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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
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Public Types

typedef core::Real Real
 
typedef core::Size Size
 
typedef utility::vector1
< core::scoring::RDC
RDC_lines
 
typedef
utility::fixedsizearray0
< core::Real, 3 > 
rvec
 
typedef
utility::fixedsizearray0< rvec, 3 > 
Tensor
 
typedef
utility::fixedsizearray0
< core::Real, 5 > 
rvec5
 
typedef
utility::fixedsizearray0
< rvec5, 5 > 
Tensor5
 

Public Member Functions

 ResidualDipolarCoupling (std::string const &filename="")
 standard c'stor – will access option -in:file:rdc to read RDC data More...
 
 ResidualDipolarCoupling (RDC_lines data_in)
 alternative c'stor if you have a list of RDC lines More...
 
 ResidualDipolarCoupling (ResidualDipolarCoupling const &other)
 
ResidualDipolarCouplingoperator= (ResidualDipolarCoupling const &other)
 
 ~ResidualDipolarCoupling () override
 
basic::datacache::CacheableDataOP clone () const override
 
core::Real compute_dipscore (core::pose::Pose const &pose)
 compute dipolar score for given pose will set alignment tensor and force-fields in RDC More...
 
core::Real compute_dipscore_nls (core::pose::Pose const &pose)
 fit rdc using RDC data More...
 
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)
 
core::Real compute_dipscore_nls (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 More...
 
void preprocess_data ()
 fill internal buffers... call always when RDC lines change. More...
 
void release_buffers ()
 free memory of buffers More...
 
void reserve_buffers ()
 get memory for buffers More...
 
RDC_lines const & get_RDC_data () const
 get the raw RDC data More...
 
Real Q () const
 return the Q value ( cornilescu ) — only valid after compute_dipscore More...
 
Real R () const
 return the R value ( M Clore ) — only valid after compute_dipscore More...
 
core::Size get_n_alignments () const
 
utility::vector0< Tensor > & tensor ()
 return tensor of certain experiment... exp_id starts at 1 More...
 
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 core::Real *par) const
 
void do_correct_NH (utility::vector1< core::scoring::RDC >::const_iterator it, numeric::xyzVector< Real > &r, core::Real &r2, core::Real &invr)
 

Private Member Functions

void read_RDC_file (Size nex, std::string const &filename)
 read RDC data from file More...
 
RDC_linesget_RDC_data_ref ()
 non-const reference to RDC data private use only. More...
 

Private Attributes

RDC_lines All_RDC_lines_
 some internal buffers in More...
 
utility::vector0< rvecEV_
 
utility::vector0< rvec5D_
 
utility::vector0< rvec5rhs_
 
utility::vector0< TensorS_
 
utility::vector0< Tensor5T_
 
core::Size nex_
 
core::Size nrows_
 
core::Real R_
 
core::Real rmsd_
 
utility::vector0< TensorSD_
 
utility::vector0< TensorEIG_
 
utility::vector0< core::RealFA_
 
utility::vector0< core::Realtrace_
 
utility::vector0< core::Realmaxz_
 
utility::vector0< core::Realr0_
 
utility::vector0< core::Realr1_
 
utility::vector0< core::Realr2_
 
utility::vector0< core::Realexprdc_
 
utility::vector0< core::Realrdcconst_
 
utility::vector0< core::Realrdcweight_
 
utility::vector0< core::Sizelenex_
 

Static Private Attributes

static Real const COMMON_DENOMINATOR = 36.5089/1.041/1.041/1.041
 

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

typedef utility::fixedsizearray0< core::Real, 3 > core::scoring::ResidualDipolarCoupling::rvec
typedef utility::fixedsizearray0< core::Real, 5 > core::scoring::ResidualDipolarCoupling::rvec5
typedef utility::fixedsizearray0< rvec, 3 > core::scoring::ResidualDipolarCoupling::Tensor
typedef utility::fixedsizearray0< rvec5, 5 > core::scoring::ResidualDipolarCoupling::Tensor5

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 protocols::abinitio::filename(), preprocess_data(), read_RDC_file(), release_buffers(), and reserve_buffers().

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 ( )
override

References release_buffers().

Member Function Documentation

basic::datacache::CacheableDataOP core::scoring::ResidualDipolarCoupling::clone ( ) const
inlineoverride
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_nls ( core::pose::Pose const &  pose,
utility::vector1< Real > const &  tensorDa,
utility::vector1< Real > const &  tensorR 
)
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 ( )
void core::scoring::ResidualDipolarCoupling::do_correct_NH ( utility::vector1< core::scoring::RDC >::const_iterator  it,
numeric::xyzVector< Real > &  r,
core::Real r2,
core::Real invr 
)
core::Real core::scoring::ResidualDipolarCoupling::get_al_tensor_max_z ( core::Size  ex) const
inline

References maxz_.

core::Real core::scoring::ResidualDipolarCoupling::get_al_tensor_trace ( core::Size  ex) const
inline

References trace_.

core::Size core::scoring::ResidualDipolarCoupling::get_n_alignments ( ) const
inline

References nex_.

RDC_lines const& core::scoring::ResidualDipolarCoupling::get_RDC_data ( ) const
inline
RDC_lines& core::scoring::ResidualDipolarCoupling::get_RDC_data_ref ( )
private

non-const reference to RDC data private use only.

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.

References All_RDC_lines_, nex_, and nrows_.

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 R().

Referenced by compute_dipscore(), and compute_dipscore_nls().

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

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

References R_.

Referenced by Q().

void core::scoring::ResidualDipolarCoupling::read_RDC_file ( )
void core::scoring::ResidualDipolarCoupling::read_RDC_file ( Size  nex,
std::string const &  filename 
)
private

read RDC data from file

References All_RDC_lines_, and core::scoring::tr().

void core::scoring::ResidualDipolarCoupling::release_buffers ( )
void core::scoring::ResidualDipolarCoupling::reserve_buffers ( )
void core::scoring::ResidualDipolarCoupling::show ( std::ostream &  out) const

References All_RDC_lines_.

Referenced by core::scoring::operator<<().

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 core::Real par 
) const
utility::vector0< Tensor >& core::scoring::ResidualDipolarCoupling::tensor ( )
inline

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

References S_.

Member Data Documentation

RDC_lines core::scoring::ResidualDipolarCoupling::All_RDC_lines_
private
Real const core::scoring::ResidualDipolarCoupling::COMMON_DENOMINATOR = 36.5089/1.041/1.041/1.041
staticprivate
utility::vector0< rvec5 > core::scoring::ResidualDipolarCoupling::D_
private
utility::vector0< Tensor > core::scoring::ResidualDipolarCoupling::EIG_
private
utility::vector0< rvec > core::scoring::ResidualDipolarCoupling::EV_
private
utility::vector0< core::Real > core::scoring::ResidualDipolarCoupling::exprdc_
private
utility::vector0< core::Real > core::scoring::ResidualDipolarCoupling::FA_
private

Referenced by release_buffers(), and reserve_buffers().

utility::vector0< core::Size > core::scoring::ResidualDipolarCoupling::lenex_
private
utility::vector0< core::Real > core::scoring::ResidualDipolarCoupling::maxz_
private
core::Size core::scoring::ResidualDipolarCoupling::nex_
private
core::Size core::scoring::ResidualDipolarCoupling::nrows_
private
utility::vector0< core::Real > core::scoring::ResidualDipolarCoupling::r0_
private
utility::vector0< core::Real > core::scoring::ResidualDipolarCoupling::r1_
private
utility::vector0< core::Real > core::scoring::ResidualDipolarCoupling::r2_
private
core::Real core::scoring::ResidualDipolarCoupling::R_
private
utility::vector0< core::Real > core::scoring::ResidualDipolarCoupling::rdcconst_
private
utility::vector0< core::Real > core::scoring::ResidualDipolarCoupling::rdcweight_
private
utility::vector0< rvec5 > core::scoring::ResidualDipolarCoupling::rhs_
private
core::Real core::scoring::ResidualDipolarCoupling::rmsd_
private
utility::vector0< Tensor > core::scoring::ResidualDipolarCoupling::S_
private
utility::vector0< Tensor > core::scoring::ResidualDipolarCoupling::SD_
private
utility::vector0< Tensor5 > core::scoring::ResidualDipolarCoupling::T_
private
utility::vector0< core::Real > core::scoring::ResidualDipolarCoupling::trace_
private

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