Module _protocols_stepwise_modeler_rna_sugar_

convert_sugar_modeling_to_residue_alternative_set( (SugarModeling)sugar_modeling) -> object :
    protocols/stepwise/modeler/rna/sugar/util.hh:101

    C++ signature :
        boost::shared_ptr<protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet> convert_sugar_modeling_to_residue_alternative_set(protocols::stepwise::modeler::rna::sugar::SugarModeling)

copy_bulge_res_and_sugar_torsion( (SugarModeling)sugar_modeling, (Pose)pose, (Pose)template_pose [, (bool)instantiate_sugar=False]) -> None :
    protocols/stepwise/modeler/rna/sugar/util.hh:55

    C++ signature :
        void copy_bulge_res_and_sugar_torsion(protocols::stepwise::modeler::rna::sugar::SugarModeling,core::pose::Pose {lvalue},core::pose::Pose [,bool=False])

detect_sugar_contacts( (Pose)pose, (int)moving_res [, (float)o2prime_contact_distance_cutoff_=3.2]) -> bool :
    protocols/stepwise/modeler/rna/sugar/util.hh:114

    C++ signature :
        bool detect_sugar_contacts(core::pose::Pose,unsigned long [,double=3.2])

detect_sugar_contacts( (Pose)pose) -> vector1_bool :
    protocols/stepwise/modeler/rna/sugar/util.hh:110

    C++ signature :
        utility::vector1<bool, std::allocator<bool> > detect_sugar_contacts(core::pose::Pose)

get_possible_reference_res_list_from_pose_without_fold_tree( (int)virtual_sugar_res, (Pose)pose, (int)moving_suite) -> vector1_Size :
    protocols/stepwise/modeler/rna/sugar/util.hh:75

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > get_possible_reference_res_list_from_pose_without_fold_tree(unsigned long,core::pose::Pose,unsigned long)

get_reference_res_for_each_virtual_sugar_based_on_fold_tree( (Pose)pose) -> map_Size_Size :
    protocols/stepwise/modeler/rna/sugar/util.hh:67

    C++ signature :
        std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > > get_reference_res_for_each_virtual_sugar_based_on_fold_tree(core::pose::Pose)

get_reference_res_for_each_virtual_sugar_without_fold_tree( (Pose)pose, (int)moving_suite) -> map_Size_Size :
    protocols/stepwise/modeler/rna/sugar/util.hh:64

    C++ signature :
        std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > > get_reference_res_for_each_virtual_sugar_without_fold_tree(core::pose::Pose,unsigned long)

get_reference_res_for_virtual_sugar_based_on_fold_tree( (Pose)pose, (int)n) -> int :
    protocols/stepwise/modeler/rna/sugar/util.hh:70

    C++ signature :
        unsigned long get_reference_res_for_virtual_sugar_based_on_fold_tree(core::pose::Pose,unsigned long)

instantiate_any_virtual_sugars( (Pose)pose, (object)working_parameters, (__CPP_ScoreFunction__)scorefxn, (object)options) -> VirtualSugarJustInTimeInstantiator :
    protocols/stepwise/modeler/rna/sugar/util.hh:107

    C++ signature :
        boost::shared_ptr<protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator> instantiate_any_virtual_sugars(core::pose::Pose {lvalue},boost::shared_ptr<protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters const>,boost::shared_ptr<core::scoring::ScoreFunction const>,boost::shared_ptr<protocols::stepwise::modeler::options::StepWiseModelerOptions const>)

is_sugar_virtual( (Pose)pose, (int)previous_moving_res, (int)previous_bulge_res) -> bool :
    protocols/stepwise/modeler/rna/sugar/util.hh:51

    C++ signature :
        bool is_sugar_virtual(core::pose::Pose,unsigned long,unsigned long)

is_sugar_virtual( (Pose)pose, (int)sugar_res, (int)bulge_res, (vector1_Size)bulge_residues_to_virtualize) -> bool :
    protocols/stepwise/modeler/rna/sugar/util.hh:48

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

look_for_jumps( (int)n, (Pose)pose, (bool)force_upstream) -> int :
    protocols/stepwise/modeler/rna/sugar/util.hh:79

    C++ signature :
        unsigned long look_for_jumps(unsigned long,core::pose::Pose,bool)

look_for_jumps_to_next( (int)virtual_sugar_res, (Pose)pose, (bool)force_upstream) -> int :
    protocols/stepwise/modeler/rna/sugar/util.hh:89

    C++ signature :
        unsigned long look_for_jumps_to_next(unsigned long,core::pose::Pose,bool)

look_for_jumps_to_previous( (int)virtual_sugar_res, (Pose)pose, (bool)force_upstream) -> int :
    protocols/stepwise/modeler/rna/sugar/util.hh:84

    C++ signature :
        unsigned long look_for_jumps_to_previous(unsigned long,core::pose::Pose,bool)

look_for_non_jump_reference_to_next( (int)virtual_sugar_res, (Pose)pose, (int)moving_suite) -> int :
    protocols/stepwise/modeler/rna/sugar/util.hh:99

    C++ signature :
        unsigned long look_for_non_jump_reference_to_next(unsigned long,core::pose::Pose,unsigned long)

look_for_non_jump_reference_to_previous( (int)virtual_sugar_res, (Pose)pose, (int)moving_suite) -> int :
    protocols/stepwise/modeler/rna/sugar/util.hh:94

    C++ signature :
        unsigned long look_for_non_jump_reference_to_previous(unsigned long,core::pose::Pose,unsigned long)

minimize_all_sampled_floating_bases( (Pose)viewer_pose, (object)modeling_list, (vector1_PoseOP)pose_data_list, (__CPP_ScoreFunction__)modeler_scorefxn, (object)working_parameters [, (bool)virtual_sugar_is_from_prior_step=True]) -> None :
    protocols/stepwise/modeler/rna/sugar/util.hh:44

    C++ signature :
        void minimize_all_sampled_floating_bases(core::pose::Pose {lvalue},utility::vector1<protocols::stepwise::modeler::rna::sugar::SugarModeling, std::allocator<protocols::stepwise::modeler::rna::sugar::SugarModeling> >,utility::vector1<boost::shared_ptr<core::pose::Pose>, std::allocator<boost::shared_ptr<core::pose::Pose> > > {lvalue},boost::shared_ptr<core::scoring::ScoreFunction const>,boost::shared_ptr<protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters const> [,bool=True])

modeler_starting_pose_data_list( (vector1_PoseOP)starting_pose_data_list, (object)SugarModeling_list, (Pose)pose) -> None :
    protocols/stepwise/modeler/rna/sugar/util.hh:60

    C++ signature :
        void modeler_starting_pose_data_list(utility::vector1<boost::shared_ptr<core::pose::Pose>, std::allocator<boost::shared_ptr<core::pose::Pose> > > {lvalue},utility::vector1<protocols::stepwise::modeler::rna::sugar::SugarModeling, std::allocator<protocols::stepwise::modeler::rna::sugar::SugarModeling> >,core::pose::Pose)