ó —™xTc@ s—ddlmZddlmZdefd„ƒYZedkr“dZdZeeƒZe ej ƒeeƒZe ej ƒe ej ƒƒndS( iÿÿÿÿ(tdivision(tprint_functiont pcr_parsercB s\eZd d ed„Zed„Zdd„Zdd„Zd„Z dd„Z d „Z RS( cC sÖddlm}d|_|ƒ|_|jƒ|_||_x|jD]}t|ƒqGW|jdjdƒsÈ|jr‰t dƒ‚qÈx<|jj ƒD](}|jdƒr™|jj |ƒq™q™Wn|j ƒdS(sFFunction to parse a FullProf command file into a ConfigObj It was modeled according to the FullProf manual and actual output files from FullProf and still far from being complete. :param inputstring: a string containing a whole commented pcr file like fp2k would format it. :type inputstring: string iÿÿÿÿ(t ConfigObjiit!s{ This function only works with correctly commented FullProf files! Please run fp2k on your input file first.N( t configobjRtLOtcfgt splitlinestlinestenforce_valid_commentstprintt startswitht ValueErrortcopytremovet_parse(tselft inputstringtpcrfileR Rtline((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/read_pcr.pyt__init__s      cC s;|jd7_|r#|j|jS|j|jjƒSdS(Ni(RR tsplit(Rtraw((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/read_pcr.pyt__get_next_line"st c C sú|jƒ}d}xá|jdƒD]Ð}t|ƒdkr>Pnt|ƒ|krc||jƒ}n|djƒ}|dkr¡t|jdƒƒ||jƒƒ||d?dƒ|d@ƒ||dAdƒ||dBdƒ|dCƒ||dDdƒ||dEdƒ|jdFdkr=|dGƒ||dHdƒ||dIdƒn|| t|dƒ0 not supported (yet)! IRESO={}Rs!Ipr shIOT, IPL, IPC, MAT, NXT, LST1, LST2, LST3, IPL1, IPL2, INSTRM, JCIL, JSY, JLKH, JFOU, ISHOR, IANALYs ! Lambda1 s5LAMDA1, LAMDA2, RATIO, BKPOS, WDT, CTHM, TMR, RLIM, KRs!NCY sRMCYCLE, EPS, RELAX1, RELAX2, RELAX3, RELAX4, THMIN, STEP, THMAX, ALPSD, SENT0tiftICRYGtNBCKGDiiýÿÿÿs! 2Thetat backgroundtMAXSs! Zero sAZER, FLGZER, SYCOS, FLCOS, SYSIN, FLSYN, LAMBDA, FLAMBDA, IGLMOREitIGLMOREs! Microabsorptions! P0 sCPO, Cp, CCp, Tau, CTaus! BackgroundtbackgroundpolytNPHASEs!-------s! Data for PHASEtPHSNMs!Nat saNAT, NDIST, NMAGC, PREF1, PREF2, PREF3, JBT, IRF, ISYM, ISTR, IFURT, ATZ, NVK, NPRO, IMOREtiiifffiiiiifiiitIMORERiRAtISYMs!Atom tNATs1LABEL, NTYP, X, Y, Z, B, N, IOPIN, IOPFIN, N_Typet ssfffffiiis!CX, CY, CZ, CB, CN, CMx, CMy, CMzR7s!-------> Profile s ! Scale s,S, GAM1, Bov, STR1, STR2, STR3, IstrainModeltffffffis%CS, FLGAM1, CBov, CSTR1, CSTR2, CSTR3tIRFis ! Us!U, V, W, X, Y, IG, SZ, IsizeModeltfffffffisCU, CV, CW, CX, CY CIG CSZs! a sa, b, c, alpha, beta, gammasCA, CB, CC, CD, CE, CFs ! Pref1 sG1, G2, Pas1, Pas2, Pas3, Pas4s$CG1, CG2, CPas1, CPas2, CPas3, CPas4tRATIOs!Additional U,V,Ws U2, V2, W2s CU2, CV2, CW2R.Ntfffffffft ffffffffi(R R!RR R RRt_pcr_parser__parse_linet_pcr_parser__check_commentR R+R0tabsR"RtzipROtTrue(RRt get_next_linet parse_linet check_commentR^R_RR&t lineflagsRbtvRR.RWtphaseR7R8tatom((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/read_pcr.pyRdsÒ                      (                              N( t__name__t __module__tNoneRtRtFalseRRpRqR3R1R(((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/read_pcr.pyRs     t__main__s‘ COMM CeO2 CSIRO Test 25-143 ! Current global Chi2 (Bragg contrib.) = 11.67 ! Files => DAT-file: ce1.dat, PCR-file: ce1 !Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut 0 5 1 0 0 0 0 0 0 0 0 0 0 2 0 0 0 1 1 ! !Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana 0 0 1 0 1 0 4 0 0 1 0 1 1 1 2 0 0 ! ! Lambda1 Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz 2nd-muR -> Patt# 1 1.540560 1.544330 -0.50000 25.000 15.0000 0.9100 0.0000 30.00 0.0000 0.0000 ! !NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0 6 0.10 1.00 1.00 1.00 1.00 25.0000 0.025000 143.0000 0.000 0.000 ! ! 20 !Number of refined parameters ! ! Zero Code SyCos Code SySin Code Lambda Code MORE ->Patt# 1 0.02573 11.0 0.00000 0.0 0.00000 0.0 0.000000 0.00 1 ! ! Microabsorption coefficients for Pattern# 1 ! P0 Cod_P0 Cp Cod_Cp Tau Cod_Tau 0.0000 0.00 1.2313 141.00 0.1340 151.00 ! Background coefficients/codes for Pattern# 1 (Polynomial of 6th degree) 24.538 -17.709 6.313 -0.604 0.000 0.000 21.00 31.00 41.00 51.00 0.00 0.00 !------------------------------------------------------------------------------- ! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 0.00 !------------------------------------------------------------------------------- CeO2 ! !Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More 2 0 0 1.0 1.0 1.0 0 0 0 0 0 688.480 0 5 0 ! F m 3 m <--Space group symbol !Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes Ce CE 0.00000 0.00000 0.00000 0.46033 0.02000 0 0 0 0 # color green conn O O 0.0 3.2 0.00 0.00 0.00 161.00 0.00 O O 0.25000 0.25000 0.25000 0.92218 0.04000 0 0 0 0 # color blue 0.00 0.00 0.00 171.00 0.00 !-------> Profile Parameters for Pattern # 1 ! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model 0.10216E-02 0.36723 0.00000 0.00000 0.00000 0.00000 0 61.00000 81.000 0.000 0.000 0.000 0.000 ! U V W X Y GauSiz LorSiz Size-Model 0.007618 -0.008887 0.010210 0.003351 0.000000 0.000000 0.000000 0 101.000 91.000 111.000 121.000 0.000 0.000 0.000 ! a b c alpha beta gamma #Cell Info 5.412223 5.412223 5.412223 90.000000 90.000000 90.000000 #multiple box -1 1 -1 1 0 1 71.00000 71.00000 71.00000 0.00000 0.00000 0.00000 ! Pref1 Pref2 Asy1 Asy2 Asy3 Asy4 0.00000 0.00000 0.06233 0.00000 0.00000 0.00000 0.00 0.00 131.00 0.00 0.00 0.00 !Additional U,V,W parameters for Lambda2 0.007461 -0.005255 0.008197 <-- U2,V2,W2 for lambda(2) 191.000000 201.000000 181.000000 ! Limits for selected parameters : 14 0.0010 2.0000 0.0000 0 Cp_mabs_pat1 15 0.0010 2.0000 0.0000 0 Tau_mabs_pat1 ! 2Th1/TOF1 2Th2/TOF2 Pattern # 1 25.000 143.000 1 sÌCOMM unnamed ! Files => DAT-file: rnd_27A_15L_10M_02H_P_1_25_, PCR-file: rnd_27A_15L_10M_02H_P_1_25_ !Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut 2 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 ! !Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana 2 0 1 1 1 0 4 0 0 1 10 0 1 4 2 0 0 ! ! Lambda1 Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz 2nd-muR -> Patt# 1 1.541800 1.541800 1.00000 60.000 5.0000 0.0000 0.0000 50.00 0.0000 0.0000 ! !NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0 1 0.01 1.00 1.00 1.00 1.00 10.0000 0.100000 100.0000 0.000 0.000 ! ! 0 !Number of refined parameters ! ! Zero Code SyCos Code SySin Code Lambda Code MORE ->Patt# 1 0.00000 0.0 0.00000 0.0 0.00000 0.0 0.000000 0.00 0 ! Background coefficients/codes for Pattern# 1 (Polynomial of 6th degree) 0.000 0.000 0.000 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 !------------------------------------------------------------------------------- ! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 0.00 !------------------------------------------------------------------------------- Phase_1 ! !Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More 27 0 0 0.0 0.0 1.0 0 0 0 0 0 924.976 0 0 0 ! P 1 <--Space group symbol !Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes Cs1 Cs 0.25575 0.74218 0.01280 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Cs2 Cs 0.76337 0.84611 0.64963 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C1 C 0.80799 0.01687 0.87219 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C2 C 0.95999 0.89218 0.97716 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C3 C 0.61730 0.40423 0.22206 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C4 C 0.96991 0.50496 0.26698 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C5 C 0.27434 0.34505 0.32297 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C6 C 0.51741 0.89889 0.90591 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C7 C 0.28570 0.06143 0.11813 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C8 C 0.85987 0.32773 0.87587 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C9 C 0.57367 0.37951 0.94405 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C10 C 0.74819 0.35206 0.92477 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C11 C 0.11661 0.17692 0.48152 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C12 C 0.68782 0.53267 0.57410 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C13 C 0.35920 0.22199 0.20957 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C14 C 0.54158 0.59845 0.57855 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 C15 C 0.10057 0.16401 0.79612 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti1 Ti 0.42526 0.93883 0.93721 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti2 Ti 0.81513 0.52398 0.20025 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti3 Ti 0.51151 0.35888 0.34305 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti4 Ti 0.43735 0.05657 0.82934 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti5 Ti 0.96559 0.21095 0.23956 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti6 Ti 0.59096 0.29067 0.09393 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti7 Ti 0.24350 0.09520 0.50214 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti8 Ti 0.60861 0.39336 0.54098 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti9 Ti 0.80180 0.14419 0.13294 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 Ti10 Ti 0.49678 0.67274 0.97981 0.39478 1.00000 0 0 0 0 0.00 0.00 0.00 0.00 0.00 !-------> Profile Parameters for Pattern # 1 ! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model 0.10000E-01 0.00000 0.03837 0.00000 0.00000 0.00000 0 0.00000 0.000 0.000 0.000 0.000 0.000 ! U V W X Y GauSiz LorSiz Size-Model 1.706310 -1.179299 0.405540 0.000000 0.000000 0.000000 0.000000 0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 ! a b c alpha beta gamma #Cell Info 9.422933 12.249814 16.018988 83.000000 109.000000 129.000000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ! Pref1 Pref2 Asy1 Asy2 Asy3 Asy4 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00 0.00 0.00 0.00 0.00 0.00 ! 2Th1/TOF1 2Th2/TOF2 Pattern # 1 10.000 100.000 1 N( t __future__RRtobjectRR|t testfile1t testfile2txR RR1(((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/read_pcr.pytsÛ Ah