Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine. More...

#include <SampleFarnesylMover.hh>

Inheritance diagram for protocols::farnesyl::SampleFarnesylMover:

[legend]

Public Member Functions
	SampleFarnesylMover ()
	Constructors ///. More...

	SampleFarnesylMover (SampleFarnesylMover const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~SampleFarnesylMover () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

void	sample_farnesyl (core::pose::Pose &pose, core::Size const cys_idx, core::Size const dma_one_idx, core::Size const dma_two_idx, core::Size const dma_three_idx)
	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	set_score_function (core::scoring::ScoreFunctionOP const &sfxn)

void	set_enumerate (bool const enumerate)

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	sfxn_ = nullptr

bool	enumerate_ = true

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

Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine.

Constructor & Destructor Documentation

protocols::farnesyl::SampleFarnesylMover::SampleFarnesylMover ( )

Constructors ///.

Default constructor

protocols::farnesyl::SampleFarnesylMover::SampleFarnesylMover ( SampleFarnesylMover const & src )

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::farnesyl::SampleFarnesylMover::~SampleFarnesylMover ( )

override

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

Member Function Documentation

void protocols::farnesyl::SampleFarnesylMover::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover.

Apply the mover

Loop through every residue in the pose. If it's not cysteine – move on. if it has no conjugation – move on. If it doesn't have 3 pendant DMAs – move on. Then... you've found farnesyl cysteine; go to the sampling function.

Implements protocols::moves::Mover.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_cys, core::chemical::ResidueType::atom_index(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection_id_for_atom(), core::pose::Pose::residue_type(), sample_farnesyl(), core::chemical::SC_BRANCH_POINT, core::pose::Pose::size(), and protocols::TR().

protocols::moves::MoverOP protocols::farnesyl::SampleFarnesylMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::farnesyl::SampleFarnesylMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::farnesyl::SampleFarnesylMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::farnesyl::SampleFarnesylMover::mover_name ( )

static

Referenced by get_name(), protocols::farnesyl::SampleFarnesylMoverCreator::keyname(), and provide_xml_schema().

void protocols::farnesyl::SampleFarnesylMover::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::scoring::parse_score_function(), set_enumerate(), and set_score_function().

void protocols::farnesyl::SampleFarnesylMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::farnesyl::SampleFarnesylMoverCreator::provide_xml_schema().

void protocols::farnesyl::SampleFarnesylMover::sample_farnesyl	(	core::pose::Pose &	pose,
		core::Size const	cys_idx,
		core::Size const	dma_one_idx,
		core::Size const	dma_two_idx,
		core::Size const	dma_three_idx
	)

Mover Methods ///.

Sample a particular farnesyl

Draw torsion combinations from a small library of options. Someone else (TM) can turn this rigorous (with explicit management of their relative probabilities, and perhaps registering these conformations in a useful way, and perhaps expanded and/or made dependent on CYS more explicitly. Or the InstallFarnesylMover could give you a custom library, optionally for this particular farnesyl. Plus, this should all be read in from a DB file). What a useful task list for someone else (TM)! Actually – the sampling process we've been using is pretty fast. I am going to actually use that every time. Why not! The fixed library subset paradigm can be used later. So now we do all this sampling and then take the best conformation forward.

References protocols::minimization_packing::MinMover::apply(), core::id::BB, core::chemical::rna::CHI, enumerate_, core::scoring::get_score_function(), protocols::hybridization::score, protocols::stepwise::sampler::StepWiseSamplerComb::set_random(), core::pose::Pose::set_torsion(), sfxn_, and protocols::TR().

Referenced by apply().

void protocols::farnesyl::SampleFarnesylMover::set_enumerate ( bool const enumerate )

inline

References enumerate_.

Referenced by parse_my_tag().

void protocols::farnesyl::SampleFarnesylMover::set_score_function ( core::scoring::ScoreFunctionOP const & sfxn )

inline

References sfxn_.

Referenced by parse_my_tag().

void protocols::farnesyl::SampleFarnesylMover::show ( std::ostream & output = std::cout ) const

overridevirtual