#include <RamaCheck.hh>

Inheritance diagram for protocols::loops::loop_closure::ccd::RamaCheck1B:

Public Member Functions
	RamaCheck1B ()
	constructor More...

	RamaCheck1B (RamaCheck1B const &object_to_copy)
	Copy constructor. More...

RamaCheck1B &	operator= (RamaCheck1B const &object_to_copy)

virtual	~RamaCheck1B ()

virtual std::string	name () const
	Return "RamaCheck1B". More...

virtual RamaCheckBaseOP	clone () const
	Return a pointer to a new, fully configured copy of RamaCheck1B. More...

virtual core::Real	compute_rama_score (core::pose::Pose const &pose, core::uint const seqpos, core::Real const phi, core::Real const psi) const
	Compute the Ramachandran score of residue <seqpos> in <pose> with a hypothetical conformation <phi>, <psi>. The score is independent of 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)

virtual	~RamaCheckBase ()

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 (RamaCheck1B &to, RamaCheck1B const &from) const

Private Attributes
core::scoring::RamachandranCOP	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::RamaCheck1B::RamaCheck1B ( )

constructor

Initialize RamaCheck1B with a pointer to the Ramachandran potential.

Referenced by clone().

protocols::loops::loop_closure::ccd::RamaCheck1B::RamaCheck1B ( RamaCheck1B const & object_to_copy )

Copy constructor.

References copy_data().

protocols::loops::loop_closure::ccd::RamaCheck1B::~RamaCheck1B ( )

virtual

Member Function Documentation

RamaCheckBaseOP protocols::loops::loop_closure::ccd::RamaCheck1B::clone ( ) const

virtual

Return a pointer to a new, fully configured copy of RamaCheck1B.

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

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

References RamaCheck1B().

core::Real protocols::loops::loop_closure::ccd::RamaCheck1B::compute_rama_score	(	core::pose::Pose const &	pose,
		core::uint const	seqpos,
		core::Real const	phi,
		core::Real const	psi
	)		const

virtual

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

The neighbor-independent Ramachandran maps are used to compute the score for a residue in the conformation defined by <phi> and <psi>. These values represent the conformation preferences of the residue in its average sequence context.

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

References core::pose::Pose::aa(), core::chemical::aa_unk, core::conformation::Residue::backbone_aa(), rama_, and core::pose::Pose::residue().