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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::loops::loop_closure::ccd::RamaCheck1B Class Reference

#include <RamaCheck.hh>

Inheritance diagram for protocols::loops::loop_closure::ccd::RamaCheck1B:
Inheritance graph
[legend]

Public Member Functions

 RamaCheck1B ()
 constructor More...
 
 RamaCheck1B (RamaCheck1B const &object_to_copy)
 Copy constructor. More...
 
RamaCheck1Boperator= (RamaCheck1B const &object_to_copy)
 
 ~RamaCheck1B () override
 
std::string name () const override
 Return "RamaCheck1B". More...
 
RamaCheckBaseOP clone () const override
 Return a pointer to a new, fully configured copy of RamaCheck1B. 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 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...
 
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 (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.

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

Copy constructor.

References copy_data().

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

Member Function Documentation

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

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.

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
overridevirtual

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().

void protocols::loops::loop_closure::ccd::RamaCheck1B::copy_data ( RamaCheck1B to,
RamaCheck1B const &  from 
) const
private

References rama_.

Referenced by operator=(), and RamaCheck1B().

std::string protocols::loops::loop_closure::ccd::RamaCheck1B::name ( ) const
overridevirtual

Return "RamaCheck1B".

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

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

Member Data Documentation

core::scoring::RamachandranCOP protocols::loops::loop_closure::ccd::RamaCheck1B::rama_
private

Referenced by compute_rama_score(), and copy_data().


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