def exercise():
from mmtbx.regression.make_fake_anomalous_data import generate_calcium_inputs
base = "tst_pick_ca"
mtz_file, pdb_file = generate_calcium_inputs(file_base=base,
anonymize=True)
time.sleep(2)
args = [
"\"%s\"" % pdb_file,
"\"%s\"" % mtz_file, "wavelength=1.1", "nproc=1", "use_phaser=False",
"fpp_ratio_max=1.2"
]
result = easy_run.fully_buffered("mmtbx.water_screen %s" %
" ".join(args)).raise_if_errors()
n_ca = 0
for line in result.stdout_lines:
if "Probable cation: CA+2" in line:
n_ca += 1
if (n_ca != 1):
print("\n".join(result.stdout_lines))
raise RuntimeError("Expected 1 Ca2+, found %d" % n_ca)
os.remove(pdb_file)
os.remove(mtz_file)
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():
try :
import svm # import dependency
import svmutil # import dependency
except ImportError :
print "libsvm not available, skipping this test"
return
from mmtbx.regression.make_fake_anomalous_data import generate_calcium_inputs
base = "tst_pick_ca_svm"
mtz_file, pdb_file = generate_calcium_inputs(file_base=base, anonymize=True)
args = ["\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "wavelength=1.1",
"nproc=1", "use_phaser=False", "use_svm=True", "elements=CA,ZN"]
result = easy_run.fully_buffered("mmtbx.water_screen %s" % " ".join(args)
).raise_if_errors()
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")
n_ca = 0
for line in result.stdout_lines:
if ("Final choice: CA" in line):
n_ca += 1
if (n_ca != 1):
print "\n".join(result.stdout_lines)
raise RuntimeError("Expected 1 Ca2+, found %d" % n_ca)
print "OK"
def exercise_omit_atom_selection():
# combine an omit selection with a CCP4 map selection - this used to crash
from mmtbx.regression.make_fake_anomalous_data import generate_calcium_inputs
import mmtbx.command_line.maps
mtz_file, pdb_file = generate_calcium_inputs(
file_base="tst_mmtbx_maps_misc2")
with open("tst_mmtbx_maps_misc2.eff", "w") as f:
f.write("""\
maps {
map {
map_type = 2mFo-DFc
format = xplor *ccp4
file_name = tst_mmtbx_maps_misc2.ccp4
region = *selection cell
atom_selection = "resname HOH"
}
}""")
mmtbx.command_line.maps.run(args=[
mtz_file,
pdb_file,
"tst_mmtbx_maps_misc2.eff",
"omit.selection=\"resname TRP\"",
"prefix=tst_mmtbx_maps_misc2",
],
log=null_out())
def exercise () :
from mmtbx.regression.make_fake_anomalous_data import generate_calcium_inputs
from mmtbx.command_line import find_peaks_holes
mtz_file, pdb_file = generate_calcium_inputs(
file_base = "tst_find_peaks_holes", anonymize = True)
out = StringIO()
peaks_holes = find_peaks_holes.run(
args=[pdb_file, mtz_file],
out=out)
peaks_holes.save_pdb_file(file_name="tst_fph_peaks.pdb", log=null_out())
p = easy_pickle.dumps(peaks_holes)
s = peaks_holes.get_summary()
sp = easy_pickle.dumps(s)
out2 = StringIO()
s.show(out=out2)
lines = out2.getvalue().splitlines()
assert (""" anomalous H2O (anomalous > 3): 1""" in lines)
assert (""" anomalous non-water atoms: 0""" in lines)
assert (""" mFo-DFc > 9: 0""" in lines)
peaks_holes = find_peaks_holes.run(
args=[pdb_file, mtz_file, "filter_peaks_by_2fofc=1.0"],
out=null_out())
out3 = StringIO()
peaks_holes.get_summary().show(out=out3)
lines = out3.getvalue().splitlines()
assert (""" anomalous > 3: 0""" in lines)
out3 = StringIO()
peaks_holes = find_peaks_holes.run(
args=[pdb_file, mtz_file, "include_peaks_near_model=True",],
out=out3)
lines = out3.getvalue().splitlines()
assert (""" mFo-DFc > 9: 1""" in lines)
os.remove(mtz_file)
os.remove(pdb_file)
def exercise () :
try :
import svm # import dependency
import svmutil # import dependency
except ImportError :
print "libsvm not available, skipping this test"
return
from mmtbx.regression.make_fake_anomalous_data import generate_calcium_inputs
base = "tst_pick_ca_svm"
mtz_file, pdb_file = generate_calcium_inputs(file_base=base, anonymize=True)
args = ["\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "wavelength=1.1",
"nproc=1", "use_phaser=False", "use_svm=True", "elements=CA,ZN"]
result = easy_run.fully_buffered("mmtbx.water_screen %s" % " ".join(args)
).raise_if_errors()
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")
n_ca = 0
for line in result.stdout_lines:
if ("Final choice: CA" in line) :
n_ca += 1
if (n_ca != 1) :
print "\n".join(result.stdout_lines)
raise RuntimeError("Expected 1 Ca2+, found %d" % n_ca)
print "OK"
def exercise_calcium_substitution () :
from mmtbx.regression.make_fake_anomalous_data import generate_calcium_inputs
from iotbx.file_reader import any_file
anom_mtz_file, pdb_file = generate_calcium_inputs(
file_base = "tst_isomorphous_difference_misc_anom", anonymize = False)
hoh_file = generate_calcium_inputs(
file_base = "tst_isomorphous_difference_misc_hoh", anonymize = True)[1]
mtz_file = "tst_isomorphous_difference_misc.mtz"
args = [
"phenix.fmodel",
hoh_file,
"high_resolution=1.5",
"r_free_flags_fraction=0.1",
"type=real",
"output.file_name=" + mtz_file
]
easy_run.fully_buffered(args).raise_if_errors()
time.sleep(2)
assert os.path.isfile(mtz_file)
minus_mtz_file = "tst_isomorphous_difference_misc_anon_minus.mtz"
args = [
"phenix.fobs_minus_fobs_map",
"f_obs_1_file=" + anom_mtz_file,
"f_obs_2_file=" + mtz_file,
pdb_file,
"omit_selection=\"element CA\"",
"multiscale=True",
"output_file=" + minus_mtz_file,
]
result = easy_run.fully_buffered(args).raise_if_errors()
assert os.path.isfile(minus_mtz_file)
assert ("1 atoms selected for removal" in result.stdout_lines)
f = any_file(minus_mtz_file)
coeffs = f.file_server.miller_arrays[0]
fft_map = coeffs.fft_map(resolution_factor=0.25)
minus_map = fft_map.apply_sigma_scaling().real_map_unpadded()
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
xrs = pdb_in.file_object.xray_structure_simple()
for i_seq, atom in enumerate(hierarchy.atoms()) :
if (atom.element == "CA") :
site_frac = xrs.sites_frac()[i_seq]
val = minus_map.eight_point_interpolation(site_frac)
assert (val > 40)
def exercise_calcium_substitution():
from mmtbx.regression.make_fake_anomalous_data import generate_calcium_inputs
from iotbx.file_reader import any_file
anom_mtz_file, pdb_file = generate_calcium_inputs(
file_base="tst_isomorphous_difference_misc_anom", anonymize=False)
hoh_file = generate_calcium_inputs(
file_base="tst_isomorphous_difference_misc_hoh", anonymize=True)[1]
mtz_file = "tst_isomorphous_difference_misc.mtz"
args = [
"phenix.fmodel", hoh_file, "high_resolution=1.5",
"r_free_flags_fraction=0.1", "type=real",
"output.file_name=" + mtz_file
]
easy_run.fully_buffered(args).raise_if_errors()
time.sleep(2)
assert os.path.isfile(mtz_file)
minus_mtz_file = "tst_isomorphous_difference_misc_anon_minus.mtz"
args = [
"phenix.fobs_minus_fobs_map",
"f_obs_1_file=" + anom_mtz_file,
"f_obs_2_file=" + mtz_file,
pdb_file,
"omit_selection=\"element CA\"",
"multiscale=True",
"output_file=" + minus_mtz_file,
]
result = easy_run.fully_buffered(args).raise_if_errors()
assert os.path.isfile(minus_mtz_file)
assert ("1 atoms selected for removal" in result.stdout_lines)
f = any_file(minus_mtz_file)
coeffs = f.file_server.miller_arrays[0]
fft_map = coeffs.fft_map(resolution_factor=0.25)
minus_map = fft_map.apply_sigma_scaling().real_map_unpadded()
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
xrs = pdb_in.file_object.xray_structure_simple()
for i_seq, atom in enumerate(hierarchy.atoms()):
if (atom.element == "CA"):
site_frac = xrs.sites_frac()[i_seq]
val = minus_map.eight_point_interpolation(site_frac)
assert (val > 40)
def exercise_1 () :
from mmtbx.regression import make_fake_anomalous_data
import mmtbx.maps.utils
import mmtbx.utils
from iotbx.file_reader import any_file
mtz_file, pdb_file = make_fake_anomalous_data.generate_calcium_inputs(
"tst_map_utils")
# create_map_from_pdb_and_mtz
mfn1 = "tst_map_utils_1.mtz"
mmtbx.maps.utils.create_map_from_pdb_and_mtz(
pdb_file=pdb_file,
mtz_file=mtz_file,
output_file=mfn1,
fill=False,
out=null_out())
assert (os.path.isfile(mfn1))
maps_in = any_file(mfn1)
assert (len(maps_in.file_server.miller_arrays) == 3)
# generate_water_omit_map
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
xrs = pdb_in.file_object.xray_structure_simple()
mtz_in = any_file(mtz_file)
f_obs = mtz_in.file_server.miller_arrays[0]
flags = mtz_in.file_server.miller_arrays[1]
flags = flags.customized_copy(data=flags.data()==1)
fmodel = mmtbx.utils.fmodel_simple(
f_obs=f_obs,
r_free_flags=flags,
scattering_table="n_gaussian",
xray_structures=[xrs],
bulk_solvent_correction=False,
skip_twin_detection=True)
omit = mmtbx.maps.utils.generate_water_omit_map(
fmodel=fmodel,
pdb_hierarchy=hierarchy,
log=null_out())
assert (omit.n_waters == 3)
mfn2 = "tst_map_utils_2.mtz"
pdbfn2 = "tst_map_utils_2.pdb"
omit.write_map_coeffs(mfn2)
omit.write_pdb_file(pdbfn2)
for fn in [mfn1, mfn2, pdbfn2] :
os.remove(fn)
def exercise():
from mmtbx.regression.make_fake_anomalous_data import generate_calcium_inputs
base = "tst_validate_ca"
mtz_file, pdb_file = generate_calcium_inputs(file_base=base, anonymize=False)
time.sleep(2)
args = ["\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "wavelength=1.12",
"nproc=1"]
result = easy_run.fully_buffered("mmtbx.validate_ions %s" % " ".join(args)
).raise_if_errors()
n_ca, n_bad = 0, 0
for line in result.stdout_lines:
if "| CA" in line:
n_ca += 1
if "!!!" in line:
n_bad += 1
assert n_ca == 1 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_calcium_inputs
base = "tst_validate_ca"
mtz_file, pdb_file = generate_calcium_inputs(file_base=base, anonymize=False)
time.sleep(2)
args = ["\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "wavelength=1.12",
"nproc=1"]
result = easy_run.fully_buffered("mmtbx.validate_ions %s" % " ".join(args)
).raise_if_errors()
n_ca, n_bad = 0, 0
for line in result.stdout_lines:
if "| CA" in line:
n_ca += 1
if "!!!" in line:
n_bad += 1
assert n_ca == 1 and n_bad == 0
for ext in [".pdb", ".mtz", "_fmodel.eff"]:
os.remove(base + ext)
print "OK"
def exercise_1():
from mmtbx.regression import make_fake_anomalous_data
import mmtbx.maps.utils
import mmtbx.utils
from iotbx.file_reader import any_file
mtz_file, pdb_file = make_fake_anomalous_data.generate_calcium_inputs(
"tst_map_utils")
# create_map_from_pdb_and_mtz
mfn1 = "tst_map_utils_1.mtz"
mmtbx.maps.utils.create_map_from_pdb_and_mtz(pdb_file=pdb_file,
mtz_file=mtz_file,
output_file=mfn1,
fill=False,
out=null_out())
assert (os.path.isfile(mfn1))
maps_in = any_file(mfn1)
assert (len(maps_in.file_server.miller_arrays) == 3)
# generate_water_omit_map
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
xrs = pdb_in.file_object.xray_structure_simple()
mtz_in = any_file(mtz_file)
f_obs = mtz_in.file_server.miller_arrays[0]
flags = mtz_in.file_server.miller_arrays[1]
flags = flags.customized_copy(data=flags.data() == 1)
fmodel = mmtbx.utils.fmodel_simple(f_obs=f_obs,
r_free_flags=flags,
scattering_table="n_gaussian",
xray_structures=[xrs],
bulk_solvent_correction=False,
skip_twin_detection=True)
omit = mmtbx.maps.utils.generate_water_omit_map(fmodel=fmodel,
pdb_hierarchy=hierarchy,
log=null_out())
assert (omit.n_waters == 3)
mfn2 = "tst_map_utils_2.mtz"
pdbfn2 = "tst_map_utils_2.pdb"
omit.write_map_coeffs(mfn2)
omit.write_pdb_file(pdbfn2)
for fn in [mfn1, mfn2, pdbfn2]:
os.remove(fn)
def exercise () :
from mmtbx.regression.make_fake_anomalous_data import generate_calcium_inputs
base = "tst_pick_ca"
mtz_file, pdb_file = generate_calcium_inputs(file_base=base, anonymize=True)
time.sleep(2)
args = ["\"%s\"" % pdb_file, "\"%s\"" % mtz_file, "wavelength=1.1",
"nproc=1", "use_phaser=False", "fpp_ratio_max=1.2"]
result = easy_run.fully_buffered("mmtbx.water_screen %s" % " ".join(args)
).raise_if_errors()
n_ca = 0
for line in result.stdout_lines:
if "Probable cation: CA+2" in line:
n_ca += 1
if (n_ca != 1) :
print "\n".join(result.stdout_lines)
raise RuntimeError("Expected 1 Ca2+, found %d" % n_ca)
os.remove(pdb_file)
os.remove(mtz_file)
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_omit_atom_selection () :
# combine an omit selection with a CCP4 map selection - this used to crash
from mmtbx.regression.make_fake_anomalous_data import generate_calcium_inputs
import mmtbx.command_line.maps
mtz_file, pdb_file = generate_calcium_inputs(
file_base="tst_mmtbx_maps_misc2")
open("tst_mmtbx_maps_misc2.eff", "w").write("""\
maps {
map {
map_type = 2mFo-DFc
format = xplor *ccp4
file_name = tst_mmtbx_maps_misc2.ccp4
region = *selection cell
atom_selection = "resname HOH"
}
}""")
mmtbx.command_line.maps.run(args=[
mtz_file,
pdb_file,
"tst_mmtbx_maps_misc2.eff",
"omit.selection=\"resname TRP\"",
"prefix=tst_mmtbx_maps_misc2",
], log=null_out())
