protocols::calc_taskop_filters Namespace Reference

Classes
class	ConservedPosMutationFilter
class	ConservedPosMutationFilterCreator
class	IdManager
class	MultipleSigmoids
	simply takes a list of pdbs and creates relative pose then extract sigmoids and call operator (product) More...
class	MultipleSigmoidsFilterCreator
class	Operator
	simply take a list of filters and combine them using the operation above More...
class	OperatorFilterCreator
class	RelativePoseFilter
class	RelativePoseFilterCreator
class	RotamerBoltzmannWeight
class	RotamerBoltzmannWeight2
	Next-generation RotamerBoltzmannWeight filter. More...
class	RotamerBoltzmannWeight2Creator
class	RotamerBoltzmannWeightFilterCreator
class	Sigmoid
	transform the output from a regular filter into a sigmoid ranging from 0-1 according to: fx = 1/[1 + exp[ ( x - offset ) * steepness ] The function asymptotically reaches 1 at negative values and 0 at positive values. It's 0.5 at the offset and steepness determines its slope at the offset More...
class	SigmoidFilterCreator

Typedefs
typedef utility::pointer::shared_ptr < ConservedPosMutationFilter >	ConservedPosMutationFilterOP
typedef utility::pointer::shared_ptr < ConservedPosMutationFilter const >	ConservedPosMutationFilterCOP
typedef utility::pointer::shared_ptr < MultipleSigmoids >	MultipleSigmoidsOP
typedef utility::pointer::shared_ptr < MultipleSigmoids const >	MultipleSigmoidsCOP
typedef utility::pointer::shared_ptr < Operator >	OperatorOP
typedef utility::pointer::shared_ptr < Operator const >	OperatorCOP
typedef utility::pointer::shared_ptr < RelativePoseFilter >	RelativePoseFilterOP
typedef utility::pointer::shared_ptr < RelativePoseFilter const >	RelativePoseFilterCOP
typedef utility::pointer::shared_ptr < RotamerBoltzmannWeight >	RotamerBoltzmannWeightFilterOP
typedef utility::pointer::shared_ptr < RotamerBoltzmannWeight const >	RotamerBoltzmannWeightFilterCOP
typedef utility::pointer::shared_ptr < RotamerBoltzmannWeight2 >	RotamerBoltzmannWeight2OP
typedef utility::pointer::shared_ptr < RotamerBoltzmannWeight2 const >	RotamerBoltzmannWeight2COP
typedef utility::pointer::shared_ptr < Sigmoid >	SigmoidOP
typedef utility::pointer::shared_ptr < Sigmoid const >	SigmoidCOP

Enumerations
enum	Operation {   SUM, PRODUCT, NORMALIZED_SUM, MAX,   MIN, SUBTRACT, ABS, BOOLEAN_OR,   XOR }

Functions
static basic::Tracer	TR ("protocols.calc_taskop_filters.MultipleSigmoids")
std::string	subtag_for_multiple_sigmoids (std::string const &foo)
static basic::Tracer	TR ("protocols.calc_taskop_filters.Operator")
static basic::Tracer	TR ("protocols.simple_filters.RelativePoseFilter")
static basic::Tracer	TR ("protocols.simple_filters.RotamerBoltzmannWeight")
std::string	RotBoltzWeight_subelement_ct_name (std::string const &name)
core::Real	compute_mean_probability (protocols::pose_metric_calculators::RotamerProbabilities const &probs)
core::Real	compute_probability (protocols::pose_metric_calculators::RotamerProbabilities const &probs)
core::Real	compute_max_probability (protocols::pose_metric_calculators::RotamerProbabilities const &probs)
core::Real	compute_min_probability (protocols::pose_metric_calculators::RotamerProbabilities const &probs)
static basic::Tracer	TR ("protocols.simple_filters.Sigmoid")

Typedef Documentation

typedef utility::pointer::shared_ptr< ConservedPosMutationFilter const > protocols::calc_taskop_filters::ConservedPosMutationFilterCOP

typedef utility::pointer::shared_ptr< ConservedPosMutationFilter > protocols::calc_taskop_filters::ConservedPosMutationFilterOP

typedef utility::pointer::shared_ptr< MultipleSigmoids const > protocols::calc_taskop_filters::MultipleSigmoidsCOP

typedef utility::pointer::shared_ptr< MultipleSigmoids > protocols::calc_taskop_filters::MultipleSigmoidsOP

typedef utility::pointer::shared_ptr< Operator const > protocols::calc_taskop_filters::OperatorCOP

typedef utility::pointer::shared_ptr< Operator > protocols::calc_taskop_filters::OperatorOP

typedef utility::pointer::shared_ptr< RelativePoseFilter const > protocols::calc_taskop_filters::RelativePoseFilterCOP

typedef utility::pointer::shared_ptr< RelativePoseFilter > protocols::calc_taskop_filters::RelativePoseFilterOP

typedef utility::pointer::shared_ptr< RotamerBoltzmannWeight2 const > protocols::calc_taskop_filters::RotamerBoltzmannWeight2COP

typedef utility::pointer::shared_ptr< RotamerBoltzmannWeight2 > protocols::calc_taskop_filters::RotamerBoltzmannWeight2OP

typedef utility::pointer::shared_ptr< RotamerBoltzmannWeight const > protocols::calc_taskop_filters::RotamerBoltzmannWeightFilterCOP

typedef utility::pointer::shared_ptr< RotamerBoltzmannWeight > protocols::calc_taskop_filters::RotamerBoltzmannWeightFilterOP

typedef utility::pointer::shared_ptr< Sigmoid const > protocols::calc_taskop_filters::SigmoidCOP

typedef utility::pointer::shared_ptr< Sigmoid > protocols::calc_taskop_filters::SigmoidOP

Enumeration Type Documentation

enum protocols::calc_taskop_filters::Operation

Enumerator
SUM
PRODUCT
NORMALIZED_SUM
MAX
MIN
SUBTRACT
ABS
BOOLEAN_OR
XOR

Function Documentation

core::Real protocols::calc_taskop_filters::compute_max_probability

(

protocols::pose_metric_calculators::RotamerProbabilities const &

probs

)

References protocols::mean_field::max().

Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_score().

core::Real protocols::calc_taskop_filters::compute_mean_probability

(

protocols::pose_metric_calculators::RotamerProbabilities const &

probs

)

References core::simple_metrics::metrics::sum.

Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_score().

core::Real protocols::calc_taskop_filters::compute_min_probability

(

protocols::pose_metric_calculators::RotamerProbabilities const &

probs

)

References protocols::mean_field::min().

Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_score().

core::Real protocols::calc_taskop_filters::compute_probability

(

protocols::pose_metric_calculators::RotamerProbabilities const &

probs

)

Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_score().

std::string protocols::calc_taskop_filters::RotBoltzWeight_subelement_ct_name

(

std::string const &

name

)

Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeight::provide_xml_schema().

std::string protocols::calc_taskop_filters::subtag_for_multiple_sigmoids

(

std::string const &

foo

)

Referenced by protocols::calc_taskop_filters::MultipleSigmoids::provide_xml_schema().

static basic::Tracer protocols::calc_taskop_filters::TR ( "protocols.simple_filters.Sigmoid"  )

static

static basic::Tracer protocols::calc_taskop_filters::TR ( "protocols.calc_taskop_filters.MultipleSigmoids"  )

static

Referenced by protocols::calc_taskop_filters::Operator::apply(), protocols::calc_taskop_filters::Operator::compute(), protocols::calc_taskop_filters::RelativePoseFilter::compute(), protocols::calc_taskop_filters::MultipleSigmoids::compute(), protocols::calc_taskop_filters::Sigmoid::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_modified_ddg(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), protocols::calc_taskop_filters::Operator::modify_relative_filters_pdb_names(), protocols::calc_taskop_filters::Operator::parse_my_tag(), protocols::calc_taskop_filters::Sigmoid::parse_my_tag(), protocols::calc_taskop_filters::MultipleSigmoids::parse_my_tag(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::register_calculator(), protocols::calc_taskop_filters::Operator::report_sm(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::report_sm(), protocols::calc_taskop_filters::Operator::reset_baseline(), protocols::calc_taskop_filters::MultipleSigmoids::reset_baseline(), protocols::calc_taskop_filters::Sigmoid::reset_baseline(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::RotamerBoltzmannWeight2(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), and protocols::calc_taskop_filters::RotamerBoltzmannWeight2::unregister_calculator().

static basic::Tracer protocols::calc_taskop_filters::TR ( "protocols.calc_taskop_filters.Operator"  )

static

static basic::Tracer protocols::calc_taskop_filters::TR ( "protocols.simple_filters.RelativePoseFilter"  )

static

static basic::Tracer protocols::calc_taskop_filters::TR ( "protocols.simple_filters.RotamerBoltzmannWeight"  )

static