ó ‘™xTc@ s¦dZddlmZddlmZddlmZddlmZ ddl m Z ddl mZddl mZdd lmZdd lmZdd lmZddlm Zddlm Zddlm Zdd lm Z dd l!m"Z"ddl!m#Z#ddl$m%Z%ddl&m'Z'm(Z(ddl)Z)ddl*Z*ddl+Z*ddl,Z,d„Z-d„Z.de/fd„ƒYZ0e1e2ddd„Z4d„Z5dS(sÎ This module provides a generic frontend to all of the reflection file formats supported in ``iotbx``. Note that this module can also be used indirectly via the even more generic :py:mod:`iotbx.file_reader` module, which provides a unified API for reading in any file (but calls :py:class:`iotbx.reflection_file_reader.any_reflection_file` internally). Currently, the supported formats include: - **CIF**: Crystallographic Information Format, the common syntax for specifying most structured data encountered in crystallography (but more widely used in small-molecule versus macromolecular crystallography), usually as ASCII text. May encapsulate a variety of other data types, but only reflection data (of any type) is handled by this particular module. Uses :py:mod:`iotbx.cif` internally. - **MTZ**: Binary file format established by `CCP4 `_ capable of storing any numerical data, and used by most major macromolecular crystallography software packages. Because of its speed and broad compatibility, this is the primary interchange format for reflection data in Phenix. Uses :py:mod:`iotbx.mtz` internally. - **Scalepack**: Fixed-format ASCII text produced by the program of the same name and the HKL2000 graphical interface. This is actually two separate formats: one for merged intensities (with or without Friedel mates), another for unmerged intensities and associated processing metadata. Uses either :py:mod:`iotbx.scalepack.merge` or :py:mod:`iotbx.scalepack.no_merge_original_index` internally. - **CNS**: ASCII format, not as flexible as MTZ or CIF but able to store either amplitudes or intensities, R-free flags, and Hendrickson-Lattman coefficients. Uses :py:mod:`iotbx.cns.reflection_reader` internally. - **SHELX**: Fixed-format ASCII used by the eponymous software suite. This format has significan disadvantages, discussed below. Uses :py:mod:`iotbx.shelx.hklf` internally. - **XDS**: ASCII format for processed intensities (both merged and unmerged). Uses :py:mod:`iotbx.xds.read_ascii` internally. - **D*Trek**: ASCII format produced by software sold by Rigaku. Independently, the :py:class:`cctbx.miller.array` class defines output methods for CIF, MTZ, CNS, SHELX, and unmerged Scalepack files (although only the first two are recommended for routine use). Note that the underlying formats do not always contain complete information about the crystal or even the data type. SHELX format is especially problematic as it not only omits crystal symmetry, but the same format may be used to store either amplitudes or intensities, without any distinguishing features. As a crude workaround for the latter problem, the data type may be specified as part of the file name:: hkl_file = any_reflection_file("data.hkl=hklf4") hkl_file = any_reflection_file("data.hkl=intensities") Other formats (CNS, unmerged Scalepack) may have incomplete or missing crystal symmetry. MTZ, XDS, and (usually) CIF files will be more complete. iÿÿÿÿ(tdivision(tmtz(tmerge(tno_merge_original_index(treader(treflection_reader(tindex_fobs_sigma_reader(treflnlist_reader(thklf(tcrystal_symmetry_from_ins(t option_parser(tmiller(tcrystal(t easy_pickle(tSorrytdetect_binary_fileNcC s_tj|ƒ}t|tjƒr(|gSt|ƒ}x$|D]}t|tjƒs;dSq;W|S(N(R tloadt isinstanceR tarraytlisttNone(t file_nametresultt miller_array((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_reader.pytunpickle_miller_arraysKs  cC s}ytjd|ƒ}Wntk r)n Xd|fStjd|ƒrŽytd|ƒ}Wn$tk ro‚ntk rn Xd|fSdSyt j t |ƒƒ}Wnt j k r½n Xd|fSyt jd|ƒ}Wntk rñn Xd|fSytjt |ƒƒ}Wntjk r+n Xd|fSytj|ƒ}Wn$tk r_‚ntk ron Xd|fSytjt |ƒƒ}Wn$tk r©‚ntk r¹n Xd|fSytjd|ƒ}Wn$tk rð‚ntk rn Xd |fSygtd |ƒ}t}x<|jƒjƒD](}d |ksTd |kr6t}Pq6q6W|sqt‚nWn$tk rˆ‚ntk r˜n Xd |fSytt |ƒƒ}Wn$tk rÏ‚ntk rßn Xd|fSytƒ}|j|ƒWn$tk r‚ntk r*n Xd|fSytd|ƒ}Wn$tk r^‚ntk rnn Xd|fSdS(NRtccp4_mtzscctbx.miller.arraytcns_reflection_filetcns_index_fobs_sigmatscalepack_merget!scalepack_no_merge_original_indextdtrek_reflnlistt shelx_hklft file_patht_refln_index_hs_refln.index_htcift xds_asciitxds_integrate_hklt solve_fpfm(NN(NN(Rtobjectt RuntimeErrorRtfrom_initial_blockRtKeyboardInterruptt ExceptionRtcns_reflection_readerRtopentCNS_input_Errortcns_index_fobs_sigma_readerRRt FormatErrortscalepack_no_mergetdtrek_reflnlist_readert reflnlistRt cif_readertFalsetmodeltvaluestTruetxds_ascii_readertxds_integrate_hkl_readert read_filetsolve_fpfm_reader(Rtcontenttlooks_like_a_reflection_filetblock((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_reader.pyttry_all_readersUsº                                    tany_reflection_filecB sPeZdZeed„Zd„Zd„Zd„Zde eddd„Z RS(s³ Proxy object for reading a reflection file of unspecified format, and extracting the Miller arrays contained therein. Examples -------- >>> from iotbx.reflection_file_reader import any_reflection_file >>> hkl_file = any_reflection_file("data.mtz") >>> print hkl_file.file_type() 'ccp4_mtz' >>> print type(hkl_file.file_content()) >>> miller_arrays = hkl_file.as_miller_arrays() cC s|jdƒsK|jdƒsK|jdƒsK|jdƒsK|jdƒrl|jddƒ\|_|_n~|jdƒs·|jd ƒs·|jd ƒs·|jd ƒs·|jd ƒrØ|jddƒ\|_|_n||_d|_|jd krd|_n|jdkr d|_nd|_|j}yt|ƒWn/tk rq}|rmt t |ƒƒ‚ndSX|jdk ræyt j d|ƒ|_ Wn=tk r°‚qtk rÙt d||jfƒ‚qXd|_ntd|ƒ\|_|_ dS(Ns amplitudes=shklf3=s intensities=shklf4=s hklf+ins/res=t=is =amplitudess=hklf3s =intensitiess=hklf4s =hklf+ins/resthklf3t amplitudesthklf4t intensitiesRsRNot a SHELX reflection file: %s =%s can only be used for SHELX reflection files.R(t startswithtsplitt_observation_typet _file_nametendswithRt _file_typeR,tIOErrorRtstrRRt _file_contentR)R*R?(tselfRtensure_read_accesststrictte((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_reader.pyt__init__§sL!!          cC s|jS(sReturns the file name.(RI(RO((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_reader.pyRÑscC s|jS(s=Return a string specifying the format type (e.g. 'ccp4_mtz').(RK(RO((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_reader.pyt file_typeÕscC s|jS(s-Return the underlying format-specific object.(RN(RO((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_reader.pyt file_contentÙsc C s|d'kst‚|jd&kr%gS|j}|jdƒsL|jdƒrY|d}n|d&krƒtjd|d|jƒ}n|jdkrcg}xÄ|jD]¹}|jƒ} | d&ksÓt | tjƒ rÜ|} n|| _ t j d |j ƒd |jƒd tƒ| _|j|jd |jd |d|d tƒƒj| ƒj|jƒƒƒq¢W|S|d&ks|j ƒd&kr |jdkr tjj|jƒ\} } | dkrÒtjj| ƒ\} } nx[d| d| fD].} yt| ƒ} PWqçtk rqçqçXqçWtd| fdƒ‚tjd| ƒ}| j dƒ| j!ƒ}| j"ƒt#j$d|t#j%t#j&Bt#j'Bƒ}|d&kr­td| j(ƒ‚n|j)dƒdkrÎd|_q |j)dƒdkrïd|_q td|j)dƒƒ‚n|jj*d |d|d|d|ƒ}|j+ƒdkr |jdks_|dkr|dj|djƒjd d!d"gƒƒ|dj,ƒq |jdks¸|dkrö|dj|djƒjd d#d$gƒƒ|dj-ƒq td%|jƒ‚n|S((sŽ Convert the contents of the reflection file into a list of :py:class:`cctbx.miller.array` objects, each of which may contain multiple columns of data from the underlying file. By default this will automatically merge redundant observations to obtain a unique set under symmetry. :param crystal_symmetry: :py:class:`cctbx.crystal.symmetry` object (defaults to using internally specified symmetry, if any) :param force_symmetry: TODO :param merge_equivalents: merge redundant obervations (default=True) :param base_array_info: :py:class:`cctbx.miller.array_info` object containing basic information to be propagated to the arrays :param assume_shelx_observation_type_is: if specified, instead of raising an exception if the SHELX file type is not known from the file name plus data type tag, the function will force the specified data type. RCREs./s.\itsourcet source_typescctbx.miller.arrayt unit_celltspace_group_infot%raise_sorry_if_incompatible_unit_celltcrystal_symmetrytother_symmetrytforces hklf+ins/ress.hkls%s.inss%s.ressDCan't open files %s.ins or %s.resrequired by the option hklf+ins/restfileis ^HKLF\s*(\d)s2%s does not contain the mandatory HKLF instructionit4t3sHKLF %s not supportedtforce_symmetrytmerge_equivalentstbase_array_infoRtlabelstIobstSigIobstFobstSigFobssUnresolved amplitude/intensity ambiguity: %s SHELX reflection files may contain amplitudes or intensities. Please append =amplitudes or =hklf3 or =intensities or =hklf4 to the file name argument or parameter to resolve the ambiguity. If a corresponding .ins file is available, look for the HKLF codeword. Alternatively, run the phenix.reflection_statistics command twice, once with =amplitudes and once with =intensities. Inspect the /()^2 statistics. For acentric structures the values should fluctuate around 2.0, for centric structures around 3.0. If the statistics are not conclusive it will be best to recover the original reflection data, such as SCALEPACK, SCALA MTZ, XDS, or d*TREK files.N(Ns amplitudess intensities(.RtAssertionErrorRKRIRFR t array_infoRNtinfoRRVR tsymmetryRXRYR7tcrystal_symmetry_from_filetappendtcustomized_copyt join_symmetrytset_infotset_observation_typetobservation_typeRHtostpathtsplitextR,RLRR t extract_fromtseektreadtclosetretsearchtXtMtStnametgrouptas_miller_arraysRTt#set_observation_type_xray_intensityt#set_observation_type_xray_amplitude(ROR[RaRbRct assume_shelx_observation_type_ist info_sourceRRRkR€texttshelx_file_namet shelx_filet remainingtm((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_reader.pyR‚Ýsš                        &       N( t__name__t __module__t__doc__R7RSRRTRURR4R‚(((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_reader.pyR@—s*   ic C sJ|dkrtj}n|r'd}ng}x|D]}|dkrg|J|dI|IJ|jƒnt|ƒ} |dkrœ|dI| jƒIJ|Jn| jd|d|d|ƒ} xo| D]g} |dkrÁ|dkrò| jd|ƒn| jd|ƒ|d kr!| j d|ƒn|JqÁqÁW|s4|j | ƒq4q4W|S( Nis file_name:s file_type:R[RaRbitfi( RtsyststdouttflushR@RTR‚tshow_comprehensive_summaryt show_summaryt show_arraytextend( t file_namesR[RaRbtdiscard_arraystverboset report_outRRtreflection_filet miller_arraysR((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_reader.pytcollect_arraysYs:               c C stddddƒjƒjdddddtd d ƒjdd dddtd d ƒjdd ddddd dddƒjd|ƒ}t|jƒdkr­|jj ƒdS|j j rÂd}nd}t d|jd|j d|j j d|j jdkd|dtjƒ}|dk r t|ƒdkr t|ƒdkrN|d}n|j j}|dkrÊt|jƒdkrŠtd ƒ‚ntjj|jdƒ}|jƒjd!ƒrÊtd"ƒ‚qÊn|jƒjd!ƒsì|d!7}nHd#G|GHtj||ƒHndS($Ntusages:iotbx.reflection_file_reader [options] reflection_file ...t descriptions:Example: iotbx.reflection_file_reader w1.sca w2.mtz w3.cnss--weak_symmetrytactiont store_truetdefaultthelps?symmetry on command line is weaker than symmetry found in filess --show_datas*show Miller indices and data of all arrayss--pickletstorettypetstrings?write all data to FILE ('--pickle .' copies name of input file)tmetavartFILEtargsiiiR—R[RaR˜R™Ršit.s:Ambiguous name for pickle file (more than one input file).s.pickles$Input file is already a pickle file.s"Writing all Miller arrays to file:(R tenable_symmetry_comprehensivetoptionRR4tprocesstlenR©tparsert show_helptoptionst show_dataRRlt weak_symmetrytpickleRR‘RRtRutbasenametlowerRJR tdump(R©t command_lineR™tall_miller_arraystpickle_file_name((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_reader.pytruns^                    (6RŽt __future__RtiotbxRtiotbx.scalepackRRRR0t iotbx.cifRR3t iotbx.cnsRR+RR.t iotbx.dtrekRR1t iotbx.shelxRRR tiotbx.xds.read_asciiR8tiotbx.xds.integrate_hklR9tiotbx.solve.fpfm_readerR;tiotbx.option_parserR tcctbxR R tlibtbxR t libtbx.utilsRRRRttos.pathR{RR?R&R@R7R4RRR»(((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/reflection_file_reader.pyt4s8$  BÆ !