o Rŀg^<@sbdZddlZddlmZddlmZddlmZddlmZdgdiZ eZ Gd d d eZ dS) zcWrite an mmCIF file. See https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax for syntax. N) defaultdict)Select) StructureIO)StructureBuilder _atom_site) group_PDBid type_symbol label_atom_id label_alt_id label_comp_id label_asym_idlabel_entity_id label_seq_idpdbx_PDB_ins_codeCartn_xCartn_yCartn_z occupancyB_iso_or_equivpdbx_formal_charge auth_seq_id auth_comp_id auth_asym_id auth_atom_idpdbx_PDB_model_numc@s^eZdZdZddZddZedfddZd d Zd d Z d dZ ddZ ddZ ddZ dS)MMCIFIOaWrite a Structure object or a mmCIF dictionary as a mmCIF file. Examples -------- >>> from Bio.PDB import MMCIFParser >>> from Bio.PDB.mmcifio import MMCIFIO >>> parser = MMCIFParser() >>> structure = parser.get_structure("1a8o", "PDB/1A8O.cif") >>> io=MMCIFIO() >>> io.set_structure(structure) >>> io.save("bio-pdb-mmcifio-out.cif") >>> import os >>> os.remove("bio-pdb-mmcifio-out.cif") # tidy up cCsdS)z Initialise.N)selfrrC/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/mmcifio.py__init__EszMMCIFIO.__init__cCs"||_t|drt|ddSdS)z+Set the mmCIF dictionary to be written out. structureN)dichasattrdelattr)rr"rrrset_dictHs zMMCIFIO.set_dictFcCsnt|tr t|d}d}n|}d}t|dr||||nt|dr)||ntd|r5|dSdS)aSave the structure to a file. :param filepath: output file :type filepath: string or filehandle :param select: selects which entities will be written. :type select: object Typically select is a subclass of L{Select}, it should have the following methods: - accept_model(model) - accept_chain(chain) - accept_residue(residue) - accept_atom(atom) These methods should return 1 if the entity is to be written out, 0 otherwise. wTFr!r"zKUse set_structure or set_dict to set a structure or dictionary to write outN) isinstancestropenr#_save_structure _save_dict ValueErrorclose)rfilepathselectpreserve_atom_numberingfp close_filerrrsaveOs      z MMCIFIO.savec Csi}|jD]9}|dkr|j|}qtd|}t|dkr9|d|vr/||d|dq|dg||d<qtd||D];\}}|tvr~g}|D] }z |t||WqOtyo|tt|YqOwddt t ||D||<qC|r| d|d n| d |D].\}}|j|d |d} t| } |D]/}|j|d |} t | t rt | tst| | kst | trt | t rtd |d |qt | tst | t r}| |d |dd||<|j|d |D]"} t| }|| r{|| s{|d7}|||kr|||<qeqKt| D]$}|D]}| ||j|d ||||dq| dqn tdtt| | dqdS)Ndata_z\.rz!Invalid key in mmCIF dictionary: cSsg|]\}}|qSrr).0_krrr sz&MMCIFIO._save_dict..z # zdata_ # .z-Inconsistent list sizes in mmCIF dictionary: z {k: <{width}})r9width zloop_ z"Invalid type in mmCIF dictionary: z# )r"resplitlenappendr,items mmcif_orderindexsortedzipwriter'listr(format_format_mmcif_col_requires_quote_requires_newlinerangetype)rout_file key_listskeydata_valskey_listindsi sample_valn_valsvalm value_no_list col_widthslen_valcolrrrr+ws                 zMMCIFIO._save_dictcCsb||r d|dS||r*d|vrdjd|d|dSdjd|d|dSdj||dS)Nz ;z ; ' z {v: <{width}}")vr=')rMrLrJ)rrZ col_widthrrrrKs   zMMCIFIO._format_mmcif_colcCs d|vs d|vrd|vrdSdS)Nr>r`z" TFrrrZrrrrMszMMCIFIO._requires_newlinecCs>d|vsd|vsd|vs|ddvs|ds|dvrdSd S) N rcrar)r8#$[];)r4save_)loop_stop_global_TF) startswithrerrrrLs zMMCIFIO._requires_quotecCsH|}d}|dkr"|dd}|td|7}t||d}|dks|S)Nrr6A)chrint)r entity_iddivoutmodrrr_get_label_asym_id s zMMCIFIO._get_label_asym_idc Cstt}|jD]T}||sq |jdkrd}nt|j}d}|s%d}|D]3} || s2q)| } | dkrr4)rrIr!get_list accept_model serial_numr( accept_chainget_idget_unpacked_listaccept_residue get_resnamerz accept_atomrBget_serial_numberelementstripget_name get_altloc get_coord get_occupancy get_bfactorrreplacer"r+)rrPr/r0 atom_dictmodelmodel_nrv atom_numberchainchain_idresidue_numberprev_residue_type prev_resnameresiduehetfieldresseqicode residue_typerresnamer atomraltloccoord structure_idcrrrr*s             OzMMCIFIO._save_structureN)__name__ __module__ __qualname____doc__r r%_selectr3r+rKrMrLrzr*rrrrr3s(h r) rr? collectionsr Bio.PDB.PDBIOrrBio.PDB.StructureBuilderrrDrrrrrrs