Rosetta 3.4
Public Types | Public Member Functions
core::scoring::ResidualDipolarCoupling Class Reference

ResidualDipolarCouplings are mainly handled by this class related classed: RDC --- a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingEnergy -- an energy method which triggers computations handled by this class. More...

#include <ResidualDipolarCoupling.hh>

Inheritance diagram for core::scoring::ResidualDipolarCoupling:
Inheritance graph
[legend]
Collaboration diagram for core::scoring::ResidualDipolarCoupling:
Collaboration graph
[legend]

List of all members.

Public Types

typedef core::Real Real
typedef core::Size Size
typedef utility::vector1
< core::scoring::RDC
RDC_lines
typedef core::Real Tensor [3][3]
typedef core::Real rvec [3]

Public Member Functions

 ResidualDipolarCoupling (std::string const &filename="")
 standard c'stor -- will access option -in:file:rdc to read RDC data
 ResidualDipolarCoupling (RDC_lines data_in)
 alternative c'stor if you have a list of RDC lines
 ResidualDipolarCoupling (ResidualDipolarCoupling const &other)
ResidualDipolarCouplingoperator= (ResidualDipolarCoupling const &other)
virtual ~ResidualDipolarCoupling ()
basic::datacache::CacheableDataOP clone () const
core::Real compute_dipscore (core::pose::Pose const &pose)
 compute dipolar score for given pose will set alignment tensor and force-fields in RDC
core::Real compute_dipscore_nls (core::pose::Pose const &pose)
 fit rdc using RDC data
core::Real compute_dipscore_nlsDa (core::pose::Pose const &pose, utility::vector1< Real > const tensorDa)
core::Real compute_dipscore_nlsR (core::pose::Pose const &pose, utility::vector1< Real > const tensorR)
core::Real compute_dipscore_nlsDaR (core::pose::Pose const &pose, utility::vector1< Real > const tensorDa, utility::vector1< Real > const tensorR)
Real iterate_tensor_weights (core::pose::Pose const &pose, core::Real sigma2, core::Real tolerance, bool reset)
void show (std::ostream &) const
void read_RDC_file ()
 read RDC data from file
void preprocess_data ()
 fill internal buffers... call always when RDC lines change.
void release_buffers ()
 free memory of buffers
void reserve_buffers ()
 get memory for buffers
RDC_lines const & get_RDC_data () const
 get the raw RDC data
Real Q () const
 return the Q value ( cornilescu ) --- only valid after compute_dipscore
Real R () const
 return the R value ( M Clore ) --- only valid after compute_dipscore
core::Size get_n_alignments () const
Tensortensor ()
 return tensor of certain experiment... exp_id starts at 1
core::Real get_al_tensor_trace (core::Size ex) const
core::Real get_al_tensor_max_z (core::Size ex) const
void compute_tensor_stats ()
void show_tensor_stats (std::ostream &, core::Size ex) const
void show_tensor_matrix (std::ostream &, core::Size ex) const
void show_rdc_values (std::ostream &, core::Size ex) const
void show_tensor_stats_nls (std::ostream &, core::Size ex, const double *par) const

Detailed Description

ResidualDipolarCouplings are mainly handled by this class related classed: RDC --- a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingEnergy -- an energy method which triggers computations handled by this class.


Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::ResidualDipolarCoupling::ResidualDipolarCoupling ( std::string const &  filename = "") [inline]

standard c'stor -- will access option -in:file:rdc to read RDC data

References preprocess_data(), read_RDC_file(), release_buffers(), and reserve_buffers().

Referenced by clone().

core::scoring::ResidualDipolarCoupling::ResidualDipolarCoupling ( RDC_lines  data_in) [inline]

alternative c'stor if you have a list of RDC lines

References preprocess_data(), and reserve_buffers().

core::scoring::ResidualDipolarCoupling::ResidualDipolarCoupling ( ResidualDipolarCoupling const &  other)
core::scoring::ResidualDipolarCoupling::~ResidualDipolarCoupling ( ) [virtual]

References release_buffers().


Member Function Documentation

basic::datacache::CacheableDataOP core::scoring::ResidualDipolarCoupling::clone ( ) const [inline]
Real core::scoring::ResidualDipolarCoupling::compute_dipscore ( core::pose::Pose const &  pose)
Real core::scoring::ResidualDipolarCoupling::compute_dipscore_nls ( core::pose::Pose const &  pose)
Real core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa ( core::pose::Pose const &  pose,
utility::vector1< Real > const  tensorDa 
)
Real core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR ( core::pose::Pose const &  pose,
utility::vector1< Real > const  tensorDa,
utility::vector1< Real > const  tensorR 
)
Real core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR ( core::pose::Pose const &  pose,
utility::vector1< Real > const  tensorR 
)
void core::scoring::ResidualDipolarCoupling::compute_tensor_stats ( )
core::Real core::scoring::ResidualDipolarCoupling::get_al_tensor_max_z ( core::Size  ex) const [inline]
core::Real core::scoring::ResidualDipolarCoupling::get_al_tensor_trace ( core::Size  ex) const [inline]
core::Size core::scoring::ResidualDipolarCoupling::get_n_alignments ( ) const [inline]
RDC_lines const& core::scoring::ResidualDipolarCoupling::get_RDC_data ( ) const [inline]
Real core::scoring::ResidualDipolarCoupling::iterate_tensor_weights ( core::pose::Pose const &  pose,
core::Real  sigma2,
core::Real  tolerance,
bool  reset 
)
ResidualDipolarCoupling & core::scoring::ResidualDipolarCoupling::operator= ( ResidualDipolarCoupling const &  other)
void core::scoring::ResidualDipolarCoupling::preprocess_data ( )

fill internal buffers... call always when RDC lines change.

Referenced by operator=(), read_RDC_file(), and ResidualDipolarCoupling().

Real core::scoring::ResidualDipolarCoupling::Q ( ) const [inline]

return the Q value ( cornilescu ) --- only valid after compute_dipscore

References make_table_of_pilot_apps::f, and R().

Referenced by compute_dipscore(), compute_dipscore_nls(), compute_dipscore_nlsDa(), compute_dipscore_nlsDaR(), and compute_dipscore_nlsR().

Real core::scoring::ResidualDipolarCoupling::R ( ) const [inline]

return the R value ( M Clore ) --- only valid after compute_dipscore

Referenced by Q().

void core::scoring::ResidualDipolarCoupling::read_RDC_file ( )
void core::scoring::ResidualDipolarCoupling::release_buffers ( )
void core::scoring::ResidualDipolarCoupling::reserve_buffers ( )

get memory for buffers

References core::scoring::tr().

Referenced by operator=(), read_RDC_file(), and ResidualDipolarCoupling().

void core::scoring::ResidualDipolarCoupling::show ( std::ostream &  out) const
void core::scoring::ResidualDipolarCoupling::show_rdc_values ( std::ostream &  out,
core::Size  ex 
) const
void core::scoring::ResidualDipolarCoupling::show_tensor_matrix ( std::ostream &  out,
core::Size  ex 
) const
void core::scoring::ResidualDipolarCoupling::show_tensor_stats ( std::ostream &  out,
core::Size  ex 
) const
void core::scoring::ResidualDipolarCoupling::show_tensor_stats_nls ( std::ostream &  out,
core::Size  ex,
const double *  par 
) const
Tensor* core::scoring::ResidualDipolarCoupling::tensor ( ) [inline]

return tensor of certain experiment... exp_id starts at 1


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines