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Classes | Typedefs | Enumerations | Functions
protocols::calc_taskop_filters Namespace Reference

Classes

class  ConservedPosMutationFilter
 
class  ConservedPosMutationFilterCreator
 
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  IdManager
 
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< ConservedPosMutationFilterConservedPosMutationFilterOP
 
typedef utility::pointer::shared_ptr< ConservedPosMutationFilter const > ConservedPosMutationFilterCOP
 
typedef utility::pointer::shared_ptr< MultipleSigmoidsMultipleSigmoidsOP
 
typedef utility::pointer::shared_ptr< MultipleSigmoids const > MultipleSigmoidsCOP
 
typedef utility::pointer::shared_ptr< OperatorOperatorOP
 
typedef utility::pointer::shared_ptr< Operator const > OperatorCOP
 
typedef utility::pointer::shared_ptr< RelativePoseFilterRelativePoseFilterOP
 
typedef utility::pointer::shared_ptr< RelativePoseFilter const > RelativePoseFilterCOP
 
typedef utility::pointer::shared_ptr< RotamerBoltzmannWeightRotamerBoltzmannWeightFilterOP
 
typedef utility::pointer::shared_ptr< RotamerBoltzmannWeight const > RotamerBoltzmannWeightFilterCOP
 
typedef utility::pointer::shared_ptr< RotamerBoltzmannWeight2RotamerBoltzmannWeight2OP
 
typedef utility::pointer::shared_ptr< RotamerBoltzmannWeight2 const > RotamerBoltzmannWeight2COP
 
typedef utility::pointer::shared_ptr< SigmoidSigmoidOP
 
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

◆ ConservedPosMutationFilterCOP

◆ ConservedPosMutationFilterOP

◆ MultipleSigmoidsCOP

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

◆ MultipleSigmoidsOP

◆ OperatorCOP

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

◆ OperatorOP

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

◆ RelativePoseFilterCOP

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

◆ RelativePoseFilterOP

◆ RotamerBoltzmannWeight2COP

◆ RotamerBoltzmannWeight2OP

◆ RotamerBoltzmannWeightFilterCOP

◆ RotamerBoltzmannWeightFilterOP

◆ SigmoidCOP

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

◆ SigmoidOP

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

Enumeration Type Documentation

◆ Operation

Enumerator
SUM 
PRODUCT 
NORMALIZED_SUM 
MAX 
MIN 
SUBTRACT 
ABS 
BOOLEAN_OR 
XOR 

Function Documentation

◆ compute_max_probability()

core::Real protocols::calc_taskop_filters::compute_max_probability ( protocols::pose_metric_calculators::RotamerProbabilities const &  probs)

◆ compute_mean_probability()

core::Real protocols::calc_taskop_filters::compute_mean_probability ( protocols::pose_metric_calculators::RotamerProbabilities const &  probs)

◆ compute_min_probability()

core::Real protocols::calc_taskop_filters::compute_min_probability ( protocols::pose_metric_calculators::RotamerProbabilities const &  probs)

◆ compute_probability()

core::Real protocols::calc_taskop_filters::compute_probability ( protocols::pose_metric_calculators::RotamerProbabilities const &  probs)

◆ RotBoltzWeight_subelement_ct_name()

std::string protocols::calc_taskop_filters::RotBoltzWeight_subelement_ct_name ( std::string const &  name)

◆ subtag_for_multiple_sigmoids()

std::string protocols::calc_taskop_filters::subtag_for_multiple_sigmoids ( std::string const &  foo)

◆ TR() [1/5]

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::MultipleSigmoids::compute(), protocols::calc_taskop_filters::Operator::compute(), protocols::calc_taskop_filters::RelativePoseFilter::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute(), protocols::calc_taskop_filters::Sigmoid::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::MultipleSigmoids::parse_my_tag(), protocols::calc_taskop_filters::Operator::parse_my_tag(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::calc_taskop_filters::Sigmoid::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::MultipleSigmoids::reset_baseline(), protocols::calc_taskop_filters::Operator::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().

◆ TR() [2/5]

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

◆ TR() [3/5]

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

◆ TR() [4/5]

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

◆ TR() [5/5]

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