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_pairing_interact:[17,33],add_beta_carbon_vector:[16,32],add_biogrid_edg:[10,15,27,38],add_biogrid_metadata:[15,27],add_bond_ord:[16,21],add_bond_typ:[14,26],add_cation_pi_interact:[16,20,24,32,34],add_contacts_edg:16,add_contour:16,add_delaunay_triangul:[16,21,32],add_distance_threshold:[8,14,16,26,32],add_disulfide_interact:[16,24,28,32,34],add_dssp_df:16,add_dssp_featur:[16,30],add_edg:32,add_fully_connected_edg:[14,26],add_h:[14,26],add_histidine_histidine_edg:32,add_hydrogen_bond_interact:[16,24,25,30,32,34],add_hydrophobic_interact:[16,20,28,34],add_interacting_gen:12,add_interacting_protein:15,add_interacting_resi:16,add_ionic_interact:[16,20,24,25,32,34],add_k_nn_edg:[14,16,26,30,32],add_nod:15,add_nodes_to_graph:[14,16,32],add_peptide_bond:[8,16,21,24,25,28,30,32,34],add_phosphodiester_bond:[17,33],add_pseudoknot:[17,33],add_regnetwork_edg:[10,12,23,38],add_ring_statu:[16,21],add_separ:[16,28],add_sequence_distance_edg:16,add_sequence_neighbour_vector:[16,32],add_sequence_to_nod:[12,15,23,27],add_sidechain_vector:[16,32],add_string_biogrid_metadata:[15,27],add_string_edg:[10,15,27,38],add_string_metadata:[15,27],add_trrust_edg:[10,12,23,38],add_vector_to_plot:[16,32],addit:[4,6,10,12,14,15,16,18,23,25,29,32,38],addition:16,additionalidentifiertyp:15,address:[0,10,38],adenyl:31,adj:18,adjac:[16,17,18],adjacency_matrix:24,adjacency_matrix_pow:[],adjuv:16,adp:[16,31],advanc:0,advantag:32,ae:16,aectylcitrullin:31,af:16,af_vers:22,aforement:34,after:[1,6,10,16,18,20,22,29,38],ag:[0,14,16],again:[24,27,29,32,34],against:16,aggegation_typ:16,aggreg:[16,24,32],aggregate_feature_over_chain:32,aggregate_graph_feature_over_chain:16,aggregation_typ:[16,32],agnost:[10,38],agp:27,ah:16,ahead:1,ai:[16,20,25,27,32,33],aib:16,aicompet:[10,38],aid:16,ak:16,akap8:27,akap8l:27,akap9:27,al:[14,16,25,35],ala:[16,21,24,25,28,32,34,36],alanin:16,alert:36,alex:2,alexand:16,alg11:27,alg5:27,alg8:27,algorithm:[1,15,17],alia:[14,16],align:[0,16,20],aligned_scor:[10,16,20,38],alik:[10,38],aliv:29,all:[0,1,2,6,10,11,14,15,16,17,18,21,29,32,34,36,38],all_bond_typ:14,all_bond_types_to_channel:14,all_composition_descriptor:16,all_ctd_descriptor:16,all_distribution_descriptor:16,all_info:[],all_stereo_to_channel:14,all_stereo_typ:14,all_transition_descriptor:16,allow:[1,7,10,14,16,17,27,30,38],allowable_nod:[16,21],allowable_set:[14,16,18],allowable_ss_el:16,allowed_bond_typ:14,allowed_bond_type_to_channel:14,allowed_degre:14,allowed_hybrid:14,allowed_num_h:14,allowed_val:14,alon:20,alpha:[16,21,25,32,34,36],alpha_helixfasman:28,alpha_helixlevitt:28,alpha_helixroux:28,alphabet:[16,28,36],alphafold2:35,alphafold:[16,22,27,37],alphafolddb:[20,22],alreadi:[1,12,29,34],also:[0,1,6,7,10,15,16,20,21,25,27,28,29,32,34,36,38],alt:[10,38],alt_loc:[32,34],alter:[22,29,32],altern:[6,10,22,36,38],alwai:[2,10,36],am:16,amalgam:17,amat_kwarg:[],amemiya:5,amino:[14,16,18,28,32,36],amino_acid:[8,16,18,20,21,25,27,28,32,34],amino_acid_composit:16,amino_acid_composition_:16,amino_acid_one_hot:[16,32],amino_acid_properti:[28,32],amino_group:16,aminoacid:16,aminobutyric_acid:16,aminoisobutyric_acid:16,amongst:18,amorehead:2,amount:[21,32],amp:[16,31],an:[0,1,6,11,14,16,17,18,20,21,22,23,25,29,30,32,34,36],anaconda3:[15,17,22,23,24,30,32],anaconda:6,analys:[7,10,38],analysi:[1,7,10,25,29,37,38],analyt:[16,37],angl:[14,16,25],angstrom:[14,16,32],ani:[0,1,8,11,14,15,16,18,28,32],anim:36,annot:[4,9,12,14,15,16,17,18,21],annotate_edge_metadata:[18,32],annotate_graph_metadata:[18,32],annotate_node_featur:18,annotate_node_metadata:[18,32],ano6:27,anoth:[14,16,32,36],answer:[0,1],antiparallelbeta_strand:[28,32],anyth:1,ap2a2:27,ap2m1:27,ap3b1:27,ap:16,apart:[16,32],api:[8,10,12,15,16,22,25,27,33,37,38],appar:36,appear:0,append:[30,32],appli:[0,10,12,18,21,22,32,36,38],applic:[10,21,25,32,38],appoint:0,approach:1,appropri:[0,10,38],approx:18,approxim:18,apt:[21,24,28,29,32,34],aq:16,ar:[0,1,2,4,6,10,12,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,32,33,34,36,38],arang:30,arbirari:25,arbitrari:[14,16,32],arc:16,arf6:27,arg10:36,arg:[12,16,21,24,30,32,34],arginin:16,argmax:30,argument:[8,14,16,18,25,27,29,32],arian:[0,2,10,11,14,16,38],arian_jamasb:1,arianjamasb:[15,16,17,20,21,22,23,24,25,27,28,29,32,34],aris:11,arl6ip6:27,aromat:[14,16,20,24,26,28,32,34],aromatic_resi:16,aromatic_sulphur:16,around:[16,25,29],arrai:[14,16,18,21,26,32],art:1,articl:[10,16,38],artifici:16,arxiv:16,asa:[16,28],asid:1,ask:1,asn:[16,21,24,25,28,32,34],asp:[16,21,24,25,32,34],asparagin:16,aspart:16,aspirin:26,assembl:16,assert:[30,34],assertionerror:18,asset:[10,38],assig:23,assign:[16,21,32,34,36],assign_bond_states_to_datafram:16,assign_covalent_radii_to_datafram:16,assign_node_id_to_datafram:16,assist:10,associ:[11,16,20,32,34],assort:24,assum:6,assumpt:18,asteroid:37,asteroid_plot:[16,25],astyp:25,asx:16,at1g58602:20,ate1:27,atj39:30,atla:25,atom:[10,20,26,27,28,32,36,37,38],atom_bond_st:16,atom_df_processing_func:[16,32],atom_nam:[16,32,34],atom_numb:[32,34],atom_typ:[14,16,25,3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