ó Û™xTc@ sšddlmZddlmZddlmZddlmZd„Zd„Z d„Z d„Z d „Z e d kr–eƒe ƒe ƒd GHnd S( iÿÿÿÿ(tdivision(tbuilding(tnull_out(tStringIOcC s%tƒ}|jjƒjƒdjƒdjƒ}|jjƒjdƒ}tj d|jd|j j ƒd|ƒ}t |j ƒƒdddd d gks¡t‚d d lm}d d lm}|jƒ}|jƒ}xt|jƒD]f\}} | jƒjƒjƒjƒ}tj||ƒ} t| ƒdkræ|jd!ksLt‚qæqæWd"d#d$d%d&d'd(g} d dl} | jjjddƒ} xC| D];\}}| jjjdd|d|ƒ}| j|ƒq–Wtƒ}tj| jƒd|ddƒ|j ƒd ks!t|j ƒƒ‚dS()Nis resname TYRt pdb_hierarchytxray_structuret selectioni;i<i=i>i?iÿÿÿÿ(t idealized_aa(tservertALAtGLYititAiiii tBtidtresseqs%4dticodetouttprefixs s chain 'A': 1-2A,4-6,10B (R R (iR (iR (iR (iR (iR (iR (i R (!t get_1yjp_pdbt hierarchyt only_modeltchainstresidue_groupstonly_atom_grouptatom_selection_cacheRRtget_nearby_water_selectiontinputtxray_structure_simpletlistt iselectiontAssertionErrortmmtbx.monomer_libraryRRt residue_dictt iteritemst only_chaintonly_residue_grouptgenerate_sidechain_clusterstlentresnametiotbx.pdb.hierarchytpdbtchaint residue_grouptappend_residue_groupRtshow_chain_resseq_rangestgetvalue(tpdb_intresiduetselet water_selRRt mon_lib_srvt ideal_dictR'RtresulttresidstiotbxR*RRtrgR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/tst.pytexercise_model_utilss6 )   -   " c C s‚tƒ}|jjƒ}|jddƒjƒ}|jddƒ}|jƒjƒ}|jj ƒ}|j dƒ}|j ƒj ƒ}|j dd|ƒ|jjƒj|j ƒƒ|j ƒj ƒ}tjd|d |jd|d |d tddd tƒƒ} |jjƒj| ƒ|j|ƒ} | d ks8t‚|j| ƒ| ksSt‚|j|ƒj| j|ƒƒdks€t‚| j|ƒj|j|ƒƒdks­t‚|j|ƒj| j|ƒƒdksÜt‚tjd |jd|ddd |d|ddd tƒƒ} | j| jdƒ| jƒ| jƒ| jƒ} |j| ƒdksft‚| jƒdks~t‚dS(Ntd_mingø?tresolution_factorgÐ?s resseq 4:5g333333Ó?RRRt target_maptrsr_after_annealRgš™™™™™¹?itprocessed_pdb_fileg{®Gáz”?i(RRRtstructure_factorstf_calctfft_maptapply_sigma_scalingtreal_map_unpaddedRRRt sites_cartt deep_copytshake_sites_in_placetatomstset_xyzRtrun_real_space_annealingtFalseRtrms_differenceRtselecttbox_build_refine_basetNonetrestrain_atomst others_in_boxtgeometry_minimizationtreal_space_refinetupdate_original_coordinatestmean_density_at_sites( R/txrstfctfc_ffttfc_mapt sel_cachetselt sites_origt sites_shakent sites_newt rmsd_startt box_builder((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/tst.pytexercise_box_rebuild%sP    --/      c C s­tƒ\}}|jƒ}|jdƒ}|jdƒ}|jjddd|ƒ|jdtƒtj|ƒ\}}tj d|d|d |d |jƒ}t ƒ}|j d |d d ƒg|j ƒj ƒD]} | jdƒd^qÐ} t| ƒdkst‚|jddƒjddƒjƒjƒ} |jƒdksIt‚|jƒdksat‚tjd|d|d| d|jjƒd|jjƒd|jƒƒ} dS(Ns.resseq 5 and (name CD or name OE1 or name NE2)sresseq 5tfactorgà?Rt update_f_calctfofc_mapt two_fofc_maptatom_selectionRRttwo_fofc_cutoffg@t:itmap_typetFcR;gÐ?igR<t model_mapt unit_cellRDt pdb_atoms(tget_1yjp_pdb_and_fmodelRRRt scale_adptupdate_xray_structuretTrueRtget_difference_mapstlocal_density_qualityRtshow_atoms_outside_densityR.t splitlinestsplitR&Rtmap_coefficientsRARBRCt$number_of_atoms_below_fofc_map_levelt+fraction_of_nearby_grid_points_above_cutofftget_model_map_statsRkRDRG( RtfmodelRYR1tsele_allRdRct map_statsRtltpdb_strsRXtstats((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/tst.pytexercise_map_utilsOs6    2 c C s›ddl}tƒ}|jjƒ}t|jddƒjƒƒ}|jƒ|jƒ}|j j d|gd|d|ddd t d t ƒ}|j |fS( NiÿÿÿÿR:gø?txray_structurestf_obst r_free_flagstscattering_tablet n_gaussiantbulk_solvent_and_scalingtskip_twin_detection(t mmtbx.utilsRRRtabsR?R@t#set_observation_type_xray_amplitudetgenerate_r_free_flagstutilst fmodel_simpleRJRpR(tmmtbxR/RUR@tflagsRz((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/tst.pyRmss       cC s"ddl}|jjjddƒS(Niÿÿÿÿt pdb_strings­CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 12.15 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 12.82 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.05 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 13.48 N ATOM 21 N GLN A 4 -1.005 2.228 3.598 1.00 10.29 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 1.00 10.53 C ATOM 23 C GLN A 4 1.435 2.606 4.088 1.00 10.24 C ATOM 24 O GLN A 4 1.547 3.843 4.115 1.00 8.86 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 1.00 9.80 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 1.00 10.25 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 0.80 12.43 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 0.80 14.62 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 0.80 9.05 N ATOM 30 N GLN A 5 2.154 1.821 4.871 1.00 10.38 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 1.00 11.39 C ATOM 32 C GLN A 5 4.594 1.768 5.172 1.00 11.52 C ATOM 33 O GLN A 5 4.768 0.546 5.054 1.00 12.05 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 1.00 11.96 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 1.00 10.81 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 0.80 13.10 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 0.80 10.65 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 0.80 12.30 N ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O TER HETATM 61 O HOH A 8 -6.471 5.227 7.124 1.00 22.62 O HETATM 62 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O HETATM 63 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 64 O HOH A 11 11.808 4.179 9.970 1.00 23.99 O HETATM 65 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O HETATM 66 O HOH A 13 -2.749 3.429 10.024 1.00 39.15 O HETATM 67 O HOH A 14 -1.500 0.682 10.967 1.00 43.49 O END (R(R)RR(R7((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/tst.pyRƒs Ft__main__tOKN(t __future__RRŽRt libtbx.utilsRt cStringIORR9R`R€RmRt__name__(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/tst.pyts 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