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core::scoring::epr_deer Namespace Reference

Namespaces

 metrics
 

Classes

class  DEERDataCache
 
class  DEERIO
 
class  EPRSpinLabel
 
class  Simulated4PDEERTrace
 
class  Simulated4PDEERTraceFactory
 

Typedefs

typedef
utility::pointer::shared_ptr
< DEERDataCache
DEERDataCacheOP
 
typedef
utility::pointer::shared_ptr
< DEERDataCache const > 
DEERDataCacheCOP
 
typedef
utility::pointer::shared_ptr
< DEERIO
DEERIOOP
 
typedef
utility::pointer::shared_ptr
< DEERIO const > 
DEERIOCOP
 
using SplitLine = utility::vector1< std::string >
 
using SplitLines = utility::vector1< SplitLine >
 
using SplitLineMap = std::map< std::string, SplitLines >
 
using PairSizeString = std::pair< Size, std::string >
 Alias to asve space when defining residues and spin labels. More...
 
typedef
utility::pointer::shared_ptr
< EPRSpinLabel
EPRSpinLabelOP
 
typedef
utility::pointer::shared_ptr
< EPRSpinLabel const > 
EPRSpinLabelCOP
 
using PseudoSL = std::pair< numeric::xyzVector< Real >, Real >
 Alias to save space throughout core/scoring/epr_deer. More...
 
typedef
utility::pointer::shared_ptr
< Simulated4PDEERTrace
Simulated4PDEERTraceOP
 
typedef
utility::pointer::shared_ptr
< Simulated4PDEERTrace const > 
Simulated4PDEERTraceCOP
 
using TriVec = std::tuple< utility::vector1< Real >, utility::vector1< Real >, utility::vector1< Real > >
 
using TriVecC = std::tuple< utility::vector1< Real > const, utility::vector1< Real > const, utility::vector1< Real > const >
 
typedef
utility::pointer::shared_ptr
< Simulated4PDEERTraceFactory
Simulated4PDEERTraceFactoryOP
 
typedef
utility::pointer::shared_ptr
< Simulated4PDEERTraceFactory
const > 
Simulated4PDEERTraceFactoryCOP
 

Functions

static basic::Tracer TR ("core.scoring.epr_deer.metrics.DEERDataCache")
 Tracer used for error messages. More...
 
static basic::Tracer TR ("core.scoring.epr_deer.DEERIO")
 Tracer used for error messages. More...
 
static basic::Tracer TR ("core.scoring.epr_deer.EPRSpinLabel")
 Tracer used for error messages. More...
 
static const
numeric::xyzVector< Real
vrt_cb_ (-1.3116,-0.5715, 0.5398)
 Virtual, idealized CB atom for center-of-mass calculation. More...
 
static basic::Tracer TR ("core.scoring.epr_deer.Simulated4PDEERTrace")
 Tracer used for error messages. More...
 
static basic::Tracer TR ("core.scoring.epr_deer.Simulated4PDEERTraceFactory")
 Tracer used for error messages. More...
 
utility::vector1< Realadd_bckg (utility::vector1< Real > const &sim_trace, utility::vector1< Real > const &time_pts, Real depth, Real slope, Real dim, bool const thru_sigmoid)
 Function for adding non-3D background coupling to DEER trace. More...
 
void unpack (void const *data, utility::vector1< Real > &time_pts, utility::vector1< Real > &exp_trace, utility::vector1< Real > &sim_trace)
 Unpacks data passed to lmmin function. More...
 
void minimize_sumsq (Real const *par, int m_dat, void const *data, Real *fvec, int *)
 LM function for optimizing non-3D background coupling. More...
 
void minimize_sumsq_nodim (Real const *par, int m_dat, void const *data, Real *fvec, int *)
 LM function for optimizing 3D background coupling. More...
 
static basic::Tracer TR ("core.scoring.epr_deer.util")
 Tracer used for error messages. More...
 
Real gauss (Real const &x, Real const &avg, Real const &stdev)
 Compute amplitude at a given point of a normal distribution. More...
 
Real probit (Real const &x)
 Calculate probit function given a certain value. More...
 
Real logit (Real const &x, Real const &lo, Real const &hi)
 Calculate logit function given certain value. More...
 
Real ln (Real const &q)
 Safe version of log() that doesn't crash when zero is passed. More...
 
std::tuple< Size, Sizemin_max (std::map< Size, Real > const &histr1, std::map< Size, Real > const &histr2)
 Return the minimum and maximum bins from two distributions. More...
 
Real sigmoid (Real const &x, Real const &min, Real const &max)
 Sigmoid function implementation. More...
 
template<typename T1 , typename T2 >
void add_to_map (std::map< T1, T2 > &map, T1 const &key, T2 const &val)
 Simple fxn to avoid repeating this code everywhere. More...
 
template<typename T1 , typename T2 >
void append_to_map (std::map< T1, utility::vector1< T2 > > &map, T1 const &key, T2 const &val)
 Simple fxn to avoid repeating this code everywhere. More...
 

Variables

static std::map< Size,
metrics::DEERDataOP
epr_deer_input_data_
 
static scoring::AtomVDWOP atom_vdw_ = scoring::AtomVDWOP( nullptr )
 Object use to calculate VDW radii of centroid atoms. More...
 
static std::map< std::string,
utility::vector1< PseudoSL > > 
deflt_coords_
 Default coordinates map. More...
 
static Real const mindepth_ = 0.01
 Minimum modulation depth (passed to sigmoid function) More...
 
static Real const maxdepth_ = 0.9
 Maximum modulation depth (passed to sigmoid function) More...
 
static Real const minslope_ = 0.0
 Minimum background slope (passed to sigmoid function) More...
 
static Real const maxslope_ = 1.0
 Maximum background slope (passed to sigmoid function) More...
 
static Real const mindim_ = 2.0
 Minimum dimensionality (passed to sigmoid function) More...
 
static Real const maxdim_ = 3.5
 Maximum dimensionality (passed to sigmoid function) More...
 
static Real const dim3d_ = 0.69314717
 Default dimensionality to yield 3.0 (passed to sigmoid function) More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< DEERDataCache const > core::scoring::epr_deer::DEERDataCacheCOP
typedef utility::pointer::shared_ptr< DEERDataCache > core::scoring::epr_deer::DEERDataCacheOP
typedef utility::pointer::shared_ptr< DEERIO const > core::scoring::epr_deer::DEERIOCOP
typedef utility::pointer::shared_ptr< DEERIO > core::scoring::epr_deer::DEERIOOP
typedef utility::pointer::shared_ptr< EPRSpinLabel const > core::scoring::epr_deer::EPRSpinLabelCOP
typedef utility::pointer::shared_ptr< EPRSpinLabel > core::scoring::epr_deer::EPRSpinLabelOP
typedef std::pair< Size, std::string > core::scoring::epr_deer::PairSizeString

Alias to asve space when defining residues and spin labels.

using core::scoring::epr_deer::PseudoSL = typedef std::pair< numeric::xyzVector< Real >, Real >

Alias to save space throughout core/scoring/epr_deer.

typedef utility::pointer::shared_ptr< Simulated4PDEERTrace const > core::scoring::epr_deer::Simulated4PDEERTraceCOP
using core::scoring::epr_deer::SplitLine = typedef utility::vector1< std::string >
using core::scoring::epr_deer::SplitLineMap = typedef std::map< std::string, SplitLines >
using core::scoring::epr_deer::SplitLines = typedef utility::vector1< SplitLine >
using core::scoring::epr_deer::TriVec = typedef std::tuple< utility::vector1< Real >, utility::vector1< Real >, utility::vector1< Real > >
using core::scoring::epr_deer::TriVecC = typedef std::tuple< utility::vector1< Real > const, utility::vector1< Real > const, utility::vector1< Real > const >

Function Documentation

utility::vector1< Real > core::scoring::epr_deer::add_bckg ( utility::vector1< Real > const &  sim_trace,
utility::vector1< Real > const &  time_pts,
Real  depth,
Real  slope,
Real  dim,
bool const  thru_sigmoid 
)

Function for adding non-3D background coupling to DEER trace.

Parameters
sim_traceSimulated DEER trace (intramolecular)
time_ptsTime points for DEER trace
depthModulation deoth
slopeBackground slope
dimBackground dimensionality Note that this is a "friend" function, not part of the factory Also note that all values need to pass through sigmoid function

References maxdepth_, maxdim_, mindepth_, mindim_, and sigmoid().

Referenced by core::scoring::epr_deer::Simulated4PDEERTraceFactory::initial_search(), minimize_sumsq(), minimize_sumsq_nodim(), and core::scoring::epr_deer::Simulated4PDEERTraceFactory::opt_bckg().

template<typename T1 , typename T2 >
void core::scoring::epr_deer::add_to_map ( std::map< T1, T2 > &  map,
T1 const &  key,
T2 const &  val 
)

Simple fxn to avoid repeating this code everywhere.

Parameters
mapSimulated DEER histogram to modify
keyBin/X-value
valY-value to either add or append

References protocols::hybridization::val.

Referenced by core::scoring::epr_deer::metrics::DEERData::convolute(), core::scoring::epr_deer::EPRSpinLabel::histogram(), core::energy_methods::DEEREnergy::iter_over_labels(), and core::energy_methods::DEEREnergy::setup_for_derivatives().

template<typename T1 , typename T2 >
void core::scoring::epr_deer::append_to_map ( std::map< T1, utility::vector1< T2 > > &  map,
T1 const &  key,
T2 const &  val 
)

Simple fxn to avoid repeating this code everywhere.

Parameters
mapSimulated DEER histogram to modify
keyBin/X-value
valY-value to either add or append

Referenced by core::scoring::epr_deer::DEERIO::parse_data(), core::scoring::epr_deer::DEERIO::parse_input(), and core::scoring::epr_deer::DEERIO::pull_coords().

Real core::scoring::epr_deer::gauss ( Real const &  x,
Real const &  avg,
Real const &  stdev 
)

Compute amplitude at a given point of a normal distribution.

Parameters
xThe point of interest
avgAverage value of distribution
stdevWidth of distribution
Returns
Amplitude

Referenced by core::scoring::epr_deer::metrics::DEERData::convolute(), and core::scoring::epr_deer::EPRSpinLabel::histogram().

Real core::scoring::epr_deer::ln ( Real const &  q)

Safe version of log() that doesn't crash when zero is passed.

Parameters
qValue to take logarithm
Returns
natural logarithm of q, or arbitrarily large number of q=0.0

References protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by core::scoring::epr_deer::metrics::DEERJSMethod::get_score(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::get_score(), and core::scoring::SecondaryStructurePotential::rsigma_dot_initializer().

Real core::scoring::epr_deer::logit ( Real const &  x,
Real const &  lo,
Real const &  hi 
)

Calculate logit function given certain value.

Parameters
xValue to calculate
loLower bound
hiUpper bound
Returns
: Logit value

Referenced by core::scoring::epr_deer::Simulated4PDEERTraceFactory::initial_search().

std::tuple< Size, Size > core::scoring::epr_deer::min_max ( std::map< Size, Real > const &  histr1,
std::map< Size, Real > const &  histr2 
)

Return the minimum and maximum bins from two distributions.

Parameters
histr1First distribution
histr2Second distribution
Returns
Tuple of minimum and maximum, in that order

References protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by core::scoring::epr_deer::metrics::DEEROverlapMethod::get_score(), core::scoring::epr_deer::metrics::DEERJSMethod::get_score(), core::scoring::epr_deer::metrics::DEERMiscMethod::get_score(), and core::scoring::epr_deer::metrics::DEERJaccardMethod::get_score().

void core::scoring::epr_deer::minimize_sumsq ( Real const *  par,
int  m_dat,
void const *  data,
Real *  fvec,
int *   
)

LM function for optimizing non-3D background coupling.

Parameters
parC-style parameter array
m_datNumber of data points
dataGeneric data pointer object that needs to be unpacked
fvecVector of residuals used by lmmin()
null(not used) Note that this is a "friend" function, not part of the factory

References add_bckg(), and unpack().

Referenced by core::scoring::epr_deer::Simulated4PDEERTraceFactory::opt_bckg().

void core::scoring::epr_deer::minimize_sumsq_nodim ( Real const *  par,
int  m_dat,
void const *  data,
Real *  fvec,
int *   
)

LM function for optimizing 3D background coupling.

Parameters
parC-style parameter array
m_datNumber of data points
dataGeneric data pointer object that needs to be unpacked
fvecVector of residuals used by lmmin()
null(not used) Note that this is a "friend" function, not part of the factory

References add_bckg(), dim3d_, and unpack().

Referenced by core::scoring::epr_deer::Simulated4PDEERTraceFactory::opt_bckg().

Real core::scoring::epr_deer::probit ( Real const &  x)

Calculate probit function given a certain value.

Parameters
xValue to calculate
Returns
Probit function of x

Referenced by core::scoring::epr_deer::metrics::DEERDistanceDistribution::get_prs().

Real core::scoring::epr_deer::sigmoid ( Real const &  x,
Real const &  min,
Real const &  max 
)
static basic::Tracer core::scoring::epr_deer::TR ( "core.scoring.epr_deer.Simulated4PDEERTrace"  )
static

Tracer used for error messages.

Global to avoid re-instantiating tracer with every new object

static basic::Tracer core::scoring::epr_deer::TR ( "core.scoring.epr_deer.util"  )
static

Tracer used for error messages.

Global to avoid re-instantiating tracer with every new object

static basic::Tracer core::scoring::epr_deer::TR ( "core.scoring.epr_deer.metrics.DEERDataCache"  )
static
static basic::Tracer core::scoring::epr_deer::TR ( "core.scoring.epr_deer.Simulated4PDEERTraceFactory"  )
static

Tracer used for error messages.

Global to avoid re-instantiating tracer with every new object

static basic::Tracer core::scoring::epr_deer::TR ( "core.scoring.epr_deer.EPRSpinLabel"  )
static

Tracer used for error messages.

Global to avoid re-instantiating tracer with every new object

static basic::Tracer core::scoring::epr_deer::TR ( "core.scoring.epr_deer.DEERIO"  )
static

Tracer used for error messages.

Global to avoid re-instantiating tracer with every new object

void core::scoring::epr_deer::unpack ( void const *  data,
utility::vector1< Real > &  time_pts,
utility::vector1< Real > &  exp_trace,
utility::vector1< Real > &  sim_trace 
)

Unpacks data passed to lmmin function.

Parameters
dataThe data passed to lmmin
time_pointsTime point vector to assign
exp_traceExperimental DEER trace to assign
sim_traceSimulated DEER trace to assign

Referenced by minimize_sumsq(), and minimize_sumsq_nodim().

static const numeric::xyzVector< Real > core::scoring::epr_deer::vrt_cb_ ( -1.  3116,
-0.  5715,
0.  5398 
)
static

Virtual, idealized CB atom for center-of-mass calculation.

Global to avoid reinstantiation with every new object

Referenced by core::scoring::epr_deer::EPRSpinLabel::calc_sl_for_res().

Variable Documentation

scoring::AtomVDWOP core::scoring::epr_deer::atom_vdw_ = scoring::AtomVDWOP( nullptr )
static

Object use to calculate VDW radii of centroid atoms.

Global to avoid re-instantiating with every new object

Referenced by core::scoring::epr_deer::EPRSpinLabel::init_vdw(), and core::scoring::epr_deer::EPRSpinLabel::weight().

std::map< std::string, utility::vector1< PseudoSL > > core::scoring::epr_deer::deflt_coords_
static

Default coordinates map.

Global to avoid re-reading from database with every new object

Referenced by core::scoring::epr_deer::EPRSpinLabel::label().

Real const core::scoring::epr_deer::dim3d_ = 0.69314717
static

Default dimensionality to yield 3.0 (passed to sigmoid function)

Referenced by minimize_sumsq_nodim().

std::map< Size, metrics::DEERDataOP > core::scoring::epr_deer::epr_deer_input_data_
static
Real const core::scoring::epr_deer::maxdepth_ = 0.9
static
Real const core::scoring::epr_deer::maxdim_ = 3.5
static

Maximum dimensionality (passed to sigmoid function)

Referenced by add_bckg(), and core::scoring::epr_deer::Simulated4PDEERTraceFactory::dim().

Real const core::scoring::epr_deer::maxslope_ = 1.0
static

Maximum background slope (passed to sigmoid function)

Real const core::scoring::epr_deer::mindepth_ = 0.01
static
Real const core::scoring::epr_deer::mindim_ = 2.0
static

Minimum dimensionality (passed to sigmoid function)

Referenced by add_bckg(), and core::scoring::epr_deer::Simulated4PDEERTraceFactory::dim().

Real const core::scoring::epr_deer::minslope_ = 0.0
static

Minimum background slope (passed to sigmoid function)