i \ddlZddlmZdZdZdZdZdZdZd Z d Z d Z d Z d Z dS)N) constantsc n||}||}||}|j|j} |j|j} |j|j} |j|j} |j|j} |j|j}|j|j}||| | | | | |||| dS)aAdd the atomic data to the DataTransferInterface. :param data_api the data api from where to get the data :param data_setters the class to push the data to :param atom_nams the list of atom names for the group :param element_names the list of element names for this group :param atom_charges the list formal atomic charges for this group :param group_atom_ind the index of this atom in the groupN) alt_loc_list atom_counter atom_id_list x_coord_list y_coord_list z_coord_listoccupancy_list b_factor_list set_atom_info)data_api data_setters atom_names element_names atom_chargesgroup_atom_ind atom_nameelementchargealternative_location_id serial_numberxyz occupancytemperature_factors b/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/mmtf/utils/decoder_utils.py add_atom_datars>*IN+G . )F&3H4IJ)(*?@Mh34Ah34Ah34A'(=>I!/0EFy-9P !Q 3EwPVXXXXXctt|D]4}|||dz||dzdz||5dS)zAdd the bonds for this group. :param data_setters the class to push the data to :param bond_indices the indices of the atoms in the group that are bonded (in pairs) :param bond_orders the orders of the bondsN)rangelenset_group_bond)r bond_indices bond_orders bond_indexs radd_group_bondsr*sk C ,,--uu ##LA$>|JWXLYZN?[\ghr\sttttuur c |j|}t|j|d}|j|}||j|d|j|||j|d||j|j|d|j||j| t|D]Y}t|||j|d|j|d|j|d||xj dz c_ Zt||j|d|j|d |S) zAdd the data for a whole group. :param data_api the data api from where to get the data :param data_setters the class to push the data to :param group_index the index for this group atomNameList groupName chemCompTypesingleLetterCode elementListformalChargeListr# bondAtomList bondOrderList) group_type_listr% group_list ins_code_listset_group_info group_id_list num_bondssequence_index_listsec_struct_listr$rrr*)rr group_indexgroup_type_ind atom_countinsertion_coders r add_groupr@$si -k:NX(8HIIJ+K8N 3N CK P ( 6{ C^ ( 3N CN S *H,> ( 3N CDV W ( <[ I ( 8 E GGG ++""h ).9.I).9-H).9:LM$  & & & !L'7G'7HJJJ r c,|j|}|j|}|j|}|||||j|z}|j}t ||D]#}t ||||xjdz c_$|xjdz c_dS)zAdd the data for a whole chain. :param data_api the data api from where to get the data :param data_setters the class to push the data to :param chain_index the index for this chainr#N) chain_id_listchain_name_listgroups_per_chainset_chain_info group_counterr$r@ chain_counter) rr chain_indexchain_id chain_name num_groupsnext_indlast_ind group_inds radd_chain_inforO@s %k2H)+6J*;7J*jAAA% 2H%H8X..## (L)444" Ar c|jD]b}||j||j|z}|j}t ||D]}t ||||xjdz c_cdS)zAdd all the structural information. :param data_api the data api from where to get the data :param data_setters the class to push the data tor#N)chains_per_modelset_model_info model_counterrGr$rO)rr model_chainstot_chains_this_modellast_chain_counterrHs radd_atomic_informationrWQs!1"" ##H$:LIII ( 6 E%3 !35JKK @ @K 8\; ? ? ? ?! ""r cd}|jD]5}|dz }|dD]%}|||d|d&6dS)zGenerate the bioassembly data. :param data_api the interface to the decoded data :param struct_inflator the interface to put the data into the client objectrr# transformListchainIndexListmatrixN) bio_assemblyset_bio_assembly_trans)rstruct_inflatorbioassembly_count bioassembly transforms rgenerate_bio_assemblyrb^s,HH Q$_5 H HI  2 23D3<=M3N3rs XXX,uuu8" " " " H H HJJJ C C C:::" 8 8 8r