#include <RamaCheck.hh>

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

Public Member Functions
	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)

virtual std::string	name () const =0
	Return the name of the RamaCheck class being used. More...

virtual RamaCheckBaseOP	clone () const =0
	Return a pointer to a new, fully configured copy of RamaCheckBase. More...

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...

virtual core::Real	compute_rama_score (core::pose::Pose const &pose, core::uint const seqpos, core::Real const phi, core::Real const psi) const =0
	Compute the Ramachandran score of residue <seqpos> in <pose> with a hypothetical conformation <phi>, <psi> More...

Static Public Member Functions
static void	register_options ()
	Register options with the option system. More...

Private Types
typedef utility::VirtualBase	Parent

typedef utility::vector1 < core::Real >	RamaScoreVector

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

void	init ()

void	init_options ()

bool	accept_new_conformation (core::Real const current_score, core::Real const proposed_score, core::Real const starting_score) const

Private Attributes
core::Real	temperature_

core::Real	max_rama_score_increase_

RamaScoreVector	starting_rama_scores_

Static Private Attributes
static core::Real const	BAD_SCORE = 500.0

Member Typedef Documentation

typedef utility::VirtualBase protocols::loops::loop_closure::ccd::RamaCheckBase::Parent

private

typedef utility::vector1< core::Real > protocols::loops::loop_closure::ccd::RamaCheckBase::RamaScoreVector

private

Constructor & Destructor Documentation

protocols::loops::loop_closure::ccd::RamaCheckBase::RamaCheckBase ( )

constructor

Initialize the VirtualBase and the private data

References init().

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

Copy constructor.

References copy_data().

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

overridedefault

Member Function Documentation

bool protocols::loops::loop_closure::ccd::RamaCheckBase::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.

Returns: true if the move should be accepted, false if it should be rejected.

New conformations are accepted using the Metropolis criterion. More specifically, if the new conformation has an improved score, it is always accepted. If the score gets worse (increases), it is accepted with a penalty based on the difference of energy between the two states. Even if a score is accepted with a penalty, it may be rejected if it exceeds the maximum score increase cutoff, which can be accessed by max_rama_score_increase().

References compute_rama_score(), initialize_starting_rama_scores(), core::conformation::Residue::is_protein(), core::pose::Pose::phi(), core::id::phi_torsion(), core::pose::Pose::psi(), core::id::psi_torsion(), core::pose::Pose::residue(), core::id::TorsionID::rsd(), core::pose::Pose::size(), starting_rama_scores_, core::id::TorsionID::torsion(), and protocols::loops::loop_closure::ccd::TR().

bool protocols::loops::loop_closure::ccd::RamaCheckBase::accept_new_conformation	(	core::Real const	current_score,
		core::Real const	proposed_score,
		core::Real const	starting_score
	)		const

private

References protocols::mean_field::max(), max_rama_score_increase_, protocols::simple_moves::bb_sampler::probability, and temperature_.

core::Real protocols::loops::loop_closure::ccd::RamaCheckBase::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>.

Returns: The average change in Ramachandran score.

The average change in Ramachandran score is the total net change in Ramachandran score divided by the number of residues in the range [<first_res>, <last_res>].

Note: <first_res> must be a smaller value than <last_res> and all values in [<first_res>, <last_res>] must correspond to valid residue numbers in <pose>.

References total_net_change_in_rama_score_over_range().

virtual RamaCheckBaseOP protocols::loops::loop_closure::ccd::RamaCheckBase::clone ( ) const

pure virtual

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

Note: The clone method should be used to copy an instance of RamaCheck if the derived class type is unknown.

Implemented in protocols::loops::loop_closure::ccd::RamaCheck2B, and protocols::loops::loop_closure::ccd::RamaCheck1B.

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

pure virtual

Compute the Ramachandran score of residue <seqpos> in <pose> with a hypothetical conformation <phi>, <psi>

Implemented in protocols::loops::loop_closure::ccd::RamaCheck2B, and protocols::loops::loop_closure::ccd::RamaCheck1B.

Referenced by accept_new_conformation(), initialize_starting_rama_scores(), and total_net_change_in_rama_score_over_range().

void protocols::loops::loop_closure::ccd::RamaCheckBase::copy_data	(	RamaCheckBase &	to,
		RamaCheckBase const &	from
	)		const

private

References max_rama_score_increase_, starting_rama_scores_, and temperature_.

Referenced by operator=(), and RamaCheckBase().

void protocols::loops::loop_closure::ccd::RamaCheckBase::init ( void )

private

References max_rama_score_increase_, starting_rama_scores_, and temperature_.

Referenced by RamaCheckBase().

void protocols::loops::loop_closure::ccd::RamaCheckBase::init_options ( )

private

References max_rama_score_increase(), and temperature().

void protocols::loops::loop_closure::ccd::RamaCheckBase::initialize_starting_rama_scores ( core::pose::Pose const & pose ) const

Store the Ramachandran scores of each residue in the supplied pose.

References BAD_SCORE, compute_rama_score(), core::conformation::Residue::is_protein(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::size(), starting_rama_scores_, and protocols::loops::loop_closure::ccd::TR().

Referenced by accept_new_conformation(), and total_net_change_in_rama_score_over_range().

core::Real protocols::loops::loop_closure::ccd::RamaCheckBase::max_rama_score_increase ( ) const

inline

Get the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.

Note: This value will only be used if the option for checking the rama score is turned on.

References max_rama_score_increase_.

Referenced by init_options(), and parse_my_tag().

void protocols::loops::loop_closure::ccd::RamaCheckBase::max_rama_score_increase ( core::Real input_max_rama_score_increase )

inline

Set the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.

Note: This value will only be used if the option for checking the rama score is turned on.

References max_rama_score_increase_.

virtual std::string protocols::loops::loop_closure::ccd::RamaCheckBase::name ( ) const

pure virtual

Return the name of the RamaCheck class being used.

Implemented in protocols::loops::loop_closure::ccd::RamaCheck2B, and protocols::loops::loop_closure::ccd::RamaCheck1B.

Referenced by show().

RamaCheckBase & protocols::loops::loop_closure::ccd::RamaCheckBase::operator= ( RamaCheckBase const & object_to_copy )

References copy_data().

Referenced by protocols::loops::loop_closure::ccd::RamaCheck1B::operator=(), and protocols::loops::loop_closure::ccd::RamaCheck2B::operator=().

void protocols::loops::loop_closure::ccd::RamaCheckBase::parse_my_tag ( utility::tag::TagCOP tag )

virtual

Enable the RamaCheck classes to parse tags with options for "max_rama_score_increase" and "temperature".

References max_rama_score_increase(), and temperature().

void protocols::loops::loop_closure::ccd::RamaCheckBase::register_options ( )

static

Register options with the option system.

Associate the RamaCheck classes with the -loops:ccd:max_rama_score_increase and -loops:ccd:temperature options

Referenced by protocols::loops::loop_closure::ccd::CCDLoopClosureMover::register_options().

void protocols::loops::loop_closure::ccd::RamaCheckBase::show ( std::ostream & output = std::cout ) const

virtual

Generate a string representation of RamaCheck for debugging purposes.

Print the RamaCheck's basic information and details about the instance's configuration.

References max_rama_score_increase_, name(), and temperature_.

Referenced by protocols::loops::loop_closure::ccd::operator<<().

core::Real protocols::loops::loop_closure::ccd::RamaCheckBase::temperature ( ) const

inline

Get the "temperature" used for rama score-checking with the Metropolis criterion.

Note: This value will only be used if the option for checking the rama score is turned on.

References temperature_.

Referenced by init_options(), and parse_my_tag().

void protocols::loops::loop_closure::ccd::RamaCheckBase::temperature ( core::Real input_temperature )

inline

Set the "temperature" used for rama score-checking with the Metropolis criterion.

Note: This value will only be used if the option for checking the rama score is turned on.

References temperature_.

core::Real protocols::loops::loop_closure::ccd::RamaCheckBase::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>.

Returns: The total net change in Ramachandran score.

The total net change in Ramachandran score is simply the sum of the differences of the current Ramachandran score and the initial Ramachandran score of each residue in the range <first_res>, <last_res>.

Note: <first_res> must be a smaller value than <last_res> and all values in [<first_res>, <last_res>] must correspond to valid residue numbers in <pose>.

References compute_rama_score(), initialize_starting_rama_scores(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::size(), starting_rama_scores_, and protocols::loops::loop_closure::ccd::TR().

Referenced by average_change_in_rama_score_over_range().