ó —™xTc@ sddlmZddlmZddlmZejdƒjƒdddd„Zejdƒjƒde dd„Z d d „Z e d krþdd l mZdd lmZejdejddƒddgdddƒZeee eƒd ƒƒndS(iÿÿÿÿ(tdivision(tprint_function(t wavelengthstCUc C s=|||gjdƒdkr-tdƒ‚nddlm}ddl}ddl}ddl}y|jdddtƒ} Wnt k r“‚nX| j } |j j | ƒd } || |d d d |d |ƒ| j ƒy6|dk r|j|| d ƒn|dk rnWnt k r(‚nXt| dd ƒdS(s´This function tries to rietveld refine a structure using FullProf. If I_obs is given neither a Profile or a ProfileFile may be specified. 'Profile' and 'ProfileFile' are also exclusive. :param crystalstructure: the starting model for the refinement :type crystalstructure: cctbx.xray.structure :param wavelength: the x-ray wavelength for the given intensity data :type wavelength: float :param I_obs: observed Intensities :type I_obs: cctbx.miller :param Profile: a XRD profile given as a list/tuple of (2-theta, intensity)-tuples :type Profile: list/tuple(tuple(2theta,I)) :param ProfileFile: path to a XRD profile as FullProf .prf file :type ProfileFile: string is7You may only pass one of I_obs, Profile and ProfileFileiÿÿÿÿ(t write_pcrNtsuffixs.pcrtdeleteitjobtypet wavelengthtI_obss.dattverbose(NN(tcounttNonet ValueErrorRttempfiletshutiltostNamedTemporaryFiletFalsetIOErrortnametpathtsplitexttclosetcopyfilet run_fullprof( tcrystalstructureRR tProfilet ProfileFileRRRRtftpcrfiletbasepath((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/__init__.pytrietveld_refine_structure s0          tgð?c C sŽddlm}ddlm}ddl}ddl}y:|dkrb|jdddtƒ} nt|d ƒ} Wntk rˆ‚nX| j } |j j | ƒd } || |d d d |d|ƒ| j ƒ|dkrã‚nt | dd ƒ| d} t| dƒ} | jƒd} | j ƒ| d} |tkrS|j| | dƒnt| d ƒ} | j| ƒ| j ƒd}y5|d| ƒ}|jd|jƒddƒd }WnGtk rÊ‚n4tk rýt|d |d|d|d|dƒSXd}|tkr„xqdddddd d!d"ddd#d$g D]B}y|j| |ƒWq;tk rl‚q;tk r|q;Xq;Wn||fS(%s@ Get integrated intensities and a a simulated XRD profile calculated with FullProf (has to be installed and callable via "fp2k"). :param crystalstructure: a crystal structure to calculate the intensities for :type crystalstructure: cctbx.xray.structure :param wavelength: x-ray wavelength in angstroms :type wavelength: float :param filename: a filepath to save the in- and output of FullProf to :type filename: string :param keep_results: keep the (temporary) files from FullProf for a later manual inspection :type keep_results: boolean :param scale_down: factor to divide intensities by (to avoid overflows) :type scale_down: float :returns: calculated integral intensities, calculated profile :rtype: cctbx.miller, list(tuple(float,int)) XXX Todo: implement extraction of calculated profile iÿÿÿÿ(R(tany_reflection_fileNR!Rs.pcrRtwiRiRt scale_downi'R s.foutris.hkls.hkldatat file_nametcrystal_symmetryt assume_shelx_observation_type_ist intensitiestfilenamet keep_resultsg$@s.syms.inss.prfs.sims.sums.outs1.fsts1.sub(Rtiotbx.reflection_file_readerR"RRRRtopenRRRRRRt readlinestTruetrenamet writelinesR tas_miller_arraysR'tKeyboardInterruptt Exceptiontsimulate_powder_patterntunlink(RRR*R+R$RR"RRRRRthklfiletlinestf_calctrftprofiletext((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/__init__.pyR5>sf                       ic C sñddlm}ddl}ddl}|jjƒ|jjƒ|jƒjdƒrp|j j |ƒd}n|j j |dƒs™t |dƒ‚n|j j |ƒ}|jƒ}|j j|ƒd}y"|j|ƒ|j|dƒWn$tk r‚ntk rnX|jdd|j j|ƒd ƒjƒj}dsQ|rox|D]}t|ƒqXWnt|dd ƒ} | jƒ}| jƒ|jjƒds±|rÓx|D]}t|d ƒq¸Wn|jjƒ|j|ƒdS( Niÿÿÿÿ(teasy_runs.pcris.pcr not found!s.outtcommandsfp2k iR%(tlibtbxR=tsysRtstdouttflushtstderrtlowertendswithRRtexistsRtabspathtgetcwdtsplittchdirR6R3R4tfully_bufferedtraise_if_errorst stdout_linestprintR-R.R( RR R=R@Rtold_cwdtworkdirt fullprof_outtlR((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/__init__.pyR‘s>      /        t__main__(tsgtbx(trandom_structuretspace_group_infotnumberitelementstCi tu_isog{®Gázt?N(t __future__RRt cctbx.eltbxRtcharacteristict as_angstromR R RR5Rt__name__tcctbxRTtcctbx.developmentRUtxray_structureRVtxrsRNtlist(((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/fullprof/__init__.pyts  2 O $