def exercise():
from mmtbx.regression.make_fake_anomalous_data import generate_magnessium_inputs
base = "tst_pick_mg"
mtz_file, pdb_file = generate_magnessium_inputs(file_base=base,
anonymize=True)
time.sleep(2)
args = [
"\"%s\"" % pdb_file,
"\"%s\"" % mtz_file, "nproc=1", "use_phaser=False", "elements=MG"
]
result = easy_run.fully_buffered("mmtbx.water_screen %s" %
" ".join(args)).raise_if_errors()
n_mg = 0
for line in result.stdout_lines:
if ("Probable cation: MG+2" in line):
n_mg += 1
if n_mg != 2:
print "\n".join(result.stdout_lines)
raise RuntimeError("Expected 2 MG+2, found %d" % n_mg)
os.remove(pdb_file)
os.remove(mtz_file)
# "zn_frag_hoh.pdb" => "zn_frag_fmodel.eff"
os.remove(os.path.splitext(pdb_file)[0][:-4] + ".pdb")
os.remove(os.path.splitext(pdb_file)[0][:-4] + "_fmodel.eff")
print "OK"
def exercise () :
from mmtbx.regression.make_fake_anomalous_data import generate_magnessium_inputs
base = "tst_validate_mg"
mtz_file, pdb_file = generate_magnessium_inputs(file_base=base, anonymize=False)
time.sleep(2)
args = ["\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "nproc=1"]
result = easy_run.fully_buffered("mmtbx.validate_ions %s" % " ".join(args)
).raise_if_errors()
n_mg, n_bad = 0, 0
for line in result.stdout_lines :
if "| MG" in line:
n_mg += 1
if "!!!" in line:
n_bad += 1
assert n_mg == 2 and n_bad == 0
for ext in [".pdb", ".mtz", "_fmodel.eff"]:
os.remove(base + ext)
print "OK"
def exercise():
from mmtbx.regression.make_fake_anomalous_data import generate_magnessium_inputs
base = "tst_validate_mg"
mtz_file, pdb_file = generate_magnessium_inputs(file_base=base, anonymize=False)
time.sleep(2)
args = ["\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "nproc=1"]
result = easy_run.fully_buffered("mmtbx.validate_ions %s" % " ".join(args)
).raise_if_errors()
n_mg, n_bad = 0, 0
for line in result.stdout_lines :
if "| MG" in line:
n_mg += 1
if "!!!" in line:
n_bad += 1
assert n_mg == 2 and n_bad == 0
for ext in [".pdb", ".mtz", "_fmodel.eff"]:
os.remove(base + ext)
print("OK")
def exercise () :
from mmtbx.regression.make_fake_anomalous_data import generate_magnessium_inputs
base = "tst_pick_mg"
mtz_file, pdb_file = generate_magnessium_inputs(file_base=base, anonymize=True)
time.sleep(2)
args = [ "\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "nproc=1",
"use_phaser=False", "elements=MG" ]
result = easy_run.fully_buffered("mmtbx.water_screen %s" % " ".join(args)
).raise_if_errors()
n_mg = 0
for line in result.stdout_lines :
if ("Probable cation: MG+2" in line) :
n_mg += 1
if n_mg != 2:
print "\n".join(result.stdout_lines)
raise RuntimeError("Expected 2 MG+2, found %d" % n_mg)
os.remove(pdb_file)
os.remove(mtz_file)
# "zn_frag_hoh.pdb" => "zn_frag_fmodel.eff"
os.remove(os.path.splitext(pdb_file)[0][:-4] + ".pdb")
os.remove(os.path.splitext(pdb_file)[0][:-4] + "_fmodel.eff")
print "OK"
