Module _protocols_generalized_kinematic_closure_

copy_loop_pose_to_original( (Pose)original_pose, (Pose)loop_pose, (vector1_pair_Size_Size)residue_map, (vector1_pair_Size_Size)tail_residue_map) -> None :
    Copy the atom positions of the residues in the loop pose to the original pose.
    

    C++ signature :
        void copy_loop_pose_to_original(core::pose::Pose {lvalue},core::pose::Pose,utility::vector1<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >,utility::vector1<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >)

general_set_phi( (Pose)pose, (int)residue_index, (float)phi_value) -> None :
    Sets phi for an L-alpha amino acid, even if the nitrogen has a nonstandard connection.
    

    C++ signature :
        void general_set_phi(core::pose::Pose {lvalue},unsigned long,double)

general_set_psi( (Pose)pose, (int)residue_index, (float)psi_value) -> None :
    Sets psi for an L-alpha amino acid, even if the carbonyl carbon has a nonstandard connection.
    

    C++ signature :
        void general_set_psi(core::pose::Pose {lvalue},unsigned long,double)

get_original_pose_rsd( (int)perturbedloop_rsd, (vector1_pair_Size_Size)residue_map) -> int :
    Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >,
    and a residue index in the perturbed loop, return the corresponding residue index in the original pose.
    

    C++ signature :
        unsigned long get_original_pose_rsd(unsigned long,utility::vector1<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >)

is_in_list( (int)val, (vector1_Size)list) -> bool :
    Function to determine whether a value is in a list.
    

    C++ signature :
        bool is_in_list(unsigned long,utility::vector1<unsigned long, std::allocator<unsigned long> >)

original_pose_residue_is_in_residue_map( (int)residue_index, (vector1_pair_Size_Size)residue_map) -> bool :
    function to determine whether a residue index from the original pose is in the residue_map list.
    

    C++ signature :
        bool original_pose_residue_is_in_residue_map(unsigned long,utility::vector1<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >)

set_loop_pose( (Pose)pose, (object)atomlist, (vector1_Real)t_ang) -> None :
    Set the loop pose conformation based on a set of results from kinematic closure.
    This version ONLY sets mainchain torsions, and does no rebuilding of mainchain O or H atoms.
    [in,out] pose -- A pose consisting of the loop to be closed only.
    [in] atomlist -- A list of AtomIDs and corresponding xyz coordinates (though we don't use the latter) of the chain of atoms closed by KIC.  Note that the residue indices refer to the loop pose, not the original pose.
    [in] torsions -- The torsion angles values to set.
    

    C++ signature :
        void set_loop_pose(core::pose::Pose {lvalue},utility::vector1<std::pair<core::id::AtomID, numeric::xyzVector<double> >, std::allocator<std::pair<core::id::AtomID, numeric::xyzVector<double> > > >,utility::vector1<double, std::allocator<double> >)

set_loop_pose( (Pose)pose, (object)atomlist, (vector1_Real)t_ang, (vector1_Real)b_ang, (vector1_Real)b_len) -> None :
    Set the loop pose conformation based on a set of results from kinematic closure.
    [in,out] pose -- A pose consisting of the loop to be closed only.
    [in] atomlist -- A list of AtomIDs and corresponding xyz coordinates (though we don't use the latter) of the chain of atoms closed by KIC.  Note that the residue indices refer to the loop pose, not the original pose.
    [in] torsions -- The torsion angles values to set.
    [in] bondangles -- The bond angle values to set.
    [in] bondlengths -- The bond length values to set.
    

    C++ signature :
        void set_loop_pose(core::pose::Pose {lvalue},utility::vector1<std::pair<core::id::AtomID, numeric::xyzVector<double> >, std::allocator<std::pair<core::id::AtomID, numeric::xyzVector<double> > > >,utility::vector1<double, std::allocator<double> >,utility::vector1<double, std::allocator<double> >,utility::vector1<double, std::allocator<double> >)