ó ³™xTc@ siddlmZddlZddlmZddlmZddlmZddlmZddl m Z m Z ddl Z ddl mZdd l mZdd l mZddlZdd lmZdd lmZdd lmZddlZddlZdefd„ƒYZd„Ze jjdƒZd„Zd„Z e!dkree ej"dƒndS(iÿÿÿÿ(tdivisionN(tcrystal(tsgtbx(txray(tflex(tSorryt multi_out(treflection_file_utils(tcrystal_symmetry_from_any(tpdb(tabsolute_scaling(tf_model(tStringIOt error_swapcB s,eZdddd„Zd„Zd„ZRS(iig@c C s@||_||_||_|jj|jƒ|_|jj|jƒ|_tj|jdtƒ}tj|jdtƒ}tj|jdtƒ} |jjƒ|_ |jjƒ|_ | jjƒ|_ |j |_ |j |_| j |_||_||_||_|jjd|jƒ|jj|jƒ|jj|jƒ|j j|jƒ|j j|jƒ|j j|jƒ|j jƒj|j ƒ|_d|_|jƒ|j jd|jjƒ|jjƒjƒjƒtj |jƒd|jj!ƒ|jjƒjƒjƒtj |jƒƒj|jƒ|_dS(Nt auto_kerneltn_binstdatatsigmas("t miller_obst miller_calct miller_mockt common_setR tkernel_normalisationtTruetnormalised_miller_dev_epst f_sq_as_ft norma_obst norma_calct norma_mocktnormalizer_for_miller_arraytnorma_obs_consttnorma_calc_consttnorma_mock_consttthrest n_reso_binstn_e_binst setup_binnert use_binner_oft deep_copytset_observation_typet new_norma_obstNonetnew_obstswap_ittcustomized_copyRtepsilonst as_doubleRtsqrtR( tselfRRRR"R#R!t norma_obs_objtnorma_calc_objtnorma_mock_obj((sW/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/examples/simulate_experimental_data.pyt__init__s<            8;cC sóxì|jjƒjƒD]Õ}|jjƒjƒ|k}|jj|ƒ}|jj|ƒ}|jj|ƒ}|j|jƒ|j ƒ|jƒ|jƒƒ\}}|jj d|jjƒj ||ƒd|jj ƒj ||ƒƒ|_ qWdS(NRR( Rtbinnert range_usedt bin_indicestselectRRtdo_something_cleverRRR,t set_selectedR((R0tibint selectiont tmp_norm_obst tmp_norm_calct tmp_norm_mocktnew_etnew_se((sW/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/examples/simulate_experimental_data.pyR+Fs   c C sîtj|ƒ}|jƒ}|j|ƒ}|j|ƒ}|j|ƒ} |j|ƒ} tj| ƒ} tj|ƒtj| ƒ} | jƒ} t|jƒƒ|j}t |ƒd}tj ƒ}d}xHt |jƒƒD]4}||dkrÿ|d7}n|j |dƒqÜWx–t |jƒD]…}tj ||kƒ}|j tƒ}tjtj|ƒƒ}| j|ƒ}|j|ƒ}|j|ƒ}|j|ƒ}tj|ƒ}tjtj||ƒ||ƒ}tj tj||ƒ|j|kƒ}|j tƒdkr…|j|ƒ}tjtj|j tƒƒƒ}|j|ƒ}|d|j tƒ!}|j|jƒ|ƒ}n| j||ƒ} |j||ƒ}q$W| | } tj| ƒ} | j|ƒ}|j|ƒ}||fS(Nii(Rtsort_permutationtinverse_permutationR8tlogR&tfloattsizeR#tinttxrangetappendtbooltcountRt random_doubletmeantmathR/tabsR!R:t iselectiontexp( R0tobstsobstcalctmockt sort_ordertinverse_sort_ordert sorted_obst sorted_sobst sorted_calct sorted_mocktlog_calctdeltast old_deltastbin_sizetebinRKtiiR;tthis_bin_selectionttmp_ntpermutetselected_deltast selected_sobst mean_deltat std_deltatoutlierst non_out_deltat tmp_permutt tmp_deltatnew_fobstnew_sobs((sW/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/examples/simulate_experimental_data.pyR9XsR    $)" (t__name__t __module__R4R+R9(((sW/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/examples/simulate_experimental_data.pyR s  , cC s_tjddddƒ}|dk r?|jd|dtƒ}n|dk rf|jd|dtƒ}n|jƒdkrÌxQ|D]F}|jƒ}|dk rtjd|d|jƒdtƒ}PqqWnx&|D]}|jd|dtƒ}qÓW|jƒdkr[xQ|D]F}|jƒ}|dk rtjd|jƒd|dtƒ}PqqWn|S(Nt unit_celltspace_group_infotother_symmetrytforcetassert_is_compatible_unit_cell(RtsymmetryR)t join_symmetrytFalseRqRr(tfrom_command_linetfrom_parameter_filetfrom_coordinate_filestfrom_reflection_filestresulttcrystal_symmetryRqRr((sW/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/examples/simulate_experimental_data.pytselect_crystal_symmetry¡s<                     s“simul_utils{ input{ unit_cell=None .type=unit_cell space_group=None .type=space_group xray_data{ file_name=None .type=path labels=None .type=str } model{ file_name=None .type=path } mock_model{ file_name=None .type=path } } output{ logfile=simul.log .type=str hklout=simul.mtz .type=str } } cC s dGHdS(Ns¦ mmtbx.simulate_data: Allows one to quickly simulate data 'experimental' data with similar Fobs-Fcalc distribution as in the given model/data pair. The keywords are sumarized below and should be self explanatory: simul_utils{ input{ unit_cell=None space_group=None xray_data{ file_name=None labels=None } model{ file_name=None } mock_model{ file_name=None } } output{ logfile=simul.log hklout=simul.mtz } } The main purpose of this file is to generate data with errors that look real. This is what is done: 1. The pdb file 'model.file_name' is scaled to the observed data 'xray_data.file_name' (Fcalc and Fobs are now available and on the same scale) 2. Structure factors are computed for 'mock_model.file_name' with same bulk solvent parameters as 'model.file_name' (call this Fmock) 3a. For each resolution bin, generate about 20 E value bins. 3b. In each E value bin, compute ratio=Fobs/Fcalc (or log Fobs - log Fcalc so you will) 3c. make a random permuation of these ratios log differences (call this array random_ratio) 3d. Fmockobs = F_mock*random_ratio 4. Write out Fmockobs The data generated in this manner has similar F/sigF (the sigmas are permuted along with the ratios) and R value properties. If no mock model is supplied, the model will be the mock model. The mock model is supposed to be in the same unit cell/spacegroup (this is enforced). 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