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()
