B b @sdZddlZddlmZddZddZdd Zd d ZGd d d Ze dkrddl Z ddl m Z e Z e de jdZeede jddS)aHWrappers for PSEA, a program for secondary structure assignment. See this citation for P-SEA, PMID: 9183534 Labesse G, Colloc'h N, Pothier J, Mornon J-P: P-SEA: a new efficient assignment of secondary structure from C_alpha. Comput Appl Biosci 1997 , 13:291-295 ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/ N)is_aacCs2td|g|dd}|dd}|dS)aERun PSEA and return output filename. Note that this assumes the P-SEA binary is called "psea" and that it is on the path. Note that P-SEA will write an output file in the current directory using the input filename with extension ".sea". Note that P-SEA will write output to the terminal while run. psea/.rz.sea) subprocessZcallsplit)fnameZlastbaser +lib/python3.7/site-packages/Bio/PDB/PSEA.pyrun_pseas r c Cspt|}d}d}t|N}xF|D]>}|dddkr:d}q |s@q |ddkrNP||dd}q WWdQRX|S) zParse PSEA output file.rz>p-sea rN)r open)Zpnamer startssfplr r r r)s   rcCsHg}x>|D]6}|dkrd}n|dkr*d}n |dkr6d}||q W|S)z3Translate PSEA secondary structure string into HEC.aHbEcC)append)Zpseqseqrnr r r psea2HEC;s r cCs|d}|}g}x|D]}t|r||qWt|}|t|ks`td|t|fx$td|D]}||||jd<qlWdS)z;Apply secondary structure information to residues in model.rzLength mismatch %i %iZSS_PSEAN)Zget_listrrlen ValueErrorrangeZxtra)mss_seqrallZresiduesZresLir r r annotateIs   r)c@s eZdZdZddZddZdS)PSEAziDefine PSEA class. PSEA object is a wrapper to PSEA program for secondary structure assignment. cCs$t|}t|}t||||_dS)zInitialize the class.N)rr r)r%)selfZmodelfilenamer%r r r __init__`s z PSEA.__init__cCs|jS)z"Return secondary structure string.)r%)r+r r r get_seqgsz PSEA.get_seqN)__name__ __module__ __qualname____doc__r-r.r r r r r*Zsr*__main__) PDBParserXr)r2rZBio.PDB.Polypeptiderr rr r)r*r/sysZBio.PDBr4pZ get_structureargvsr r r r s