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protocols::loops::loop_closure::ccd::RamaCheck2B Class Reference

#include <RamaCheck.hh>

Inheritance diagram for protocols::loops::loop_closure::ccd::RamaCheck2B:
Inheritance graph
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Public Member Functions

 RamaCheck2B ()
 constructor More...
 
 RamaCheck2B (RamaCheck2B const &object_to_copy)
 Copy constructor. More...
 
RamaCheck2Boperator= (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...
 
RamaCheckBaseoperator= (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().

void protocols::loops::loop_closure::ccd::RamaCheck2B::copy_data ( RamaCheck2B to,
RamaCheck2B const &  from 
) const
private

References rama_.

Referenced by operator=(), and RamaCheck2B().

std::string protocols::loops::loop_closure::ccd::RamaCheck2B::name ( ) const
overridevirtual

Return "RamaCheck2B".

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

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

Member Data Documentation

core::scoring::Ramachandran2BCOP protocols::loops::loop_closure::ccd::RamaCheck2B::rama_
private

Referenced by compute_rama_score(), and copy_data().


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