Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::frag_picker::scores::RDCScore Class Reference

scores a fragment by its crmsd to the given reference structure More...

#include <RDCScore_Gront.hh>

Public Member Functions

 RDCScore (Size, Real, bool)
 creates a RDC-based scoring function. More...
 
void do_caching (VallChunkOP)
 In this case caching means copying coordinates of relevant atoms from a chunk's pose. More...
 
void clean_up ()
 Erases the internal array of coordinates. More...
 
bool cached_score (FragmentCandidateOP, FragmentScoreMapOP)
 
bool score (FragmentCandidateOP, FragmentScoreMapOP)
 
 RDCScore (Size, Real, bool, Size)
 Prepare the scoring method. More...
 
void do_caching (VallChunkOP)
 In this case caching means copying coordinates of relevant atoms from a chunk's pose. More...
 
void clean_up ()
 Erases the internal array of coordinates. More...
 
bool score (FragmentCandidateOP, FragmentScoreMapOP)
 Evaluate the score. More...
 
- Public Member Functions inherited from protocols::frag_picker::scores::AtomBasedConstraintsScore
 AtomBasedConstraintsScore (Size, Real, bool, Size, utility::vector1< std::string >, std::string)
 Prepare an atom-based score that utilizes some user-defined atoms. More...
 
 AtomBasedConstraintsScore (Size, Real, bool, Size, std::string)
 Prepare an atom-based score that utilizes the following predefined atoms: N, CA, C, O and CB. More...
 
bool has_atom (Size residue_id, Size atom_id)
 Returns true if a given atom has been successfully cached and one can use its coordinates. More...
 
numeric::xyzVector< Realget_atom_coordinates (Size residue_id, Size atom_id)
 Returns coordinates for a given atom. More...
 
std::map< std::string, Sizeget_constrainable_atoms_map ()
 Returns a map that defines all constrained atoms used by this scoring method. More...
 
Size get_constrained_atom_id (std::string atom_name)
 returns an internal ID assigned to a given atom name More...
 
std::string get_constrained_atom_name (Size atom_id)
 returns a name of a constrained atom when its internal ID is known More...
 
Size get_query_size ()
 provides an access to the size of the length of a query sequence More...
 
- Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
 CachingScoringMethod (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name)
 
- Public Member Functions inherited from protocols::frag_picker::scores::FragmentScoringMethod
 FragmentScoringMethod (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name)
 
std::stringget_score_name ()
 Returns a name of this scoring method. More...
 
Size get_id ()
 Returns an integer index assigned to this scoring method by a scoring manager. More...
 
void set_id (Size id)
 Sets a new integer index for this scoring method. More...
 
Size get_priority ()
 Returns a priority of this scoring method. More...
 
Real get_min_allowed_score ()
 Returns the lowest acceptable score value for this scoring method. More...
 
bool get_use_lowest ()
 Returns the boolean choice on using the above lowest acceptable score value. More...
 
void set_min_allowed_score (Real lowest_acceptable_value)
 Sets a new value of the lowest acceptable score. More...
 

Private Member Functions

utility::vector1< std::string > & rdc_atoms ()
 
void read_RDC_file (std::string const &, Size)
 
Real sqr (Real x) const
 
Real iprod (const Real a[3], const Real b[3]) const
 
void mvmul (Real a[3][3], const Real src[3], Real dest[3]) const
 
void jacobi (Real a[5][5], Real d[], Real v[5][5], int *nrot)
 
int m_inv_gen (Real m[5][5], int n, Real minv[5][5])
 

Private Attributes

core::scoring::ResidualDipolarCouplingOP rdc_file_
 
core::scoring::ResidualDipolarCoupling::RDC_lines rdc_raw_data_
 
utility::vector1
< core::scoring::RDC
rdc_data_
 
utility::vector1< std::stringrdc_atoms_
 
utility::vector1< std::stringrdc_atom_names_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
Size id_
 
Size priority_
 
std::string name_
 
Real lowest_acceptable_value_
 
bool use_lowest_
 

Detailed Description

scores a fragment by its crmsd to the given reference structure

Calculates a score for a fragment based on RDC experimental data.

Constructor & Destructor Documentation

protocols::frag_picker::scores::RDCScore::RDCScore ( Size  priority,
Real  lowest_acceptable_value,
bool  use_lowest 
)

creates a RDC-based scoring function.

References rdc_file_, and rdc_raw_data_.

protocols::frag_picker::scores::RDCScore::RDCScore ( Size  priority,
Real  lowest_acceptable_value,
bool  use_lowest,
Size  query_size 
)

Prepare the scoring method.

Parameters
priority- the priority for this scoring method. The lower the priority, the later the score will be evaluated Because a fragment may be discarded when a score is too low, the most accurate && meaningful scores should have the highest priority
lowest_acceptable_value- a fragment for which this score is below a certain threshold will be discarded
rdc_file_name- from this file RDC data will be obtained
query_size- the number of residues in the query sequence

Member Function Documentation

bool protocols::frag_picker::scores::RDCScore::cached_score ( FragmentCandidateOP  fragment,
FragmentScoreMapOP  empty_map 
)
virtual
void protocols::frag_picker::scores::RDCScore::clean_up ( )
virtual

Erases the internal array of coordinates.

Reimplemented from protocols::frag_picker::scores::AtomBasedConstraintsScore.

void protocols::frag_picker::scores::RDCScore::clean_up ( )
virtual

Erases the internal array of coordinates.

Reimplemented from protocols::frag_picker::scores::AtomBasedConstraintsScore.

void protocols::frag_picker::scores::RDCScore::do_caching ( VallChunkOP  chunk)
virtual

In this case caching means copying coordinates of relevant atoms from a chunk's pose.

Reimplemented from protocols::frag_picker::scores::AtomBasedConstraintsScore.

References protocols::frag_picker::VallChunk::chunk_key().

void protocols::frag_picker::scores::RDCScore::do_caching ( VallChunkOP  )
virtual

In this case caching means copying coordinates of relevant atoms from a chunk's pose.

Reimplemented from protocols::frag_picker::scores::AtomBasedConstraintsScore.

Real protocols::frag_picker::scores::RDCScore::iprod ( const Real  a[3],
const Real  b[3] 
) const
inlineprivate
void protocols::frag_picker::scores::RDCScore::jacobi ( Real  a[5][5],
Real  d[],
Real  v[5][5],
int nrot 
)
private

References protocols::match::upstream::b, c, ROTATE, s, and t.

Referenced by m_inv_gen().

int protocols::frag_picker::scores::RDCScore::m_inv_gen ( Real  m[5][5],
int  n,
Real  minv[5][5] 
)
private

References jacobi(), and s.

void protocols::frag_picker::scores::RDCScore::mvmul ( Real  a[3][3],
const Real  src[3],
Real  dest[3] 
) const
inlineprivate
utility::vector1< std::string > & protocols::frag_picker::scores::RDCScore::rdc_atoms ( )
private

References rdc_atoms_.

void protocols::frag_picker::scores::RDCScore::read_RDC_file ( std::string const &  filename,
Size  exp_id = 1 
)
private
bool protocols::frag_picker::scores::RDCScore::score ( FragmentCandidateOP  fragment,
FragmentScoreMapOP  empty_map 
)
virtual
bool protocols::frag_picker::scores::RDCScore::score ( FragmentCandidateOP  ,
FragmentScoreMapOP   
)
virtual

Evaluate the score.

Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.

Real protocols::frag_picker::scores::RDCScore::sqr ( Real  x) const
inlineprivate

Member Data Documentation

utility::vector1<std::string> protocols::frag_picker::scores::RDCScore::rdc_atom_names_
private
utility::vector1<std::string> protocols::frag_picker::scores::RDCScore::rdc_atoms_
private

Referenced by rdc_atoms().

utility::vector1<core::scoring::RDC> protocols::frag_picker::scores::RDCScore::rdc_data_
private

Referenced by read_RDC_file().

core::scoring::ResidualDipolarCouplingOP protocols::frag_picker::scores::RDCScore::rdc_file_
private

Referenced by RDCScore().

core::scoring::ResidualDipolarCoupling::RDC_lines protocols::frag_picker::scores::RDCScore::rdc_raw_data_
private

Referenced by RDCScore(), and score().


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