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- g -
gap_distance() :
protocols::hybridization
gather_coords() :
protocols::comparative_modeling
gaussian_deriv() :
core::scoring::constraints
gaussian_jump_move() :
protocols::rigid
gdtha() :
core::scoring
gdtsc() :
core::scoring
generate_bb_coordinate_constraints() :
protocols::relax
generate_beta_database_test() :
protocols::swa::protein
generate_centroid_constraints() :
protocols::hybridization
generate_empty_jump_frame() :
protocols::jumping
generate_extended_pose() :
protocols::star
generate_fullatom_constraints() :
protocols::hybridization
generate_jump_frame() :
protocols::jumping
generate_relax_from_cmd() :
protocols::relax
generate_rigid_from_alignment() :
protocols::topology_broker
generate_taskfactory_and_add_task_awareness() :
protocols::protein_interface_design::movers
generate_unique_name() :
protocols::ligand_docking
generate_unique_structure_id() :
protocols::wum
GEOMETRIES() :
core::scoring::methods
get_2way_orientation() :
core::scoring
get_A() :
core::scoring::electron_density
get_abego() :
core::util
get_all_comments() :
core::pose
get_all_score_line_strings() :
core::pose
get_anchor_and_root_atoms() :
core::conformation
get_anchor_atomno() :
core::conformation
get_angles() :
core::scoring
get_asymm_unit_fold_tree() :
core::conformation::symmetry
get_asymmetric_pose_copy_from_symmetric_pose() :
core::pose::symmetry
get_atom_coordinates() :
protocols::swa::rna
get_base_centroid_and_rotation_matrix() :
protocols::swa
get_base_pair_params() :
core::scoring::dna
get_base_pair_params_old() :
core::scoring::dna
get_base_pair_stub() :
core::scoring::dna
get_base_pair_stub_slow() :
core::scoring::dna
get_base_pair_y_axis_atom_xyz() :
core::scoring::dna
get_base_pairing_info() :
protocols::rna
get_base_pairing_list() :
protocols::rna
get_base_pucker() :
core::scoring::dna
get_base_step_params() :
core::scoring::dna
get_base_stub() :
core::scoring::dna
get_batch_id() :
protocols::features
get_bbcsts() :
protocols::protein_interface_design
get_binary_rna_silent_struct_safe() :
protocols::swa::rna
get_binary_rna_silent_struct_safe_wrapper() :
protocols::swa::rna
get_bounds_intersection() :
protocols::sic_dock
get_branching_atoms2() :
protocols::branch_angle
get_burial_3() :
core::scoring::hbonds
get_C4_C3_distance_range() :
protocols::swa::rna
get_CA_vectors() :
core::scoring::dssp
,
protocols::jumping
get_CB_Vecs() :
protocols::sic_dock
get_cen_scorefxn() :
protocols::loops
get_chain2range() :
core::conformation::symmetry
get_chain_from_chain_id() :
core::pose
get_chain_from_jump_id() :
core::pose
get_chain_id_from_chain() :
core::pose
get_chain_id_from_jump_id() :
core::pose
get_chain_ids_from_chain() :
core::pose
get_chain_residues() :
core::pose
get_chemical_root_and_anchor_atomnos() :
core::conformation
get_chiral_residue_type() :
protocols::simple_moves::chiral
get_closest_residue_pair() :
protocols::seeded_abinitio
get_comment() :
core::pose
get_component_contiguous_foldtree() :
core::conformation::symmetry
get_component_lower_bound() :
core::pose::symmetry
get_component_of_residue() :
core::pose::symmetry
get_component_upper_bound() :
core::pose::symmetry
get_contact_features() :
protocols::simple_filters
get_coordinate_system() :
protocols::jumping
get_core() :
protocols::abinitio
get_cst_fa_file_option() :
core::scoring::constraints
get_cst_file_option() :
core::scoring::constraints
get_current_job() :
protocols::jd2
get_current_jobs_starting_pose() :
protocols::jd2
get_current_model_score() :
protocols::features
get_current_structure_count() :
protocols::features
get_DB_filter_ptr() :
protocols::features
get_default_allowed_bulge_res() :
protocols::swa::rna
get_delta_magnetic_anisotropy_deriv() :
core::scoring::rna::chemical_shift
get_density_map() :
core::scoring::electron_density_atomwise
get_DFIRE_potential() :
core::scoring::methods::dfire
get_distribution() :
protocols::ligand_docking
get_DNA_backbone_bin() :
core::scoring::dna
get_Dock_ScoreFxn() :
protocols::antibody2
get_edge_from_num() :
core::scoring::rna
get_environment_dependent_weight() :
core::scoring::hbonds
get_enzcst_io() :
protocols::enzdes::enzutil
get_enzdes_observer() :
protocols::toolbox::match_enzdes_util
Get_euler_angles() :
protocols::swa::rna
get_euler_angles() :
protocols::swa
Get_euler_stub_bin() :
protocols::swa::rna
get_fa_scorefxn() :
protocols::loops
get_fade_correction() :
core::scoring::rna
get_file_name() :
protocols::swa
get_filenames() :
protocols::motifs
get_final_rot_probs() :
protocols::MakeRotLib
get_final_rots() :
protocols::MakeRotLib
get_first_protein_residue() :
protocols::toolbox::match_enzdes_util
get_foldtree_seqsep() :
protocols::fldsgn::potentials::sspot
get_full_edge_from_num() :
core::scoring::rna
get_full_LW_orientation_from_num() :
core::scoring::rna
get_full_orientation_from_num() :
core::scoring::rna
get_gdtmm() :
protocols::hybridization
get_hash_excluding_chain() :
core::pose
get_hash_from_chain() :
core::pose
get_hb_acc_chem_type() :
core::scoring::hbonds
get_hb_don_chem_type() :
core::scoring::hbonds
get_hbe_acc_hybrid() :
core::scoring::hbonds
get_hbond_energies() :
core::scoring::hbonds
get_hbond_weight_type() :
core::scoring::hbonds
get_highest_score_from_job_data_statement() :
protocols::features
get_highest_score_from_score_data_statement() :
protocols::features
get_incomplete_connections() :
protocols::ligand_docking
get_joint_id() :
core::scoring::methods::dfire
get_jump_id_from_chain() :
core::pose
get_jump_id_from_chain_id() :
core::pose
get_jump_ids_from_chain() :
core::pose
get_jump_ids_from_chain_ids() :
core::pose
get_jump_name_to_components() :
core::pose::symmetry
get_jump_name_to_subunits() :
core::pose::symmetry
get_K_cluster_engine() :
protocols::toolbox
get_km() :
core::scoring::electron_density
get_last_protein_residue() :
protocols::toolbox::match_enzdes_util
get_leap_6dof() :
protocols::sic_dock
get_leap_lower_stub() :
protocols::sic_dock
get_leap_upper_stub() :
protocols::sic_dock
get_ligand_seqpos() :
protocols::ligand_docking
get_ligand_torsion_constraints() :
protocols::ligand_docking
get_LigandMotifLibrary_user() :
protocols::motifs
get_line() :
core::scoring::electron_density::SplineInterp
get_LoopCentral_ScoreFxn() :
protocols::antibody2
get_LoopHighRes_ScoreFxn() :
protocols::antibody2
get_masks() :
core::scoring
get_max_centroid_to_atom_distance() :
protocols::swa::rna
get_max_seq_num_from_res_map() :
protocols::swa::rna
get_maximum_scores() :
core::sequence
get_membrane_depth_dependent_weight() :
core::scoring::hbonds
get_midstep_stub() :
core::scoring::dna
get_mindis_with_plane_hashes() :
protocols::sic_dock
get_motif_build_position_defs_user() :
protocols::motifs
get_motif_build_positions_user() :
protocols::motifs
get_MotifLibrary_user() :
protocols::motifs
get_moving_residue_case() :
protocols::swa::monte_carlo
get_ncac() :
protocols::jumping
get_nearest_neighbor() :
core::conformation
get_nth_lowest_score_from_job_data_statement() :
protocols::features
get_nth_lowest_score_from_score_data_statement() :
protocols::features
get_num_bytes() :
core::scoring
get_num_residues_nonvirt() :
protocols::hybridization
Get_num_side_chain_atom_from_res_name() :
protocols::swa::rna
get_number_base_stacks() :
protocols::rna
get_o1p_o2p_sign() :
protocols::rna
Get_one_letter_name() :
protocols::swa::rna
get_orientation() :
core::scoring
,
core::scoring::packstat::old
get_orientation_from_num() :
core::scoring::rna
get_out_tag() :
protocols::vip
get_output_tag() :
protocols::jobdist
get_overlap() :
core::scoring::packstat::old
,
core::scoring
get_overlap_pos() :
protocols::loops::loop_closure::ccd
get_Pack_ScoreFxn() :
protocols::antibody2
get_pairing_geometry() :
core::scoring::dssp
,
protocols::jumping
get_parallel_h_for_arg() :
core::scoring::methods
get_pdb_code_from_pose_tag() :
protocols::enzdes::enzutil
get_per_residue_score() :
protocols::nonlocal
get_per_residue_scores() :
protocols::relax
get_pleating() :
core::scoring::dssp
,
protocols::jumping
get_position_in_vector() :
core::scoring::carbon_hbonds
,
core::scoring::rna
get_potential_add_residues() :
protocols::swa::monte_carlo
get_potential_delete_residues() :
protocols::swa::monte_carlo
get_pretend_phi_explicit() :
protocols::swa::protein
get_pretend_psi_explicit() :
protocols::swa::protein
get_protocol_and_batch_id() :
protocols::features
get_random_residue_at_chain_terminus() :
protocols::swa::monte_carlo
get_rb_atr_and_rep_scores() :
protocols::ligand_docking
get_rb_number() :
core::id
get_rb_type() :
core::id
get_res_aa_from_BASE_name() :
core::scoring::rna::chemical_shift
Get_residue_base_state() :
protocols::swa::rna
get_residue_connections() :
core::conformation
get_residue_current_energy() :
core::pack
Get_residue_from_seq_num() :
protocols::swa::rna
Get_residue_list_from_fasta() :
protocols::swa::rna
get_residue_path_distances() :
core::chemical
Get_residue_pucker_state() :
protocols::swa::rna
get_residue_weight_by_ss() :
core::scoring::methods
get_resnum() :
core::pose
get_resnum_from_cstid() :
protocols::enzdes::enzutil
get_resnum_from_cstid_list() :
protocols::enzdes::enzutil
get_resnum_list() :
core::pose
get_resnum_list_ordered() :
core::pose
get_restag() :
core::scoring::methods
get_rho_and_z() :
core::scoring::rna::chemical_shift
Get_ribose_stub() :
protocols::swa::rna
get_rigid_body_jumps() :
protocols::rna
get_ring_current_deriv() :
core::scoring::rna::chemical_shift
get_ring_current_term_derivatives() :
core::scoring::rna::chemical_shift
get_rmsd() :
protocols::loophash
get_rna_base_centroid() :
core::scoring::rna
get_rna_base_coordinate_system() :
core::scoring::rna
get_rna_base_coordinate_system_from_CS_params() :
core::scoring::rna::chemical_shift
get_rna_secstruct() :
protocols::rna
get_root_atomno() :
core::conformation
get_root_residue_root_atomno() :
core::conformation
get_rosetta_hatom_name() :
core::scoring::rna::chemical_shift
get_rotamer_angle() :
protocols::swa::protein
get_rt_over_leap() :
protocols::loophash
get_rt_over_leap_fast() :
protocols::loophash
get_rt_over_leap_without_foldtree_bs() :
protocols::loophash
get_sasa_dot_locations() :
core::scoring::packstat
get_score_for_struct_id_and_score_term_from_job_data() :
protocols::features
get_score_for_struct_id_and_score_term_from_score_data() :
protocols::features
get_score_line_string() :
core::pose
get_score_map() :
protocols::jobdist
get_score_type_id_from_score_term() :
protocols::features
get_scratch_atom_id() :
core::pose
get_section_name() :
core::scoring::constraints
get_seq_sep() :
core::scoring::hbonds
get_set_from_datamap() :
protocols::moves
get_sha1_hash_excluding_chain() :
core::pose
get_something_from_database() :
protocols::features
get_specific_atom_coordinate() :
protocols::swa::rna
get_struct_id_with_highest_score_from_job_data() :
protocols::features
get_struct_id_with_highest_score_from_score_data() :
protocols::features
get_struct_id_with_lowest_score_from_job_data() :
protocols::features
get_struct_id_with_lowest_score_from_score_data() :
protocols::features
get_struct_id_with_nth_lowest_score_from_job_data() :
protocols::features
get_struct_id_with_nth_lowest_score_from_score_data() :
protocols::features
get_structure_count_statement() :
protocols::features
get_stub_stub_params() :
core::scoring::dna
get_subunit_name_to_component() :
core::pose::symmetry
get_sugar_centroid() :
protocols::rna
get_superposition_transformation() :
protocols::hybridization
get_surf_tot() :
core::scoring::packing
get_surf_vol() :
core::scoring::packing
get_surf_vol_deriv() :
core::scoring::packing
get_surrounding_O2star_hydrogen() :
protocols::swa::rna
get_sym_aware_jump_num() :
core::pose::symmetry
get_symdof_subunits() :
core::pose::symmetry
get_symm_axis() :
core::pose::symmetry
get_tag_from_pdb_filename() :
protocols::swa::rna
get_target_position_map_make_dna_mutations() :
protocols::motifs
get_target_positions_make_dna_mutations() :
protocols::motifs
get_targetconformers_user() :
protocols::motifs
get_task_operations() :
protocols::rosetta_scripts
get_tenA_neighbor_residues() :
protocols::loops
get_termini_from_pose() :
protocols::sic_dock
Get_three_letter_name() :
protocols::swa::rna
get_time() :
protocols::wum
get_token() :
core::pack::task
get_torsion_axis() :
protocols::loops::loop_closure::ccd
get_torsion_bin() :
core::conformation
get_total_energy_for_state() :
core::pack
get_watson_crick_base_pair_atoms() :
core::scoring::rna
get_write_delete_pair() :
protocols::features
get_xform_stats() :
protocols::sic_dock
get_y_axis() :
core::scoring::dna
get_y_axis_atoms() :
core::scoring::dna
get_z_axis() :
core::scoring::dna
getAVG() :
protocols::sparta
getDensityMap() :
core::scoring::electron_density
getDensityMap_legacy() :
core::scoring::electron_density
getDiff() :
protocols::sparta
getPoseExtraScores() :
core::pose
getRG() :
protocols::moves
getRMS() :
protocols::sparta
getScoreFunction() :
core::scoring
getScoreFunctionName() :
core::scoring
getSTD() :
protocols::sparta
getxform() :
core::fragment
global_loop_rmsd() :
protocols::antibody2
glu_corrections() :
protocols::MakeRotLib
grad3() :
core::scoring::electron_density::SplineInterp
graphics_main() :
protocols::star
,
protocols::medal
grid_rotamer_trials() :
protocols::ligand_docking
grid_rotamer_trials_atr_rep() :
protocols::ligand_docking
grid_score() :
protocols::ligand_docking
grid_score_atr_rep() :
protocols::ligand_docking
grid_to_kin() :
protocols::ligand_docking
GridBaseTracer() :
protocols::qsar::scoring_grid
GridManagerTracer() :
protocols::qsar::scoring_grid
grow() :
protocols::ligand_docking
grow_left_r() :
protocols::forge::methods
grow_left_rtype() :
protocols::forge::methods
grow_ligand_tracer() :
protocols::ligand_docking
grow_right_r() :
protocols::forge::methods
grow_right_rtype() :
protocols::forge::methods
guess_rbsegs_from_pose() :
protocols::rbsegment_relax
guess_torsion_type_of_dof_id() :
core::conformation::symmetry
gzip() :
core::io::silent
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