i TddlmZddlZddlmZdZGddeZdZGdd eZ Gd d e Z dS) ) encode_arrayN) constantsc2i}||d<||d<||d<||d<|S)N descriptiontypechainIndexListsequence) chain_indicesr r entity_typeout_ds ^/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/mmtf/api/mmtf_writer.pymake_entity_dictrs4 E&E-E&M+E  E* Lc eZdZdZdZdZdS)Groupc&|j|jkrdS|j|jkrdS|j|jkrdS|j|jkrdS|j|jkrdS|j|jkrdS|j|jkrdS|j|jkrdSdS)zFunction to define equalityFT)atom_name_list charge_list element_list group_type group_namesingle_letter_codebond_atom_listbond_order_list)selfothers r__eq__z Group.__eq__s  %"6 6 65  u0 0 05   2 2 25 ?e. . .5 ?e. . .5  "e&> > >5  %"6 6 65  5#8 8 85trcg|_g|_g|_g|_g|_t j|_t j|_ t j |_ dS)N) rrrrrrUNKOWN_GROUP_NAMErUNKOWN_GROUP_TYPEr UNKNOWN_SLrrs r__init__zGroup.__init__#sO ! #5#5"+"6rci}|j|d<|j|d<|j|d<|j|d<|j|d<|j|d<|j|d<|j|d<|S) z/Convert the group object to an appropriate DICT groupName atomNameList elementList bondOrderList bondAtomListformalChargeListsingleLetterCode chemCompType)rrrrrrrr)rout_dicts rconvert_to_dictzGroup.convert_to_dict-st $#'#6 "&"3$($8!#'#6 '+'7#$'+'>#$#'? rN)__name__ __module__ __qualname__rr$r/r rrrr sA(777     rrcFg}|D]}||vr|||S)z(Function to get a unique list of groups.)append) input_listout_listitems rget_unique_groupsr8;s9H"" x   OOD ! ! ! OrcZeZdZdZdZdZdZdZdZdZ dZ d Z d Z d Z d Zd ZdS)TemplateEncoderzSTemplate class to be used by third parties to pass data into other data structures.ct)Initialise the structure object. :param total_num_bonds: the number of bonds in the structure :param total_num_atoms: the number of atoms in the structure :param total_num_groups: the number of groups in the structure :param total_num_chains: the number of chains in the structure :param total_num_models: the number of models in the structure :param structure_id the: id of the structure (e.g. PDB id) NotImplementedErrorrtotal_num_bondstotal_num_atomstotal_num_groupstotal_num_chainstotal_num_models structure_ids rinit_structurezTemplateEncoder.init_structureG "!rc t)Create an atom object an set the information. :param atom_name: the atom name, e.g. CA for this atom :param serial_number: the serial id of the atom (e.g. 1) :param alternative_location_id: the alternative location id for the atom, if present :param x: the x coordiante of the atom :param y: the y coordinate of the atom :param z: the z coordinate of the atom :param occupancy: the occupancy of the atom :param temperature_factor: the temperature factor of the atom :param element: the element of the atom, e.g. C for carbon. According to IUPAC. Calcium is Ca :param charge: the formal atomic charge of the atom r= r atom_name serial_numberalternative_location_idxyz occupancytemperature_factorelementcharges r set_atom_infozTemplateEncoder.set_atom_infoTs "!rct)Set the chain information. :param chain_id: the asym chain id from mmCIF :param chain_name: the auth chain id from mmCIF :param num_groups: the number of groups this chain has r=rchain_id chain_name num_groupss rset_chain_infozTemplateEncoder.set_chain_infoe "!rct)NSet the entity level information for the structure. :param chain_indices: the indices of the chains for this entity :param sequence: the one letter code sequence for this entity :param description: the description for this entity :param entity_type: the entity type (polymer,non-polymer,water) r=rr r rr s rset_entity_infozTemplateEncoder.set_entity_infoos "!rc t)ESet the information for a group :param group_name: the name of this group,e.g. LYS :param group_number: the residue number of this group :param insertion_code: the insertion code for this group :param group_type: a string indicating the type of group (as found in the chemcomp dictionary. Empty string if none available. :param atom_count: the number of atoms in the group :param bond_count: the number of unique bonds in the group :param single_letter_code: the single letter code of the group :param sequence_index: the index of this group in the sequence defined by the enttiy :param secondary_structure_type: the type of secondary structure used (types are according to DSSP and number to type mappings are defined in the specification) r= rr group_numberinsertion_coder atom_count bond_countrsequence_indexsecondary_structure_types rset_group_infozTemplateEncoder.set_group_infoys "!rct)Set the information for a model. :param model_id: the index for the model :param chain_count: the number of chains in the model r=rmodel_id chain_counts rset_model_infozTemplateEncoder.set_model_infor]rct)Set the crystallographic information for the structure :param space_group: the space group name, e.g. "P 21 21 21" :param unit_cell: an array of length 6 with the unit cell parameters in order: a, b, c, alpha, beta, gamma r=r space_group unit_cells r set_xtal_infozTemplateEncoder.set_xtal_info "!rct)Sets the header information. :param r_free: the measured R-Free for the structure :param r_work: the measure R-Work for the structure :param resolution: the resolution of the structure :param title: the title of the structure :param deposition_date: the deposition date of the structure :param release_date: the release date of the structure :param experimnetal_methods: the list of experimental methods in the structure r=rr_freer_work resolutiontitledeposition_date release_dateexperimental_methodss rset_header_infozTemplateEncoder.set_header_inforGrct)vSet the Bioassembly transformation information. A single bioassembly can have multiple transforms, :param bio_assembly_index: the integer index of the bioassembly :param input_chain_indices: the list of integer indices for the chains of this bioassembly :param input_transformation: the list of doubles for the transform of this bioassmbly transformr=)rbio_assembly_indexinput_chain_indicesinput_transforms rset_bio_assembly_transz&TemplateEncoder.set_bio_assembly_transrxrct).Any functions needed to cleanup the structure.r=r#s rfinalize_structurez"TemplateEncoder.finalize_structures!!rct)!Add bonds within a group. :param atom_index_one: the integer atom index (in the group) of the first partner in the bond :param atom_index_two: the integer atom index (in the group) of the second partner in the bond :param bond_order: the integer bond order r=ratom_index_oneatom_index_two bond_orders rset_group_bondzTemplateEncoder.set_group_bondr]rct) Add bonds between groups. :param atom_index_one: the integer atom index (in the structure) of the first partner in the bond :param atom_index_two: the integer atom index (in the structure) of the second partner in the bond :param bond_order the bond order r=rs rset_inter_group_bondz$TemplateEncoder.set_inter_group_bondr]rN)r0r1r2__doc__rFrUr\rarkrqrwrrrrrr rrr:r:Ds]] " " """"""""""""""("""""" " " """"""" """"""""rr:cheZdZdZdZdZdZdZdZdZ dZ d Z d Z d Z d Zd ZdZdZdS) MMTFEncoderci}t|jdd|d<t|jdd|d<t|jdd|d<t|jdd|d<t|jdd |d <t|jd d |d <t|jd d|d<t|jdd|d<t|j dd|d<t|j d d|d<|j |d<t|j d d|d<t|j dd|d<t|jdd|d<t|jdd|d<t|jdd|d<t|jdd|d<|j|d<|j|d<|j|d<|j|d<|j|d <|j|d!<|j|d"<|j|d#<|j|d$<|j|d%<|j|d&<|j|d'<|j|d(<|j|d)<|j |d*<|j!|d+<|j"|d,<|j#|d-<|j$|d.<|j%|d/<|j&|d0<|S)1z!Encode the data back into a dict.r groupTypeList i xCoordList yCoordList zCoordListd bFactorList occupancyList atomIdList altLocList insCodeList groupIdList groupListsequenceIndexList chainNameList chainIdListr*r) secStructListchainsPerModelgroupsPerChain spaceGroup mmtfVersion mmtfProducer structureId entityListbioAssemblyListrFreerWorkr~rexperimentalMethodsdepositionDate releaseDateunitCellnumBonds numChains numModelsnumAtoms numGroups)'rgroup_type_list x_coord_list y_coord_list z_coord_list b_factor_listoccupancy_list atom_id_list alt_loc_list ins_code_list group_id_list group_listsequence_index_listchain_name_list chain_id_listrrsec_struct_listchains_per_modelgroups_per_chainru mmtf_version mmtf_producerrE entity_list bio_assemblyr|r}r~rrrrrv num_bonds num_chains num_models num_atomsr[)r output_datas r encode_datazMMTFEncoder.encode_datas '3D4H!Q'O'O O$$01BB$M$M L!$01BB$M$M L!$01BB$M$M L!%1$2Db#%N%N M"'3D4GC'P'P O$$01BAq$I$I L!$01BAq$I$I L!%1$2Da%K%K M"%1$2Da%K%K M"#'? K +78PRSUV+W+W '('3D4H!Q'O'O O$%1$2Da%K%K M"&243F1&M&M N#'3D4H!Q'O'O O$'3D4H!Q'O'O O$(,(= $%(,(= $%$($4 L!%)%6 M"&*&8 N#%)%6 M"$($4 L!)-): %&#{ G#{ G$(O L!#z G-1-F )*(,(< $%%)%6 M""&. J"&. J#'? K #'? K "&. J#'? K rcRtj|dS)z$Get the msgpack of the encoded data.T) use_bin_type)msgpackpackbrr#s r get_msgpackzMMTFEncoder.get_msgpacks#}T--//dCCCCrct|d5}||ddddS#1swxYwYdS)Nwb)openwriter)r file_pathout_fs r write_filezMMTFEncoder.write_files )T " " ,e KK((** + + + , , , , , , , , , , , , , , , , , ,s(AA  A ctj|_tj|_||_||_||_||_||_ ||_ g|_ g|_ g|_ g|_g|_g|_g|_g|_g|_g|_g|_g|_g|_g|_g|_g|_g|_g|_g|_g|_d|_g|_ dS)r<N)!r MMTF_VERSIONrPRODUCERrrrr[rrrErrrrrrrrrrrrrrrrrrrr current_grouprr?s rrFzMMTFEncoder.init_structures&2&/((***(! #% ! !! " "!rc ,|j||j||j||j||j||j||j||jj ||jj | |jj | dS)rIN) rr4rrrrrrrrrrrJs rrUzMMTFEncoder.set_atom_info3s   ###   ###   ###   ///   !8999 ""9--- !!"4555 )00;;; &--f555 '..w77777rc|j||j||j|dS)rWN)rr4rrrXs rr\zMMTFEncoder.set_chain_infoNsO !!(+++ ##J/// $$Z00000rcZ|jt||||dS)r_N)rr4rr`s rrazMMTFEncoder.set_entity_infoYs1  0x T_ ` `aaaaarc |j|j|j|j||j||j||j| t|_||j_||j_ ||j_ dS)rcN) rrr4rrrrrrrrrds rrkzMMTFEncoder.set_group_infocs"   ) O " "4#5 6 6 6 !!,/// !!.111  ''777 ##$<==="WW(2%(2%0B---rc:|j|dS)rmN)rr4rns rrqzMMTFEncoder.set_model_infos! $$[11111rc"||_||_dS)rsN)rurvrts rrwzMMTFEncoder.set_xtal_infos '"rch||_||_||_||_||_||_||_dS)rzN)r|r}r~rrrrr{s rrzMMTFEncoder.set_header_infos>  $ .($8!!!rc&d}|jD]}|dt|kr|}n |st|gd}n|j||d||d|j|dS)rNname)r transformListr)rmatrix)rstrremover4)rrrr this_bioassbioasss rrz"MMTFEncoder.set_bio_assembly_transs  '  Ff~%7!8!888$ 9 2#&'9#:#:RPPKK   $ $[ 1 1 1O$++>Q\k,l,lmmm   -----rc|j|jt|j}|jD]/}|j||0d|D|_dS)rc6g|]}|Sr )r/).0rNs r z2MMTFEncoder.finalize_structure..s$BBB11,,..BBBrN)rr4rr8rindex)r group_setr7s rrzMMTFEncoder.finalize_structuresz t1222%do66 O ? ?D  ' ' (=(= > > > >BB BBBrc|jj||jj||jj|dS)rN)rrr4rrs rrzMMTFEncoder.set_group_bondsX )00@@@ )00@@@ *11*=====rc|j||j||j|dS)rN)rr4rrs rrz MMTFEncoder.set_inter_group_bondsO "">222 "">222 ##J/////rN)r0r1r2rrrrFrUr\rarkrqrwrrrrrr rrrrs)))XDDD ,,, )))X8886111bbbCCC<222###999(...$CCC>>>00000rr) mmtf.codecsrr mmtf.utilsrrobjectrr8r:rr rrr s$$$$$$ +++++F+++\G"G"G"G"G"fG"G"G"VE0E0E0E0E0/E0E0E0E0E0r