Module _core_fragment_

apply_best_scoring_fragdata( (Pose)pose, (Frame)frame, (ScoreFunction)sfxn) -> None :
    goes through all frag_data in the frame and puts the
    best scoring one into the pose, i.e. quenches the frame
    

    C++ signature :
        void apply_best_scoring_fragdata(core::pose::Pose {lvalue},core::fragment::Frame,core::scoring::ScoreFunction)

chop_fragments( (FragSet)source, (FragSet)dest) -> None :
    Function for chopping the X-sized fragments in source into fragments that
    go into N-sized fragments in dest. Sizes are encoded by the value of
    max_frag_length() in both source and dest.
    

    C++ signature :
        void chop_fragments(core::fragment::FragSet {lvalue},core::fragment::FragSet {lvalue})

compute_per_residue_coverage( (FragSet)frags, (vector1_Size)nr_frags) -> None :
    core/fragment/util.hh:90

    C++ signature :
        void compute_per_residue_coverage(core::fragment::FragSet,utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue})

dump_frames_as_pdb( (Pose)pose, (vector1_FrameOP)frames, (str)filename [, (int)start_frag=1]) -> None :
    writes FragData in multimodel pdb format
    start_tag can be used to only write a subset
    of the contained frag data
    

    C++ signature :
        void dump_frames_as_pdb(core::pose::Pose,utility::vector1<boost::shared_ptr<core::fragment::Frame>, std::allocator<boost::shared_ptr<core::fragment::Frame> > >,std::string [,unsigned long=1])

fill_template_frames_from_pdb( (Pose)pose, (vector1_FrameOP)template_frames, (str)filename) -> bool :
    filling a frameset from a multimodel pdb file
    returns true if no error occured
    

    C++ signature :
        bool fill_template_frames_from_pdb(core::pose::Pose,utility::vector1<boost::shared_ptr<core::fragment::Frame>, std::allocator<boost::shared_ptr<core::fragment::Frame> > >,std::string)

flatten_list( (FrameList)frames, (object)frag_ids) -> None :
    core/fragment/util.hh:97

    C++ signature :
        void flatten_list(core::fragment::FrameList {lvalue},utility::vector1<core::fragment::FragID, std::allocator<core::fragment::FragID> > {lvalue})

fragment_set_slice( (ConstantLengthFragSet)fragset, (vector1_Size)slice_res) -> None :
    core/fragment/util.hh:139

    C++ signature :
        void fragment_set_slice(boost::shared_ptr<core::fragment::ConstantLengthFragSet> {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> >)

fragment_set_slice( (ConstantLengthFragSet)fragset, (int)min_res, (int)max_res) -> None :
    core/fragment/util.hh:135

    C++ signature :
        void fragment_set_slice(boost::shared_ptr<core::fragment::ConstantLengthFragSet> {lvalue},unsigned long,unsigned long)

getxform( (xyzVector_Real)m1, (xyzVector_Real)m2, (xyzVector_Real)m3, (xyzVector_Real)f1, (xyzVector_Real)f2, (xyzVector_Real)f3) -> Stub :
    core/fragment/util.hh:43

    C++ signature :
        core::kinematics::Stub getxform(numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>)

make_pose_from_frags( (Pose)pose, (str)sequence, (object)frags [, (bool)chains=False]) -> None :
    core/fragment/util.hh:142

    C++ signature :
        void make_pose_from_frags(core::pose::Pose {lvalue},std::string,utility::vector1<boost::shared_ptr<core::fragment::FragData const>, std::allocator<boost::shared_ptr<core::fragment::FragData const> > > [,bool=False])

make_simple_fold_tree_from_jump_frame( (Frame), (int)total_residue, (FoldTree)new_fold_tree) -> None :
    given a JumpFrame with Up and DownJumpSRFDs as LAST SRFDs this will make a fold-tree compatible with the
    Frame...   this is NOT GOOD for sampling, since it introduces cut-points outside of fragments
    later for sampling: one could probably write a routine that looks if it can move existing Jumps in Fold-tree to
    fit the FRAME ... if not it returns failure...
    

    C++ signature :
        void make_simple_fold_tree_from_jump_frame(core::fragment::Frame,unsigned long,core::kinematics::FoldTree {lvalue})

merge_frags( (FragSet)good_frags, (FragSet)filling, (int)min_nr_frags [, (bool)bRandom=True]) -> FragSet :
    core/fragment/util.hh:95

    C++ signature :
        boost::shared_ptr<core::fragment::FragSet> merge_frags(core::fragment::FragSet,core::fragment::FragSet,unsigned long [,bool=True])

read_std_frags_from_cmd( (FragSet)fragset_large, (FragSet)fragset_small) -> None :
    core/fragment/util.hh:126

    C++ signature :
        void read_std_frags_from_cmd(boost::shared_ptr<core::fragment::FragSet> {lvalue},boost::shared_ptr<core::fragment::FragSet> {lvalue})

retain_top( (int)k, (FragSet)fragments) -> None :
    Removes all but the top <k> fragments from <fragments>
    

    C++ signature :
        void retain_top(unsigned long,boost::shared_ptr<core::fragment::FragSet>)

steal_constant_length_frag_set_from_pose( (Pose)pose, (ConstantLengthFragSet)fragset) -> None :
    core/fragment/util.hh:55

    C++ signature :
        void steal_constant_length_frag_set_from_pose(core::pose::Pose,core::fragment::ConstantLengthFragSet {lvalue})

steal_frag_set_from_pose( (Pose)pose_in, (FragSet)fragset, (__CPP_FragData__)frag_type, (set_Size)active_residues) -> None :
    core/fragment/util.hh:76

    C++ signature :
        void steal_frag_set_from_pose(core::pose::Pose,core::fragment::FragSet {lvalue},boost::shared_ptr<core::fragment::FragData const>,std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> >)

steal_frag_set_from_pose( (Pose)pose_in, (int)begin, (int)end, (FragSet)fragset, (__CPP_FragData__)frag_type) -> None :
    core/fragment/util.hh:69

    C++ signature :
        void steal_frag_set_from_pose(core::pose::Pose,unsigned long,unsigned long,core::fragment::FragSet {lvalue},boost::shared_ptr<core::fragment::FragData const>)

steal_frag_set_from_pose( (Pose)pose_in, (FragSet)fragset, (__CPP_FragData__)frag_type) -> None :
    core/fragment/util.hh:61

    C++ signature :
        void steal_frag_set_from_pose(core::pose::Pose,core::fragment::FragSet {lvalue},boost::shared_ptr<core::fragment::FragData const>)

xform_pose( (Pose)pose, (Stub)s [, (int)sres=1 [, (int)eres=0]]) -> None :
    core/fragment/util.hh:48

    C++ signature :
        void xform_pose(core::pose::Pose {lvalue},core::kinematics::Stub [,unsigned long=1 [,unsigned long=0]])