ó —™xTc@ sƒddlmZddlmZddlmZdddd„Zdd d d ejd ƒjƒdd „Zgd „Z dd d d ejd ƒjƒddd „Z e dkrddl m Z ddlmZddlmZejdejddƒddgdddƒZejdejddƒddgdddƒZe ƒZe eeefddƒeejƒƒejndS(iÿÿÿÿ(tdivision(tprint_function(t wavelengthsitgð?c s|jƒ|dkr(djˆƒ}n|jƒ}|jƒ}djdˆd|dt|ƒddd |jƒƒ}xo|D]g}|d jd |jd |jƒd |jdd|jdd|jdd|j ƒd|j ƒ7}q}W|j ƒj ƒ\}} } } } } |djdd|d|d| d| d| d| d| dˆƒ7}‡fd†}|||j ƒjƒƒd 7}|d!7}|S("sCreate a pcr phase block skelleton with placeholder strings for different refinement options. (for internal use) :param phase: a crystal structucture :type phase: cctbx.xray_structure :param number: the number of the phase :type number: integer :param name: a title to be used for the phase in the pcr file :type name: string :param scale_down: factor to divide intensities by (to avoid overflows) :type scale_down: float :returns: the pcr phase block skelleton as a string :rtype: string Rs Phase_{0}s!------------------------------------------------------------------------------- ! Data for PHASE number: {number} ==> Current R_Bragg for Pattern# {number}: !------------------------------------------------------------------------------- {name:s} ! !Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More {nat:>4d} 0 0 0.0 0.0 0.0 0 0 0 0 0 {atz} 0 0 0 ! {space_group} <--Space group symbol !Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes tnumbertnametnattatzgt space_groups—{lbl:s} {stype:s} {x:f} {y:f} {z:f} {biso:7.5f} {occ:7.5f} 0 0 0 0 ##_ap*_## ##_ap*_## ##_ap*_## 0.00 0.00 tlbltstypetxityitzitbisotoccs˜!-------> Profile Parameters for Pattern # 1 ! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model {scale:f} 0.10033 0.03837 0.00000 0.00000 0.00000 0 ##_scf_## ##_shp1.{n}_## ##_shp2.{n}_## 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 ##_prfu.{n}_## ##_prfv.{n}_## ##_prfw.{n}_## 0.000 0.000 0.000 0.000 ! a b c alpha beta gamma #Cell Info {a:f} {b:f} {c:f} {alpha:f} {beta:f} {gamma:f} tscaleg{®Gáz„?tatbtctalphatbetatgammatnc s‘|jƒ}|dkr%djˆƒS|dkr>djˆƒS|dkrWdjˆƒS|dkrpd jˆƒS|d kr‰d jˆƒSd SdS(Nt triclinicsU ##_lp1.{0}_## ##_lp2.{0}_## ##_lp3.{0}_## ##_lp4.{0}_## ##_lp5.{0}_## ##_lp6.{0}_##t monoclinicsP ##_lp1.{0}_## ##_lp2.{0}_## ##_lp3.{0}_## ##_lp4.{0}_## 0.00 ##_lp5.{0}_##t orthorhombicsF ##_lp1.{0}_## ##_lp2.{0}_## ##_lp3.{0}_## 0.00 0.00 0.00ttrigonalt hexagonalt tetragonalsF ##_lp1.{0}_## ##_lp1.{0}_## ##_lp2.{0}_## 0.00 0.00 0.00tcubicsF ##_lp1.{0}_## ##_lp1.{0}_## ##_lp1.{0}_## 0.00 0.00 0.00s6 0.00 0.00 0.00 0.00 0.00 0.00(RRR(tlowertformat(t xtal_system(R(sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/write_pcr.pyt__constraints_from_symmFs           s s¥! 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 (t/make_scatterer_labels_shelx_compatible_in_placeR t scattererstcrystal_symmetrytlentspace_group_infotlabeltelement_symboltsitetb_isot occupancyt unit_cellt parametersRtcrystal_system(tphaseRRt scale_downtscatttsymmttmptatomRRRRRRR"((RsF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/write_pcr.pyt_make_phase_blocks>             $   tunnameditCUc C s¹t|ƒ}d|d}|dj||||d|dkrDdndƒ7}|djd d d |ƒ7}|d 7}x>t|ƒD]0} |t|| d | dddd|ƒ7}qW|S(sßCreate a pcr skelleton with placeholder strings for different refinement options. (for internal use) :param phases: a list/tuple/set of structures :type phases: list(cctbx.xray_structure) :param title: a title to be used in the pcr file :type title: string :param jobtype: the jobtype to be used :type jobtype: integer :param nprof: the default peak profile to be used :type nprof: integer :param nbckgd: the type of background to be used :type nbckgd: integer :param wavelength: the wavelength to be used in Angstroms :type wavelength: float :param scale_down: factor to divide intensities by (to avoid overflows) :type scale_down: float :returns: the pcr skelleton as a string :rtype: string sCOMM s s¥!Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut {0} {1} {2} {3} 0 0 0 {dum} 0 0 0 0 0 0 0 0 0 0 1 tdumiiis! !Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 Syo Prf Ins Rpa Sym Hkl Fou Sho Ana 2 0 1 1 1 0 0 0 1 1 {filetype} 0 1 4 2 0 0 ! ! lambda1 Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz ->Patt# 1 {xlambda} {xlambda} 1.0000 60.000 5.0000 0.0000 0.0000 50.00 0.0000 ! !NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0 20 0.01 1.00 1.00 1.00 1.00 10.0000 0.100000 100.0000 0.000 0.000 ! ! #__npar__# !Number of refined parameters tfiletypet0txlambdasz! ! 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 RRRR1(R&R trangeR6( tphasesttitletjobtypetnproftnbckgdt wavelengthR1tnphasetretti((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/write_pcr.pyt_pcr_skelleton]s 1 .c C sddl}d}|}tƒ}d„}|gk r§xn|D]c}|dkr‹xN|jd|ƒD]"}||||ƒ}|d7}qbWq=|dkr x|jd|ƒD]Z}|jd ƒ|krå|||jd ƒ<|d7}n|||||jd ƒƒ}qªWq=|d kr‹x†|jd |ƒD]Z}|jd ƒ|kre|||jd ƒ<|d7}n|||||jd ƒƒ}q*Wq=td j|ƒƒ‚q=WnxT|jd |ƒD]@}||jƒ djt|jd ƒƒƒ||j ƒ}qºW|j dt |dƒƒ}|S(sëParse a pcr skelleton to enable or disable the different refinement parameters. The placeholder string for a parameter starts with '##_' and ends with '_##'. (for internal use) Allowed values in the freeparams list are: * 'scale' --> free all scale factors * 'lattice' --> free all lattice parameters * 'profile' --> free all profile parameters The parameters are freed according to their order inside the list. If an empty list is passed all parameters will be fixed. :param inputstring: a string containing placeholders for different refinement variables :type inputstring: string :param freeparams: a list of parameter sets to free :type freeparams: list :returns: the parsed string :rtype: string iÿÿÿÿNicS sMt|jdƒƒ}dj|ƒj|ƒ}||jƒ |||jƒS(Nis {0:>d}1.00(R&tgroupR trjusttstarttend(tstringtmatchtvartmlentreplace((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/write_pcr.pyt__replace_match¹sRs ##_scf_##tlattices ##_lp.*?_##itprofiles ##_prf*?_##sunknown parameter type: '{0}'s ##_.*?_##s0.00s #__npar__#( tretdicttfinditerRHt ValueErrorR RJRIR&RKRPtstr( t inputstringt freeparamsRTtvarcountREt param_to_varRQtparamtm((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/write_pcr.pyt_set_ref_flagsžs8        &  &>c C s›t|tttfƒs$|f}ntd|d|d|d|d|d|ƒ} |dkrlt| ƒ} nt| dd d d gƒ} t| d |ƒd S(sFWrite a pcr file to a file or IO buffer. :param s: a buffer/file to write to :type s: StringIO or filestream :param phases: a list/tuple/set of structures or a single crystal structucture :type phases: list(cctbx.xray_structure) or cctbx.xray_structure :param title: a title to be used in the pcr file :type title: string :param jobtype: the jobtype to be used (0=xray refine, 2=xray powdersim) :type jobtype: integer :param nprof: the default peak profile to be used :type nprof: integer :param nbckgd: the type of background to be used :type nbckgd: integer :param wavelength: the wavelength to be used in Angstroms :type wavelength: float :param I_obs: observed intensities :type I_obs: cctbx.miller :param scale_down: factor to divide intensities by (to avoid overflows) :type scale_down: float R>R?R@RARBR1iRZRRRRStfileN(t isinstancettupletlisttsetRGR_tprint( tsR>R?R@RARBRCtI_obsR1tpcrfile((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/write_pcr.pyt write_pcrÚs    t__main__(tStringIO(tsgtbx(trandom_structureR'RtelementstCi tu_isog{®Gázt?i{iR@iN(t __future__RRt cctbx.eltbxRR6tcharacteristict as_angstromRGR_tNoneRit__name__RktcctbxRltcctbx.developmentRmtxray_structureR'txrs1txrs2tbufferRetgetvaluetclose(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/write_pcr.pyts>Y ; > (