TODO: De-duplicate shared code from RotateJumpAxisMover (angle picking code) More...

#include <TorsionDOFMover.hh>

Inheritance diagram for protocols::simple_moves::TorsionDOFMover:

[legend]

Public Member Functions
	TorsionDOFMover ()
	default ctor More...

	TorsionDOFMover (core::id::AtomID const &atom1, core::id::AtomID const &atom2, core::id::AtomID const &atom3, core::id::AtomID const &atom4)
	constructor for random distribution (just needs torsion) More...

	TorsionDOFMover (core::id::AtomID const &atom1, core::id::AtomID const &atom2, core::id::AtomID const &atom3, core::id::AtomID const &atom4, core::Angle const upper, core::Angle const lower)
	constructor for range - these angles are in degrees, not radians! More...

	TorsionDOFMover (core::id::AtomID const &atom1, core::id::AtomID const &atom2, core::id::AtomID const &atom3, core::id::AtomID const &atom4, core::Angle const angle)
	constructor for single value - these angles are in degrees, not radians! More...

	~TorsionDOFMover () 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...

void	set_angle_range (core::Angle const upper, core::Angle const lower)
	set range of desired change - on [180, -180) degrees More...

void	get_angle_range (core::Angle &upper, core::Angle &lower) const
	return range of allowed angles More...

void	set_DOF (core::id::AtomID const &atom1, core::id::AtomID const &atom2, core::id::AtomID const &atom3, core::id::AtomID const &atom4)
	change the torsion DOF under consideration More...

void	get_DOF (core::id::AtomID &atom1, core::id::AtomID &atom2, core::id::AtomID &atom3, core::id::AtomID &atom4) const
	return DOF More...

void	check_mmt (bool const setting)
	(de)activate scoring check More...

bool	check_mmt () const
	getter for scoring check More...

void	temp (core::Real const setting)
	set temperature for scoring check More...

core::Real	temp () const
	getter for temperature for scoring check More...

void	tries (core::Size const setting)
	set number of tries More...

core::Size	tries () const
	getter for number of tries 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
core::Angle	calc_angle ()
	calculate angle for perturbation - call to RNG More...

core::Energy	score_torsion (core::pose::Pose &pose)
	calculate mmt score for the moving bond More...

bool	boltzmann (core::Energy const pre_score, core::Energy const post_score)
	boltzmann calculation - is the new score acceptable? More...

Private Attributes
core::id::AtomID	atom1_
	these atoms define the torsion More...

core::id::AtomID	atom2_

core::id::AtomID	atom3_

core::id::AtomID	atom4_

core::Angle	upper_angle_
	these angles define the range of transformations More...

core::Angle	lower_angle_

bool	check_MMT_
	boolean - should we restrict moves based on MMTorsionEnergy? More...

core::scoring::ScoreFunctionOP	mmt_
	MMTorsionEnergy scorefunction. More...

core::Real	temp_
	temperature for accepting moves More...

core::Size	tries_
	number of attempts at finding a valid move More...

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...

Detailed Description

TODO: De-duplicate shared code from RotateJumpAxisMover (angle picking code)

This mover rotates a specific AtomTree Torsion degree of freedom (any valid 4-body torsion). It can rotate by a fixed amount, within a range, or randomly. Optionally, the mover will attempt to internally score the move with MMTorsionEnergy (similar to check_rama in Small/ShearMover). The mover will print a warning message at apply time if the specified DOF is bad. For now this mover only allows one DOF; if you want to have it consider multiple DOF's that might be a good idea. The DOF is determined by a set of 4 atoms; this allows the mover to check the validity of the DOF. I found it conceptually simpler to think about the 4 atoms involved in the torsion than try to trace DOF_IDs.

Constructor & Destructor Documentation

◆ TorsionDOFMover() [1/4]

protocols::simple_moves::TorsionDOFMover::TorsionDOFMover ( )

default ctor

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

◆ TorsionDOFMover() [2/4]

protocols::simple_moves::TorsionDOFMover::TorsionDOFMover	(	core::id::AtomID const &	atom1,
		core::id::AtomID const &	atom2,
		core::id::AtomID const &	atom3,
		core::id::AtomID const &	atom4
	)

constructor for random distribution (just needs torsion)

random angle constructor. Magic numbers 180 and -179.9999999... maintain the uniform range. I'm sure there's a better way to get [180, -180) but I can't figure out what it is.

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

◆ TorsionDOFMover() [3/4]

protocols::simple_moves::TorsionDOFMover::TorsionDOFMover	(	core::id::AtomID const &	atom1,
		core::id::AtomID const &	atom2,
		core::id::AtomID const &	atom3,
		core::id::AtomID const &	atom4,
		core::Angle const	upper,
		core::Angle const	lower
	)

constructor for range - these angles are in degrees, not radians!

range of angles constructor - takes DEGREES not RADIANS.

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

◆ TorsionDOFMover() [4/4]

protocols::simple_moves::TorsionDOFMover::TorsionDOFMover	(	core::id::AtomID const &	atom1,
		core::id::AtomID const &	atom2,
		core::id::AtomID const &	atom3,
		core::id::AtomID const &	atom4,
		core::Angle const	angle
	)

constructor for single value - these angles are in degrees, not radians!

particular angle constructor - takes DEGREES not RADIANS.

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

◆ ~TorsionDOFMover()

protocols::simple_moves::TorsionDOFMover::~TorsionDOFMover ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::simple_moves::TorsionDOFMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References atom1_, atom2_, atom3_, atom4_, core::pose::Pose::atom_tree(), boltzmann(), calc_angle(), check_MMT_, core::pose::Pose::conformation(), core::scoring::mm_twist, mmt_, score_torsion(), core::conformation::Conformation::set_torsion_angle(), core::kinematics::AtomTree::torsion_angle(), core::kinematics::AtomTree::torsion_angle_dof_id(), protocols::simple_moves::TR(), tries_, and core::id::DOF_ID::valid().

◆ boltzmann()

bool protocols::simple_moves::TorsionDOFMover::boltzmann	(	core::Energy const	pre_score,
		core::Energy const	post_score
	)

private

boltzmann calculation - is the new score acceptable?

References protocols::mean_field::max(), protocols::simple_moves::bb_sampler::probability, core::scoring::rg, and temp_.

Referenced by apply().

◆ calc_angle()

core::Angle protocols::simple_moves::TorsionDOFMover::calc_angle ( )

private

calculate angle for perturbation - call to RNG

References lower_angle_, core::scoring::rg, and upper_angle_.

Referenced by apply().

◆ check_mmt() [1/2]

bool protocols::simple_moves::TorsionDOFMover::check_mmt ( ) const

inline

getter for scoring check

References check_MMT_.

◆ check_mmt() [2/2]

void protocols::simple_moves::TorsionDOFMover::check_mmt ( bool const setting )

inline

(de)activate scoring check

References check_MMT_.

◆ get_angle_range()

void protocols::simple_moves::TorsionDOFMover::get_angle_range	(	core::Angle &	upper,
		core::Angle &	lower
	)		const

inline

return range of allowed angles

References lower_angle_, and upper_angle_.

◆ get_DOF()

void protocols::simple_moves::TorsionDOFMover::get_DOF	(	core::id::AtomID &	atom1,
		core::id::AtomID &	atom2,
		core::id::AtomID &	atom3,
		core::id::AtomID &	atom4
	)		const

inline

return DOF

References atom1_, atom2_, atom3_, and atom4_.

◆ get_name()

std::string protocols::simple_moves::TorsionDOFMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ score_torsion()

core::Energy protocols::simple_moves::TorsionDOFMover::score_torsion ( core::pose::Pose & pose )

private

calculate mmt score for the moving bond

calculate mmt score for the moving bond This is the stupidest possible method - score the whole pose. It would be much better if this could directly use MMTorsionEnergy to calculate about just the one bond in question, but I can't figure out how to reliably look up exactly the set of residues modified by this torsion (remember that changing this 4-body torsion affects other 4-bodies with a shared central bond).

References mmt_.

Referenced by apply().

◆ set_angle_range()

void protocols::simple_moves::TorsionDOFMover::set_angle_range	(	core::Angle const	upper,
		core::Angle const	lower
	)

inline

set range of desired change - on [180, -180) degrees

getters, setters////////////////////////////////////////

References lower_angle_, and upper_angle_.

◆ set_DOF()

void protocols::simple_moves::TorsionDOFMover::set_DOF	(	core::id::AtomID const &	atom1,
		core::id::AtomID const &	atom2,
		core::id::AtomID const &	atom3,
		core::id::AtomID const &	atom4
	)

inline

change the torsion DOF under consideration

References atom1_, atom2_, atom3_, and atom4_.

◆ temp() [1/2]

core::Real protocols::simple_moves::TorsionDOFMover::temp ( ) const

inline

getter for temperature for scoring check

References temp_.

◆ temp() [2/2]

void protocols::simple_moves::TorsionDOFMover::temp ( core::Real const setting )

inline

set temperature for scoring check

References temp_.

◆ tries() [1/2]

core::Size protocols::simple_moves::TorsionDOFMover::tries ( ) const

inline

getter for number of tries

References tries_.

◆ tries() [2/2]

void protocols::simple_moves::TorsionDOFMover::tries ( core::Size const setting )

inline

set number of tries

References tries_.

Member Data Documentation

◆ atom1_

core::id::AtomID protocols::simple_moves::TorsionDOFMover::atom1_

private

these atoms define the torsion

Referenced by apply(), get_DOF(), and set_DOF().

◆ atom2_

core::id::AtomID protocols::simple_moves::TorsionDOFMover::atom2_

private

Referenced by apply(), get_DOF(), and set_DOF().

◆ atom3_

core::id::AtomID protocols::simple_moves::TorsionDOFMover::atom3_

private

Referenced by apply(), get_DOF(), and set_DOF().

◆ atom4_

core::id::AtomID protocols::simple_moves::TorsionDOFMover::atom4_

private

Referenced by apply(), get_DOF(), and set_DOF().

◆ check_MMT_

bool protocols::simple_moves::TorsionDOFMover::check_MMT_

private

boolean - should we restrict moves based on MMTorsionEnergy?

Referenced by apply(), and check_mmt().

◆ lower_angle_

core::Angle protocols::simple_moves::TorsionDOFMover::lower_angle_

private

Referenced by calc_angle(), get_angle_range(), and set_angle_range().

◆ mmt_

core::scoring::ScoreFunctionOP protocols::simple_moves::TorsionDOFMover::mmt_

private

MMTorsionEnergy scorefunction.

Referenced by apply(), and score_torsion().

◆ temp_

core::Real protocols::simple_moves::TorsionDOFMover::temp_

private

temperature for accepting moves

Referenced by boltzmann(), and temp().

◆ tries_

core::Size protocols::simple_moves::TorsionDOFMover::tries_

private

number of attempts at finding a valid move

Referenced by apply(), and tries().

◆ upper_angle_

core::Angle protocols::simple_moves::TorsionDOFMover::upper_angle_

private

these angles define the range of transformations

Referenced by calc_angle(), get_angle_range(), and set_angle_range().

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

src/protocols/simple_moves/TorsionDOFMover.hh
src/protocols/simple_moves/TorsionDOFMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TorsionDOFMover() [1/4]

◆ TorsionDOFMover() [2/4]

◆ TorsionDOFMover() [3/4]

◆ TorsionDOFMover() [4/4]

◆ ~TorsionDOFMover()

Member Function Documentation

◆ apply()

◆ boltzmann()

◆ calc_angle()

◆ check_mmt() [1/2]

◆ check_mmt() [2/2]

◆ get_angle_range()

◆ get_DOF()

◆ get_name()

◆ score_torsion()

◆ set_angle_range()

◆ set_DOF()

◆ temp() [1/2]

◆ temp() [2/2]

◆ tries() [1/2]

◆ tries() [2/2]

Member Data Documentation

◆ atom1_

◆ atom2_

◆ atom3_

◆ atom4_

◆ check_MMT_

◆ lower_angle_

◆ mmt_

◆ temp_

◆ tries_

◆ upper_angle_