B ‰°b;$ã@sbdZdZGdd„dƒZGdd„dƒZdd„Zdd „Zd d „Zd d „Zedkr^ddl m Z e ƒdS)z:Tools to manipulate data from nmrview .xpk peaklist files.éc@seZdZdZdd„ZdS)ÚXpkEntrya‰Provide dictonary access to single entry from nmrview .xpk file. This class is suited for handling single lines of non-header data from an nmrview .xpk file. This class provides methods for extracting data by the field name which is listed in the last line of the peaklist header. Parameters ---------- xpkentry : str The line from an nmrview .xpk file. xpkheadline : str The line from the header file that gives the names of the entries. This is typically the sixth line of the header, 1-origin. Attributes ---------- fields : dict Dictionary of fields where key is in header line, value is an entry. Variables are accessed by either their name in the header line as in self.field["H1.P"] will return the H1.P entry for example. self.field["entrynum"] returns the line number (1st field of line) cCsT| ¡}| ¡}tt||dd…ƒƒ|_y|d|jd<Wntk rNYnXdS)zInitialize the class.éNéZentrynum)ÚsplitÚdictÚzipÚfieldsÚ IndexError)ÚselfÚentryZheadlineZdatlistZheadlist©r ú/lib/python3.7/site-packages/Bio/NMR/xpktools.pyÚ__init__%szXpkEntry.__init__N)Ú__name__Ú __module__Ú __qualname__Ú__doc__rr r r r r src@s(eZdZdZdd„Zdd„Zdd„ZdS) ÚPeaklista;Provide access to header lines and data from a nmrview xpk file. Header file lines and file data are available as attributes. Parameters ---------- infn : str The input nmrview filename. Attributes ---------- firstline : str The first line in the header. axislabels : str The axis labels. dataset : str The label of the dataset. sw : str The sw coordinates. sf : str The sf coordinates. datalabels : str The labels of the entries. data : list File data after header lines. Examples -------- >>> from Bio.NMR.xpktools import Peaklist >>> peaklist = Peaklist('../Doc/examples/nmr/noed.xpk') >>> peaklist.firstline 'label dataset sw sf ' >>> peaklist.dataset 'test.nv' >>> peaklist.sf '{599.8230 } { 60.7860 } { 60.7860 }' >>> peaklist.datalabels ' H1.L H1.P H1.W H1.B H1.E H1.J 15N2.L 15N2.P 15N2.W 15N2.B 15N2.E 15N2.J N15.L N15.P N15.W N15.B N15.E N15.J vol int stat ' c Cs t|ƒŽ}| ¡ d¡d|_| ¡ d¡d|_| ¡ d¡d|_| ¡ d¡d|_| ¡ d¡d|_| ¡ d¡d|_dd„|Dƒ|_ WdQRXdS)zInitialize the class.Ú rcSsg|]}| d¡d‘qS)rr)r)Ú.0Úliner r r ú lsz%Peaklist.__init__..N) ÚopenÚreadlinerÚ firstlineÚ axislabelsÚdatasetÚswÚsfÚ datalabelsÚdata)r ZinfnZinfiler r r r_s zPeaklist.__init__c CsÒd}d}i|_x¨|jD]ž}t||jƒj|d}| d¡d}t|ƒ}|dkrR|}|dkr^|}t||gƒ}t||gƒ}t |ƒ}y|j|  |¡Wqt k r²|g|j|<YqXqW||jd<||jd<|jS)aªReturn a dict of lines in 'data' indexed by residue number or a nucleus. The nucleus should be given as the input argument in the same form as it appears in the xpk label line (H1, 15N for example) Parameters ---------- index : str The nucleus to index data by. Returns ------- resdict : dict Mappings of index nucleus to data line. Examples -------- >>> from Bio.NMR.xpktools import Peaklist >>> peaklist = Peaklist('../Doc/examples/nmr/noed.xpk') >>> residue_d = peaklist.residue_dict('H1') >>> sorted(residue_d.keys()) ['10', '3', '4', '5', '6', '7', '8', '9', 'maxres', 'minres'] >>> residue_d['10'] ['8 10.hn 7.663 0.021 0.010 ++ 0.000 10.n 118.341 0.324 0.010 +E 0.000 10.n 118.476 0.324 0.010 +E 0.000 0.49840 0.49840 0'] éÿÿÿÿz.LÚ.rÚmaxresÚminres) rr rrrrÚintÚmaxÚminÚstrÚappendÚKeyError)r Úindexr#r$rZindÚkeyÚresr r r Ú residue_dictns*     zPeaklist.residue_dictc Csžt|dƒŠ}| |j¡| d¡| |j¡| d¡| |j¡| d¡| |j¡| d¡| |j¡| d¡| |j¡| d¡WdQRXdS)z7Write header lines from input file to handle ``outfn``.ÚwrN)rÚwriterrrrrr)r ZoutfnZoutfiler r r Ú write_header©s            zPeaklist.write_headerN)rrrrrr.r1r r r r r4s);rcCsJt||ƒ}t||d… ¡dƒ}|d|…t|ƒ|||d…}|S)zËReplace an entry in a string by the field number. No padding is implemented currently. Spacing will change if the original field entry and the new field entry are of different lengths. Nr)Ú_find_start_entryÚlenrr()rZfieldnZnewentryÚstartÚlengÚnewliner r r Ú replace_entryºs $r7cCsš|dkr dSd}t|ƒ}|ddkr.d}d}nd}d}xZ||kr||kr|r†||dkrn||ddkrnd}n||dkr†d}|d7}|d7}q8W|dS)a"Find the starting character for entry ``n`` in a space delimited ``line`` (PRIVATE). n is counted starting with 1. The n=1 field by definition begins at the first character. Returns ------- starting character : str The starting character for entry ``n``. rrú FT)r3)rÚnÚcr5ZinfieldZfieldr r r r2És$   r2cCsðg}t||ƒ\}}|dd}|dd}x4|D],}||dkrH|d}||dkr0|d}q0W|} x†| |krêd} t| ƒ} | } xN|D]F}|| } | |krº| dt|| d| ƒj|} n| d7} | d7} q„W| d7} | | ¡| d7} qfW|S)azGenerate a data table from a list of input xpk files. Parameters ---------- fn_list : list List of .xpk file names. datalabel : str The data element reported. keyatom : str The name of the nucleus used as an index for the data table. Returns ------- outlist : list List of table rows indexed by ``keyatom``. rr$r#ú z *rr)Ú _read_dictsr(rrr))Úfn_listZ datalabelÚkeyatomZoutlistÚ dict_listZlabel_line_listZminrZmaxrÚ dictionaryr-Úcountr,rZlabelr r r Ú data_tableõs0        "   rBcCsFg}g}x4|D],}t|ƒ}| |¡}| |¡| |j¡qW||gS)zBRead multiple files into a list of residue dictionaries (PRIVATE).)rr.r)r)r=r>r?Zdatalabel_listÚfnZpeaklistr@r r r r<+s   r<Ú__main__r)Ú run_doctestN) rZ HEADERLENrrr7r2rBr<rZ Bio._utilsrEr r r r Ús),6