ó ¼™xTc@ sêddlmZddlmZddlZddlmZddlZddl m Z ddl m Z m Z mZddlZejjdƒZd„Zd „Zd „Zd „Zd „Zd „Zd„Zd„Zdd„ZdS(iÿÿÿÿ(tdivision(tmillerN(tSorry(txray_structure(t fa_estimationt pair_analysestrelative_scalingsê task = *get_dano get_diso lsq_scale sfcalc custom None .type=choice .help="Possible tasks" output_label_root=None .type=str .help="Output label root" get_dano .help="Get ||F+| - |F-|| from input data." { input_data = None .type=str } get_diso .help="Get |Fder|-|Fnat|" { native = None .type=str .help="Name of native data" derivative = None .type=str .help="Name of derivative data" use_intensities=True .type=bool .help="Scale on intensities" use_weights=True .type=bool .help="Use experimental sigmas as weights in scaling" scale_weight=True .type=bool .help="Whether or not to scale the sigmas during scaling" } lsq_scale{ input_data_1 = None .type=str .help="Reference data" input_data_2 = None .type=str .help="Data to be scaled" use_intensities=True .type=bool .help="Scale on intensities" use_weights=True .type=bool .help="Use experimental sigmas as weights in scaling" scale_weight=True .type=bool .help="Whether or not to scale the sigmas during scaling" } sfcalc{ fobs = None .type=str .help = "Data name of observed data" output = 2mFo-DFc mFo-DFc *complex_fcalc abs_fcalc intensities .type=choice .help="Output coefficients" use_bulk_and_scale = *as_estimated user_upplied .type=choice .help = "estimate or use parameters given by user" bulk_and_scale_parameters .help = "Parameters used in the structure factor calculation. Ignored if experimental data is given" { d_min = 2.0 .type=float .help = "resolution of the data to be calculated." overall .help = "Bulk solvent and scaling parameters" { b_cart .help = "Anisotropic B values" { b_11 = 0 .type=float b_22 = 0 .type=float b_33 = 0 .type=float b_12 = 0 .type=float b_13 = 0 .type=float b_23 = 0 .type=float } k_overall = 0.1 .type=float .help = "Overall scalar" } solvent .help = "Solvent parameters" { k_sol = 0.3 .type=float .help="Solvent scale" b_sol = 56.0 .type=float .help="Solvent B" } } } custom .help = "A custom script that uses miller_array data names as variables." { code = None .help = "A piece of python code" .type=str show_instructions = True .help = "Some instructions" .type = bool } cC s_g}xRt|tt|ƒƒƒD]5\}}d||f}|jt|ddƒƒq"W|S(Ns%%s = miller_arrays[ %i ].deep_copy()stexec(tziptrangetlentappendtcompile(tnamestresulttnametnumbert tmp_result((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip_tasks.pytpatch_miller_arrays_as_namess (c C sèd}|jdkr7t|ƒdkri|d}qin2|j|jƒr]|||j}n tdƒ‚|jƒr„|jƒ}n|jƒs–t‚t j |ƒ}|j j ƒ}|j j ƒ}tj||ƒ} | jj ƒ} | S(NiisUnknown data name.(tNonet input_dataR thas_keyRtis_xray_intensity_arrayt f_sq_as_ftis_xray_amplitude_arraytAssertionErrorRt ano_scalingtx1pt deep_copytx1nRtdelta_generatort abs_delta_f( R t miller_arraysRt parameterstoutt miller_arraytpair_generatortplustminust delta_gentdeltas((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip_tasks.pytget_dano‹s"    c C sd|jdkrtdƒ‚n|jdkr<tdƒ‚nd}d}|j|jƒrt|||jjƒ}ntd|jƒ‚|j|jƒr³|||jjƒ}ntd|jƒ‚tjd|d|d|jd|j d|j ƒ}|j d |ƒ|j ƒr$|j ƒ}n|j ƒr?|j ƒ}ntj||ƒ}|jjƒ} | S( NsPlease define native data names"Please define derivative data namesUnknown data name: >>%s<>%s<| jƒj ddƒ} n|jdkrh| jƒj ddƒ} n| dk szt!‚| S(Niÿÿÿÿ(tf_modelt complex_fcalct abs_fcalct intensitiessDExperimental data is needed for %s coefficients. Please supply Fobstd_mintanomalous_flagtfractiongš™™™™™¹?tmax_freeiÿàõRt r_free_flagst target_namet ls_wunit_k1tf_obstb_carttk_soltb_solt as_estimatedR"s2mFo-DFctmap_types2m*Fobs-D*FmodelsmFo-DFc(R;R<R=(R;R<R=("tmmtbxR:RtfobstoutputRtabststructure_factorstbulk_and_scale_parametersR>tFalsetf_calcRRRtgenerate_r_free_flagstoverallRFtb_11tb_22tb_33tb_12tb_13tb_23tmanagertsolventRGRHtuse_bulk_and_scaletupdate_solvent_and_scalet f_as_f_sqtelectron_density_maptmap_coefficientsR( R R RR!R"R:REtflagsRFtfmodelR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip_tasks.pytsfcalcésX      cC s-|dIJx|D]}|d|IJqWdS(NsRestricted data set names are:s - %s((trestricted_namesR"trn((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip_tasks.pytshow_restricted_custom_names#s  cC s^|dIJ|dIJ|dIJ|dIJ|dIJ|dIJ|dIJ|dIJ|d IJdS( NscThe custom function in the manipulate miller task of xmanip allows one to submit a small (or large)sesnippet of python code, have it executed and have a single miller array returned and written to file.sdIf one is familiar with python and the cctbx in general, this function allows one to quickly performs`complex tasks relating reflection files without having the overhead of writing a user interface.slData set names given to the miller arrays in the main (user specified) input file, are actual variable namessjand are stored as a cctbx.miller.array object. A pdb file that was read in, is stored in the object named sixray_structure. Note that not many safeguards are in place: make sure your code snippet is proper python!snPlease note that there are some restriction on variable names: the should not contains spaces or have the namesRof local variables or functions. By default, a variable named 'result' is returned((R"((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip_tasks.pytprint_custom_instructions(s        c B s#ddddddddd d d d d dg}|jrSe|ƒe||ƒnxV|D]N}d|kred|ƒ‚n||krZe|ƒed|ƒ‚qZqZWe|ƒ}x|D]}|dUq¿Wd} |dIJ|dIJ||jIJ|dIJe|jddƒ} | dU| S(NReR R tparamsR"R)R5tcustomtsfalcRR9tmanipulate_millerRgRht sMSorry, no spaces allowed in data set name >%s< to avoid compilation problems.sCThe data set name >%s< is restricted to avoid compilation problems.s*Trying to evaluate the code as shown belows*------------------------------------------sR(tshow_instructionsRhRgRRRtcodeR ( R R RRiR"ReRt tmp_namest instructionRt user_code((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip_tasks.pyRj5s.             c B s‹|dkrej}nied6ed6ed6ed6ed6}d}ed|j ddƒ}|dU||j |||||ƒ}|S( NR)R5R9RdRjsfunction_arguments = params.%ssR( RtsyststdoutR)R5R9RdRjR ttask( R R RRiR"tfunction_pointertfunction_argumentstpatchR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip_tasks.pyRlXs"     (t __future__RtcctbxRtcctbx.xray.structure_factorst libtbx.utilsRt iotbx.philtiotbxt iotbx.pdbRt mmtbx.scalingRRRRstphiltparset master_paramsRR)R5R9RdRgRhRjRRl(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/xmanip_tasks.pyts$    t   '  :  #