ó ЙxTc @ s;ddlmZddlZddlZddlmZddlZddlm Z ddl Zddl m Z dZ dZdd d „Zed kr7ejƒZd ZxueegD]gZx^egD]SZxJeegD]<ZeGeGeGHed edededeƒed7ZqÙWqÆWq¶WdejƒeGHndS(iÿÿÿÿ(tdivisionN(tflex(tmonomer_library(t RotamerEvals™CRYST1 14.074 16.834 17.360 90.00 90.00 90.00 P 1 ATOM 1 N ARG A 21 8.318 11.834 9.960 1.00 10.00 N ATOM 2 CA ARG A 21 7.146 11.154 9.422 1.00 10.00 C ATOM 3 C ARG A 21 6.012 11.120 10.440 1.00 10.00 C ATOM 4 O ARG A 21 5.000 10.449 10.235 1.00 10.00 O ATOM 5 CB ARG A 21 7.505 9.732 8.987 1.00 10.00 C ATOM 6 CG ARG A 21 7.923 8.820 10.129 0.30 20.00 C ATOM 7 CD ARG A 21 8.312 7.441 9.621 0.30 20.00 C ATOM 8 NE ARG A 21 8.694 6.545 10.708 0.30 20.00 N ATOM 9 CZ ARG A 21 7.839 5.785 11.385 0.30 20.00 C ATOM 10 NH1 ARG A 21 6.546 5.811 11.088 0.30 20.00 N ATOM 11 NH2 ARG A 21 8.275 5.000 12.360 0.30 20.00 N TER ATOM 9 O HOH B 21 8.776 10.791 4.311 1.00 5.00 O ATOM 10 O HOH B 22 7.708 11.548 4.090 1.00 5.00 O ATOM 11 O HOH B 23 9.698 10.663 3.367 1.00 5.00 O TER END s™CRYST1 14.074 16.834 17.360 90.00 90.00 90.00 P 1 ATOM 1 N ARG A 21 8.318 11.834 9.960 1.00 10.00 N ATOM 2 CA ARG A 21 7.248 10.924 9.570 1.00 10.00 C ATOM 3 C ARG A 21 6.012 11.120 10.440 1.00 10.00 C ATOM 4 O ARG A 21 5.064 10.337 10.375 1.00 10.00 O ATOM 5 CB ARG A 21 7.724 9.472 9.652 1.00 10.00 C ATOM 6 CG ARG A 21 8.797 9.112 8.637 1.00 10.00 C ATOM 7 CD ARG A 21 9.187 7.647 8.741 1.00 10.00 C ATOM 8 NE ARG A 21 10.266 7.301 7.820 1.00 10.00 N ATOM 9 CZ ARG A 21 10.871 6.118 7.790 1.00 10.00 C ATOM 10 NH1 ARG A 21 10.505 5.162 8.634 1.00 10.00 N ATOM 11 NH2 ARG A 21 11.844 5.891 6.920 1.00 10.00 N TER ATOM 9 O HOH B 21 8.776 10.791 4.311 1.00 5.00 O ATOM 10 O HOH B 22 7.708 11.548 4.090 1.00 5.00 O ATOM 11 O HOH B 23 9.698 10.663 3.367 1.00 5.00 O TER END gð?gš™™™™™¹?cC s[tjjdddtƒ}|jddƒ|jƒ}tjjdddtƒ}|jƒ}|jd|ƒjƒ} | j d|ƒ} | j ƒ| j ƒ} | j ddƒ} | j ƒ} | jdd ƒtjjƒ}tjjd |d tjjƒd tjtjƒƒd tdtddƒ}|jj}|jƒ}|jƒ}|jddƒtƒ}tjj}d}x]|jƒD]O}xF|j ƒD]8}x/|j!ƒj"ƒD]}||j#ƒdkr®t$j$ƒ}t%j&j'j(d|ddd|j)ƒj*ƒƒ}t%j&j'j+d|d| d|ddƒ}dt$j$ƒ|GHt%j&j'j,j-d|d |d|j.ƒd|d|d|d |d!|ƒ|j/|j)ƒj*ƒ|j)ƒj0ƒƒd"t$j$ƒ|GHq®q®Wq•Wq‚W|j1|ƒ}|j2|ƒ|jdd#ƒ|j3d$|ƒ}|d)kr:|d'ksRt4|ƒ‚n|d(ksRt4|ƒ‚|GHdS(*Nt source_infotlinest file_names answer.pdbtd_mintresolution_factortcolumn_root_labeltFCmaps answer.mtzt mon_lib_srvtener_libt raw_recordststrict_conflict_handlingtforce_symmetrytlogspoor.pdbtcommon_amino_acidtxray_structuretselection_within_radiusit iselectiontmap_datatnegate_selectiont atom_radiusis time (negate map): %6.4ft target_maptspecial_position_settingstresiduetrotamer_managert use_slopetuse_torsion_searchtuse_rotamer_iteratorstime (refine): %6.4fs refined.pdbtotheriigú~j¼t“h?g¸…ëQ¸Î?(ii(5tiotbxtpdbtinputtNonet pdb_answertwrite_pdb_filetxray_structure_simpletstructure_factorstf_calctfft_maptapply_sigma_scalingtreal_map_unpaddedtas_mtz_datasett mtz_objecttwriteRtservertpdb_interpretationtprocessR Rt std_stringtpdb_poort splitlinestTruetall_chain_proxiest pdb_hierarchyRt sites_cartRtcommon_residue_names_get_classtmodelstchainstonly_conformertresiduestresnamettimetmmtbxt refinementt real_spacetselection_around_to_negatetatomst extract_i_seqt6negate_map_around_selected_atoms_except_selected_atomst fit_residuetmanagerRt set_selectedt extract_xyztreplace_sites_carttadopt_xray_structuret max_distancetAssertionError(RRRtcntrRRtpdb_inpt xrs_answertxrs_mapR(R)Rt mtz_datasetR-R tprocessed_pdb_filetpdb_hierarchy_poortxrs_poortsites_cart_poorRt get_classt residue_poortmodeltchainRtt0Rt target_map_tdist((s[/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/real_space/tst_fit_residue_4.pytexercise4s|               "  t__main__iRRRROis Time: %6.4f(t __future__Rt(mmtbx.monomer_library.pdb_interpretationR@t iotbx.mtzR tcctbx.array_familyRR?Rt'mmtbx.refinement.real_space.fit_residuetmmtbx.rotamer.rotamer_evalRR$R3R_t__name__R\ROR5tFalseRRR(((s[/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/real_space/tst_fit_residue_4.pyts0    L