Ri:$rdZdZGddZGddZdZdZdZd Zed k(rd d l m Z e y y )z:Tools to manipulate data from nmrview .xpk peaklist files.ceZdZdZdZy)XpkEntryaProvide dictionary access to single entry from nmrview .xpk file. This class is suited for handling single lines of non-header data from an nmrview .xpk file. This class provides methods for extracting data by the field name which is listed in the last line of the peaklist header. Parameters ---------- xpkentry : str The line from an nmrview .xpk file. xpkheadline : str The line from the header file that gives the names of the entries. This is typically the sixth line of the header, 1-origin. Attributes ---------- fields : dict Dictionary of fields where key is in header line, value is an entry. Variables are accessed by either their name in the header line as in self.field["H1.P"] will return the H1.P entry for example. self.field["entrynum"] returns the line number (1st field of line) c|j}|j}tt||dd|_ |d|jd<y#t$rYywxYw)Initialize the class.Nentrynum)splitdictzipfields IndexError)selfentryheadlinedatlistheadlists H/home/agent/.friday_env/lib/python3.12/site-packages/Bio/NMR/xpktools.py__init__zXpkEntry.__init__$s]++->>#3x56  &-ajDKK #   sA AAN)__name__ __module__ __qualname____doc__rrrr s 2 rrc"eZdZdZdZdZdZy)Peaklista;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 ' cpt|5}|jjdd|_|jjdd|_|jjdd|_|jjdd|_|jjdd|_|jjdd|_|Dcgc]}|jddc}|_ dddycc}w#1swYyxYw)r rN) openreadliner firstline axislabelsdatasetswsf datalabelsdata)rinfninfilelines rrzPeaklist.__init__^s $Z C6#__.44V>> from Bio.NMR.xpktools import Peaklist >>> peaklist = Peaklist('../Doc/examples/nmr/noed.xpk') >>> residue_d = peaklist.residue_dict('H1') >>> sorted(residue_d.keys()) ['10', '3', '4', '5', '6', '7', '8', '9', 'maxres', 'minres'] >>> residue_d['10'] ['8 10.hn 7.663 0.021 0.010 ++ 0.000 10.n 118.341 0.324 0.010 +E 0.000 10.n 118.476 0.324 0.010 +E 0.000 0.49840 0.49840 0'] z.L.rmaxresminres) r r(rr'r r intmaxminstrappendKeyError)rindexr/r0r+indkeyress r residue_dictzPeaklist.residue_dictls6 II (D4188FC))C.#Cc(C||&#'F&#'Fc(C ( #%%d+# (,% ($ (yy ("& # (sCC:9C:cVt|d5}|j|j|jd|j|j|jd|j|j|jd|j|j |jd|j|j |jd|j|j|jddddy#1swYyxYw)z7Write header lines from input file to handle ``outfn``.wrN)r writer"r#r$r%r&r')routfnoutfiles r write_headerzPeaklist.write_headers %  " MM$.. ) MM& ! MM$// * MM& ! MM$,, ' MM& ! MM$'' " MM& ! MM$'' " MM& ! MM$// * MM& ! " " "s D DD(N)rrrrrr;rArrrrr3s(T C9v"rrct||}t||djd}|d|t|z|||zdz}|S)zReplace an entry in a string by the field number. No padding is implemented currently. Spacing will change if the original field entry and the new field entry are of different lengths. Nr)_find_start_entrylenr r4)r+fieldnnewentrystartlengnewlines r replace_entryrJsX dF +E tEF|!!#A& 'D6ElS]*T54<2B-CCG Nrc|dk(ryd}t|}|ddk(rd}d}nd}d}||kr<||kr7|r%||dk(r||dz dk7rd}n||dk7rd}|dz }|dz }||kr||kr7|dz S)a"Find the starting character for entry ``n`` in a space delimited ``line`` (PRIVATE). n is counted starting with 1. The n=1 field by definition begins at the first character. Returns ------- starting character : str The starting character for entry ``n``. rr FT)rD)r+ncrHinfieldfields rrCrCs Av A t9D Aw#~ d(uqy Aw#~$q1u+"47c>"GQJE Q d(uqy q5Lrczg}t||\}}|dd}|dd}|D]}||dkr|d}||dkDs|d}|} | |krpd} t| } | } |D];}|| } | |vr&| dzt|| d| j|z} n| dz } | dz } =| dz } |j | | dz } | |krp|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``. rr0r/ z *rr) _read_dictsr4rr r5)fn_list datalabelkeyatomoutlist dict_listlabel_line_listminrmaxr dictionaryr:countr9r+labels r data_tabler_s'&G!,Wg!>I Q< !D Q< !D( *X& &h'D *X& &h'D ( C +#h# J#E*Ej 4K(:c?1+=u"E"L"LY"WW  QJE   t q +" Nrcg}g}|D]J}t|}|j|}|j||j|jL||gS)zBRead multiple files into a list of residue dictionaries (PRIVATE).)rr;r5r')rTrVrXdatalabel_listfnpeaklistr\s rrSrS)scIN3B<**73 $h112 3 ~ &&r__main__r) run_doctestN) r HEADERLENrrrJrCr_rSr Bio._utilsrerrrrhsU A &&RB"B"J )X3l ' z&Mr