_last_move_status(), core::pose::Pose::size(), core::kinematics::AtomTree::torsion_angle(), and protocols::TR().

Referenced by apply().

◆ apply()

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover.

Apply the mover

Implements protocols::moves::Mover.

References amide_mm_, analyze_and_filter(), atomIDs, core::pack::task::TaskFactory::create_packer_task(), core::pose::Pose::fold_tree(), fullatom_scorefunction_, GTPase_lys_, initialize(), loop_, core::pose::Pose::size(), protocols::loops::Loop::start(), starting_pose_, protocols::loops::Loop::stop(), task_factory_, and protocols::TR().

Referenced by initialize().

◆ clone()

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.

◆ fresh_instance()

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.

◆ get_amide_mm()

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

References amide_mm_.

◆ get_atom_IDs()

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

References atomIDs.

◆ get_extra_bodies()

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

References extra_bodies_.

◆ get_extra_bodies_chains()

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

References extra_bodies_chains_.

◆ get_fullatom_scorefunction()

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

References fullatom_scorefunction_.

◆ get_GTPase_lys()

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

References GTPase_lys_.

◆ get_IAM()

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

References IAM_.

◆ get_InterfaceSasaDefinition()

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

References InterfaceSasaDefinition_.

◆ get_loop()

protocols::loops::Loop const & protocols::chemically_conjugated_docking::UBQ_GTPaseMover::get_loop ( ) const

References loop_.

◆ get_n_tail_res()

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

References n_tail_res_.

◆ get_name()

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().

◆ get_SASAfilter()

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

References SASAfilter_.

◆ get_scorefilter()

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

References scorefilter_.

◆ get_selector()

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

References selector_.

Referenced by parse_my_tag().

◆ get_starting_pose()

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

References starting_pose_.

◆ get_task_factory()

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

References task_factory_.

◆ get_UBQpdb()

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

References UBQpdb_.

◆ initialize()

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(), core::chemical::ResidueType::atom_index(), atomIDs, core::conformation::Conformation::chain_end(), 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::conformation::Conformation::insert_chain_ending(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Conformation::insert_ideal_geometry_at_residue_connection(), core::pose::metrics::CalculatorFactory::Instance(), loop_, core::chemical::ResidueType::lower_connect_id(), core::chemical::ResidueType::n_possible_residue_connections(), 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::Pose::prepend_polymer_residue_before_seqpos(), 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::set_chi(), core::conformation::Conformation::set_torsion_angle(), core::pose::Pose::size(), protocols::loops::Loop::start(), starting_pose_, protocols::loops::Loop::stop(), task_factory_, protocols::TR(), UBQpdb_, and core::chemical::ResidueType::upper_connect_id().

Referenced by apply().

◆ make_index_selector()

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().

◆ mover_name()

std::string protocols::chemically_conjugated_docking::UBQ_GTPaseMover::mover_name ( )

static

Referenced by get_name(), protocols::chemically_conjugated_docking::UBQ_GTPaseMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Rosetta Scripts Support ///.

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References core::select::residue_selector::get_residue_selector(), get_selector(), make_index_selector(), set_extra_bodies(), set_n_tail_res(), set_SASAfilter(), set_scorefilter(), set_selector(), set_UBQpdb(), and protocols::TR().

◆ provide_xml_schema()

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::chemically_conjugated_docking::UBQ_GTPaseMoverCreator::provide_xml_schema().

◆ set_amide_mm()

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_amide_mm ( core::kinematics::MoveMapOP const & mm )

References amide_mm_.

◆ set_atom_IDs()

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

References atomIDs.

◆ set_extra_bodies()

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

References extra_bodies_.

Referenced by parse_my_tag().

◆ set_extra_bodies_chains()

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

References extra_bodies_chains_.

◆ set_fullatom_scorefunction()

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

References fullatom_scorefunction_.

◆ set_GTPase_lys()

void protocols::chemically_conjugated_docking::UBQ_GTPaseMover::set_GTPase_lys ( core::Size const lys )

References GTPase_lys_.

◆ set_IAM()

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

References IAM_.

◆ set_loop()

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

References loop_.

◆ set_n_tail_res()

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

References n_tail_res_.

Referenced by parse_my_tag().

◆ set_SASAfilter()

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

References SASAfilter_.

Referenced by parse_my_tag().

◆ set_scorefilter()

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

References scorefilter_.

Referenced by parse_my_tag().

◆ set_selector()

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

References selector_.

Referenced by parse_my_tag().

◆ set_task_factory()

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

References task_factory_.

◆ set_UBQpdb()

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

References UBQpdb_.

Referenced by parse_my_tag().

◆ show()

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

◆ amide_mm_

core::kinematics::MoveMapOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::amide_mm_

private

Referenced by apply(), get_amide_mm(), initialize(), and set_amide_mm().

◆ atomIDs

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().

◆ extra_bodies_

bool protocols::chemically_conjugated_docking::UBQ_GTPaseMover::extra_bodies_

private

Referenced by analyze_and_filter(), get_extra_bodies(), initialize(), and set_extra_bodies().

◆ extra_bodies_chains_

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().

◆ fullatom_scorefunction_

core::scoring::ScoreFunctionOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::fullatom_scorefunction_

private

Referenced by analyze_and_filter(), apply(), get_fullatom_scorefunction(), set_fullatom_scorefunction(), and UBQ_GTPaseMover().

◆ GTPase_lys_

core::Size protocols::chemically_conjugated_docking::UBQ_GTPaseMover::GTPase_lys_ = 0

private

Referenced by analyze_and_filter(), apply(), get_GTPase_lys(), initialize(), and set_GTPase_lys().

◆ IAM_

protocols::analysis::InterfaceAnalyzerMoverOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::IAM_

private

Referenced by analyze_and_filter(), get_IAM(), set_IAM(), and UBQ_GTPaseMover().

◆ InterfaceSasaDefinition_

std::string const protocols::chemically_conjugated_docking::UBQ_GTPaseMover::InterfaceSasaDefinition_

private

Referenced by analyze_and_filter(), get_InterfaceSasaDefinition(), and UBQ_GTPaseMover().

◆ job_me_

protocols::jd2::JobOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::job_me_

private

◆ loop_

protocols::loops::Loop protocols::chemically_conjugated_docking::UBQ_GTPaseMover::loop_

private

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

◆ n_tail_res_

core::Size protocols::chemically_conjugated_docking::UBQ_GTPaseMover::n_tail_res_

private

Referenced by get_n_tail_res(), initialize(), and set_n_tail_res().

◆ SASAfilter_

core::Real protocols::chemically_conjugated_docking::UBQ_GTPaseMover::SASAfilter_

private

Referenced by analyze_and_filter(), get_SASAfilter(), and set_SASAfilter().

◆ scorefilter_

core::Real protocols::chemically_conjugated_docking::UBQ_GTPaseMover::scorefilter_

private

Referenced by analyze_and_filter(), get_scorefilter(), and set_scorefilter().

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::selector_

private

Referenced by get_selector(), initialize(), make_index_selector(), and set_selector().

◆ starting_pose_

core::pose::Pose protocols::chemically_conjugated_docking::UBQ_GTPaseMover::starting_pose_

private

Referenced by apply(), get_starting_pose(), and initialize().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::chemically_conjugated_docking::UBQ_GTPaseMover::task_factory_

private

Referenced by apply(), get_task_factory(), initialize(), and set_task_factory().

◆ UBQpdb_

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:

src/protocols/chemically_conjugated_docking/UBQ_GTPaseMover.hh
src/protocols/chemically_conjugated_docking/UBQ_GTPaseMover.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ UBQ_GTPaseMover() [1/2]

◆ UBQ_GTPaseMover() [2/2]

◆ ~UBQ_GTPaseMover()

Member Function Documentation

◆ analyze_and_filter()

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_amide_mm()

◆ get_atom_IDs()

◆ get_extra_bodies()

◆ get_extra_bodies_chains()

◆ get_fullatom_scorefunction()

◆ get_GTPase_lys()

◆ get_IAM()

◆ get_InterfaceSasaDefinition()

◆ get_loop()

◆ get_n_tail_res()

◆ get_name()

◆ get_SASAfilter()

◆ get_scorefilter()

◆ get_selector()

◆ get_starting_pose()

◆ get_task_factory()

◆ get_UBQpdb()

◆ initialize()

◆ make_index_selector()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_amide_mm()

◆ set_atom_IDs()

◆ set_extra_bodies()

◆ set_extra_bodies_chains()

◆ set_fullatom_scorefunction()

◆ set_GTPase_lys()

◆ set_IAM()

◆ set_loop()

◆ set_n_tail_res()

◆ set_SASAfilter()

◆ set_scorefilter()

◆ set_selector()

◆ set_task_factory()

◆ set_UBQpdb()

◆ show()

Member Data Documentation

◆ amide_mm_

◆ atomIDs

◆ extra_bodies_

◆ extra_bodies_chains_

◆ fullatom_scorefunction_

◆ GTPase_lys_

◆ IAM_

◆ InterfaceSasaDefinition_

◆ job_me_

◆ loop_

◆ n_tail_res_

◆ SASAfilter_

◆ scorefilter_

◆ selector_

◆ starting_pose_

◆ task_factory_

◆ UBQpdb_