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protocols::loops::loop_closure::ccd::RamaCheckBase Class Referenceabstract

#include <RamaCheck.hh>

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

 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)
 
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

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
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
void protocols::loops::loop_closure::ccd::RamaCheckBase::init ( void  )
private
void protocols::loops::loop_closure::ccd::RamaCheckBase::init_options ( )
private
void protocols::loops::loop_closure::ccd::RamaCheckBase::initialize_starting_rama_scores ( core::pose::Pose const &  pose) const
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)
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().

Member Data Documentation

core::Real const protocols::loops::loop_closure::ccd::RamaCheckBase::BAD_SCORE = 500.0
staticprivate
core::Real protocols::loops::loop_closure::ccd::RamaCheckBase::max_rama_score_increase_
private
RamaScoreVector protocols::loops::loop_closure::ccd::RamaCheckBase::starting_rama_scores_
mutableprivate
core::Real protocols::loops::loop_closure::ccd::RamaCheckBase::temperature_
private

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