:>"^ @sdZddlZddlmZddZddZdd Zd d ZGd d d eZ e dkrddl Z ddl m Z e Zejde jdZe ede 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_aacCs?tjd||jdd}|jdd}|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. zpsea /.rz.sea)ossystemsplit)fnamelastbaser 1/tmp/pip-build-ww9dw3qa/biopython/Bio/PDB/PSEA.pyrun_pseas rc Cst|}d}d}t|dk}xa|jD]S}|dddkr\d}q7|seq7|ddkrvP||dd }q7WWdQRX|S) zParse PSEA output file.rrz>p-sear Nr)ropen readlines)Zpnamer startssfplr r rpsea)s rcCsdg}xW|D]O}|dkr(d}n'|dkr=d}n|dkrOd}|j|q W|S)z3Translate PSEA secondary structure string into HEC.aHbEcC)append)Zpseqseqrnr r rpsea2HEC;s      r$cCs|jd}|j}g}x'|D]}t|r)|j|q)Wt|}|t|kstd|t|fx,td|D]}||||jds