def exercise_pdb_input_error_handling():
from libtbx.test_utils import open_tmp_file
from libtbx.test_utils import Exception_expected
bad_pdb_string = """\
ATOM 1 CB LYS 109 16.113 7.345 47.084 1.00 20.00 A
ATOM 2 CG LYS 109 17.058 6.315 47.703 1.00 20.00 A
ATOM 3 CB LYS 109 26.721 1.908 15.275 1.00 20.00 B
ATOM 4 CG LYS 109 27.664 2.793 16.091 1.00 20.00 B
"""
f = open_tmp_file(suffix="bad.pdb")
f.write(bad_pdb_string)
f.close()
try:
pdb_inp = pdb.input(file_name=f.name, source_info=None)
except ValueError as e:
err_message = str(e)
assert bad_pdb_string.splitlines()[0] in err_message
else:
raise Exception_expected
bad_cif_loop_string = """\
data_cif
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.auth_asym_id
_atom_site.auth_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.type_symbol
_atom_site.pdbx_formal_charge
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
#_atom_site.pdbx_PDB_model_num
ATOM 47 CA . THR C 22 ? -7.12300 19.28700 -2.26800 1.000 8.32783 C ? B ? 11 1
ATOM 52 CA . ASN C 25 ? -11.06500 18.97000 -5.48100 1.000 8.20531 C ? C ? 12 1
ATOM 60 CA . VAL C 26 ? -12.16900 22.54800 -4.78000 1.000 8.45988 C ? C ? 13 1
"""
f = open_tmp_file(suffix="bad.cif")
f.write(bad_cif_loop_string)
f.close()
try:
pdb_inp = pdb.input(file_name=f.name, source_info=None)
except iotbx.cif.CifParserError as e:
err_message = str(e)
assert err_message == \
"Wrong number of data items for loop containing _atom_site.group_PDB"
else:
raise Exception_expected
def exercise_spots_xds():
txt = """\
1104.20 1290.27 2.20 632. -4 -3 -1
912.22 1303.37 3.49 346. 0 0 0
1427.55 1339.93 3.34 259. 7 3 -1
1380.54 1187.54 3.58 243. 4 3 4
1222.32 1220.09 3.95 241. -1 0 2
1491.71 1322.33 2.72 237. 9 4 0
1053.50 1227.71 2.87 221. -6 -4 1
"""
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.write(txt)
f.close()
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(
spots_in.centroid,
[[1104.2, 1290.27, 2.2], [912.22, 1303.37, 3.49],
[1427.55, 1339.93, 3.34], [1380.54, 1187.54, 3.58],
[1222.32, 1220.09, 3.95], [1491.71, 1322.33, 2.72],
[1053.5, 1227.71, 2.87]])
assert approx_equal(
spots_in.intensity,
[632.0, 346.0, 259.0, 243.0, 241.0, 237.0, 221.0])
assert approx_equal(
spots_in.miller_index,
[[-4, -3, -1], [0, 0, 0], [7, 3, -1], [4, 3, 4],
[-1, 0, 2], [9, 4, 0], [-6, -4, 1]])
spots_out = spot_xds.writer(
spots_in.centroid, spots_in.intensity, spots_in.miller_index)
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.close()
spots_out.write_file(filename=f.name)
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(spots_in.centroid, spots_out.centroids)
assert approx_equal(spots_in.intensity, spots_out.intensities)
assert approx_equal(spots_in.miller_index, spots_out.miller_indices)
# now without miller indices
spots_out = spot_xds.writer(spots_in.centroid, spots_in.intensity)
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.close()
spots_out.write_file(filename=f.name)
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(spots_in.centroid, spots_out.centroids)
assert approx_equal(spots_in.intensity, spots_out.intensities)
assert len(spots_in.miller_index) == 0
def exercise_writer():
from iotbx import csv_utils
x = (1, 2, 3, 4, 5)
y = (6, 7, 8, 9, 10)
f = open_tmp_file()
field_names = ('x', 'y')
csv_utils.writer(f, (x, y), field_names=field_names)
f.close()
f = open(f.name, 'r')
content = [l.strip() for l in f.readlines()]
text = ['x,y']
text += ['%s,%s' % (row[0], row[1]) for row in zip(x, y)]
assert content == text
f.close()
x = (1, 2, 3, 4, 5)
y = (6, 7, 8, 9, 10)
f = open_tmp_file()
csv_utils.writer(f, (x, y), delimiter=';')
f.close()
f = open(f.name, 'r')
content = [l.strip() for l in f.readlines()]
text = ['%s;%s' % (row[0], row[1]) for row in zip(x, y)]
assert content == text
f.close()
x = flex.int(x)
y = flex.int(y)
f = open_tmp_file()
csv_utils.writer(f, (x, y), field_names=field_names)
f.close()
f = open(f.name, 'r')
content = [l.strip() for l in f.readlines()]
text = ['x,y']
text += ['%s,%s' % (row[0], row[1]) for row in zip(x, y)]
assert content == text
f.close()
y.append(11)
f = open_tmp_file()
try:
csv_utils.writer(f, (x, y), field_names=field_names)
except AssertionError:
pass
else:
raise Exception_expected
f.close()
def exercise_spots_xds():
txt = """\
1104.20 1290.27 2.20 632. -4 -3 -1
912.22 1303.37 3.49 346. 0 0 0
1427.55 1339.93 3.34 259. 7 3 -1
1380.54 1187.54 3.58 243. 4 3 4
1222.32 1220.09 3.95 241. -1 0 2
1491.71 1322.33 2.72 237. 9 4 0
1053.50 1227.71 2.87 221. -6 -4 1
"""
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.write(txt)
f.close()
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(spots_in.centroid,
[[1104.2, 1290.27, 2.2], [912.22, 1303.37, 3.49],
[1427.55, 1339.93, 3.34], [1380.54, 1187.54, 3.58],
[1222.32, 1220.09, 3.95], [1491.71, 1322.33, 2.72],
[1053.5, 1227.71, 2.87]])
assert approx_equal(spots_in.intensity,
[632.0, 346.0, 259.0, 243.0, 241.0, 237.0, 221.0])
assert approx_equal(spots_in.miller_index,
[[-4, -3, -1], [0, 0, 0], [7, 3, -1], [4, 3, 4],
[-1, 0, 2], [9, 4, 0], [-6, -4, 1]])
spots_out = spot_xds.writer(spots_in.centroid, spots_in.intensity,
spots_in.miller_index)
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.close()
spots_out.write_file(filename=f.name)
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(spots_in.centroid, spots_out.centroids)
assert approx_equal(spots_in.intensity, spots_out.intensities)
assert approx_equal(spots_in.miller_index, spots_out.miller_indices)
# now without miller indices
spots_out = spot_xds.writer(spots_in.centroid, spots_in.intensity)
f = open_tmp_file(suffix="SPOTS.XDS", mode="wb")
f.close()
spots_out.write_file(filename=f.name)
spots_in = spot_xds.reader()
spots_in.read_file(f.name)
assert approx_equal(spots_in.centroid, spots_out.centroids)
assert approx_equal(spots_in.intensity, spots_out.intensities)
assert len(spots_in.miller_index) == 0
def exercise_density_modification():
cci_structure_lib = os.environ.get("CCI_STRUCTURE_LIB")
if cci_structure_lib is None:
print "Skipping exercise_density_modification(): $CCI_STRUCTURE_LIB is not set"
return
rnase_s_path = os.path.join(cci_structure_lib, "rnase-s")
from libtbx.test_utils import open_tmp_file
tmp_file = open_tmp_file(suffix=".params")
tmp_file.write(params % (rnase_s_path, rnase_s_path))
tmp_file.close()
#dm = density_modification.run(
#args=[tmp_file.name, "%s/model/1RGE.pdb"%rnase_s_path])
args = (
tmp_file.name,
op.join(rnase_s_path, "model", "1RGE.pdb"))
for arg in args:
assert arg.find('"') < 0
cmd = 'mmtbx.density_modification "%s" "%s"' % args
print cmd
result = easy_run.fully_buffered(command=cmd).raise_if_errors()
assert result.stdout_lines[-5].startswith('Starting dm/model correlation:')
assert result.stdout_lines[-4].startswith('Final dm/model correlation:')
assert approx_equal(float(result.stdout_lines[-5].split()[-1]), 0.59, 0.01)
assert approx_equal(float(result.stdout_lines[-4].split()[-1]), 0.80, 0.01)
def exercise_compilation():
ucif_dist = libtbx.env.dist_path(module_name="ucif")
antlr3_dist = libtbx.env.under_dist("ucif", "antlr3")
os.environ["LIBTBX_UCIF"] = ucif_dist
os.environ["LIBTBX_ANTLR3"] = antlr3_dist
assert ucif_dist.find('"') < 0
if sys.platform == "win32":
cmd = '"%s/examples/build_cif_parser.bat"' %ucif_dist
ext = ".exe"
else:
cmd = '. "%s/examples/build_cif_parser.sh"' %ucif_dist
ext = ""
result = easy_run.fully_buffered(cmd)
if result.return_code:
if len(result.stderr_lines) > 0:
raise RuntimeError, result.show_stderr()
raise RuntimeError, result.show_stdout()
assert os.path.exists("cif_parser"+ext)
f = open_tmp_file(suffix=".cif")
f.write(cif_string)
f.close()
cmd = 'cif_parser "%s"' %f.name
cmd = os.path.join(".", cmd)
r = easy_run.fully_buffered(cmd).raise_if_errors()
assert r.stdout_lines[0].startswith("Congratulations!")
def exercise_compilation():
ucif_dist = libtbx.env.dist_path(module_name="ucif")
antlr3_dist = libtbx.env.under_dist("ucif", "antlr3")
os.environ["LIBTBX_UCIF"] = ucif_dist
os.environ["LIBTBX_ANTLR3"] = antlr3_dist
assert ucif_dist.find('"') < 0
if sys.platform == "win32":
cmd = '"%s/examples/build_cif_parser.bat"' % ucif_dist
ext = ".exe"
else:
cmd = '"%s/examples/build_cif_parser.sh"' % ucif_dist
ext = ""
result = easy_run.fully_buffered(cmd)
if result.return_code:
if len(result.stderr_lines) > 0:
raise RuntimeError, result.show_stderr()
raise RuntimeError, result.show_stdout()
assert os.path.exists("cif_parser" + ext)
f = open_tmp_file(suffix=".cif")
f.write(cif_string)
f.close()
cmd = 'cif_parser "%s"' % f.name
cmd = os.path.join(".", cmd)
r = easy_run.fully_buffered(cmd).raise_if_errors()
assert r.stdout_lines[0].startswith("Congratulations!")
def exercise_writer():
from iotbx import csv_utils
x = (1,2,3,4,5)
y = (6,7,8,9,10)
f = open_tmp_file()
field_names = ('x','y')
csv_utils.writer(f, (x,y), field_names=field_names)
f.close()
f = open(f.name, 'r')
content = f.readlines()
text = ['x,y\r\n']
text += ['%s,%s\r\n' %(row[0],row[1]) for row in zip(x,y)]
assert content == text
f.close()
x = (1,2,3,4,5)
y = (6,7,8,9,10)
f = open_tmp_file()
csv_utils.writer(f, (x,y), delimiter=';')
f.close()
f = open(f.name, 'r')
content = f.readlines()
text = ['%s;%s\r\n' %(row[0],row[1]) for row in zip(x,y)]
assert content == text
x = flex.int(x)
y = flex.int(y)
f = open_tmp_file()
csv_utils.writer(f, (x,y), field_names=field_names)
f.close()
f = open(f.name, 'r')
content = f.readlines()
text = ['x,y\r\n']
text += ['%s,%s\r\n' %(row[0],row[1]) for row in zip(x,y)]
assert content == text
f.close()
y.append(11)
f = open_tmp_file()
try:
csv_utils.writer(f, (x,y), field_names=field_names)
except AssertionError:
pass
else:
raise Exception_expected
f.close()
def exercise_reader():
from iotbx import csv_utils
x = (1,2,3,4,5)
y = (6,7,8,9,10)
f = open_tmp_file()
field_names = ('x','y')
csv_utils.writer(f, (x,y), field_names=field_names,delimiter=';')
f.close()
f = open(f.name, 'r')
a = csv_utils.reader(f, data_type=int, field_names=True,delimiter=';')
f.close()
assert tuple(a.data[0]) == x
assert tuple(a.data[1]) == y
x = (1,2,3,4,5)
y = (1.1,2.2,3.3,4.4,5.5)
f = open_tmp_file()
csv_utils.writer(f, (x,y))
f.close()
f = open(f.name, 'r')
data_type_list = (int, float)
a = csv_utils.reader(f, data_type_list=data_type_list)
f.close()
assert tuple(a.data[0]) == x
assert tuple(a.data[1]) == y
f = open(f.name, 'r')
data_type_list = (int, float)
try:
a = csv_utils.reader(f, data_type=int,
data_type_list=data_type_list)
# Can't pass data_type AND data_type_list
except AssertionError:
pass
else:
raise Exception_expected
f.close()
f = open(f.name, 'r')
a = csv_utils.reader(f)
f.close()
assert list(a.data[0]) == [str(i) for i in x]
assert list(a.data[1]) == [str(i) for i in y]
def exercise_crystal_symmetry():
cm = cif.reader(input_string=p1_sym_ops).model()
cs_builder = cif.builders.crystal_symmetry_builder(cm["r1e5xsf"])
assert cs_builder.crystal_symmetry.space_group_info().symbol_and_number() \
== 'P 1 (No. 1)'
file_object = open_tmp_file(suffix=".cif")
file_object.write(p1_sym_ops)
file_object.close()
cs = crystal_symmetry_from_any.extract_from(file_name=file_object.name)
assert cs.space_group_info().symbol_and_number() == 'P 1 (No. 1)'
def exercise_reader():
from iotbx import csv_utils
x = (1, 2, 3, 4, 5)
y = (6, 7, 8, 9, 10)
f = open_tmp_file()
field_names = ('x', 'y')
csv_utils.writer(f, (x, y), field_names=field_names, delimiter=';')
f.close()
f = open(f.name, 'r')
a = csv_utils.reader(f, data_type=int, field_names=True, delimiter=';')
f.close()
assert tuple(a.data[0]) == x
assert tuple(a.data[1]) == y
x = (1, 2, 3, 4, 5)
y = (1.1, 2.2, 3.3, 4.4, 5.5)
f = open_tmp_file()
csv_utils.writer(f, (x, y))
f.close()
f = open(f.name, 'r')
data_type_list = (int, float)
a = csv_utils.reader(f, data_type_list=data_type_list)
f.close()
assert tuple(a.data[0]) == x
assert tuple(a.data[1]) == y
f = open(f.name, 'r')
data_type_list = (int, float)
try:
a = csv_utils.reader(f, data_type=int, data_type_list=data_type_list)
# Can't pass data_type AND data_type_list
except AssertionError:
pass
else:
raise Exception_expected
f.close()
f = open(f.name, 'r')
a = csv_utils.reader(f)
f.close()
assert list(a.data[0]) == [str(i) for i in x]
assert list(a.data[1]) == [str(i) for i in y]
def exercise_crystal_symmetry():
cm = cif.reader(input_string=p1_sym_ops).model()
cs_builder = cif.builders.crystal_symmetry_builder(cm["r1e5xsf"])
assert cs_builder.crystal_symmetry.space_group_info().symbol_and_number() \
== 'P 1 (No. 1)'
file_object = open_tmp_file(suffix=".cif")
file_object.write(p1_sym_ops)
file_object.close()
cs = crystal_symmetry_from_any.extract_from(file_name=file_object.name)
assert cs.space_group_info().symbol_and_number() == 'P 1 (No. 1)'
def exercise_mmcif():
input_4edr = """\
data_4EDR
_cell.length_a 150.582
_cell.length_b 150.582
_cell.length_c 38.633
_cell.angle_alpha 90.000
_cell.angle_beta 90.000
_cell.angle_gamma 120.000
#
_symmetry.space_group_name_H-M 'P 61'
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 1 N N . SER A 1 1 21.138 -69.073 17.360 1.00 23.68 108 SER A N 1
ATOM 2 C CA . SER A 1 1 22.164 -68.793 18.358 1.00 22.98 108 SER A CA 1
ATOM 3 C C . SER A 1 1 23.173 -67.799 17.805 1.00 21.13 108 SER A C 1
ATOM 4 O O . SER A 1 1 23.251 -67.594 16.595 1.00 19.34 108 SER A O 1
ATOM 5 C CB . SER A 1 1 22.882 -70.080 18.766 1.00 22.68 108 SER A CB 1
ATOM 6 O OG . SER A 1 1 23.683 -70.569 17.703 1.00 24.00 108 SER A OG 1
HETATM 2650 MN MN . MN F 4 . 9.296 -44.783 -6.320 1.00 44.18 505 MN A MN 1
"""
f = open_tmp_file(suffix="cif", mode="w")
print >> f, input_4edr
f.close()
mmcif = any_file(f.name)
mmcif.assert_file_type("pdb")
mmcif.check_file_type("pdb")
symm = mmcif.crystal_symmetry()
assert (str(symm.space_group_info()) == "P 61")
assert (str(symm.unit_cell()) == "(150.582, 150.582, 38.633, 90, 90, 120)")
assert mmcif.file_description == 'Model'
hierarchy = mmcif.file_object.hierarchy
assert len(hierarchy.atoms()) == 7
remarks = mmcif.file_object.input.remark_section()
assert (len(remarks) == 0)
def exercise_mmcif():
input_4edr = """\
data_4EDR
_cell.length_a 150.582
_cell.length_b 150.582
_cell.length_c 38.633
_cell.angle_alpha 90.000
_cell.angle_beta 90.000
_cell.angle_gamma 120.000
#
_symmetry.space_group_name_H-M 'P 61'
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 1 N N . SER A 1 1 21.138 -69.073 17.360 1.00 23.68 108 SER A N 1
ATOM 2 C CA . SER A 1 1 22.164 -68.793 18.358 1.00 22.98 108 SER A CA 1
ATOM 3 C C . SER A 1 1 23.173 -67.799 17.805 1.00 21.13 108 SER A C 1
ATOM 4 O O . SER A 1 1 23.251 -67.594 16.595 1.00 19.34 108 SER A O 1
ATOM 5 C CB . SER A 1 1 22.882 -70.080 18.766 1.00 22.68 108 SER A CB 1
ATOM 6 O OG . SER A 1 1 23.683 -70.569 17.703 1.00 24.00 108 SER A OG 1
HETATM 2650 MN MN . MN F 4 . 9.296 -44.783 -6.320 1.00 44.18 505 MN A MN 1
"""
f = open_tmp_file(suffix="cif", mode="w")
print >> f, input_4edr
f.close()
mmcif = any_file(f.name)
mmcif.assert_file_type("pdb")
mmcif.check_file_type("pdb")
symm = mmcif.crystal_symmetry()
assert (str(symm.space_group_info()) == "P 61")
assert (str(symm.unit_cell()) == "(150.582, 150.582, 38.633, 90, 90, 120)")
assert mmcif.file_description == 'Model'
hierarchy = mmcif.file_object.hierarchy
assert len(hierarchy.atoms()) == 7
remarks = mmcif.file_object.input.remark_section()
assert (len(remarks) == 0)
def exercise_to_xds():
if not libtbx.env.has_module("dials"):
print "Skipping test: dials not present"
return
if not libtbx.env.has_module("dials_regression"):
print "Skipping exercise_to_xds(): dials_regression not present"
return
data_dir = libtbx.env.find_in_repositories(
relative_path="dials_regression/centroid_test_data",
test=os.path.isdir)
template = os.path.join(data_dir, "centroid_00*.cbf")
file_names = glob.glob(template)
sweep = ImageSetFactory.new(file_names)[0]
to_xds = xds.to_xds(sweep)
s1 = StringIO()
to_xds.XDS_INP(out=s1)
s2 = StringIO()
real_space_a = (-5.327642, -39.034747, -4.988286)
real_space_b = (-35.253495, 7.596265, -22.127661)
real_space_c = (-22.673623, -1.486119, 35.793463)
to_xds.xparm_xds(real_space_a,
real_space_b,
real_space_c,
space_group=1,
out=s2)
# run coordinate frame converter on xparm.xds as a sanity check
f = open_tmp_file(suffix="XPARM.XDS", mode="wb")
s2.seek(0)
f.writelines(s2.readlines())
f.close()
from rstbx.cftbx import coordinate_frame_helpers
converter = coordinate_frame_helpers.import_xds_xparm(f.name)
scan = sweep.get_scan()
detector = sweep.get_detector()
goniometer = sweep.get_goniometer()
beam = sweep.get_beam()
assert approx_equal(real_space_a, converter.get_real_space_a())
assert approx_equal(real_space_b, converter.get_real_space_b())
assert approx_equal(real_space_c, converter.get_real_space_c())
assert approx_equal(goniometer.get_rotation_axis(),
converter.get_rotation_axis())
assert approx_equal(beam.get_direction(),
converter.get_sample_to_source().elems)
assert approx_equal(detector[0].get_fast_axis(),
converter.get_detector_fast())
assert approx_equal(detector[0].get_slow_axis(),
converter.get_detector_slow())
assert approx_equal(detector[0].get_origin(),
converter.get_detector_origin())
def exercise_pdb_input_error_handling():
from libtbx.test_utils import open_tmp_file
from libtbx.test_utils import Exception_expected
bad_pdb_string = """\
ATOM 1 CB LYS 109 16.113 7.345 47.084 1.00 20.00 A
ATOM 2 CG LYS 109 17.058 6.315 47.703 1.00 20.00 A
ATOM 3 CB LYS 109 26.721 1.908 15.275 1.00 20.00 B
ATOM 4 CG LYS 109 27.664 2.793 16.091 1.00 20.00 B
"""
f = open_tmp_file(suffix="bad.pdb")
f.write(bad_pdb_string)
f.close()
try: pdb_inp = pdb.input(file_name=f.name, source_info=None)
except ValueError, e:
err_message = str(e)
assert bad_pdb_string.splitlines()[0] in err_message
def exercise_pdb_input_error_handling():
from libtbx.test_utils import open_tmp_file
from libtbx.test_utils import Exception_expected
bad_pdb_string = """\
ATOM 1 CB LYS 109 16.113 7.345 47.084 1.00 20.00 A
ATOM 2 CG LYS 109 17.058 6.315 47.703 1.00 20.00 A
ATOM 3 CB LYS 109 26.721 1.908 15.275 1.00 20.00 B
ATOM 4 CG LYS 109 27.664 2.793 16.091 1.00 20.00 B
"""
f = open_tmp_file(suffix="bad.pdb")
f.write(bad_pdb_string)
f.close()
try:
pdb_inp = pdb.input(file_name=f.name, source_info=None)
except ValueError, e:
err_message = str(e)
assert bad_pdb_string.splitlines()[0] in err_message
def exercise_to_xds():
if not libtbx.env.has_module("dials_regression"):
print "Skipping exercise_to_xds(): dials_regression not present"
return
data_dir = libtbx.env.find_in_repositories(
relative_path="dials_regression/centroid_test_data",
test=os.path.isdir)
template = os.path.join(data_dir, "centroid_00*.cbf")
file_names = glob.glob(template)
sweep = ImageSetFactory.new(file_names)[0]
to_xds = xds.to_xds(sweep)
s1 = StringIO()
to_xds.XDS_INP(out=s1)
s2 = StringIO()
real_space_a = (-5.327642, -39.034747, -4.988286)
real_space_b = (-35.253495, 7.596265, -22.127661)
real_space_c = (-22.673623, -1.486119, 35.793463)
to_xds.xparm_xds(real_space_a, real_space_b, real_space_c, space_group=1, out=s2)
# run coordinate frame converter on xparm.xds as a sanity check
f = open_tmp_file(suffix="XPARM.XDS", mode="wb")
s2.seek(0)
f.writelines(s2.readlines())
f.close()
from rstbx.cftbx import coordinate_frame_helpers
converter = coordinate_frame_helpers.import_xds_xparm(f.name)
scan = sweep.get_scan()
detector = sweep.get_detector()
goniometer = sweep.get_goniometer()
beam = sweep.get_beam()
assert approx_equal(real_space_a, converter.get_real_space_a())
assert approx_equal(real_space_b, converter.get_real_space_b())
assert approx_equal(real_space_c, converter.get_real_space_c())
assert approx_equal(goniometer.get_rotation_axis(),
converter.get_rotation_axis())
assert approx_equal(
beam.get_direction(), converter.get_sample_to_source().elems)
assert approx_equal(detector[0].get_fast_axis(), converter.get_detector_fast())
assert approx_equal(detector[0].get_slow_axis(), converter.get_detector_slow())
assert approx_equal(detector[0].get_origin(), converter.get_detector_origin())
def exercise_density_modification():
cci_structure_lib = os.environ.get("CCI_STRUCTURE_LIB")
if cci_structure_lib is None:
print "Skipping exercise_density_modification(): $CCI_STRUCTURE_LIB is not set"
return
rnase_s_path = os.path.join(cci_structure_lib, "rnase-s")
from libtbx.test_utils import open_tmp_file
tmp_file = open_tmp_file(suffix=".params")
tmp_file.write(params % (rnase_s_path, rnase_s_path))
tmp_file.close()
#dm = density_modification.run(
#args=[tmp_file.name, "%s/model/1RGE.pdb"%rnase_s_path])
args = (tmp_file.name, op.join(rnase_s_path, "model", "1RGE.pdb"))
for arg in args:
assert arg.find('"') < 0
cmd = 'mmtbx.density_modification "%s" "%s"' % args
print cmd
result = easy_run.fully_buffered(command=cmd).raise_if_errors()
assert result.stdout_lines[-5].startswith('Starting dm/model correlation:')
assert result.stdout_lines[-4].startswith('Final dm/model correlation:')
assert approx_equal(float(result.stdout_lines[-5].split()[-1]), 0.59, 0.01)
assert approx_equal(float(result.stdout_lines[-4].split()[-1]), 0.80, 0.01)
def exercise_density_modification():
pdb_path = libtbx.env.find_in_repositories(
relative_path="phenix_regression/density_modification/1RGE.pdb",
test=os.path.isfile)
reflection_path = libtbx.env.find_in_repositories(
relative_path="phenix_regression/density_modification/scale.hkl",
test=os.path.isfile)
phases_path = libtbx.env.find_in_repositories(
relative_path="phenix_regression/density_modification/ir_phase.hkl",
test=os.path.isfile)
if pdb_path is None or reflection_path is None or phases_path is None:
print(
"Skipping exercise_density_modification(): phenix_regression is not available"
)
return
from libtbx.test_utils import open_tmp_file
tmp_file = open_tmp_file(suffix=".params")
tmp_file.write(params % (reflection_path, phases_path))
tmp_file.close()
#dm = density_modification.run(
#args=[tmp_file.name, "%s/model/1RGE.pdb"%rnase_s_path])
args = (tmp_file.name, pdb_path)
for arg in args:
assert arg.find('"') < 0
cmd = 'mmtbx.density_modification "%s" "%s"' % args
print(cmd)
result = easy_run.fully_buffered(command=cmd).raise_if_errors()
assert result.stdout_lines[-5].startswith('Starting dm/model correlation:')
assert result.stdout_lines[-4].startswith('Final dm/model correlation:')
assert approx_equal(float(result.stdout_lines[-5].split()[-1]), 0.59, 0.01)
assert approx_equal(float(result.stdout_lines[-4].split()[-1]), 0.80, 0.01)
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.type_symbol
_atom_site.pdbx_formal_charge
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
#_atom_site.pdbx_PDB_model_num
ATOM 47 CA . THR C 22 ? -7.12300 19.28700 -2.26800 1.000 8.32783 C ? B ? 11 1
ATOM 52 CA . ASN C 25 ? -11.06500 18.97000 -5.48100 1.000 8.20531 C ? C ? 12 1
ATOM 60 CA . VAL C 26 ? -12.16900 22.54800 -4.78000 1.000 8.45988 C ? C ? 13 1
"""
f = open_tmp_file(suffix="bad.cif")
f.write(bad_cif_loop_string)
f.close()
try:
pdb_inp = pdb.input(file_name=f.name, source_info=None)
except iotbx.cif.CifParserError, e:
err_message = str(e)
assert err_message == "Wrong number of data items for loop containing _atom_site.group_PDB"
else:
raise Exception_expected
def exercise_extract_authors():
pdb_in = """
AUTHOR R.B.SUTTON,J.A.ERNST,A.T.BRUNGER
"""
def exercise_angle_edits_change(mon_lib_srv, ener_lib):
edits = """\
refinement.geometry_restraints.edits {
n_2_selection = chain A and resname ALA and resid 2 and name N
ca_2_selection = chain A and resname ALA and resid 2 and name CA
c_2_selection = chain A and resname ALA and resid 2 and name C
angle {
action = *change
atom_selection_1 = $n_2_selection
atom_selection_2 = $ca_2_selection
atom_selection_3 = $c_2_selection
angle_ideal = 100.00
sigma = 5
}
}"""
gm_phil = iotbx.phil.parse(
monomer_library.pdb_interpretation.grand_master_phil_str,
process_includes=True)
edits_phil = iotbx.phil.parse(edits)
working_phil = gm_phil.fetch(edits_phil)
params = working_phil.extract()
# print params.geometry_restraints.edits.parallelity[0].atom_selection_1
assert params.geometry_restraints.edits.angle[0].atom_selection_1.find(
"name N")
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=None,
raw_records=raw_records2,
params=params.pdb_interpretation,
log=None)
grm = processed_pdb_file.geometry_restraints_manager(
params_edits=params.geometry_restraints.edits,
params_remove=params.geometry_restraints.remove)
assert grm.angle_proxies.size() == 20
user_defined = grm.angle_proxies.proxy_select(
origin_id=origin_ids.get_origin_id('edits'))
assert user_defined.size() == 1
udp = user_defined[0]
assert list(udp.i_seqs) == [5, 6, 7]
assert approx_equal(udp.angle_ideal, 100, eps=1e-4)
assert approx_equal(udp.weight, 0.04, eps=1e-4)
from libtbx.test_utils import open_tmp_file
from libtbx import easy_run
pdb_file = open_tmp_file(suffix="aaa.pdb")
pdb_file.write('\n'.join(raw_records2))
pdb_file.close()
edits_file = open_tmp_file(suffix="tau.edits")
edits_file.write(edits)
edits_file.close()
cmd = "phenix.pdb_interpretation \"%s\" \"%s\" write_geo_files=True" % (
pdb_file.name, edits_file.name)
result = easy_run.fully_buffered(cmd).raise_if_errors()
geo_file = open(pdb_file.name + '.geo', "r")
# geo_file = open(pdb_file.name.replace(".pdb", '_minimized.geo'), "r")
geo_file_str = geo_file.read()
assert '''User supplied angle restraints: 1
Sorted by residual:
angle pdb=" N ALA A 2 " segid="A "
pdb=" CA ALA A 2 " segid="A "
pdb=" C ALA A 2 " segid="A "
ideal model delta sigma weight residual
100.00''' in geo_file_str
def exercise_to_xds():
if not libtbx.env.has_module("dials"):
print "Skipping test: dials not present"
return
if not libtbx.env.has_module("dials_regression"):
print "Skipping exercise_to_xds(): dials_regression not present"
return
data_dir = libtbx.env.find_in_repositories(
relative_path="dials_regression/centroid_test_data",
test=os.path.isdir)
template = os.path.join(data_dir, "centroid_*.cbf")
file_names = glob.glob(template)
expected_output = """\
DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=495976
SENSOR_THICKNESS= 0.320
DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000
DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000
NX=2463 NY=2527 QX=0.1720 QY=0.1720
DETECTOR_DISTANCE= 190.180
ORGX= 1235.84 ORGY= 1279.58
ROTATION_AXIS= 1.00000 0.00000 0.00000
STARTING_ANGLE= 0.000
OSCILLATION_RANGE= 0.200
X-RAY_WAVELENGTH= 0.97950
INCIDENT_BEAM_DIRECTION= -0.000 -0.000 1.021
FRACTION_OF_POLARIZATION= 0.999
POLARIZATION_PLANE_NORMAL= 0.000 1.000 0.000
NAME_TEMPLATE_OF_DATA_FRAMES= %s
TRUSTED_REGION= 0.0 1.41
UNTRUSTED_RECTANGLE= 487 495 0 2528
UNTRUSTED_RECTANGLE= 981 989 0 2528
UNTRUSTED_RECTANGLE= 1475 1483 0 2528
UNTRUSTED_RECTANGLE= 1969 1977 0 2528
UNTRUSTED_RECTANGLE= 0 2464 195 213
UNTRUSTED_RECTANGLE= 0 2464 407 425
UNTRUSTED_RECTANGLE= 0 2464 619 637
UNTRUSTED_RECTANGLE= 0 2464 831 849
UNTRUSTED_RECTANGLE= 0 2464 1043 1061
UNTRUSTED_RECTANGLE= 0 2464 1255 1273
UNTRUSTED_RECTANGLE= 0 2464 1467 1485
UNTRUSTED_RECTANGLE= 0 2464 1679 1697
UNTRUSTED_RECTANGLE= 0 2464 1891 1909
UNTRUSTED_RECTANGLE= 0 2464 2103 2121
UNTRUSTED_RECTANGLE= 0 2464 2315 2333
DATA_RANGE= 1 9
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT\
""" % (template.replace("*", "????"))
cmd = " ".join(["dxtbx.to_xds"] + file_names)
result = easy_run.fully_buffered(cmd)
# allow extra lines to have been added (these may be comments)
for record in expected_output.split('\n'):
assert record.strip() in "\n".join(result.stdout_lines), record
# now test reading from a json file
sweep = ImageSetFactory.new(file_names)[0]
f = open_tmp_file(suffix="sweep.json", mode="wb")
dump.imageset(sweep, f)
f.close()
cmd = " ".join(["dxtbx.to_xds", f.name])
print cmd
result = easy_run.fully_buffered(cmd)
# allow extra lines to have been added (these may be comments)
for record in expected_output.split('\n'):
assert record.strip() in "\n".join(result.stdout_lines), record
def exercise_lex_parse_build():
exercise_parser(cif.reader, cif.builders.cif_model_builder)
cm = cif.reader(input_string=cif_quoted_string).model()
assert cm['global']['_a'] == 'a"b'
assert cm['global']['_b'] == "a dog's life"
stdout = sys.stdout
s = StringIO()
sys.stdout = s
try:
cif.reader(input_string=cif_invalid_missing_value)
except CifParserError:
pass
else:
raise Exception_expected
r = cif.reader(input_string=cif_invalid_missing_value,
raise_if_errors=False)
assert r.error_count() == 1
try:
cif.reader(input_string=cif_invalid_string)
except CifParserError:
pass
else:
raise Exception_expected
a = cif.reader(input_string=cif_cod)
assert a.error_count() == 0
try:
cif.reader(input_string=cif_invalid_semicolon_text_field)
except CifParserError:
pass
else:
raise Exception_expected
d = cif.reader(input_string=cif_valid_semicolon_text_field)
assert d.error_count() == 0
assert d.model()['1']['_a'] == '\n1\n'
e = cif.reader(input_string=cif_unquoted_string_semicolon)
assert not show_diff(
str(e.model()), """\
data_1
_a ;1
_b ;
_c 2
""")
cif_str_1 = """\
data_1
_a 1
"""
cif_str_2 = """\
data_2
_b 2
"""
cm = cif.reader(input_string=cif_str_1).model()
assert list(cm.keys()) == ['1']
cif.reader(input_string=cif_str_2, cif_object=cm).model()
assert list(cm.keys()) == ['1', '2']
try:
cm = cif.reader(input_string=cif_invalid_loop).model()
except CifParserError:
pass
else:
raise Exception_expected
try:
cm = cif.reader(input_string=cif_invalid_loop_2).model()
except CifParserError:
pass
else:
raise Exception_expected
sys.stdout = stdout
arrays = miller.array.from_cif(file_object=StringIO(
cif_miller_array_template %
('_refln_F_calc', '_refln_F_meas', '_refln_F_sigma')),
data_block_name='global')
assert sorted(arrays.keys()) == ['_refln_F_calc', '_refln_F_meas']
assert arrays['_refln_F_calc'].sigmas() is None
assert isinstance(arrays['_refln_F_meas'].sigmas(), flex.double)
arrays = miller.array.from_cif(file_object=StringIO(
cif_miller_array_template %
('_refln_A_calc', '_refln_B_calc', '_refln_F_meas')),
data_block_name='global')
assert sorted(arrays.keys()) == ['_refln_A_calc', '_refln_F_meas']
assert arrays['_refln_A_calc'].is_complex_array()
arrays = miller.array.from_cif(file_object=StringIO(
cif_miller_array_template %
('_refln_A_meas', '_refln_B_meas', '_refln_F_meas')),
data_block_name='global')
assert sorted(arrays.keys()) == ['_refln_A_meas', '_refln_F_meas']
assert arrays['_refln_A_meas'].is_complex_array()
arrays = miller.array.from_cif(
file_object=StringIO(cif_miller_array_template %
('_refln_intensity_calc', '_refln_intensity_meas',
'_refln_intensity_sigma')),
data_block_name='global')
assert sorted(
arrays.keys()) == ['_refln_intensity_calc', '_refln_intensity_meas']
arrays = miller.array.from_cif(file_object=StringIO(
cif_miller_array_template %
('_refln_F_calc', '_refln_phase_calc', '_refln_F_sigma')),
data_block_name='global')
assert sorted(arrays.keys()) == ['_refln_F_calc']
assert arrays['_refln_F_calc'].is_complex_array()
for data_block_name in (None, "global"):
miller_arrays = cif.reader(
file_object=StringIO(cif_miller_array_template %
('_refln_F_calc', '_refln_F_meas',
'_refln_F_sigma'))).as_miller_arrays(
data_block_name=data_block_name)
assert " ".join(sorted([str(ma.info()) for ma in miller_arrays])) \
== "cif:global,_refln_F_calc cif:global,_refln_F_meas,_refln_F_sigma"
f = open_tmp_file(suffix="cif")
f.write(cif_miller_array_template %
('_refln_F_calc', '_refln_F_meas', '_refln_F_sigma'))
f.close()
miller_arrays = any_reflection_file(file_name=f.name).as_miller_arrays()
assert len(miller_arrays) == 2
cs = crystal.symmetry(space_group_info=sgtbx.space_group_info("P1"))
miller_arrays = any_reflection_file(file_name=f.name).as_miller_arrays(
crystal_symmetry=cs, force_symmetry=True, anomalous=True)
assert miller_arrays[0].anomalous_flag() is True
assert miller_arrays[0].crystal_symmetry().space_group() == cs.space_group(
)
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.type_symbol
_atom_site.pdbx_formal_charge
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
#_atom_site.pdbx_PDB_model_num
ATOM 47 CA . THR C 22 ? -7.12300 19.28700 -2.26800 1.000 8.32783 C ? B ? 11 1
ATOM 52 CA . ASN C 25 ? -11.06500 18.97000 -5.48100 1.000 8.20531 C ? C ? 12 1
ATOM 60 CA . VAL C 26 ? -12.16900 22.54800 -4.78000 1.000 8.45988 C ? C ? 13 1
"""
f = open_tmp_file(suffix="bad.cif")
f.write(bad_cif_loop_string)
f.close()
try: pdb_inp = pdb.input(file_name=f.name, source_info=None)
except iotbx.cif.CifParserError, e:
err_message = str(e)
assert err_message == \
"Wrong number of data items for loop containing _atom_site.group_PDB"
else: raise Exception_expected
def exercise_extract_authors():
pdb_in = """
AUTHOR R.B.SUTTON,J.A.ERNST,A.T.BRUNGER
"""
assert iotbx.pdb.input(source_info=None, lines=pdb_in).extract_authors()==\
['B.R.SUTTON', 'A.ERNST.J', 'A.BRUNGER.T']
def exercise_mmcif_support():
from libtbx.test_utils import open_tmp_file
f = open_tmp_file(suffix="pdbtools.cif")
f.write("""\
data_phenix
_space_group.name_H-M_alt 'C 1 2 1'
_space_group.name_Hall ' C 2y'
_cell.length_a 46.053
_cell.length_b 9.561
_cell.length_c 20.871
_cell.angle_alpha 90.0
_cell.angle_beta 97.43
_cell.angle_gamma 90.0
_cell.volume 9112.60599144
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.auth_asym_id
_atom_site.auth_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.type_symbol
_atom_site.pdbx_formal_charge
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_model_num
ATOM 2 CA . LYS A 1 ? 7.49733 -0.62028 4.35289 1.000 10.25989 C ? A ? 1 1
ATOM 11 CA . LEU A 2 ? 3.72032 -0.19320 3.89326 1.000 7.80433 C ? A ? 2 1
ATOM 19 CA . VAL A 3 ? 0.78668 -0.39555 6.35234 1.000 5.03864 C ? A ? 3 1
ATOM 26 CA . PHE A 4 ? -2.75438 -0.21383 5.02429 1.000 8.93080 C ? A ? 4 1
ATOM 37 CA . PHE A 5 ? -6.05155 -0.46197 6.85390 1.000 9.57417 C ? A ? 5 1
ATOM 48 CA . ALA A 6 ? -9.57646 -0.10942 5.55847 1.000 17.73488 C ? A ? 6 1
ATOM 54 CA . LYS B 1 ? -8.86604 -5.20044 5.46515 1.000 16.15297 C ? B ? 7 1
""")
f.close()
cmd = " ".join(["phenix.pdbtools", "\"%s\"" % f.name,
"rename_chain_id.old_id=A",
"rename_chain_id.new_id=C"])
run_command(command=cmd, verbose=False)
assert os.path.isfile(f.name+"_modified.pdb")
pdb_inp = iotbx.pdb.input(file_name=f.name+"_modified.pdb")
assert pdb_inp.file_type() == "pdb"
hierarchy = pdb_inp.construct_hierarchy()
assert [chain.id for chain in hierarchy.chains()] == ['C', 'B']
cmd = " ".join(["phenix.pdbtools", "\"%s\"" % f.name,
"adp.convert_to_anisotropic=True",
"output.format=mmcif"])
run_command(command=cmd, verbose=False)
assert os.path.isfile(f.name+"_modified.cif")
pdb_inp = iotbx.pdb.input(file_name=f.name+"_modified.cif")
assert pdb_inp.file_type() == "mmcif"
xs = pdb_inp.xray_structure_simple()
assert xs.use_u_aniso().all_eq(True)
def exercise_mmcif_support():
from libtbx.test_utils import open_tmp_file
f = open_tmp_file(suffix="pdbtools.cif")
f.write("""\
data_phenix
_space_group.name_H-M_alt 'C 1 2 1'
_space_group.name_Hall ' C 2y'
_cell.length_a 46.053
_cell.length_b 9.561
_cell.length_c 20.871
_cell.angle_alpha 90.0
_cell.angle_beta 97.43
_cell.angle_gamma 90.0
_cell.volume 9112.60599144
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.auth_asym_id
_atom_site.auth_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.type_symbol
_atom_site.pdbx_formal_charge
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_model_num
ATOM 2 CA . LYS A 1 ? 7.49733 -0.62028 4.35289 1.000 10.25989 C ? A ? 1 1
ATOM 11 CA . LEU A 2 ? 3.72032 -0.19320 3.89326 1.000 7.80433 C ? A ? 2 1
ATOM 19 CA . VAL A 3 ? 0.78668 -0.39555 6.35234 1.000 5.03864 C ? A ? 3 1
ATOM 26 CA . PHE A 4 ? -2.75438 -0.21383 5.02429 1.000 8.93080 C ? A ? 4 1
ATOM 37 CA . PHE A 5 ? -6.05155 -0.46197 6.85390 1.000 9.57417 C ? A ? 5 1
ATOM 48 CA . ALA A 6 ? -9.57646 -0.10942 5.55847 1.000 17.73488 C ? A ? 6 1
ATOM 54 CA . LYS B 1 ? -8.86604 -5.20044 5.46515 1.000 16.15297 C ? B ? 7 1
""")
f.close()
cmd = " ".join([
"phenix.pdbtools",
"\"%s\"" % f.name, "rename_chain_id.old_id=A",
"rename_chain_id.new_id=C"
])
run_command(command=cmd, verbose=False)
assert os.path.isfile(f.name + "_modified.pdb")
pdb_inp = iotbx.pdb.input(file_name=f.name + "_modified.pdb")
assert pdb_inp.file_type() == "pdb"
hierarchy = pdb_inp.construct_hierarchy()
assert [chain.id for chain in hierarchy.chains()] == ['C', 'B']
cmd = " ".join([
"phenix.pdbtools",
"\"%s\"" % f.name, "adp.convert_to_anisotropic=True",
"output.format=mmcif"
])
run_command(command=cmd, verbose=False)
assert os.path.isfile(f.name + "_modified.cif")
pdb_inp = iotbx.pdb.input(file_name=f.name + "_modified.cif")
assert pdb_inp.file_type() == "mmcif"
xs = pdb_inp.xray_structure_simple()
assert xs.use_u_aniso().all_eq(True)
def exercise_to_xds():
if not libtbx.env.has_module("dials_regression"):
print "Skipping exercise_to_xds(): dials_regression not present"
return
data_dir = libtbx.env.find_in_repositories(
relative_path="dials_regression/centroid_test_data",
test=os.path.isdir)
template = os.path.join(data_dir, "centroid_*.cbf")
file_names = glob.glob(template)
expected_output = """\
DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=495976
SENSOR_THICKNESS= 0.320
DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000
DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000
NX=2463 NY=2527 QX=0.1720 QY=0.1720
DETECTOR_DISTANCE= 190.180
ORGX= 1235.84 ORGY= 1279.58
ROTATION_AXIS= 1.00000 0.00000 0.00000
STARTING_ANGLE= 0.000
OSCILLATION_RANGE= 0.200
X-RAY_WAVELENGTH= 0.97950
INCIDENT_BEAM_DIRECTION= -0.000 -0.000 1.021
FRACTION_OF_POLARIZATION= 0.999
POLARIZATION_PLANE_NORMAL= 0.000 1.000 0.000
NAME_TEMPLATE_OF_DATA_FRAMES= %s
TRUSTED_REGION= 0.0 1.41
UNTRUSTED_RECTANGLE= 487 495 0 2528
UNTRUSTED_RECTANGLE= 981 989 0 2528
UNTRUSTED_RECTANGLE= 1475 1483 0 2528
UNTRUSTED_RECTANGLE= 1969 1977 0 2528
UNTRUSTED_RECTANGLE= 0 2464 195 213
UNTRUSTED_RECTANGLE= 0 2464 407 425
UNTRUSTED_RECTANGLE= 0 2464 619 637
UNTRUSTED_RECTANGLE= 0 2464 831 849
UNTRUSTED_RECTANGLE= 0 2464 1043 1061
UNTRUSTED_RECTANGLE= 0 2464 1255 1273
UNTRUSTED_RECTANGLE= 0 2464 1467 1485
UNTRUSTED_RECTANGLE= 0 2464 1679 1697
UNTRUSTED_RECTANGLE= 0 2464 1891 1909
UNTRUSTED_RECTANGLE= 0 2464 2103 2121
UNTRUSTED_RECTANGLE= 0 2464 2315 2333
DATA_RANGE= 1 9
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT\
""" %(template.replace("*", "????"))
cmd = " ".join(["dxtbx.to_xds"] + file_names)
result = easy_run.fully_buffered(cmd)
# allow extra lines to have been added (these may be comments)
for record in expected_output.split('\n'):
assert record.strip() in "\n".join(result.stdout_lines), record
# now test reading from a json file
sweep = ImageSetFactory.new(file_names)[0]
f = open_tmp_file(suffix="sweep.json", mode="wb")
dump.imageset(sweep, f)
f.close()
cmd = " ".join(["dxtbx.to_xds", f.name])
result = easy_run.fully_buffered(cmd)
# allow extra lines to have been added (these may be comments)
for record in expected_output.split('\n'):
assert record.strip() in "\n".join(result.stdout_lines), record
def run(self):
from iotbx.xds import xparm
import os
import libtbx.load_env
from libtbx.test_utils import open_tmp_file
iotbx_dir = libtbx.env.dist_path('iotbx')
filename = os.path.join(iotbx_dir, 'xds', 'tests', 'XPARM.XDS')
handle = xparm.reader()
assert handle.find_version(filename) == 1
handle.read_file(filename)
print 'OK'
filename = os.path.join(iotbx_dir, 'xds', 'tests', 'NEW_XPARM.XDS')
handle = xparm.reader()
assert handle.find_version(filename) == 2
handle.read_file(filename)
print 'OK'
f = open_tmp_file(suffix='XPARM.XDS', mode='wb')
f.close()
writer = xparm.writer(
handle.starting_frame,
handle.starting_angle,
handle.oscillation_range,
handle.rotation_axis,
handle.wavelength,
handle.beam_vector,
handle.space_group,
handle.unit_cell,
handle.unit_cell_a_axis,
handle.unit_cell_b_axis,
handle.unit_cell_c_axis,
handle.num_segments,
handle.detector_size,
handle.pixel_size,
handle.detector_origin,
handle.detector_distance,
handle.detector_x_axis,
handle.detector_y_axis,
handle.detector_normal,
handle.segments,
handle.orientation)
writer.write_file(f.name)
handle_recycled = xparm.reader()
# make sure we wrote out version 2
assert handle_recycled.find_version(f.name) == 2
handle_recycled.read_file(f.name)
for handle in (handle, handle_recycled):
# Scan and goniometer stuff
assert handle.starting_frame == 1
assert handle.starting_angle == 82.0
assert handle.oscillation_range == 0.1500
assert handle.rotation_axis == (0.999997, -0.001590, -0.001580)
# Beam stuff
assert handle.wavelength == 0.976250
assert handle.beam_vector == (0.001608, 0.004392, 1.024317)
# Detector stuff
assert handle.detector_size == (2463, 2527)
assert handle.pixel_size == (0.172, 0.172)
assert handle.detector_distance == 264.928955
assert handle.detector_origin == (1224.856812, 1187.870972)
assert handle.detector_x_axis == (1.0, 0.0, 0.0)
assert handle.detector_y_axis == (0.0, 1.0, 0.0)
assert handle.detector_normal == (0.0, 0.0, 1.0)
# Crystal stuff
assert handle.space_group == 75
assert handle.unit_cell == (57.7831, 57.7831, 150.0135, 90.000, 90.000, 90.000)
assert handle.unit_cell_a_axis == (-14.918090, -22.358297, 51.151196)
assert handle.unit_cell_b_axis == (-19.858326, 51.608330, 16.766487)
assert handle.unit_cell_c_axis == (-135.447952, -34.400188, -54.539391)
# segment stuff
assert handle_recycled.num_segments == 1
assert handle_recycled.segments == [(1, 1, 2463, 1, 2527)]
assert handle_recycled.orientation == [
(0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0)]
print 'OK'
def exercise_lex_parse_build():
exercise_parser(cif.reader, cif.builders.cif_model_builder)
cm = cif.reader(input_string=cif_quoted_string).model()
assert cm['global']['_a'] == 'a"b'
assert cm['global']['_b'] == "a dog's life"
stdout = sys.stdout
s = StringIO()
sys.stdout = s
try: cif.reader(input_string=cif_invalid_missing_value)
except CifParserError: pass
else: raise Exception_expected
r = cif.reader(
input_string=cif_invalid_missing_value, raise_if_errors=False)
assert r.error_count() == 1
try: cif.reader(input_string=cif_invalid_string)
except CifParserError: pass
else: raise Exception_expected
a = cif.reader(input_string=cif_cod)
assert a.error_count() == 0
try: cif.reader(input_string=cif_invalid_semicolon_text_field)
except CifParserError: pass
else: raise Exception_expected
d = cif.reader(input_string=cif_valid_semicolon_text_field)
assert d.error_count() == 0
assert d.model()['1']['_a'] == '\n1\n'
e = cif.reader(input_string=cif_unquoted_string_semicolon)
assert not show_diff(str(e.model()), """\
data_1
_a ;1
_b ;
_c 2
""")
cif_str_1 = """\
data_1
_a 1
"""
cif_str_2 = """\
data_2
_b 2
"""
cm = cif.reader(input_string=cif_str_1).model()
assert cm.keys() == ['1']
cif.reader(input_string=cif_str_2, cif_object=cm).model()
assert cm.keys() == ['1', '2']
try: cm = cif.reader(input_string=cif_invalid_loop).model()
except CifParserError: pass
else: raise Exception_expected
try: cm = cif.reader(input_string=cif_invalid_loop_2).model()
except CifParserError: pass
else: raise Exception_expected
sys.stdout = stdout
arrays = miller.array.from_cif(file_object=StringIO(
cif_miller_array_template %(
'_refln_F_calc', '_refln_F_meas', '_refln_F_sigma')),
data_block_name='global')
assert sorted(arrays.keys()) == ['_refln_F_calc', '_refln_F_meas']
assert arrays['_refln_F_calc'].sigmas() is None
assert isinstance(arrays['_refln_F_meas'].sigmas(), flex.double)
arrays = miller.array.from_cif(file_object=StringIO(
cif_miller_array_template %(
'_refln_A_calc', '_refln_B_calc', '_refln_F_meas')),
data_block_name='global')
assert sorted(arrays.keys()) == ['_refln_A_calc', '_refln_F_meas']
assert arrays['_refln_A_calc'].is_complex_array()
arrays = miller.array.from_cif(file_object=StringIO(
cif_miller_array_template %(
'_refln_A_meas', '_refln_B_meas', '_refln_F_meas')),
data_block_name='global')
assert sorted(arrays.keys()) == ['_refln_A_meas', '_refln_F_meas']
assert arrays['_refln_A_meas'].is_complex_array()
arrays = miller.array.from_cif(file_object=StringIO(
cif_miller_array_template %(
'_refln_intensity_calc', '_refln_intensity_meas',
'_refln_intensity_sigma')),
data_block_name='global')
assert sorted(arrays.keys()) == [
'_refln_intensity_calc', '_refln_intensity_meas']
arrays = miller.array.from_cif(file_object=StringIO(
cif_miller_array_template %(
'_refln_F_calc', '_refln_phase_calc', '_refln_F_sigma')),
data_block_name='global')
assert sorted(arrays.keys()) == ['_refln_F_calc']
assert arrays['_refln_F_calc'].is_complex_array()
for data_block_name in (None, "global"):
miller_arrays = cif.reader(file_object=StringIO(
cif_miller_array_template %(
'_refln_F_calc',
'_refln_F_meas',
'_refln_F_sigma'))).as_miller_arrays(data_block_name=data_block_name)
assert " ".join(sorted([str(ma.info()) for ma in miller_arrays])) \
== "cif:global,_refln_F_calc cif:global,_refln_F_meas,_refln_F_sigma"
f = open_tmp_file(suffix="cif")
f.write(cif_miller_array_template %(
'_refln_F_calc',
'_refln_F_meas',
'_refln_F_sigma'))
f.close()
miller_arrays = any_reflection_file(file_name=f.name).as_miller_arrays()
assert len(miller_arrays) == 2
def run(self):
from iotbx.xds import xparm
import os
import libtbx.load_env
from libtbx.test_utils import open_tmp_file
iotbx_dir = libtbx.env.dist_path('iotbx')
filename = os.path.join(iotbx_dir, 'xds', 'tests', 'XPARM.XDS')
handle = xparm.reader()
assert handle.find_version(filename) == 1
handle.read_file(filename)
print('OK')
filename = os.path.join(iotbx_dir, 'xds', 'tests', 'NEW_XPARM.XDS')
handle = xparm.reader()
assert handle.find_version(filename) == 2
handle.read_file(filename)
print('OK')
f = open_tmp_file(suffix='XPARM.XDS', mode='wb')
f.close()
writer = xparm.writer(
handle.starting_frame,
handle.starting_angle,
handle.oscillation_range,
handle.rotation_axis,
handle.wavelength,
handle.beam_vector,
handle.space_group,
handle.unit_cell,
handle.unit_cell_a_axis,
handle.unit_cell_b_axis,
handle.unit_cell_c_axis,
handle.num_segments,
handle.detector_size,
handle.pixel_size,
handle.detector_origin,
handle.detector_distance,
handle.detector_x_axis,
handle.detector_y_axis,
handle.detector_normal,
handle.segments,
handle.orientation)
writer.write_file(f.name)
handle_recycled = xparm.reader()
# make sure we wrote out version 2
assert handle_recycled.find_version(f.name) == 2
handle_recycled.read_file(f.name)
for handle in (handle, handle_recycled):
# Scan and goniometer stuff
assert handle.starting_frame == 1
assert handle.starting_angle == 82.0
assert handle.oscillation_range == 0.1500
assert handle.rotation_axis == (0.999997, -0.001590, -0.001580)
# Beam stuff
assert handle.wavelength == 0.976250
assert handle.beam_vector == (0.001608, 0.004392, 1.024317)
# Detector stuff
assert handle.detector_size == (2463, 2527)
assert handle.pixel_size == (0.172, 0.172)
assert handle.detector_distance == 264.928955
assert handle.detector_origin == (1224.856812, 1187.870972)
assert handle.detector_x_axis == (1.0, 0.0, 0.0)
assert handle.detector_y_axis == (0.0, 1.0, 0.0)
assert handle.detector_normal == (0.0, 0.0, 1.0)
# Crystal stuff
assert handle.space_group == 75
assert handle.unit_cell == (57.7831, 57.7831, 150.0135, 90.000, 90.000, 90.000)
assert handle.unit_cell_a_axis == (-14.918090, -22.358297, 51.151196)
assert handle.unit_cell_b_axis == (-19.858326, 51.608330, 16.766487)
assert handle.unit_cell_c_axis == (-135.447952, -34.400188, -54.539391)
# segment stuff
assert handle_recycled.num_segments == 1
assert handle_recycled.segments == [(1, 1, 2463, 1, 2527)]
assert handle_recycled.orientation == [
(0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0)]
print('OK')