Index

A

add_all_virtual_residues() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) add_bulge_coords_from_stems() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) add_cg() (forgi.threedee.visual.pymol.PymolPrinter method) add_cone() (forgi.threedee.visual.pymol.PyMolRNA method) add_dashed() (forgi.threedee.visual.pymol.PyMolRNA method) add_encompassing_cylinders() (forgi.threedee.visual.pymol.PymolPrinter method) add_info() (forgi.graph.bulge_graph.BulgeGraph method) add_longrange_interactions() (in module forgi.threedee.model.coarse_grain) add_loop_information_from_pdb_chains() (in module forgi.threedee.utilities.graph_pdb) add_segment() (forgi.threedee.visual.pymol.PyMolRNA method) add_sphere() (forgi.threedee.visual.pymol.PyMolRNA method) add_stem_information_from_pdb_chains() (in module forgi.threedee.utilities.graph_pdb) add_stem_like() (forgi.threedee.visual.pymol.PymolPrinter method) add_stem_like_core() (forgi.threedee.visual.pymol.PymolPrinter method) add_virtual_residues() (in module forgi.threedee.utilities.graph_pdb)

AdjacencyCorrelation (class in forgi.threedee.model.similarity) adjacent_stem_pairs_iterator() (forgi.graph.bulge_graph.BulgeGraph method) after_coordinates_changed() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) all_interactions() (in module forgi.threedee.classification.aminor) AMinorClassifier (class in forgi.threedee.classification.aminor) angle_stats (forgi.threedee.model.stats.ConstructionStats attribute) AngleStat (class in forgi.threedee.model.stats) ANGLEWEIGHT (in module forgi.threedee.classification.aminor) anisotropy() (in module forgi.threedee.model.descriptors) annotate_fallback() (in module forgi.threedee.utilities.pdb) AnnotationToolNotInstalled are_adjacent_stems() (forgi.graph.bulge_graph.BulgeGraph method) asphericity() (in module forgi.threedee.model.descriptors) atan3() (in module forgi.threedee.utilities.my_math) AtomName (class in forgi.threedee.utilities.pdb)

B

backbone_breaks_after (forgi.graph.bulge_graph.BulgeGraph attribute) (forgi.graph.sequence.Sequence attribute) base_normals() (in module forgi.threedee.utilities.graph_pdb) bases (forgi.threedee.model.coarse_grain.CoarseGrainRNA attribute) BGTransformer (class in forgi.graph.transform_graphs) bounding_boxes() (in module forgi.threedee.utilities.graph_pdb)

bpseq_to_tuples_and_seq() (in module forgi.utilities.stuff) breakpoints_from_seqids() (in module forgi.threedee.model.coarse_grain) bresenham() (in module forgi.projection.projection2d) bt() (in module forgi.utilities.debug) buildorder_of() (forgi.graph.bulge_graph.BulgeGraph method) BulgeGraph (class in forgi.graph.bulge_graph)

C

calc_R() (in module forgi.threedee.utilities.graph_pdb) center() (forgi.threedee.model.linecloud.LineSegmentStorage method) center_on_centroid() (in module forgi.threedee.utilities.vector) cg_rmsd() (in module forgi.threedee.model.similarity) CgConstructionError CgIntegrityError cgs_from_args() (in module forgi.utilities.commandline_utils) CGTransformer (class in forgi.threedee.model.transform_cg) change_basis() (in module forgi.threedee.utilities.vector) change_basis_vectorized() (in module forgi.threedee.utilities.vector) change_residue_id() (in module forgi.threedee.utilities.modified_res) circle_error() (in module forgi.threedee.utilities.graph_pdb) circle_fit() (in module forgi.threedee.utilities.graph_pdb) circles() (in module forgi.visual.mplotlib) classify_interaction() (in module forgi.threedee.classification.aminor) clean_chain() (in module forgi.threedee.utilities.pdb) clean_failed() (forgi.threedee.utilities.modified_res.ModifiedResidueLookup method) clear() (forgi.utilities.observedDict.observedDict method) clock_angle() (in module forgi.threedee.utilities.my_math) closest_point_on_seg() (in module forgi.threedee.utilities.vector) cluster_of() (forgi.threedee.model.stats.ClusteredAngleStats method) ClusteredAngleStats (class in forgi.threedee.model.stats) CoarseGrainRNA (class in forgi.threedee.model.coarse_grain) condense() (forgi.projection.projection2d.Projection2D method) condense_points() (forgi.projection.projection2d.Projection2D method)

condensed() (forgi.graph.transform_graphs.BGTransformer method) (forgi.threedee.model.transform_cg.CGTransformer method) (forgi.utilities.numbered_dotbracket.NumberedDotbracket method) conf_stats (forgi.threedee.model.stats.ConstructionStats attribute) ConformationStats (class in forgi.threedee.model.stats) connected() (forgi.graph.bulge_graph.BulgeGraph method) connected_stem_iterator() (forgi.graph.bulge_graph.BulgeGraph method) connection_ends() (forgi.graph.bulge_graph.BulgeGraph method) connection_type() (forgi.graph.bulge_graph.BulgeGraph method) constrain_stats() (forgi.threedee.model.stats.ConformationStats method) ConstructionStats (class in forgi.threedee.model.stats) consume_fields() (forgi.graph.sequence.SequenceLoader method) contains_rna() (in module forgi.threedee.utilities.pdb) CoordinateStorage (class in forgi.threedee.model.linecloud) coords (forgi.threedee.model.coarse_grain.CoarseGrainRNA attribute) coords_from_directions() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) coords_to_directions() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) count() (forgi.utilities.numbered_dotbracket.NumberedDotbracket method) create_fornac_page_for_structure() (in module forgi.visual.fornac) create_orthonormal_basis() (in module forgi.threedee.utilities.vector) create_random_function() (forgi.threedee.model.stats.RandomAngleStats method) crop_coordinates_to_bounds() (in module forgi.projection.projection2d) crossingPoints (forgi.projection.projection2d.Projection2D attribute) cylinder_line_intersection() (in module forgi.threedee.utilities.vector) cylinder_works() (in module forgi.threedee.utilities.graph_pdb)

D

data_file() (in module forgi) (in module forgi.threedee) define_a() (forgi.graph.bulge_graph.BulgeGraph method) define_length() (forgi.graph.sequence.Sequence method) define_residue_num_iterator() (forgi.graph.bulge_graph.BulgeGraph method) defines (forgi.graph.bulge_graph.BulgeGraph attribute) delete_from_stack() (in module forgi.utilities.stuff) describe_multiloop() (forgi.graph.bulge_graph.BulgeGraph method)

det3x3() (in module forgi.threedee.utilities.vector) deviation_from() (forgi.threedee.model.stats.AngleStat method) df_to_data_labels() (in module forgi.threedee.classification.aminor) diameter() (in module forgi.projection.projection2d) dict_from_pdbs() (in module forgi.threedee.utilities.modified_res) dotbracket_to_pairtable() (in module forgi.utilities.stuff) draw_bounding_boxes() (forgi.threedee.visual.pymol.PymolPrinter method) drmsd() (in module forgi.threedee.model.similarity)

E

element_coord_system() (in module forgi.threedee.utilities.graph_pdb) element_distance() (in module forgi.threedee.utilities.graph_pdb) element_length() (forgi.graph.bulge_graph.BulgeGraph method) element_physical_distance() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) element_to_nucleotide_colors() (in module forgi.visual.fornac) elements_closer_than() (forgi.threedee.model.linecloud.LineSegmentStorage method) (in module forgi.threedee.utilities.vector)

elements_to_nucleotides() (forgi.graph.bulge_graph.BulgeGraph method) enumerate_interactions_kdtree() (in module forgi.threedee.utilities.pdb) evaluate() (forgi.threedee.model.similarity.AdjacencyCorrelation method) extract_define_residues() (in module forgi.threedee.utilities.graph_pdb) extract_subchains_from_seq_ids() (in module forgi.threedee.utilities.pdb)

F

f_2() (in module forgi.threedee.utilities.graph_pdb) f_3() (in module forgi.threedee.utilities.graph_pdb) FilteredConformationStats (class in forgi.threedee.model.stats) find_bulge_loop() (forgi.graph.bulge_graph.BulgeGraph method) find_mlonly_multiloops() (forgi.graph.bulge_graph.BulgeGraph method) fit() (forgi.threedee.classification.aminor.AMinorClassifier method) fit_circle() (in module forgi.threedee.utilities.graph_pdb) fiveprime_stats (forgi.threedee.model.stats.ConstructionStats attribute) flanking_nuc_at_stem_side() (forgi.graph.bulge_graph.BulgeGraph method) floop_iterator() (forgi.graph.bulge_graph.BulgeGraph method) forgi (module) forgi.config (module) forgi.graph (module) forgi.graph.bulge_graph (module) forgi.graph.residue (module) forgi.graph.sequence (module) forgi.graph.transform_graphs (module) forgi.projection (module) forgi.projection.hausdorff (module) forgi.projection.projection2d (module) forgi.threedee (module) forgi.threedee.classification (module) forgi.threedee.classification.aminor (module) forgi.threedee.model (module) forgi.threedee.model.coarse_grain (module) forgi.threedee.model.descriptors (module) forgi.threedee.model.linecloud (module) forgi.threedee.model.similarity (module) forgi.threedee.model.stats (module) forgi.threedee.model.transform_cg (module) forgi.threedee.utilities (module) forgi.threedee.utilities.graph_pdb (module)

forgi.threedee.utilities.mcannotate (module) forgi.threedee.utilities.modified_res (module) forgi.threedee.utilities.modified_res_lookup (module) forgi.threedee.utilities.my_math (module) forgi.threedee.utilities.pdb (module) forgi.threedee.utilities.vector (module) forgi.threedee.utilities.virtual_residues (module) forgi.threedee.visual (module) forgi.threedee.visual.pymol (module) forgi.utilities (module) forgi.utilities.commandline_utils (module) forgi.utilities.debug (module) forgi.utilities.exceptions (module) forgi.utilities.graph (module) forgi.utilities.numbered_dotbracket (module) forgi.utilities.observedDict (module) forgi.utilities.stuff (module) forgi.visual (module) forgi.visual.fornac (module) forgi.visual.mplotlib (module) format_resid() (in module forgi.threedee.utilities.mcannotate) from_bg_fields() (forgi.graph.sequence.MissingResidue class method) from_bg_file() (forgi.graph.bulge_graph.BulgeGraph class method) from_bg_string() (forgi.graph.bulge_graph.BulgeGraph class method) (forgi.threedee.model.coarse_grain.CoarseGrainRNA class method) from_bpseq_str() (forgi.graph.bulge_graph.BulgeGraph class method) from_ct_string() (forgi.graph.bulge_graph.BulgeGraph class method) from_dotbracket() (forgi.graph.bulge_graph.BulgeGraph class method) from_fasta() (forgi.graph.bulge_graph.BulgeGraph class method) from_fasta_text() (forgi.graph.bulge_graph.BulgeGraph class method) from_file() (forgi.threedee.model.stats.FilteredConformationStats method) from_pdb() (forgi.threedee.model.coarse_grain.CoarseGrainRNA class method)

G

gen_random_sequence() (in module forgi.utilities.stuff) get_alignment_matrix() (in module forgi.threedee.utilities.vector) get_all_chains() (in module forgi.threedee.utilities.pdb) get_angle() (forgi.threedee.model.stats.AngleStat method) get_angle_stat_dims() (forgi.threedee.model.stats.ClusteredAngleStats method) (in module forgi.threedee.model.stats) get_angle_stat_geometry() (in module forgi.threedee.utilities.graph_pdb) get_angle_stats() (in module forgi.threedee.model.stats) get_angle_type() (forgi.graph.bulge_graph.BulgeGraph method) get_array() (forgi.threedee.model.linecloud.CoordinateStorage method) get_basepair_center() (in module forgi.threedee.utilities.graph_pdb) get_basepair_plane() (in module forgi.threedee.utilities.graph_pdb) get_bg_str() (forgi.graph.sequence.Sequence method) get_biggest_chain() (in module forgi.threedee.utilities.pdb) get_bounding_box() (forgi.projection.projection2d.Projection2D method) get_bounding_square() (forgi.projection.projection2d.Projection2D method) get_box() (in module forgi.projection.hausdorff) get_branchpoint_count() (forgi.projection.projection2d.Projection2D method) get_broken_ml_deviation() (in module forgi.threedee.utilities.graph_pdb) get_bulge_angle_stats() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) get_bulge_angle_stats_core() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) get_bulge_centroid() (in module forgi.threedee.utilities.graph_pdb) get_bulge_dimensions() (forgi.graph.bulge_graph.BulgeGraph method) get_centroid() (in module forgi.threedee.utilities.graph_pdb) get_conformation_stats() (in module forgi.threedee.model.stats) get_connected_residues() (forgi.graph.bulge_graph.BulgeGraph method) get_coordinates_array() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) get_cyclebasis_len() (forgi.projection.projection2d.Projection2D method) get_define_seq_str() (forgi.graph.bulge_graph.BulgeGraph method) get_direction() (forgi.threedee.model.linecloud.LineSegmentStorage method) get_domains() (forgi.graph.bulge_graph.BulgeGraph method) get_dotplot() (in module forgi.threedee.utilities.mcannotate) get_double_alignment_matrix() (in module forgi.threedee.utilities.vector) get_elem() (forgi.graph.bulge_graph.BulgeGraph method) get_element_color() (forgi.threedee.visual.pymol.PymolPrinter method) get_encompassing_cylinders() (in module forgi.threedee.utilities.graph_pdb) get_first_chain() (in module forgi.threedee.utilities.pdb) get_fiveprime_stats() (in module forgi.threedee.model.stats) get_flanking_handles() (forgi.graph.bulge_graph.BulgeGraph method) get_flanking_region() (forgi.graph.bulge_graph.BulgeGraph method) get_flanking_sequence() (forgi.graph.bulge_graph.BulgeGraph method) get_furthest_c_alpha() (in module forgi.threedee.utilities.graph_pdb) get_incomplete_elements() (in module forgi.threedee.utilities.graph_pdb) get_inter_distances() (in module forgi.threedee.utilities.vector) get_interacting_base_pairs() (in module forgi.threedee.utilities.mcannotate) get_leaf_leaf_distances() (forgi.projection.projection2d.Projection2D method) get_length() (forgi.graph.bulge_graph.BulgeGraph method) get_link_direction() (forgi.graph.bulge_graph.BulgeGraph method) get_longest_arm_length() (forgi.projection.projection2d.Projection2D method) get_longest_img_diameter() (in module forgi.projection.hausdorff) get_loop_flexibility() (in module forgi.threedee.classification.aminor)

get_loop_stat() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) get_loop_stats() (in module forgi.threedee.model.stats) get_maximal_path_length() (forgi.projection.projection2d.Projection2D method) get_mst() (forgi.graph.bulge_graph.BulgeGraph method) get_multiloop_nucleotides() (forgi.graph.bulge_graph.BulgeGraph method) get_multiloop_side() (forgi.graph.bulge_graph.BulgeGraph method) get_next_ml_segment() (forgi.graph.bulge_graph.BulgeGraph method) get_node_dimensions() (forgi.graph.bulge_graph.BulgeGraph method) get_node_from_residue_num() (forgi.graph.bulge_graph.BulgeGraph method) get_non_colinear_unit_vector() (in module forgi.threedee.utilities.vector) get_one_d_stat_dims() (in module forgi.threedee.model.stats) get_ordered_stem_poss() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) get_ordered_virtual_residue_poss() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) get_orthogonal_unit_vector() (in module forgi.threedee.utilities.vector) get_particular_chain() (in module forgi.threedee.utilities.pdb) get_position_in_element() (forgi.graph.bulge_graph.BulgeGraph method) get_poss_for_domain() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) get_random_vector() (in module forgi.threedee.utilities.vector) get_relative_orientation() (in module forgi.threedee.classification.aminor) get_residue_type() (in module forgi.threedee.utilities.graph_pdb) get_resseqs() (forgi.graph.bulge_graph.BulgeGraph method) get_rna_input_parser() (in module forgi.utilities.commandline_utils) get_side_nucleotides() (forgi.graph.bulge_graph.BulgeGraph method) get_sides() (forgi.graph.bulge_graph.BulgeGraph method) get_some_leaf_leaf_distances() (forgi.projection.projection2d.Projection2D method) get_stacking_helices() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) get_standard_basis() (in module forgi.threedee.utilities.vector) get_stats() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) get_stem_edge() (forgi.graph.bulge_graph.BulgeGraph method) get_stem_orientation_parameters() (in module forgi.threedee.utilities.graph_pdb) get_stem_separation_parameters() (in module forgi.threedee.utilities.graph_pdb) get_stem_stats() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) (in module forgi.threedee.model.stats) get_stem_twist_and_bulge_vecs() (in module forgi.threedee.utilities.graph_pdb) get_strand() (forgi.graph.bulge_graph.BulgeGraph method) get_threeprime_stats() (in module forgi.threedee.model.stats) get_total_length() (forgi.projection.projection2d.Projection2D method) get_trainings_data() (in module forgi.threedee.classification.aminor) get_twist_angle() (in module forgi.threedee.utilities.graph_pdb) get_twist_parameter() (in module forgi.threedee.utilities.graph_pdb) get_twists() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) get_vector_centroid() (in module forgi.threedee.utilities.vector) get_version_string() (in module forgi.utilities.stuff) get_virtual_residue() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) get_vres_by_position() (forgi.projection.projection2d.Projection2D method) GetPointsEquiAngularlyDistancedOnSphere() (in module forgi.threedee.utilities.vector) globally_minimal_distance() (in module forgi.projection.hausdorff) GraphConstructionError GraphIntegrityError grouped() (in module forgi.utilities.stuff) gyration_tensor() (in module forgi.threedee.model.descriptors)

H

has_connection() (forgi.graph.bulge_graph.BulgeGraph method) hausdorff_distance() (in module forgi.projection.hausdorff)

hide_traceback() (in module forgi.utilities.commandline_utils) hloop_iterator() (forgi.graph.bulge_graph.BulgeGraph method) hulls() (in module forgi.projection.projection2d)

I

iloop_iterator() (forgi.graph.bulge_graph.BulgeGraph method) incomplete_elements (forgi.threedee.model.coarse_grain.CoarseGrainRNA attribute) index() (forgi.graph.sequence.SeqidList method) insert_into_stack() (in module forgi.utilities.stuff) interacting_elements (forgi.threedee.model.coarse_grain.CoarseGrainRNA attribute) interchain_contacts() (in module forgi.threedee.utilities.pdb) inverse_brackets() (in module forgi.utilities.stuff) is_almost_coplanar() (in module forgi.threedee.utilities.pdb) is_almost_parallel() (in module forgi.threedee.utilities.vector) is_basepair_pair() (in module forgi.threedee.utilities.pdb) is_covalent() (in module forgi.threedee.utilities.pdb) is_filled (forgi.threedee.model.linecloud.CoordinateStorage attribute) is_loop_pseudoknot() (forgi.graph.bulge_graph.BulgeGraph method)

is_protein() (in module forgi.threedee.utilities.pdb) is_similar_to() (forgi.threedee.model.stats.AngleStat method) is_single_stranded() (forgi.graph.bulge_graph.BulgeGraph method) is_stacking() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) is_string_type() (in module forgi.utilities.stuff) is_valid() (forgi.graph.sequence.Sequence method) iter_configfiles() (in module forgi.config) iter_elements_along_backbone() (forgi.graph.bulge_graph.BulgeGraph method) iter_modifications() (forgi.graph.sequence.Sequence method) iter_resids() (forgi.graph.sequence.Sequence method) iterate_over_interactions() (in module forgi.threedee.utilities.mcannotate) iterate_over_residue_list() (in module forgi.threedee.utilities.mcannotate) iterate_over_seqid_range() (forgi.graph.bulge_graph.BulgeGraph method)

J

junction_virtual_atom_distance() (in module forgi.threedee.utilities.graph_pdb)

junction_virtual_res_distance() (in module forgi.threedee.utilities.graph_pdb) junctions (forgi.graph.bulge_graph.BulgeGraph attribute)

K

keys() (forgi.threedee.model.stats.ClusteredAngleStats method) (forgi.threedee.utilities.graph_pdb.VirtualAtomsLookup method)

L

length_one_stem_basepairs() (forgi.graph.bulge_graph.BulgeGraph method) line_segment_distance() (in module forgi.threedee.utilities.vector) line_segments_collinearity() (in module forgi.threedee.utilities.vector) LineSegmentStorage (class in forgi.threedee.model.linecloud) load_coordinates_array() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) load_rna() (in module forgi.utilities.commandline_utils) load_structure() (in module forgi.threedee.utilities.pdb) locally_minimal_distance() (in module forgi.projection.hausdorff)

log (in module forgi.projection.projection2d) (in module forgi.threedee.model.descriptors) log() (forgi.graph.bulge_graph.BulgeGraph method) longest_axis (forgi.projection.projection2d.Projection2D attribute) longrange_iterator() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) lookup_stat() (forgi.threedee.model.stats.ClusteredAngleStats method) loop_potential_interactions() (in module forgi.threedee.classification.aminor) loop_stats (forgi.threedee.model.stats.ConstructionStats attribute) LoopStat (class in forgi.threedee.model.stats)

M

magnitude() (in module forgi.threedee.utilities.vector) make_random() (forgi.threedee.model.stats.RandomAngleStats method) make_temp_directory() (in module forgi.utilities.stuff) merge_intervals() (in module forgi.utilities.stuff) middlepoint() (in module forgi.threedee.utilities.vector)

min_max_bp_distance() (forgi.graph.bulge_graph.BulgeGraph method) MissingResidue (class in forgi.graph.sequence) mloop_iterator() (forgi.graph.bulge_graph.BulgeGraph method) modified_hausdorff_distance() (in module forgi.projection.hausdorff) ModifiedResidueLookup (class in forgi.threedee.utilities.modified_res)

N

noncovalent_distances() (in module forgi.threedee.utilities.pdb) normalize() (in module forgi.threedee.utilities.vector) nucleotide_colors_to_fornac_color_string() (in module forgi.visual.fornac)

nucleotides_to_elements() (forgi.graph.bulge_graph.BulgeGraph method) num_noncovalent_clashes() (in module forgi.threedee.utilities.pdb) NumberedDotbracket (class in forgi.utilities.numbered_dotbracket)

O

observedDict (class in forgi.utilities.observedDict) offsets() (in module forgi.projection.hausdorff) on_change (forgi.threedee.model.linecloud.CoordinateStorage attribute) open_for_out() (in module forgi.utilities.commandline_utils)

orientation() (in module forgi.projection.projection2d) orientation_params() (forgi.threedee.model.stats.AngleStat method) output_chain() (in module forgi.threedee.utilities.pdb) output_multiple_chains() (in module forgi.threedee.utilities.pdb)

P

pair_distance_distribution() (in module forgi.threedee.utilities.vector) pair_distance_distribution_vectorized() (in module forgi.threedee.utilities.vector) pairing_partner() (forgi.graph.bulge_graph.BulgeGraph method) pairtable_to_dotbracket() (in module forgi.utilities.stuff) pairtable_to_elements() (in module forgi.utilities.stuff) pairtable_to_tuples() (in module forgi.utilities.stuff) parse_base_pair_id() (in module forgi.threedee.utilities.mcannotate) parse_chain_base() (in module forgi.threedee.utilities.mcannotate) parse_line() (forgi.threedee.model.stats.AngleStat method) (forgi.threedee.model.stats.LoopStat method) (forgi.threedee.model.stats.StemStat method) parse_resid() (in module forgi.threedee.utilities.mcannotate) parse_vres() (in module forgi.threedee.utilities.virtual_residues) pdb_file_rmsd() (in module forgi.threedee.utilities.pdb) pdb_rmsd() (in module forgi.threedee.utilities.pdb) pin_fits_two_cyl() (in module forgi.threedee.utilities.vector) plot() (forgi.projection.projection2d.Projection2D method) plot_pdb() (in module forgi.visual.mplotlib) plot_rna() (in module forgi.visual.mplotlib) point_in_cylinder() (in module forgi.threedee.utilities.vector) point_line_distance() (in module forgi.threedee.utilities.vector) points (forgi.projection.projection2d.Projection2D attribute) pop() (forgi.utilities.observedDict.observedDict method) popitem() (forgi.utilities.observedDict.observedDict method) pos_to_spos() (in module forgi.threedee.utilities.graph_pdb) position_params() (forgi.threedee.model.stats.AngleStat method)

potential_interactions() (in module forgi.threedee.classification.aminor) predict() (forgi.threedee.classification.aminor.AMinorClassifier method) predict_proba() (forgi.threedee.classification.aminor.AMinorClassifier method) print_brackets() (in module forgi.graph.bulge_graph) profile() (in module forgi.graph.bulge_graph) (in module forgi.projection.projection2d) (in module forgi.threedee.model.coarse_grain) (in module forgi.threedee.model.linecloud) (in module forgi.threedee.utilities.graph_pdb) (in module forgi.threedee.utilities.vector) proj_direction (forgi.projection.projection2d.Projection2D attribute) proj_graph (forgi.projection.projection2d.Projection2D attribute) project_from (forgi.threedee.model.coarse_grain.CoarseGrainRNA attribute) Projection2D (class in forgi.projection.projection2d) pseudoknotted_basepairs() (forgi.graph.bulge_graph.BulgeGraph method) pv() (in module forgi.utilities.debug) pymol_axis_string() (forgi.threedee.visual.pymol.PymolPrinter method) pymol_box_string() (forgi.threedee.visual.pymol.PyMolRNA method) pymol_color() (in module forgi.threedee.visual.pymol) pymol_intro_string() (forgi.threedee.visual.pymol.PymolPrinter method) pymol_load_cgo_string() (forgi.threedee.visual.pymol.PymolPrinter method) pymol_segments_string() (forgi.threedee.visual.pymol.PyMolRNA method) pymol_spheres_string() (forgi.threedee.visual.pymol.PyMolRNA method) pymol_string() (forgi.threedee.visual.pymol.PymolPrinter method) pymol_text_string() (forgi.threedee.visual.pymol.PyMolRNA method) PymolPrinter (class in forgi.threedee.visual.pymol) PyMolRNA (class in forgi.threedee.visual.pymol)

Q

query_PDBeChem() (in module forgi.threedee.utilities.modified_res)

R

radius_of_gyration() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) (in module forgi.threedee.model.descriptors) random_subgraph() (forgi.graph.bulge_graph.BulgeGraph method) RandomAngleStats (class in forgi.threedee.model.stats) rasterize() (forgi.projection.projection2d.Projection2D method) rasterized_2d_coordinates() (in module forgi.projection.projection2d) read_config() (in module forgi.config) remove_disordered() (in module forgi.threedee.utilities.pdb) rename_rosetta_atoms() (in module forgi.threedee.utilities.pdb) renumber_bpseq() (in module forgi.utilities.stuff) renumber_chain() (in module forgi.threedee.utilities.pdb) Res (in module forgi.graph.residue) reset_vatom_cache() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) RESID (class in forgi.graph.residue) Resid_base (in module forgi.graph.residue)

resid_from_biopython() (in module forgi.graph.residue) resid_from_str() (in module forgi.graph.residue) resid_to_str() (in module forgi.graph.residue) residuelist_rmsd() (in module forgi.threedee.utilities.pdb) rmsd() (in module forgi.threedee.model.similarity) rmsd_to() (forgi.threedee.model.linecloud.LineSegmentStorage method) RnaMissing3dError rods (forgi.graph.bulge_graph.BulgeGraph attribute) rotate() (forgi.projection.projection2d.Projection2D method) (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) (forgi.threedee.model.linecloud.CoordinateStorage method) rotate2D() (in module forgi.projection.projection2d) rotate_translate() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) rotatingCalipers() (in module forgi.projection.projection2d) rotation_matrix() (in module forgi.threedee.utilities.vector)

S

sample_stats() (forgi.threedee.model.stats.ConformationStats method) (forgi.threedee.model.stats.FilteredConformationStats method) (forgi.threedee.model.stats.RandomAngleStats method) scale_colors() (in module forgi.visual.fornac) score() (forgi.threedee.classification.aminor.AMinorClassifier method) seg_intersect() (in module forgi.threedee.utilities.vector) seq (forgi.graph.bulge_graph.BulgeGraph attribute) seq_id_to_pos() (forgi.graph.bulge_graph.BulgeGraph method) seq_length (forgi.graph.bulge_graph.BulgeGraph attribute) SeqidList (class in forgi.graph.sequence) Sequence (class in forgi.graph.sequence) sequence (forgi.graph.sequence.SequenceLoader attribute) SequenceLoader (class in forgi.graph.sequence) serialize_vres() (in module forgi.threedee.utilities.virtual_residues) set_angle_types() (forgi.graph.bulge_graph.BulgeGraph method) set_conformation_stats() (in module forgi.threedee.model.stats) set_params() (forgi.threedee.classification.aminor.AMinorClassifier method) setdefault() (forgi.utilities.observedDict.observedDict method) shortest_bg_loop() (forgi.graph.bulge_graph.BulgeGraph method) shortest_cycle() (in module forgi.utilities.graph) shortest_mlonly_multiloop() (forgi.graph.bulge_graph.BulgeGraph method) shortest_path() (forgi.graph.bulge_graph.BulgeGraph method) sniff_filetype() (in module forgi.utilities.commandline_utils) sortAlongLine() (in module forgi.threedee.utilities.vector)

sorted_edges_for_mst() (forgi.graph.bulge_graph.BulgeGraph method) (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) sorted_element_iterator() (forgi.graph.bulge_graph.BulgeGraph method) sorted_stem_iterator() (forgi.graph.bulge_graph.BulgeGraph method) spherical_cartesian_to_polar() (in module forgi.threedee.utilities.vector) spherical_polar_to_cartesian() (in module forgi.threedee.utilities.vector) ss_distance() (forgi.graph.bulge_graph.BulgeGraph method) stem2_orient_from_stem1() (in module forgi.threedee.utilities.graph_pdb) stem2_orient_from_stem1_1() (in module forgi.threedee.utilities.graph_pdb) stem2_pos_from_stem1() (in module forgi.threedee.utilities.graph_pdb) stem2_pos_from_stem1_1() (in module forgi.threedee.utilities.graph_pdb) stem_angle() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) stem_bp_iterator() (forgi.graph.bulge_graph.BulgeGraph method) stem_from_chains() (in module forgi.threedee.utilities.graph_pdb) stem_iterator() (forgi.graph.bulge_graph.BulgeGraph method) stem_length() (forgi.graph.bulge_graph.BulgeGraph method) stem_offset() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) stem_resn_to_stem_vres_side() (forgi.graph.bulge_graph.BulgeGraph method) stem_side_vres_to_resn() (forgi.graph.bulge_graph.BulgeGraph method) stem_stats (forgi.threedee.model.stats.ConstructionStats attribute) stem_stem_orientation() (in module forgi.threedee.utilities.graph_pdb) stem_vres_reference_atoms() (in module forgi.threedee.utilities.graph_pdb) StemStat (class in forgi.threedee.model.stats) steric_value() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method)

T

threeprime_stats (forgi.threedee.model.stats.ConstructionStats attribute) tloop_iterator() (forgi.graph.bulge_graph.BulgeGraph method) to_0_based() (in module forgi.graph.sequence) to_4_letter_alphabeth() (in module forgi.threedee.utilities.modified_res) to_bg_string() (forgi.graph.bulge_graph.BulgeGraph method) (forgi.graph.sequence.MissingResidue method) to_bpseq_string() (forgi.graph.bulge_graph.BulgeGraph method) to_cg_string() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) to_dotbracket_string() (forgi.graph.bulge_graph.BulgeGraph method) to_element_string() (forgi.graph.bulge_graph.BulgeGraph method) to_fasta_string() (forgi.graph.bulge_graph.BulgeGraph method) to_file() (forgi.graph.bulge_graph.BulgeGraph method) (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) to_grayscale() (in module forgi.projection.projection2d) to_integer() (forgi.graph.sequence.Sequence method) to_neato_string() (forgi.graph.bulge_graph.BulgeGraph method)

to_networkx() (forgi.graph.bulge_graph.BulgeGraph method) to_pair_table() (forgi.graph.bulge_graph.BulgeGraph method) to_pair_tuples() (forgi.graph.bulge_graph.BulgeGraph method) to_resid() (forgi.graph.sequence.Sequence method) to_rgb() (in module forgi.projection.projection2d) total_helix_rotation() (in module forgi.threedee.utilities.graph_pdb) total_length() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) transformed (forgi.graph.bulge_graph.BulgeGraph attribute) (forgi.threedee.model.coarse_grain.CoarseGrainRNA attribute) traverse_graph() (forgi.graph.bulge_graph.BulgeGraph method) trim_chain_between() (in module forgi.threedee.utilities.pdb) try_parameters() (in module forgi.projection.hausdorff) tuples_to_pairtable() (in module forgi.utilities.stuff) twist2_from_twist1() (in module forgi.threedee.utilities.graph_pdb) twist2_orient_from_stem1() (in module forgi.threedee.utilities.graph_pdb) twist2_orient_from_stem1_1() (in module forgi.threedee.utilities.graph_pdb) twist_params() (forgi.threedee.model.stats.AngleStat method)

U

update() (forgi.utilities.observedDict.observedDict method)

V

v3dposs (forgi.threedee.model.coarse_grain.CoarseGrainRNA attribute) vbases (forgi.threedee.model.coarse_grain.CoarseGrainRNA attribute) vec_angle() (in module forgi.threedee.utilities.vector) vec_distance() (in module forgi.threedee.utilities.vector) vec_dot() (in module forgi.threedee.utilities.vector) vector_rejection() (in module forgi.threedee.utilities.vector) verify_vatom_positions() (in module forgi.threedee.utilities.graph_pdb) vinvs (forgi.threedee.model.coarse_grain.CoarseGrainRNA attribute) virtual_atoms() (forgi.threedee.model.coarse_grain.CoarseGrainRNA method) (in module forgi.threedee.utilities.graph_pdb)

virtual_res_3d_pos() (in module forgi.threedee.utilities.graph_pdb) virtual_res_3d_pos_core() (in module forgi.threedee.utilities.graph_pdb) virtual_res_basis() (in module forgi.threedee.utilities.graph_pdb) virtual_res_basis_core() (in module forgi.threedee.utilities.graph_pdb) virtual_residue_atoms() (in module forgi.threedee.utilities.graph_pdb) VirtualAtomsLookup (class in forgi.threedee.utilities.graph_pdb) vposs (forgi.threedee.model.coarse_grain.CoarseGrainRNA attribute) vres_iterator (forgi.projection.projection2d.Projection2D attribute) vres_to_global_coordinates() (in module forgi.threedee.utilities.graph_pdb) vvecs (forgi.threedee.model.coarse_grain.CoarseGrainRNA attribute)

W

with_missing (forgi.graph.sequence.Sequence attribute) with_modifications (forgi.graph.sequence.Sequence attribute) without_short_helices() (forgi.utilities.numbered_dotbracket.NumberedDotbracket method)

without_substr() (forgi.utilities.numbered_dotbracket.NumberedDotbracket method) without_unpaired() (forgi.utilities.numbered_dotbracket.NumberedDotbracket method) WrongFileFormat