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

Enumeration Type Documentation

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)
core::Real protocols::calc_taskop_filters::compute_mean_probability ( protocols::pose_metric_calculators::RotamerProbabilities const &  probs)
core::Real protocols::calc_taskop_filters::compute_min_probability ( protocols::pose_metric_calculators::RotamerProbabilities const &  probs)
core::Real protocols::calc_taskop_filters::compute_probability ( protocols::pose_metric_calculators::RotamerProbabilities const &  probs)
std::string protocols::calc_taskop_filters::RotBoltzWeight_subelement_ct_name ( std::string const &  name)
std::string protocols::calc_taskop_filters::subtag_for_multiple_sigmoids ( std::string const &  foo)
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