ó í™xTc@ sÐddlmZddlZddlmZddlZddlmZd%Zde fd „ƒYZ d e fd „ƒYZ d „Z d Z dZedkrÌddlZddlZejde deƒZejdddddƒejdddddddƒejdddddddƒejddd dd!dd"ƒejƒ\ZZye eeƒWqÌe k rŽejƒejd#ƒqÌe k rÈZejd$eIJejƒejd#ƒqÌXndS(&iÿÿÿÿ(tdivisionN(tlstbx(t refinements.inss.ress.ciftcommand_line_errorcB seZRS((t__name__t __module__(((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/command_line/refine.pyR stnumber_of_arguments_errorcB seZRS((RR(((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/command_line/refine.pyR sc C sMdt|ƒkodkns.tƒ‚n|d}d}d}t|ƒdkri|d\}}nTt|ƒdkr½tjj|dƒ\}}|tkr°|d}q½|d}ntjj|ƒ\}}|säd}n|dkrý|d}n|dkrC|dkr%|d} } n|d|} } | | }ntjj|ƒ\} } x3|| fD]%}|tkrhtd |ƒ‚qhqhWx9||fD]+} tjj| ƒsžtd | ƒ‚qžqžWtjj|ƒr|j rüt j d |IJqtd |ƒ‚n|d kr9t j jd|d|ƒ} nt j jd|d|ƒ} xk| jjƒD]Z} | jjtƒ| jjƒrœ| jjtƒn| jjƒrd| jjtƒqdqdWtjjd| jƒd|jd|jd|jƒ}|j ƒ| d kr!t!d| ƒ‚nt"|dƒ}| jj#|ƒWdQXdS(Niiiis.inss.hkls.ress-outsunsupported extension: %ssNo such file %ss' WARNING: file %s will be overwritten. s@refuse to overwrite file %s (use option 'overwrite' to force it)s.ciftmodelt reflectionst ins_or_resthklt non_linear_lstn_max_iterationstgradient_thresholdtstep_thresholds"Write refined structure to %s filetw($tlenRtNonetostpathtsplitexttallowed_input_file_extensionsRtisfilet overwritetsyststderrRRtfrom_cift from_shelxtxray_structuret scattererstflagst set_grad_sitetTruet use_u_isotset_grad_u_isot use_u_anisotset_grad_u_anisoRtnormal_eqns_solvingtnaive_iterationst least_squarest max_cycleststop_if_max_derivative_belowtstop_if_shift_norm_belowtdotNotImplementedErrortopent as_cif_simple(t filenamestoptionstinput_filenametoutput_filenametreflections_filenamet_texttin_roottin_exttout_roottout_exttfilenametxmtsctstepstout((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/command_line/refine.pytrunsr"                          s‚refine [options] INPUT refine [options] INPUT REFLECTIONS refine [options] INPUT OUTPUT refine [options] INPUT REFLECTIONS OUTPUT s+Supported formats for the INPUT and OUTPUT files are CIF and ShelX whereas REFLECTIONS file format may be any of those supported by iotbx.reflection_file_reader. A certain amount of guessing is done by the program: - if INPUT lacks any extension, a .ins extension is appended; - if OUTPUT is not specified, o if INPUT is a .ins file, then OUTPUT is a .res file with the same root; o otherwise OUTPUT has the same extension as INPUT but with "-out" appended to INPUT root. - if REFLECTIONS is not specified, it is INPUT root with a .hkl extension t__main__tusaget descriptions --overwritetactiont store_truethelpsallows OUTPUT to be overwrittens--stop-if-max-derivative-belowttypetfloattdefaultgH¯¼šò×z>slStop refinement as soon as the largest absolute value of objective derivatives is below the given threshold.s--stop-if-shift-norm-belowsmStop refinement as soon as the Euclidean norm of the vector of parameter shifts is below the given threshold.s --max-cyclestintisIStop refinement as soon as the given number of cycles have been performedis ERROR: %s (s.inss.ress.cif(t __future__RRtscitbxRt scitbx.lstbx.normal_eqns_solvingtsmtbxRRt RuntimeErrorRRR?t here_usagethere_descriptionRRtoptparset OptionParsertparsert add_optiont parse_argsR0targst print_usagetexitterrRt print_help(((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/command_line/refine.pytsX   O