o Rŀg @sTdZddlZddlZddlmZdddZddZd d Zd d ZGd ddZ dS)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_aaFcCst|dd}|dd}d|g}tj|ddd}|r!t|j|js2tj |dr2|dSt d |j) alRun 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 not write output to the terminal while run unless verbose is set to True. /.rpseaT)capture_outputtextz.seazError running p-sea: ) split subprocessrunprintstdoutstderrstripospathexists RuntimeError)fnameverboselastbasecmdpr@/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/PSEA.pyrun_pseas  rcCst|}d}d}t|4}|D] }|dddkrd}q|sq|ddkr'n||dd}qWd|SWd|S1sCwY|S) zParse PSEA output file.rz>p-sea rN)ropen)pnamerstartssfplinerrrr4s*       rcCsDg}|D]}|dkr d}n |dkrd}n|dkrd}||q|S)z3Translate PSEA secondary structure string into HEC.aHbEcC)append)pseqseqr$nrrrpsea2HECFs r1cCs|d}|}g}|D] }t|r||qt|}|t|ks.td|t|ft|D] }||||jd<q2dS)z;Apply secondary structure information to residues in model.rzLength mismatch %i %iSS_PSEAN)get_listrr-len ValueErrorrangextra)mss_seqr+allresiduesresLirrrannotateTs    r?c@s eZdZdZddZddZdS)PSEAziDefine PSEA class. PSEA object is a wrapper to PSEA program for secondary structure assignment. cCs$t|}t|}t||||_dS)zInitialize the class.N)rr1r?r9)selfmodelfilenamer9rrr__init__ks  z PSEA.__init__cCs|jS)z"Return secondary structure string.)r9)rArrrget_seqrsz PSEA.get_seqN)__name__ __module__ __qualname____doc__rDrErrrrr@es r@)F) rIrr Bio.PDB.Polypeptiderrrr1r?r@rrrrs