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< Real >	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. 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, Size >	min_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

typedef utility::pointer::shared_ptr< Simulated4PDEERTraceFactory const > core::scoring::epr_deer::Simulated4PDEERTraceFactoryCOP

typedef utility::pointer::shared_ptr< Simulated4PDEERTraceFactory > core::scoring::epr_deer::Simulated4PDEERTraceFactoryOP

typedef utility::pointer::shared_ptr< Simulated4PDEERTrace > core::scoring::epr_deer::Simulated4PDEERTraceOP

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_trace	Simulated DEER trace (intramolecular)
time_pts	Time points for DEER trace
depth	Modulation deoth
slope	Background slope
dim	Background 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

map	Simulated DEER histogram to modify
key	Bin/X-value
val	Y-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

map	Simulated DEER histogram to modify
key	Bin/X-value
val	Y-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

x	The point of interest
avg	Average value of distribution
stdev	Width 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

q	Value 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

x	Value to calculate
lo	Lower bound
hi	Upper 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

histr1	First distribution
histr2	Second 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

par	C-style parameter array
m_dat	Number of data points
data	Generic data pointer object that needs to be unpacked
fvec	Vector 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

par	C-style parameter array
m_dat	Number of data points
data	Generic data pointer object that needs to be unpacked
fvec	Vector 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

x	Value 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
	)

Sigmoid function implementation.

Parameters

x	Number to convert
min	Minimum value of output
max	Maximum value of output

Returns

Y output on sigmoid function Note that neither the slope nor the y-intercept can be modified

References protocols::mean_field::min().

Referenced by add_bckg(), protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator::calculate_current_temperature(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::depth(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::dim(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), and core::scoring::epr_deer::Simulated4PDEERTraceFactory::opt_bckg().

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

Tracer used for error messages.

Global to avoid re-instantiating tracer with every new object

Referenced by core::scoring::epr_deer::EPRSpinLabel::histogram(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::kernel_mult(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::opt_bckg(), core::scoring::epr_deer::DEERIO::parse_bounds_lines(), core::scoring::epr_deer::DEERIO::parse_decay_info_lines(), core::scoring::epr_deer::DEERIO::parse_desc_lines(), core::scoring::epr_deer::DEERIO::parse_dist_datatype(), and core::scoring::epr_deer::DEERIO::pull_coords().

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

data	The data passed to lmmin
time_points	Time point vector to assign
exp_trace	Experimental DEER trace to assign
sim_trace	Simulated 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

Referenced by core::scoring::epr_deer::DEERIO::generate_data().

Real const core::scoring::epr_deer::maxdepth_ = 0.9

static

Maximum modulation depth (passed to sigmoid function)

Referenced by add_bckg(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::depth(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::initial_search(), and core::scoring::epr_deer::Simulated4PDEERTraceFactory::opt_bckg().

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

Minimum modulation depth (passed to sigmoid function)

Referenced by add_bckg(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::depth(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::initial_search(), and core::scoring::epr_deer::Simulated4PDEERTraceFactory::opt_bckg().

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)