ó ®™xTc@ s°ddlmZddlZddlmZddlZddlZddlZddlZddlZ dZ d„Z e dkr¬e j jdƒr¤e ƒdGHq¬d GHndS( iÿÿÿÿ(tdivisionN(tnull_outsrATOM 1 N ALA 1 1.558 -2.549 -1.143 1.00 0.00 N ATOM 2 CA ALA 1 1.130 -3.826 -1.702 1.00 0.00 C ATOM 3 C ALA 1 -0.241 -3.705 -2.358 1.00 0.00 C ATOM 4 O ALA 1 -0.532 -4.386 -3.342 1.00 0.00 O ATOM 5 CB ALA 1 1.108 -4.897 -0.622 1.00 0.00 C ATOM 6 N ALA 2 -1.081 -2.834 -1.807 1.00 0.00 N ATOM 7 CA ALA 2 -2.422 -2.623 -2.338 1.00 0.00 C ATOM 8 C ALA 2 -2.392 -1.711 -3.560 1.00 0.00 C ATOM 9 O ALA 2 -3.170 -1.887 -4.497 1.00 0.00 O ATOM 10 CB ALA 2 -3.331 -2.042 -1.265 1.00 0.00 C ATOM 11 N ALA 3 -1.488 -0.736 -3.541 1.00 0.00 N ATOM 12 CA ALA 3 -1.351 0.207 -4.645 1.00 0.00 C ATOM 13 C ALA 3 -0.825 -0.487 -5.898 1.00 0.00 C ATOM 14 O ALA 3 -1.270 -0.201 -7.010 1.00 0.00 O ATOM 15 CB ALA 3 -0.437 1.356 -4.251 1.00 0.00 C ATOM 16 N ALA 4 0.124 -1.398 -5.708 1.00 0.00 N ATOM 17 CA ALA 4 0.699 -2.149 -6.817 1.00 0.00 C ATOM 18 C ALA 4 -0.333 -3.092 -7.426 1.00 0.00 C ATOM 19 O ALA 4 -0.387 -3.268 -8.643 1.00 0.00 O ATOM 20 CB ALA 4 1.922 -2.926 -6.355 1.00 0.00 C ATOM 21 N ALA 5 -1.152 -3.695 -6.569 1.00 0.00 N ATOM 22 CA ALA 5 -2.204 -4.597 -7.020 1.00 0.00 C ATOM 23 C ALA 5 -3.295 -3.830 -7.757 1.00 0.00 C ATOM 24 O ALA 5 -3.850 -4.313 -8.744 1.00 0.00 O ATOM 25 CB ALA 5 -2.792 -5.358 -5.842 1.00 0.00 C ATOM 26 N ALA 6 -3.597 -2.630 -7.271 1.00 0.00 N ATOM 27 CA ALA 6 -4.599 -1.778 -7.900 1.00 0.00 C ATOM 28 C ALA 6 -4.097 -1.252 -9.240 1.00 0.00 C ATOM 29 O ALA 6 -4.879 -1.036 -10.166 1.00 0.00 O ATOM 30 CB ALA 6 -4.971 -0.626 -6.981 1.00 0.00 C ATOM 31 N ALA 7 -2.788 -1.047 -9.335 1.00 0.00 N ATOM 32 CA ALA 7 -2.176 -0.571 -10.570 1.00 0.00 C ATOM 33 C ALA 7 -2.045 -1.703 -11.583 1.00 0.00 C ATOM 34 O ALA 7 -2.052 -1.472 -12.792 1.00 0.00 O ATOM 35 CB ALA 7 -0.816 0.047 -10.286 1.00 0.00 C ATOM 36 N ALA 8 -1.927 -2.929 -11.081 1.00 0.00 N ATOM 37 CA ALA 8 -1.805 -4.100 -11.941 1.00 0.00 C ATOM 38 C ALA 8 -3.169 -4.549 -12.452 1.00 0.00 C ATOM 39 O ALA 8 -3.290 -5.046 -13.572 1.00 0.00 O ATOM 40 CB ALA 8 -1.118 -5.234 -11.197 1.00 0.00 C ATOM 41 N ALA 9 -4.195 -4.370 -11.625 1.00 0.00 N ATOM 42 CA ALA 9 -5.552 -4.755 -11.995 1.00 0.00 C ATOM 43 C ALA 9 -6.141 -3.782 -13.010 1.00 0.00 C ATOM 44 O ALA 9 -6.957 -4.163 -13.849 1.00 0.00 O ATOM 45 CB ALA 9 -6.436 -4.832 -10.760 1.00 0.00 C ATOM 46 N ALA 10 -5.722 -2.523 -12.929 1.00 0.00 N ATOM 47 CA ALA 10 -6.206 -1.494 -13.841 1.00 0.00 C ATOM 48 C ALA 10 -5.523 -1.598 -15.200 1.00 0.00 C ATOM 49 O ALA 10 -6.184 -1.624 -16.238 1.00 0.00 O ATOM 50 CB ALA 10 -5.991 -0.112 -13.243 1.00 0.00 C TER c C sÖtƒ}tjjjƒ}tjjjƒ}tjjjd|d|dtjdƒdt d|ƒ}|j }|j j ƒ}tj jjƒ}|jdtjjdƒƒ}tj jd |jd |jƒƒ}|jd|ƒ|jd|ƒ|jd|d tƒ} | j} |jd td td| jd| dt ƒ} ddlm} | jjƒjƒ} d| _ | j!|jd|ƒ}| j"| ƒ}tj#jd|d|d| jddƒ}| j%|ƒ|jj&ƒ}| j'j(ƒdksöt)‚ddl*}|j*ƒ}| j'j+ddd|j,ƒdg|D]}|j-ƒ^q3d|ƒ|j.ƒdksjt)‚|j*ƒ}| j'j/ddd|j,ƒdg|D]}|j-ƒ^q›d|ƒ|j.ƒdksÒt)‚dS(Nt mon_lib_srvtener_libt raw_recordss t6substitute_non_crystallographic_unit_cell_if_necessarytlogtsources(h_bond_restraints.remove_outliers=False t pdb_hierarchytparamstas_python_objectst show_energiestshow_nonbonded_clashscorethydrogen_bond_proxiestcustom_nonbonded_exclusionstassume_hydrogens_all_missingiÿÿÿÿ(t ramachandrantemsleytramachandran_proxiestramachandran_lookupthydrogen_bond_paramsitby_valuetresidualt sites_cartt site_labelstfs¡Hydrogen bond restraints: 4 Sorted by residual: hbond pdb=" O ALA 4 " pdb=" N ALA 8 " ideal model delta sigma weight residual 2.900 2.904 -0.004 5.00e-02 4.00e+02 4.93e-03 hbond pdb=" O ALA 2 " pdb=" N ALA 6 " ideal model delta sigma weight residual 2.900 2.903 -0.003 5.00e-02 4.00e+02 4.49e-03 hbond pdb=" O ALA 3 " pdb=" N ALA 7 " ideal model delta sigma weight residual 2.900 2.903 -0.003 5.00e-02 4.00e+02 2.92e-03 hbond pdb=" O ALA 5 " pdb=" N ALA 9 " ideal model delta sigma weight residual 2.900 2.902 -0.002 5.00e-02 4.00e+02 1.84e-03 sURamachandran plot restraints: 8 Sorted by residual: phi-psi angles formed by residual pdb=" C ALA 7 " 1.53e+01 pdb=" N ALA 8 " pdb=" CA ALA 8 " pdb=" C ALA 8 " pdb=" N ALA 9 " phi-psi angles formed by residual pdb=" C ALA 1 " 1.52e+01 pdb=" N ALA 2 " pdb=" CA ALA 2 " pdb=" C ALA 2 " pdb=" N ALA 3 " phi-psi angles formed by residual pdb=" C ALA 6 " 1.20e+01 pdb=" N ALA 7 " pdb=" CA ALA 7 " pdb=" C ALA 7 " pdb=" N ALA 8 " phi-psi angles formed by residual pdb=" C ALA 2 " 1.14e+01 pdb=" N ALA 3 " pdb=" CA ALA 3 " pdb=" C ALA 3 " pdb=" N ALA 4 " phi-psi angles formed by residual pdb=" C ALA 8 " 1.06e+01 pdb=" N ALA 9 " pdb=" CA ALA 9 " pdb=" C ALA 9 " pdb=" N ALA 10 " phi-psi angles formed by residual pdb=" C ALA 4 " 1.06e+01 pdb=" N ALA 5 " pdb=" CA ALA 5 " pdb=" C ALA 5 " pdb=" N ALA 6 " phi-psi angles formed by residual pdb=" C ALA 3 " 1.03e+01 pdb=" N ALA 4 " pdb=" CA ALA 4 " pdb=" C ALA 4 " pdb=" N ALA 5 " phi-psi angles formed by residual pdb=" C ALA 5 " 7.58e+00 pdb=" N ALA 6 " pdb=" CA ALA 6 " pdb=" C ALA 6 " pdb=" N ALA 7 " (0Rtmmtbxtmonomer_librarytserverRtpdb_interpretationtprocesstpdb_strtsplittTruetall_chain_proxiestpdb_inpt source_infotsecondary_structuretsec_str_master_philtfetchtiotbxtphiltparsetmanagerRtextracttfind_automaticallyt initializetcreate_hbond_proxiestFalsetexclude_nb_listtgeometry_restraints_managertproxiestmmtbx.geometry_restraintsRt master_philtrama_potentialtextract_proxiestlookup_managertgeometry_restraintstNonetset_generic_restraintstatomstgeneric_restraints_managert get_n_hbondstAssertionErrortStringIOtshow_sorted_hbondst extract_xyztid_strtgetvaluetshow_sorted_ramachandran(RRRtprocessed_pdb_filetacpRtdefparst custom_parst ss_managertproxies_for_grmtcustom_nb_excltgrmRR R3t rama_lookuptrestraints_helperR<R@t str_resultta((sS/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/tst_manager.pytexercise_geo_outAst                         4t__main__tksdssptOKs#skipping test, ksdssp not available(t __future__RRt libtbx.utilsRt(mmtbx.monomer_library.pdb_interpretationtmmtbx.secondary_structureR(tlibtbx.load_envtlibtbxRRRt__name__tenvt has_module(((sS/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/tst_manager.pyts      6 …