Class SecondaryStructure

__init__( (object)arg1) -> None :

    C++ signature :
        void __init__(_object*)

__init__( (object)arg1, (SecondaryStructure)) -> None :
    tiny helper class that knows the relative fractions of secondary structure  L,H,E
    @detail
    so far these fractions can be computed from a FragSet
    other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses,
    

    C++ signature :
        void __init__(_object*,core::fragment::SecondaryStructure)

__init__( (object)arg1, (object), (vector1_Real)) -> None :
    c'ctor that creates a SecondaryStructure as an average of several SecondaryStructure objects
    

    C++ signature :
        void __init__(_object*,utility::vector1<boost::shared_ptr<core::fragment::SecondaryStructure>, std::allocator<boost::shared_ptr<core::fragment::SecondaryStructure> > > {lvalue},utility::vector1<double, std::allocator<double> > {lvalue})

__init__( (object)arg1, (FragSet)frags [, (int)nres=0 [, (bool)bJustCenterResidue=False]]) -> None :
    c'stor compute fractions from fragments
    

    C++ signature :
        void __init__(_object*,core::fragment::FragSet [,unsigned long=0 [,bool=False]])

__init__( (object)arg1, (Pose)) -> None :
    c'stor compute fractions from pose ( well it won't be "fractions" )
    

    C++ signature :
        void __init__(_object*,core::pose::Pose)

Overrides: object.__init__

helper for pickle

Overrides: object.__reduce__

(inherited documentation)

__str__( (SecondaryStructure)arg1) -> object :

    C++ signature :
        _object* __str__(core::fragment::SecondaryStructure {lvalue})

Overrides: object.__str__

confidence( (SecondaryStructure)arg1, (int)pos) -> float :
    confidence at position
    

    C++ signature :
        double confidence(core::fragment::SecondaryStructure {lvalue},unsigned long)

extend( (SecondaryStructure)arg1, (int)) -> None :
    extends with pure 'L' at end until requested size is reached.
    

    C++ signature :
        void extend(core::fragment::SecondaryStructure {lvalue},unsigned long)

helix_fraction( (SecondaryStructure)arg1, (int)pos) -> float :
    helix fraction at position
    

    C++ signature :
        double helix_fraction(core::fragment::SecondaryStructure {lvalue},unsigned long)

loop_fraction( (SecondaryStructure)arg1, (int)pos) -> float :
    return loop fraction at position
    

    C++ signature :
        double loop_fraction(core::fragment::SecondaryStructure {lvalue},unsigned long)

loop_fraction( (SecondaryStructure)arg1) -> object :
    return loop fraction - FArray
    

    C++ signature :
        ObjexxFCL::FArray1D<float> loop_fraction(core::fragment::SecondaryStructure {lvalue})

read_from_file( (SecondaryStructure)arg1, (str)fn) -> None :
    read from file
    

    C++ signature :
        void read_from_file(core::fragment::SecondaryStructure {lvalue},std::string)

read_psipred_ss2( (SecondaryStructure)arg1, (std_istream)os) -> None :
    write psipred format
    

    C++ signature :
        void read_psipred_ss2(core::fragment::SecondaryStructure {lvalue},std::istream {lvalue})

read_psipred_ss2( (SecondaryStructure)arg1, (str)filename) -> None :
    write psipred format
    

    C++ signature :
        void read_psipred_ss2(core::fragment::SecondaryStructure {lvalue},std::string)

read_talos_ss( (SecondaryStructure)arg1, (std_istream)os) -> None :
    read talos+ format
    

    C++ signature :
        void read_talos_ss(core::fragment::SecondaryStructure {lvalue},std::istream {lvalue})

read_talos_ss( (SecondaryStructure)arg1, (str)filename) -> None :
    read talos+ format
    

    C++ signature :
        void read_talos_ss(core::fragment::SecondaryStructure {lvalue},std::string)

secstruct( (SecondaryStructure)arg1, (int)pos) -> str :
    returns the most probably secstruct at that position
    

    C++ signature :
        char secstruct(core::fragment::SecondaryStructure {lvalue},unsigned long)

set_fractions( (SecondaryStructure)arg1, (int)pos, (float)helix_fraction, (float)sheet_fraction, (float)loop_fraction [, (float)confidence=0]) -> None :
    sets secondary structure probabilities at a given position
    

    C++ signature :
        void set_fractions(core::fragment::SecondaryStructure {lvalue},unsigned long,double,double,double [,double=0])

sheet_fraction( (SecondaryStructure)arg1, (int)pos) -> float :
    alias for strand-fraction ...
    

    C++ signature :
        double sheet_fraction(core::fragment::SecondaryStructure {lvalue},unsigned long)

show( (SecondaryStructure)arg1, (OStream)) -> None :
    core/fragment/SecondaryStructure.hh:151

    C++ signature :
        void show(core::fragment::SecondaryStructure {lvalue},std::ostream {lvalue})

strand_fraction( (SecondaryStructure)arg1, (int)pos) -> float :
    return strand fraction at position
    

    C++ signature :
        double strand_fraction(core::fragment::SecondaryStructure {lvalue},unsigned long)

strand_fraction( (SecondaryStructure)arg1) -> object :
    return strand fraction - FArray
    

    C++ signature :
        ObjexxFCL::FArray1D<float> strand_fraction(core::fragment::SecondaryStructure {lvalue})

total_residue( (SecondaryStructure)arg1) -> int :
    number of residues for which information is available
    

    C++ signature :
        unsigned long total_residue(core::fragment::SecondaryStructure {lvalue})

write_psipred_ss2( (SecondaryStructure)arg1, (OStream)os, (str)sequence) -> None :
    write psipred format
    

    C++ signature :
        void write_psipred_ss2(core::fragment::SecondaryStructure {lvalue},std::ostream {lvalue},std::string)