ó |™xTc@ s¡ddlmZddlmZddlZddlZddlZddlZdej fd„ƒYZ dZ dZ dZ d „Zed krejƒndS( iÿÿÿÿ(tdivision(t ncs_searchNttest_find_ncs_operatorscB s>eZd„Zd„Zd„Zd„Zd„Zd„ZRS(cC sktjƒjjGHtjjdtƒ}|j}|j |j ƒdgƒ|j |j ƒddggƒdS(sr Testing one ncs group and master ncs with two chains of different length and chains are not in order t pdb_stringschain A or chain Bschain C or chain Dschain E or chain FN( tsyst _getframetf_codetco_nametiotbxtncstinputt test_pdb1tncs_to_asu_selectiont assertEqualtkeystvalues(tselft trans_objtt((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/tst_finding_ncs.pyttest_two_chain_master s  cC s°tjƒjjGHtjjdtƒ}|j}|j |j ƒddgƒ|j |j ƒdgddggƒ|j |j dddhƒ|j |j d ddhƒd S( sx Test case of: Two groups, different number of chain in each group. two chains that are NOT ncs related Rschain Dschain Aschain Eschain Bschain CiiiN( RRRRRR R t test_pdb2R R RRt ncs_group_map(RRR((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/tst_finding_ncs.pyttest_three_chain_masters %c C s}tjƒjjGHtjjdtƒ}|j}|j |j ƒdgƒ|j |j ƒddddddd d ggƒd S( sw Test that minimal number of chains in master ncs are selected (not the minimal number of transformations) Rschain Aschain Bschain Cschain Dschain Eschain Fschain Gschain Hschain IN( RRRRRR R t test_pdb3R R RR(RRR((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/tst_finding_ncs.pyt)test_master_build_from_two_related_chains$s  cC swtjƒjjGHtjjdtdtdtƒ}|j }|j |j ƒdgƒ|j |j ƒddggƒdS(sw Test that minimal number of transformations in master ncs are selected (not the minimal number of chains) Rtuse_simple_ncs_from_pdbtuse_minimal_master_ncsschain A or chain B or chain Cschain D or chain E or chain Fschain G or chain H or chain IN( RRRRRR R RtFalseR R RR(RRR((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/tst_finding_ncs.pyttest_largest_common_ncs1s   c C s%tjƒjjGHtjjdddtƒ}|j ƒ}t j d|ddddƒ}|j ƒd}t d„|jƒDƒƒ}t|ƒ}t|ƒ}|j|dƒ|jt|ƒd ƒt j||ƒ}t jd |ƒ\}}t j||ƒ} |jt| ƒd ƒ| d} |jt| jƒt| jƒƒ|jt| jƒt| jƒƒd gd gdgdgdgdgdgdgdgg } |j| j| ƒ| jd} |j| jjƒƒ|j| jjƒƒ| jd } |j| jjƒƒ|j| jjƒƒdS(t t source_infotlinestphtmin_contig_lengthitmin_fraction_domaincS sh|]}|j’qS((tid(t.0tx((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/tst_finding_ncs.pys Ls i i$t match_dictitAtBtCtDtEtFtGtHtIN(R'(RRRRRtpdbR tNoneRtconstruct_hierarchyRtsearch_ncs_relationstmodelstlisttchainstsortedtlenR tclean_chain_matchingtminimal_master_ncs_groupingtbuild_group_dictt transformstcopiest iselectionst assertTruetrtis_r3_identity_matrixRt is_col_zerot assertFalse( Rtpdb_inpR tchain_match_listtmodelt chain_idstn_chainsR&ttransform_to_groupt group_dicttgr_objtexpectedttr((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/tst_finding_ncs.pyt8test_group_chains_by_domains_minimal_master_ncs_groupingAs8       ""<  c C s©tjƒjjGHtjjdddtƒ}|j ƒ}t j d|ddddƒ}t j ||ƒ}t j d|ƒ\}}t j||ƒ}|jt|ƒdƒ|d}|jt|jƒt|jƒƒ|jt|jƒt|jƒƒd d d gd d dgdddgg}|j|j|ƒ|jd} |j| jjƒƒ|j| jjƒƒ|jd} |j| jjƒƒ|j| jjƒƒdS(s Test minimal NCS operators RRR R!iR"R&iR'R(R)R*R+R,R-R.R/N(R'R(R)(RRRRRR0R R1RR2RR3R9tminimal_ncs_operators_groupingR;R R8R<R=R>R?R@RARRBRC( RRDR RER&RIRJRKRLRM((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/tst_finding_ncs.pyt2test_group_chains_by_domains_minimal_NCS_operatorsgs,     ""*  (t__name__t __module__RRRRRNRP(((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/tst_finding_ncs.pyRs    &s¨CRYST1 577.812 448.715 468.790 90.00 90.00 90.00 P 1 ATOM 1 CA LYS A 151 10.766 9.333 12.905 1.00 44.22 C ATOM 2 CA LYS A 152 10.117 9.159 11.610 1.00 49.42 C ATOM 3 CA LYS A 153 9.099 8.000 11.562 1.00 46.15 C ATOM 4 CA LYS A 154 8.000 8.202 11.065 1.00 52.97 C ATOM 5 CA LYS A 155 11.146 9.065 10.474 1.00 41.68 C ATOM 6 CA LYS A 156 10.547 9.007 9.084 1.00 55.55 C TER ATOM 7 CA LYS B 157 11.545 9.413 8.000 1.00 72.27 C ATOM 8 CA LYS B 158 12.277 10.718 8.343 1.00 75.78 C ATOM 9 CA LYS B 159 11.349 11.791 8.809 1.00 75.88 C TER ATOM 7 CA LYS F 157 2.154 3.953 16.298 1.00 72.27 C ATOM 8 CA LYS F 158 2.014 3.732 17.811 1.00 75.78 C ATOM 9 CA LYS F 159 2.558 2.413 18.250 1.00 75.88 C TER ATOM 7 CA LYS D 157 4.334 10.965 12.119 1.00 72.27 C ATOM 8 CA LYS D 158 4.057 11.980 13.238 1.00 75.78 C ATOM 9 CA LYS D 159 3.177 11.427 14.310 1.00 75.88 C TER ATOM 1 CA LYS C 151 6.855 8.667 15.730 1.00 44.22 C ATOM 2 CA LYS C 152 5.891 8.459 14.655 1.00 49.42 C ATOM 3 CA LYS C 153 6.103 7.155 13.858 1.00 46.15 C ATOM 4 CA LYS C 154 5.138 6.438 13.633 1.00 52.97 C ATOM 5 CA LYS C 155 5.801 9.685 13.736 1.00 41.68 C ATOM 6 CA LYS C 156 4.731 9.594 12.667 1.00 55.55 C TER ATOM 1 CA LYS E 151 6.987 4.106 17.432 1.00 44.22 C ATOM 2 CA LYS E 152 6.017 3.539 16.502 1.00 49.42 C ATOM 3 CA LYS E 153 6.497 3.492 15.036 1.00 46.15 C ATOM 4 CA LYS E 154 6.348 2.458 14.400 1.00 52.97 C ATOM 5 CA LYS E 155 4.647 4.221 16.634 1.00 41.68 C ATOM 6 CA LYS E 156 3.552 3.605 15.788 1.00 55.55 C TER sJ CRYST1 577.812 448.715 468.790 90.00 90.00 90.00 P 1 ATOM 1 CA LYS A 151 10.766 9.333 12.905 1.00 44.22 C ATOM 2 CA LYS A 152 10.117 9.159 11.610 1.00 49.42 C ATOM 3 CA LYS A 153 9.099 8.000 11.562 1.00 46.15 C ATOM 4 CA LYS A 154 8.000 8.202 11.065 1.00 52.97 C ATOM 5 CA LYS A 155 11.146 9.065 10.474 1.00 41.68 C TER ATOM 222 CA LEU X 40 94.618 -5.253 91.582 1.00 87.10 C ATOM 223 CA ARG X 41 62.395 51.344 80.786 1.00107.25 C ATOM 224 CA ARG X 42 62.395 41.344 80.786 1.00107.25 C TER ATOM 1 CA THR D 1 8.111 11.080 10.645 1.00 20.00 C ATOM 2 CA THR D 2 8.000 9.722 10.125 1.00 20.00 C ATOM 3 CA THR D 3 8.075 8.694 11.249 1.00 20.00 C ATOM 4 CA THR D 4 8.890 8.818 12.163 1.00 20.00 C TER ATOM 1 CA LYS B 151 6.855 8.667 15.730 1.00 44.22 C ATOM 2 CA LYS B 152 5.891 8.459 14.655 1.00 49.42 C ATOM 3 CA LYS B 153 6.103 7.155 13.858 1.00 46.15 C ATOM 4 CA LYS B 154 5.138 6.438 13.633 1.00 52.97 C ATOM 5 CA LYS B 155 5.801 9.685 13.736 1.00 41.68 C TER ATOM 1 CA LYS C 151 6.987 4.106 17.432 1.00 44.22 C ATOM 2 CA LYS C 152 6.017 3.539 16.502 1.00 49.42 C ATOM 3 CA LYS C 153 6.497 3.492 15.036 1.00 46.15 C ATOM 4 CA LYS C 154 6.348 2.458 14.400 1.00 52.97 C ATOM 5 CA LYS C 155 4.647 4.221 16.634 1.00 41.68 C TER ATOM 222 CA LEU Y 40 194.618 5.253 81.582 1.00 87.10 C ATOM 223 CA ARG Y 41 162.395 41.344 70.786 1.00107.25 C ATOM 224 CA ARG Y 42 162.395 31.344 70.786 1.00107.25 C TER ATOM 1 CA THR E 1 8.111 -10.645 11.080 1.00 20.00 C ATOM 2 CA THR E 2 8.000 -10.125 9.722 1.00 20.00 C ATOM 3 CA THR E 3 8.075 -11.249 8.694 1.00 20.00 C ATOM 4 CA THR E 4 8.890 -12.163 8.818 1.00 20.00 C TER s@ ATOM 1 N THR A 1 13.014 18.419 8.520 1.00 20.00 N ATOM 2 CA THR A 1 12.903 17.061 8.000 1.00 20.00 C ATOM 3 C THR A 1 12.978 16.033 9.124 1.00 20.00 C ATOM 4 O THR A 1 13.793 16.157 10.038 1.00 20.00 O TER ATOM 1 N THR C 1 10.325 8.000 14.368 1.00 20.00 N ATOM 2 CA THR C 1 10.111 8.702 13.108 1.00 20.00 C ATOM 3 C THR C 1 11.313 9.570 12.750 1.00 20.00 C ATOM 4 O THR C 1 11.885 10.241 13.609 1.00 20.00 O TER ATOM 1 N THR D 1 -0.430 15.458 18.495 1.00 20.00 N ATOM 2 CA THR D 1 0.086 15.020 17.204 1.00 20.00 C ATOM 3 C THR D 1 1.440 14.334 17.355 1.00 20.00 C ATOM 4 O THR D 1 2.297 14.791 18.111 1.00 20.00 O TER ATOM 1 N THR E 1 1.895 8.366 19.752 1.00 20.00 N ATOM 2 CA THR E 1 1.682 9.068 18.491 1.00 20.00 C ATOM 3 C THR E 1 2.884 9.935 18.133 1.00 20.00 C ATOM 4 O THR E 1 3.455 10.606 18.993 1.00 20.00 O TER ATOM 1 N THR F 1 8.346 7.308 15.936 1.00 20.00 N ATOM 2 CA THR F 1 7.054 7.796 15.467 1.00 20.00 C ATOM 3 C THR F 1 6.884 9.281 15.767 1.00 20.00 C ATOM 4 O THR F 1 7.237 9.751 16.849 1.00 20.00 O TER ATOM 1 N THR G 1 0.609 -0.560 24.094 1.00 20.00 N ATOM 2 CA THR G 1 0.395 0.142 22.834 1.00 20.00 C ATOM 3 C THR G 1 1.598 1.009 22.476 1.00 20.00 C ATOM 4 O THR G 1 2.169 1.680 23.335 1.00 20.00 O TER ATOM 1 N THR H 1 7.061 -1.617 20.279 1.00 20.00 N ATOM 2 CA THR H 1 5.768 -1.130 19.810 1.00 20.00 C ATOM 3 C THR H 1 5.599 0.356 20.109 1.00 20.00 C ATOM 4 O THR H 1 5.950 0.825 21.191 1.00 20.00 O TER ATOM 1 N THR I 1 8.722 4.822 16.665 1.00 20.00 N ATOM 2 CA THR I 1 7.494 4.036 16.653 1.00 20.00 C ATOM 3 C THR I 1 6.628 4.350 17.868 1.00 20.00 C ATOM 4 O THR I 1 7.130 4.482 18.984 1.00 20.00 O TER ATOM 1 N THR B 1 8.000 15.093 13.112 1.00 20.00 N ATOM 2 CA THR B 1 8.516 14.654 11.820 1.00 20.00 C ATOM 3 C THR B 1 9.870 13.968 11.972 1.00 20.00 C ATOM 4 O THR B 1 10.727 14.426 12.727 1.00 20.00 O TER cC s%dg}tjtt|ƒƒ}|S(sà Run selected tests 1) List in "tests" the names of the particular test you want to run 2) Comment out unittest.main() 3) Un-comment unittest.TextTestRunner().run(run_selected_tests()) R(tunittestt TestSuitetmapR(tteststsuite((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/tst_finding_ncs.pytrun_selected_testss t__main__(t __future__Rt mmtbx.ncsRt iotbx.ncsRt iotbx.pdbRSRtTestCaseRR RRRXRQtmain(((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/tst_finding_ncs.pyts    Ÿ(0