Sample all points on a 2D membrane energy landscape given implicit model and protein dimensions. More...

#include <MembraneEnergyLandscapeSampler.hh>

Inheritance diagram for protocols::membrane_benchmark::MembraneEnergyLandscapeSampler:

[legend]

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

	MembraneEnergyLandscapeSampler (std::string sfxn_weights, std::string rotation_type, bool interface, core::Real start_z, core::Real end_z, core::Real flag_axis, core::Real azimuthal_delta, bool repack)
	Non-defualt cnstructor for landscape sampling. More...

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

	~MembraneEnergyLandscapeSampler () 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) const override
	Show the contents of the Mover. More...

void	show () const
	Declaring an overload. 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...

core::Vector	getaxis (core::pose::Pose &pose, core::Real flag)

core::Vector	getcenter (core::pose::Pose &pose, core::Real flag)

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 Member Functions
void	init_from_options ()
	initialize the options More...

protocols::minimization_packing::PackRotamersMoverOP	get_pH_aware_packer (core::scoring::ScoreFunctionOP sfxn) const

core::Vector	get_rotation_axis ()

protocols::membrane::RotationMoverOP	get_rotation (core::Real const normal_angle, core::Vector const axis, core::Vector const rot_center, core::Size membrane_jump, std::string rotation_type)

core::Real	get_pH_value ()
	get user input pH value More...

core::Real	count_res (std::string res, core::pose::Pose const &pose)
	count the number of residue "res" in the pose "pose" More...

core::Real	count_diff (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
	count the number of occurences the 3 letter name of residue is different in pose1 and pose2 More...

Private Attributes
core::scoring::ScoreFunctionOP	sfxn_

std::string	sfxn_weights_

std::string	rotation_type_ ="YZ"

bool	interface_ =false

core::Real	start_z_ =-60

core::Real	end_z_ =60

core::Real	flag_axis_ =1.0

core::Real	azimuthal_delta_ =30

bool	repack_ =false

bool	pH_mode_ =false

bool	dump_structures_ =false

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

Sample all points on a 2D membrane energy landscape given implicit model and protein dimensions.

Constructor & Destructor Documentation

◆ MembraneEnergyLandscapeSampler() [1/3]

protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::MembraneEnergyLandscapeSampler ( )

Constructors ///.

Default constructor

References init_from_options().

◆ MembraneEnergyLandscapeSampler() [2/3]

protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::MembraneEnergyLandscapeSampler	(	std::string	sfxn_weights,
		std::string	rotation_type,
		bool	interface,
		core::Real	start_z,
		core::Real	end_z,
		core::Real	flag_axis,
		core::Real	azimuthal_delta,
		bool	repack
	)

Non-defualt cnstructor for landscape sampling.

References init_from_options().

◆ MembraneEnergyLandscapeSampler() [3/3]

protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::MembraneEnergyLandscapeSampler ( MembraneEnergyLandscapeSampler const & src )

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~MembraneEnergyLandscapeSampler()

protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::~MembraneEnergyLandscapeSampler ( )

override

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

Member Function Documentation

◆ apply()

void protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover

Implements protocols::moves::Mover.

References azimuthal_delta_, core::pose::Pose::clone(), core::pose::Pose::conformation(), core::pose::Pose::dump_pdb(), dump_structures_, end_z_, core::scoring::f_elec_lipidlayer, core::scoring::fa_atr, core::scoring::fa_elec, core::scoring::fa_imm_elec, core::scoring::fa_rep, core::scoring::fa_sol, core::scoring::fa_water_to_bilayer, protocols::abinitio::filename(), flag_axis_, get_pH_aware_packer(), get_rotation(), getaxis(), getcenter(), interface_, core::conformation::Conformation::is_membrane(), protocols::membrane::is_membrane_fixed(), core::conformation::Conformation::membrane_info(), core::scoring::name_from_score_type(), core::pose::Pose::pdb_info(), pH_mode_, protocols::membrane::pose_tm_com(), repack_, core::pose::Pose::residue(), protocols::cluster::calibur::rotate(), rotation_type_, protocols::hybridization::score, sfxn_, sfxn_weights_, core::pose::Pose::size(), start_z_, core::id::to_string(), core::pose::Pose::total_residue(), core::scoring::total_score, protocols::TR(), and core::conformation::Residue::xyz().

◆ clone()

protocols::moves::MoverOP protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ count_diff()

core::Real protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::count_diff	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

private

count the number of occurences the 3 letter name of residue is different in pose1 and pose2

References core::conformation::Residue::name3(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

◆ count_res()

core::Real protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::count_res	(	std::string	res,
		core::pose::Pose const &	pose
	)

private

count the number of residue "res" in the pose "pose"

References core::conformation::Residue::name(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

◆ fresh_instance()

protocols::moves::MoverOP protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_pH_aware_packer()

protocols::minimization_packing::PackRotamersMoverOP protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::get_pH_aware_packer ( core::scoring::ScoreFunctionOP sfxn ) const

private

References pH_mode_.

Referenced by apply().

◆ get_pH_value()

core::Real protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::get_pH_value ( )

private

get user input pH value

References pH_mode_.

◆ get_rotation()

protocols::membrane::RotationMoverOP protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::get_rotation	(	core::Real const	normal_angle,
		core::Vector const	axis,
		core::Vector const	rot_center,
		core::Size	membrane_jump,
		std::string	rotation_type
	)