#include <FlexPepDockingAbInitio.hh>

Inheritance diagram for protocols::flexpep_docking::FlexPepDockingAbInitio:

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Public Member Functions
	FlexPepDockingAbInitio (FlexPepDockingFlags const &flags_in, core::scoring::ScoreFunctionOP scorefxn_in, core::kinematics::MoveMapOP movemap_in, core::Size const rb_jump_in=1)
	constructor for low resolution flexpible peptide docking More...

	~FlexPepDockingAbInitio () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. 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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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 Member Functions
void	setup_for_apply (core::pose::Pose &pose)
	initial setup for apply More...

void	to_centroid (core::pose::Pose &pose) const

void	to_allatom (core::pose::Pose &pose, core::pose::Pose &referencePose) const

void	torsions_monte_carlo (core::pose::Pose &pose, const int cycles, core::Real &acceptance_rate)

void	loopclosure_monte_carlo (core::pose::Pose &pose)

void	rigidbody_monte_carlo (core::pose::Pose &pose, const int cycles, const float trans_magnitude, const float rot_magnitude, core::Real &acceptance_rate)

void	convertPSERtoASP (core::pose::Pose &pose, std::set< int > &pSer_positions)

void	convertPSERtoGLU (core::pose::Pose &pose, std::set< int > &pSer_positions)

void	restorePSER (core::pose::Pose &pose, std::set< int > const &pSer_positions)

Private Attributes
FlexPepDockingFlags	flags_

core::scoring::ScoreFunctionOP	scorefxn_

core::kinematics::MoveMapOP	movemap_

core::Size	rb_jump_
	the jump number across which to do rigid_body transformations More...

moves::MonteCarloOP	mc_
	whether or not to initialize the viewer (for opengl) More...

protocols::minimization_packing::MinMoverOP	minimizer_

protocols::relax::loop::LoopRelaxMoverOP	loop_relax_mover_

core::fragment::ConstantLengthFragSetOP	fragset3mer_

core::fragment::ConstantLengthFragSetOP	fragset9mer_

core::fragment::ConstantLengthFragSetOP	fragset5mer_

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::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::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

◆ FlexPepDockingAbInitio()

FlexPepDockingAbInitio::FlexPepDockingAbInitio	(	FlexPepDockingFlags const &	flags_in,
		core::scoring::ScoreFunctionOP	scorefxn_in,
		core::kinematics::MoveMapOP	movemap_in,
		core::Size const	rb_jump_in = `1`
	)

constructor for low resolution flexpible peptide docking

References fragset3mer_, fragset5mer_, fragset9mer_, loop_relax_mover_, protocols::loops::read_loop_fragments(), and scorefxn_.

◆ ~FlexPepDockingAbInitio()

FlexPepDockingAbInitio::~FlexPepDockingAbInitio ( )

overridedefault

Member Function Documentation

◆ apply()

void FlexPepDockingAbInitio::apply ( core::pose::Pose & )

overridevirtual

◆ convertPSERtoASP()

void FlexPepDockingAbInitio::convertPSERtoASP	(	core::pose::Pose &	pose,
		std::set< int > &	pSer_positions
	)

private

References core::conformation::ResidueFactory::create_residue(), core::chemical::FULL_ATOM_t, core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::name3(), core::chemical::PHOSPHORYLATION, core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::size(), and protocols::TR().

Referenced by apply().

◆ convertPSERtoGLU()

void FlexPepDockingAbInitio::convertPSERtoGLU	(	core::pose::Pose &	pose,
		std::set< int > &	pSer_positions
	)

private

References core::conformation::ResidueFactory::create_residue(), core::chemical::FULL_ATOM_t, core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::name3(), core::chemical::PHOSPHORYLATION, core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::size(), and protocols::TR().

Referenced by apply().

◆ get_name()

std::string FlexPepDockingAbInitio::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ loopclosure_monte_carlo()

void FlexPepDockingAbInitio::loopclosure_monte_carlo ( core::pose::Pose & pose )

private

References flags_, loop_relax_mover_, movemap_, protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_last_res(), and protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres().

Referenced by apply().

◆ restorePSER()

void FlexPepDockingAbInitio::restorePSER	(	core::pose::Pose &	pose,
		std::set< int > const &	pSer_positions
	)

private

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CENTROID_t, core::conformation::ResidueFactory::create_residue(), core::sequence::end, core::chemical::PHOSPHORYLATION, core::pose::Pose::replace_residue(), and core::pose::Pose::residue_type_set_for_pose().

Referenced by apply().

◆ rigidbody_monte_carlo()

void FlexPepDockingAbInitio::rigidbody_monte_carlo	(	core::pose::Pose &	pose,
		const int	cycles,
		const float	trans_magnitude,
		const float	rot_magnitude,
		core::Real &	acceptance_rate
	)