#include <RamaCheck.hh>

Inheritance diagram for protocols::loops::loop_closure::ccd::RamaCheck2B:

Public Member Functions
	RamaCheck2B ()
	constructor More...

	RamaCheck2B (RamaCheck2B const &object_to_copy)
	Copy constructor. More...

RamaCheck2B &	operator= (RamaCheck2B const &object_to_copy)

	~RamaCheck2B () override

std::string	name () const override
	Return "RamaCheck2B". More...

RamaCheckBaseOP	clone () const override
	Return a pointer to a new, fully configured copy of RamaCheck2B. More...

core::Real	compute_rama_score (core::pose::Pose const &pose, core::uint const seqpos, core::Real const phi, core::Real const psi) const override
	Compute the Ramachandran score of residue <seqpos> in <pose> with a hypothetical conformation <phi>, <psi>. The score depends on the identity of the neighboring residues. More...

Public Member Functions inherited from protocols::loops::loop_closure::ccd::RamaCheckBase
	RamaCheckBase ()
	constructor More...

	RamaCheckBase (RamaCheckBase const &object_to_copy)
	Copy constructor. More...

RamaCheckBase &	operator= (RamaCheckBase const &object_to_copy)

	~RamaCheckBase () override

virtual void	show (std::ostream &output=std::cout) const
	Generate a string representation of RamaCheck for debugging purposes. More...

virtual void	parse_my_tag (utility::tag::TagCOP tag)

core::Real	temperature () const
	Get the "temperature" used for rama score-checking with the Metropolis criterion. More...

void	temperature (core::Real input_temperature)
	Set the "temperature" used for rama score-checking with the Metropolis criterion. More...

core::Real	max_rama_score_increase () const
	Get the maximum rama score increase allowed during rama score-checking with the Metropolis criterion. More...

void	max_rama_score_increase (core::Real input_max_rama_score_increase)
	Set the maximum rama score increase allowed during rama score-checking with the Metropolis criterion. More...

void	initialize_starting_rama_scores (core::pose::Pose const &pose) const
	Store the Ramachandran scores of each residue in the supplied pose. More...

bool	accept_new_conformation (core::pose::Pose const &pose, core::id::TorsionID const &torsion_id, core::Angle const alpha) const
	Determine whether or not a candidate conformation should be accepted based on the Ramachandran score. More...

core::Real	total_net_change_in_rama_score_over_range (core::pose::Pose const &pose, core::uint const first_res, core::uint const last_res) const
	Compute the total net change in Ramachandran score between the initial pose and the current pose from <first_res> to <last_res>. More...

core::Real	average_change_in_rama_score_over_range (core::pose::Pose const &pose, core::uint const first_res, core::uint const last_res) const
	Compute the average change in Ramachandran score between the initial pose and the current pose from <first_res> to <last_res>. More...

Private Member Functions
void	copy_data (RamaCheck2B &to, RamaCheck2B const &from) const

Private Attributes
core::scoring::Ramachandran2BCOP	rama_

Additional Inherited Members
Static Public Member Functions inherited from protocols::loops::loop_closure::ccd::RamaCheckBase
static void	register_options ()
	Register options with the option system. More...

Constructor & Destructor Documentation

protocols::loops::loop_closure::ccd::RamaCheck2B::RamaCheck2B ( )

constructor

Initialize RamaCheck2B with a pointer to the Ramachandran2B potential.

protocols::loops::loop_closure::ccd::RamaCheck2B::RamaCheck2B ( RamaCheck2B const & object_to_copy )

Copy constructor.

References copy_data().

protocols::loops::loop_closure::ccd::RamaCheck2B::~RamaCheck2B ( )

overridedefault

Member Function Documentation

RamaCheckBaseOP protocols::loops::loop_closure::ccd::RamaCheck2B::clone ( ) const

overridevirtual

Return a pointer to a new, fully configured copy of RamaCheck2B.

Return a fully configured copy of this instance upcasted to a RamaCheckOP

Implements protocols::loops::loop_closure::ccd::RamaCheckBase.

core::Real protocols::loops::loop_closure::ccd::RamaCheck2B::compute_rama_score	(	core::pose::Pose const &	pose,
		core::uint const	seqpos,
		core::Real const	phi,
		core::Real const	psi
	)		const

overridevirtual

Compute the Ramachandran score of residue <seqpos> in <pose> with a hypothetical conformation <phi>, <psi>. The score depends on the identity of the neighboring residues.

The neighbor-dependent Ramachandran maps are used to compute the score for a residue in the conformation defined by <phi> and <psi>. The neighboring residue identities are taken from the pose, and these three residues are used to compute the score. In cases where there are no neighboring residues (i.e. the first and last residues in the pose), a single neighbor-dependent score is returned. This is a little strange because these reisudes are actually missing a torsion angle (residue 1 is missing phi, residue Nres is missing psi). Accordingly, the current behavior of Ramachandran2B returns a score of zero in these circumstances.

Implements protocols::loops::loop_closure::ccd::RamaCheckBase.

References core::pose::Pose::aa(), rama_, and core::pose::Pose::size().