from __future__ import absolute_import, division, print_function from mmtbx.cablam import cablam_validate from libtbx.test_utils import show_diff from iotbx import pdb import libtbx.load_env import os ref_cablam_give_text = """residue : outlier_type : contour_level : ca_contour_level : sec struc recommendation : alpha score : beta score : three-ten score 3 ILE: :0.52764:0.49162: :0.06929:0.00000:0.00000 4 PHE: :0.83948:0.80426: try alpha helix :0.34122:0.00000:0.00936 5 GLU: :0.81271:0.79155: try alpha helix :0.31550:0.00000:0.00445 6 MET: :0.77295:0.73578: try alpha helix :0.20871:0.00000:0.01115 7 LEU: :0.70530:0.69504: try alpha helix :0.12026:0.00000:0.00484 8 ARG: :0.71859:0.72353: try alpha helix :0.18161:0.00000:0.08888 9 ILE: :0.84025:0.82510: try alpha helix :0.43515:0.00000:0.00548 10 ASP: :0.65772:0.66407: try alpha helix :0.11727:0.00000:0.00000 11 GLU: :0.17045:0.15375: :0.01055:0.00000:0.00000 12 GLY: :0.35640:0.49471: :0.00000:0.00000:0.00000 13 LEU: :0.07149:0.09040: :0.00000:0.00102:0.00000 14 ARG: :0.41594:0.41432: try beta sheet :0.00000:0.15626:0.00000 15 LEU: :0.37150:0.44845: try beta sheet :0.01142:0.00202:0.00000 16 LYS: :0.14341:0.12064: try beta sheet :0.00034:0.00045:0.00000 17 ILE: CaBLAM Outlier :0.00777:0.25439: try beta sheet :0.00000:0.00123:0.00000 18 TYR: :0.38403:0.26228: try beta sheet :0.00000:0.00048:0.00000 19 LYS: :0.23229:0.31769: :0.00000:0.00601:0.00000 20 ASP: :0.24246:0.15915: :0.00000:0.00000:0.00000 21 THR: :0.07474:0.10616: :0.00639:0.00000:0.00000 22 GLU: :0.11848:0.17442: :0.00163:0.00000:0.00000 23 GLY: :0.87986:0.86098: :0.00000:0.00000:0.00000 24 TYR: :0.26671:0.25287: :0.00000:0.00975:0.00000 25 TYR: :0.17809:0.17537: try beta sheet :0.00000:0.00060:0.00000 26 THR: :0.26444:0.16084: :0.00000:0.04956:0.00000 27 ILE: :0.13051:0.05851: :0.00003:0.00000:0.00000 28 GLY: :0.57593:0.34210: :0.00218:0.00000:0.00000 29 ILE: CaBLAM Outlier :0.00287:0.02229: :0.00006:0.00000:0.00000 30 GLY: :0.27781:0.21754: :0.00000:0.00000:0.00000 31 HIS: :0.38269:0.14269: :0.00000:0.05822:0.00000 32 LEU: :0.34286:0.57402: :0.00000:0.07717:0.00000 40C ASP: :0.94906:0.96373: :0.76901:0.00000:0.01862 41 ALA: :0.92911:0.76129: try alpha helix :0.63484:0.00000:0.00712 42 ALA: :0.96131:0.96875: try alpha helix :0.77091:0.00000:0.01214 43 LYS: :0.97552:0.87406: try alpha helix :0.83796:0.00000:0.03254 44 SER: :0.78399:0.86899: try alpha helix :0.79994:0.00000:0.01036 45 GLU: :0.87884:0.86969: try alpha helix :0.73818:0.00000:0.01058 46 LEU: :0.91916:0.88671: try alpha helix :0.74961:0.00000:0.03756 47 ASP: :0.97483:0.96910: try alpha helix :0.90420:0.00000:0.01721 48 LYS: :0.91878:0.96392: try alpha helix :0.80659:0.00000:0.01638 49 ALA: :0.72801:0.71401: try alpha helix :0.14364:0.00000:0.00469 50 ILE: :0.37448:0.38935: :0.04203:0.00000:0.00000 51 GLY: :0.53355:0.56969: :0.00000:0.00000:0.00000 52 ARG: :0.11630:0.07344: :0.00000:0.00736:0.00000 53 ASN: :0.11365:0.08824: try beta sheet :0.00000:0.00088:0.00000 54 THR: :0.05756:0.15570: :0.00000:0.07997:0.00000 55 ASN: CaBLAM Disfavored :0.02086:0.00975: :0.00010:0.00000:0.00000 56 GLY: :0.64275:0.61690: :0.00000:0.00000:0.00000 57 VAL: :0.26151:0.15786: :0.00000:0.00000:0.00000 58 ILE: :0.44409:0.45268: :0.00000:0.00268:0.00000 59 THR: :0.49656:0.40961: :0.00000:0.00063:0.00000 60 LYS: :0.57162:0.65356: :0.12322:0.00000:0.00000 61 ASP: :0.87174:0.84785: try alpha helix :0.45478:0.00000:0.04867 62 GLU: :0.94925:0.94200: try alpha helix :0.91876:0.00000:0.01601 63 ALA: :0.78514:0.94158: try alpha helix :0.89034:0.00000:0.02358 64 GLU: :0.84156:0.78750: try alpha helix :0.35344:0.00000:0.04013 65 LYS: :0.80299:0.80830: try alpha helix :0.36710:0.00000:0.03984 66 LEU: :0.86889:0.86756: try alpha helix :0.48381:0.00000:0.00890 67 PHE: :0.90189:0.88748: try alpha helix :0.54551:0.00000:0.04663 68 ASN: :0.98865:0.95803: try alpha helix :0.87462:0.00000:0.01623 69 GLN: :0.97655:0.97438: try alpha helix :0.88753:0.00000:0.01169 70 ASP: :0.78162:0.77513: try alpha helix :0.96064:0.00000:0.01640 71 VAL: :0.75300:0.94269: try alpha helix :0.96236:0.00000:0.01399 72 ASP: :0.96009:0.96323: try alpha helix :0.89004:0.00000:0.01905 73 ALA: :0.89729:0.86971: try alpha helix :0.74118:0.00000:0.02781 74 ALA: :0.96049:0.91354: try alpha helix :0.79346:0.00000:0.02381 75 VAL: :0.90762:0.90773: try alpha helix :0.63817:0.00000:0.00743 76 ARG: :0.85886:0.91395: try alpha helix :0.72908:0.00000:0.01009 77 GLY: :0.96700:0.98047: try alpha helix :0.73374:0.00000:0.03867 78 ILE: :0.98019:0.98238: try alpha helix :0.87047:0.00000:0.01631 79 LEU: :0.58012:0.90368: try alpha helix :0.72839:0.00000:0.00859 80 ARG: :0.44662:0.55775: :0.01191:0.00000:0.00000 81 ASN: :0.34785:0.31423: :0.00000:0.00031:0.00000 82 ALA: :0.29269:0.38361: :0.02096:0.00000:0.00000 83 LYS: :0.58211:0.71041: try alpha helix :0.14248:0.00000:0.00001 84 LEU: :0.41959:0.32368: try alpha helix :0.05148:0.00000:0.00626 85 LYS: :0.66986:0.51927: try three-ten :0.09610:0.00000:0.21238 86 PRO: :0.98883:0.99594: try alpha helix :0.86833:0.00000:0.01204 87 VAL: :0.75880:0.95367: try alpha helix :0.78186:0.00000:0.00912 88 TYR: :0.91356:0.90539: try alpha helix :0.58192:0.00000:0.02264 89 ASP: :0.73904:0.80679: try alpha helix :0.35668:0.00000:0.05555 90 SER: :0.55972:0.60595: try three-ten :0.00733:0.00000:0.01601 91 LEU: :0.27769:0.22558: :0.00000:0.00107:0.00000 92 ASP: :0.42270:0.36276: :0.00000:0.00000:0.00000 93 ALA: :0.45818:0.40113: :0.07442:0.00000:0.00000 94 VAL: :0.77606:0.76480: try alpha helix :0.51294:0.00000:0.00679 95 ARG: :0.73578:0.72447: try alpha helix :0.16465:0.00000:0.02319 96 ARG: :0.73291:0.70074: try three-ten :0.14308:0.00000:0.15348 97 ALA: :0.83719:0.80947: try alpha helix :0.32626:0.00000:0.05371 98 ALA: :0.86385:0.88142: try alpha helix :0.53840:0.00000:0.04449 99 LEU: :0.97900:0.93347: try alpha helix :0.84827:0.00000:0.01657 100 ILE: :0.83575:0.81549: try alpha helix :0.35748:0.00000:0.04442 101 ASN: :0.87477:0.84323: try alpha helix :0.45214:0.00000:0.04502 102 MET: :0.96302:0.94884: try alpha helix :0.86991:0.00000:0.01048 103 VAL: :0.96613:0.92822: try alpha helix :0.78662:0.00000:0.01923 104 PHE: :0.77634:0.74271: try alpha helix :0.21660:0.00000:0.00765 105 GLN: :0.56557:0.55357: try alpha helix :0.09128:0.00000:0.00000 106 MET: :0.17345:0.14246: :0.01504:0.00000:0.00000 107 GLY: :0.45772:0.54732: :0.00000:0.00000:0.00000 108 GLU: :0.46203:0.46061: :0.05310:0.00000:0.00000 109 THR: :0.92592:0.77315: try alpha helix :0.79332:0.00000:0.03679 110 GLY: :0.94492:0.92742: try alpha helix :0.34326:0.00000:0.00675 111 VAL: :0.65875:0.68327: try alpha helix :0.11230:0.00000:0.01439 112 ALA: :0.68953:0.69294: try three-ten :0.05884:0.00000:0.37750 113 GLY: :0.35710:0.61555: try three-ten :0.00122:0.00000:0.06679 114 PHE: CaBLAM Disfavored :0.02716:0.02012: :0.00000:0.00000:0.00000 115 THR: :0.21716:0.25651: :0.02337:0.00038:0.00000 116 ASN: :0.93064:0.87429: try alpha helix :0.62433:0.00000:0.00578 117 SER: :0.84801:0.85414: try alpha helix :0.42589:0.00000:0.02916 118 LEU: :0.82109:0.80540: try alpha helix :0.39810:0.00000:0.05275 119 ARG: :0.97488:0.91843: try alpha helix :0.84079:0.00000:0.02236 120 MET: :0.97381:0.94393: try alpha helix :0.85304:0.00000:0.02222 121 LEU: :0.96664:0.96247: try alpha helix :0.76570:0.00000:0.01682 122 GLN: :0.81647:0.96855: try alpha helix :0.78504:0.00000:0.03365 123 GLN: :0.38558:0.54762: :0.01131:0.00000:0.00000 124 LYS: :0.27195:0.31297: :0.00000:0.00063:0.00000 125 ARG: :0.15025:0.03510: try beta sheet :0.00000:0.01617:0.00000 126 TRP: :0.36307:0.24379: :0.01956:0.00059:0.00000 127 ASP: :0.90607:0.87620: try alpha helix :0.66236:0.00000:0.00567 128 GLU: :0.94643:0.72509: try alpha helix :0.87977:0.00000:0.01864 129 ALA: :0.78394:0.78865: try alpha helix :0.29204:0.00000:0.04696 130 ALA: :0.83281:0.80403: try alpha helix :0.35091:0.00000:0.04734 131 VAL: :0.89150:0.84481: try alpha helix :0.42877:0.00000:0.00505 132 ASN: :0.84250:0.79163: try alpha helix :0.36966:0.00000:0.01480 133 LEU: :0.72732:0.71627: try three-ten :0.12666:0.00000:0.12935 134 ALA: :0.58761:0.61900: try three-ten :0.00324:0.00000:0.37544 135 LYS: CaBLAM Disfavored :0.04655:0.16709: try three-ten :0.00000:0.00000:0.02864 136 SER: :0.21418:0.10964: :0.00000:0.00275:0.00000 137 ARG: :0.44964:0.57604: :0.05596:0.00000:0.00000 138 TRP: :0.72494:0.72727: try alpha helix :0.15493:0.00000:0.07705 139 TYR: :0.84309:0.82430: try alpha helix :0.39345:0.00000:0.00260 140 ASN: :0.72053:0.79855: try alpha helix :0.36505:0.00000:0.00554 141 GLN: :0.53741:0.51793: :0.07728:0.00000:0.00000 142 THR: :0.19896:0.17954: :0.00051:0.00000:0.00000 143 PRO: :0.66687:0.52699: :0.04263:0.00083:0.00000 144 ASN: :0.77072:0.77580: try alpha helix :0.27392:0.00000:0.00914 145 ARG: :0.74389:0.76664: try alpha helix :0.24488:0.00000:0.00073 146 ALA: :0.91235:0.91083: try alpha helix :0.60613:0.00000:0.03068 147 LYS: :0.75173:0.81694: try alpha helix :0.35878:0.00000:0.05334 148 ARG: :0.79680:0.75473: try alpha helix :0.31349:0.00000:0.01607 149 VAL: :0.82542:0.80165: try alpha helix :0.33416:0.00000:0.00323 150 ILE: :0.90417:0.91613: try alpha helix :0.63958:0.00000:0.03949 151 THR: :0.81490:0.82636: try alpha helix :0.48350:0.00000:0.03861 152 THR: :0.86653:0.84523: try alpha helix :0.45410:0.00000:0.02507 153 PHE: :0.88416:0.85966: try alpha helix :0.48595:0.00000:0.00357 154 ARG: :0.58641:0.58326: try alpha helix :0.07799:0.00000:0.00000 155 THR: :0.24379:0.24630: :0.02083:0.00000:0.00000 156 GLY: :0.59583:0.57219: :0.00000:0.00063:0.00000 157 THR: :0.32804:0.23017: :0.00000:0.00482:0.00000 158 TRP: :0.08355:0.28156: :0.00000:0.00000:0.00000 159 ASP: :0.40617:0.36789: :0.01844:0.00000:0.00000 160 ALA: :0.66012:0.75135: :0.20693:0.00000:0.06554 """ ref_cablam_give_oneline = """pdb103l.ent:151:3.3:1.3:0.00 """ class cablam_test_string(): #I wrote the regression test to use a class with a custom .write() method as a # proof of principle for learning OOP and to see if I could. Possible because # all my print functions accept an optional writeto= variable. def write(self,string): self.output += str(string) def __init__(self): self.output = "" def exercise_cablam(): regression_pdb = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/pdb103l.ent", test=os.path.isfile) #This is the same file used for tst_kinemage.py if (regression_pdb is None): print("Skipping exercise_cablam(): input pdb (pdb103l.ent) not available") return #----- pdb_io = pdb.input(regression_pdb) pdbid = os.path.basename(regression_pdb) hierarchy = pdb_io.construct_hierarchy() oneline_test = cablam_test_string() cablam_validate.oneline(hierarchy, peptide_cutoff=0.05, peptide_bad_cutoff=0.01, ca_cutoff=0.005, pdbid=pdbid, writeto=oneline_test) text_test = cablam_test_string() outliers = cablam_validate.analyze_pdb(hierarchy, outlier_cutoff=0.05, pdbid=pdbid) cablam_validate.give_text(outliers, writeto=text_test) #print '|',oneline_test.output,'|' #print '|',ref_cablam_give_oneline,'|' #print '|',text_test.output,'|' #print '|',ref_cablam_give_text,'|' assert not show_diff(oneline_test.output , ref_cablam_give_oneline) assert not show_diff(text_test.output , ref_cablam_give_text) def run(): ##if (not libtbx.env.has_module(name="probe")): ## print \ ## "Skipping kinemage test:" \ ## " probe not available" ##elif (not libtbx.env.has_module(name="reduce")): ## print \ ## "Skipping kinemage test:" \ ## " reduce not available" ##else: ## exercise_kinemage() ##print "OK" exercise_cablam() print("OK") if (__name__ == "__main__"): run()