Module _protocols_stepwise_setup_

add_cutpoint_closed( (Pose)pose, (vector1_Size)res_list, (vector1_Size)cutpoint_closed) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:144

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

add_virtual_sugar_res( (Pose)pose, (vector1_Size)res_list, (vector1_Size)virtual_sugar_res) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:152

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

check_extra_minimize_res_are_input( (vector1_Size)extra_minimize_res, (vector1_Size)input_domain_map) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:187

    C++ signature :
        void check_extra_minimize_res_are_input(utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >)

check_working_res( (vector1_Size)working_res, (vector1_Size)input_domain_map, (vector1_Size)sample_res) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:165

    C++ signature :
        void check_working_res(utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >)

cleanup( (Pose)pose) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:60

    C++ signature :
        void cleanup(core::pose::Pose {lvalue})

define_chains( (Pose)pose, (vec1_vec1_Size)all_res_in_chain, (vec1_vec1_Size)all_fixed_res_in_chain, (vector1_Size)res_list, (vector1_Size)extra_min_res) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:101

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

figure_out_dock_domain_map( (vector1_Size)cutpoint_open_in_full_model, (vec1_vec1_Size)pose_res_lists, (vector1_Size)working_res, (vector1_Size)sample_res, (int)nres) -> vector1_Size :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:198

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > figure_out_dock_domain_map(utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<utility::vector1<unsigned long, std::allocator<unsigned long> >, std::allocator<utility::vector1<unsigned long, std::allocator<unsigned long> > > >,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,unsigned long)

figure_out_fixed_domain_map( (vector1_Size)input_domain_map, (vector1_Size)extra_minimize_res) -> vector1_Size :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:191

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

figure_out_motif_mode( (vector1_Size)extra_min_res, (vector1_Size)terminal_res, (vector1_Size)working_res, (vector1_Size)input_domain_map, (vector1_Size)cutpoint_open_in_full_model) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:176

    C++ signature :
        void figure_out_motif_mode(utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >)

figure_out_sample_res( (vector1_Size)input_domain_map, (vector1_Size)working_res) -> vector1_Size :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:160

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

figure_out_working_res( (vector1_Size)input_domain_map, (vector1_Size)sample_res) -> vector1_Size :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:156

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

fill_full_model_info_from_command_line( (object)pose_pointers) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:72

    C++ signature :
        void fill_full_model_info_from_command_line(utility::vector1<core::pose::Pose*, std::allocator<core::pose::Pose*> > {lvalue})

fill_full_model_info_from_command_line( (Pose)pose, (vector1_PoseOP)other_pose_ops) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:69

    C++ signature :
        void fill_full_model_info_from_command_line(core::pose::Pose {lvalue},utility::vector1<boost::shared_ptr<core::pose::Pose>, std::allocator<boost::shared_ptr<core::pose::Pose> > > {lvalue})

fill_full_model_info_from_command_line( (vector1_PoseOP)pose_ops) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:66

    C++ signature :
        void fill_full_model_info_from_command_line(utility::vector1<boost::shared_ptr<core::pose::Pose>, std::allocator<boost::shared_ptr<core::pose::Pose> > > {lvalue})

fill_full_model_info_from_command_line( (Pose)pose) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:63

    C++ signature :
        void fill_full_model_info_from_command_line(core::pose::Pose {lvalue})

get_chain( (int)i, (vec1_vec1_Size)all_res_in_chain) -> int :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:112

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

get_other_poses( (vector1_PoseOP)other_poses, (vector1_string)other_files, (ResidueTypeSetCAP)rsd_set) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:48

    C++ signature :
        void get_other_poses(utility::vector1<boost::shared_ptr<core::pose::Pose>, std::allocator<boost::shared_ptr<core::pose::Pose> > > {lvalue},utility::vector1<std::string, std::allocator<std::string> >,boost::weak_ptr<core::chemical::ResidueTypeSet const>)

get_pdb_and_cleanup( (str)input_file, (ResidueTypeSetCAP)rsd_set) -> Pose :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:40

    C++ signature :
        boost::shared_ptr<core::pose::Pose> get_pdb_and_cleanup(std::string,boost::weak_ptr<core::chemical::ResidueTypeSet const>)

get_pdb_with_full_model_info( (str)input_file, (ResidueTypeSetCAP)rsd_set) -> Pose :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:36

    C++ signature :
        boost::shared_ptr<core::pose::Pose> get_pdb_with_full_model_info(std::string,boost::weak_ptr<core::chemical::ResidueTypeSet const>)

get_tree( (int)nres, (vector1_Size)cuts, (vector1_Size)jump_partners1, (vector1_Size)jump_partners2, (vector1_string)jump_atoms1, (vector1_string)jump_atoms2) -> FoldTree :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:134

    C++ signature :
        core::kinematics::FoldTree get_tree(unsigned long,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<std::string, std::allocator<std::string> >,utility::vector1<std::string, std::allocator<std::string> >)

get_tree( (Pose)pose, (vector1_Size)cuts, (vector1_Size)jump_partners1, (vector1_Size)jump_partners2) -> FoldTree :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:126

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

initialize_native_and_align_pose( (Pose)native_pose, (Pose)align_pose, (ResidueTypeSetCAP)rsd_set, (Pose)start_pose) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:54

    C++ signature :
        void initialize_native_and_align_pose(boost::shared_ptr<core::pose::Pose> {lvalue},boost::shared_ptr<core::pose::Pose> {lvalue},boost::weak_ptr<core::chemical::ResidueTypeSet const>,boost::shared_ptr<core::pose::Pose const>)

initialize_pose_and_other_poses_from_command_line( (ResidueTypeSetCAP)rsd_set) -> Pose :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:57

    C++ signature :
        boost::shared_ptr<core::pose::Pose> initialize_pose_and_other_poses_from_command_line(boost::weak_ptr<core::chemical::ResidueTypeSet const>)

just_modeling_RNA( (vector1_string)fasta_files) -> bool :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:203

    C++ signature :
        bool just_modeling_RNA(utility::vector1<std::string, std::allocator<std::string> >)

looks_like_reference_pose( (vector1_Size)input_domain_map) -> bool :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:179

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

parse_out_non_standard_residues( (str)sequence) -> map_Size_string :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:43

    C++ signature :
        std::map<unsigned long, std::string, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, std::string> > > parse_out_non_standard_residues(std::string {lvalue})

put_in_cutpoint( (Pose)pose, (int)i) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:147

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

reorder_pose( (Pose)pose, (vector1_Size)res_list) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:200

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

setup_fold_trees( (object)pose_pointers, (vector1_Size)cutpoint_open_in_full_model, (vector1_Size)fixed_domain_map, (vector1_Size)cutpoint_closed, (vector1_Size)extra_minimize_res, (vector1_Size)extra_minimize_jump_res, (vector1_Size)sample_res, (vector1_Size)working_res, (vector1_Size)jump_res, (vector1_Size)preferred_root_res, (vector1_Size)virtual_sugar_res, (FullModelParameters)full_model_parameters, (vec1_vec1_Size)pose_res_lists) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:87

    C++ signature :
        void setup_fold_trees(utility::vector1<core::pose::Pose*, std::allocator<core::pose::Pose*> > {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,utility::vector1<unsigned long, std::allocator<unsigned long> >,core::pose::full_model_info::FullModelParameters,utility::vector1<utility::vector1<unsigned long, std::allocator<unsigned long> >, std::allocator<utility::vector1<unsigned long, std::allocator<unsigned long> > > >)

setup_jumps( (Pose)pose, (vector1_Size)jump_partners1, (vector1_Size)jump_partners2, (vector1_pair_Size_Size)chain_connections, (vec1_vec1_Size)all_res_in_chain, (object)resnum_and_chain_in_pose) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:120

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

setup_user_defined_jumps( (vector1_Size)jump_res, (vector1_Size)jump_partners1, (vector1_Size)jump_partners2, (vector1_pair_Size_Size)chain_connections, (vector1_Size)res_list, (vec1_vec1_Size)all_res_in_chain) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:109

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

update_fixed_domain_from_extra_minimize_jump_res( (vector1_Size)fixed_domain, (Pose)pose, (vector1_Size)res_list, (vector1_Size)extra_minimize_jump_res) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:140

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

update_jump_res( (vector1_Size)jump_res, (vector1_Size)extra_minimize_jump_res) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:183

    C++ signature :
        void update_jump_res(utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> >)

update_pose_fold_tree( (Pose)pose, (vector1_Size)res_list, (vector1_Size)extra_min_res, (vector1_Size)sample_res, (vector1_Size)jump_res, (FullModelParameters)full_model_parameters) -> None :
    protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh:94

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