def exercise () : # Generic SeMet protein (actually Rv0577) args = [ "resolution=2.2", "atom_type=Se", "residues=300", "wavelength=0.9794", "include_weak_anomalous_scattering=False", "sites=12", ] result = plan_sad_experiment.run(args=args, out=null_out()).show(null_out()) #print result.representative_values[:-1] assert approx_equal(result.representative_values[:-1], [2.5, 12, 10880.374304954881, 3.8438000679016113, 97.77777777777779, 0.009, 0.9467311684652722, 0.9467311684652722, 0.7396676207890701, 0.7396676207890701, 20.9016001033, 98.3151904665], eps=0.01) assert (95 < result.representative_values[-2] < 100) # Insulin S-SAD open("tst_plan_sad_experiment.fa", "w").write(""" >1ZNI:A|PDBID|CHAIN|SEQUENCE GIVEQCCTSICSLYQLENYCN >1ZNI:B|PDBID|CHAIN|SEQUENCE FVNQHLCGSHLVEALYLVCGERGFFYTPKA >1ZNI:C|PDBID|CHAIN|SEQUENCE GIVEQCCTSICSLYQLENYCN >1ZNI:D|PDBID|CHAIN|SEQUENCE FVNQHLCGSHLVEALYLVCGERGFFYTPKA """) args = [ "seq_file=tst_plan_sad_experiment.fa", "atom_type=S", "resolution=1.2", "wavelength=1.54" ] result = plan_sad_experiment.run(args=args, out=null_out()) #print result.representative_values[:-1] assert approx_equal(result.representative_values[:-1], [2, 12, 7225.2485618841, 0.5562999844551086, 97.77777777777779, 0.009, 0.5095890245676317, 0.5095890245676317, 0.616249995680551, 0.616249995680551, 13.5861823956, 82.6264245311 ], eps=0.01) assert (78 < result.representative_values[-2] < 84) # now with worse resolution args = [ "seq_file=tst_plan_sad_experiment.fa", "atom_type=S", "resolution=3.0", "wavelength=1.54" ] result = plan_sad_experiment.run(args=args, out=null_out()) #print result.representative_values[:-1] assert approx_equal(result.representative_values[:-1], [5, 12, 462.41590796058244, 0.5562999844551086, 97.77777777777779, 0.009, 0.5095890245676317, 0.5095890245676317, 0.616249995680551, 0.616249995680551, 3.55312435872, 16.8013009611], eps=0.01) # Error handling args = [ "resolution=2.2", "atom_type=Se", "wavelength=0.9794", "sites=12", ] try : result = plan_sad_experiment.run(args=args, out=null_out()) except Sorry : pass else : raise Exception_expected
# LIBTBX_PRE_DISPATCHER_INCLUDE_SH export PHENIX_GUI_ENVIRONMENT=1 from __future__ import division import wxtbx.xtriage import wxtbx.app import sys if (__name__ == "__main__") : from mmtbx.command_line import plan_sad_experiment result = plan_sad_experiment.run(args=sys.argv[1:]) app = wxtbx.app.CCTBXApp(0) frame = wxtbx.xtriage.XtriageFrameSingleResult( parent=None, title="Plan SAD experiment", size=(900,600)) frame.SetResult(result) frame.Show() app.MainLoop()
# LIBTBX_PRE_DISPATCHER_INCLUDE_SH export PHENIX_GUI_ENVIRONMENT=1 from __future__ import division import wxtbx.xtriage import wxtbx.app import sys if (__name__ == "__main__"): from mmtbx.command_line import plan_sad_experiment result = plan_sad_experiment.run(args=sys.argv[1:]) app = wxtbx.app.CCTBXApp(0) frame = wxtbx.xtriage.XtriageFrameSingleResult(parent=None, title="Plan SAD experiment", size=(900, 600)) frame.SetResult(result) frame.Show() app.MainLoop()