def exercise_cablam():
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/pdb103l.ent",
test=os.path.isfile) #This is the same file used for tst_kinemage.py
if (regression_pdb is None):
print(
"Skipping exercise_cablam(): input pdb (pdb103l.ent) not available"
)
return
#-----
pdb_io = pdb.input(regression_pdb)
pdbid = os.path.basename(regression_pdb)
hierarchy = pdb_io.construct_hierarchy()
oneline_test = cablam_test_string()
cablam_validate.oneline(hierarchy,
peptide_cutoff=0.05,
peptide_bad_cutoff=0.01,
ca_cutoff=0.005,
pdbid=pdbid,
writeto=oneline_test)
text_test = cablam_test_string()
outliers = cablam_validate.analyze_pdb(hierarchy,
outlier_cutoff=0.05,
pdbid=pdbid)
cablam_validate.give_text(outliers, writeto=text_test)
#print '|',oneline_test.output,'|'
#print '|',ref_cablam_give_oneline,'|'
#print '|',text_test.output,'|'
#print '|',ref_cablam_give_text,'|'
assert not show_diff(oneline_test.output, ref_cablam_give_oneline)
assert not show_diff(text_test.output, ref_cablam_give_text)
def exercise_correct_rhombohedral_setting_if_necessary():
for symbol in sgtbx.rhombohedral_hermann_mauguin_symbols:
for p, z in [("20 20 21 90 90 120", "R"), ("31 31 31 85 85 85", "H")]:
uc = uctbx.unit_cell(p)
cs = crystal.symmetry(
unit_cell=uc,
space_group_symbol=symbol + ":" + z,
correct_rhombohedral_setting_if_necessary=True)
assert cs.unit_cell().is_similar_to(uc)
other_z = {"R": "H", "H": "R"}[z]
assert not show_diff(cs.space_group_info().type().lookup_symbol(),
symbol + " :" + other_z)
cs = crystal.symmetry(unit_cell="20 20 21 90 89 120",
space_group_symbol="R3:R",
correct_rhombohedral_setting_if_necessary=True,
assert_is_compatible_unit_cell=False)
sio = StringIO()
cs.show_summary(f=sio)
assert not show_diff(
sio.getvalue(), """\
Unit cell: (20.3388, 20.3388, 20.3388, 98.9315, 98.9315, 98.9315)
Space group: R 3 :R (No. 146)
""")
cs = crystal.symmetry(unit_cell="31 31 31 85 85 86",
space_group_symbol="R3:H",
correct_rhombohedral_setting_if_necessary=True,
assert_is_compatible_unit_cell=False)
sio = StringIO()
cs.show_summary(f=sio)
assert not show_diff(
sio.getvalue(), """\
Unit cell: (36.4146, 36.4146, 31, 90, 90, 120)
Space group: R 3 :H (No. 146)
""")
def exercise_converter():
textures = []
gl.glGenTextures(3, textures)
assert textures == [0, 0, 0]
for i in range(10000):
textures = []
gl.glGenTextures(3, textures)
assert textures == [0, 0, 0]
for i in range(10000):
textures = [9, 3, 5]
gl.glGenTextures(3, textures)
assert textures == [9, 3, 5]
try:
textures = [9, 3, 5]
gl.glGenTextures(4, textures)
except RuntimeError as e:
assert not show_diff(
str(e), """\
Argument "textures" has the wrong number of elements:
expected size: 4
given size: 3""")
else:
raise Exception_expected
try:
textures = [9, "foo", 5]
gl.glGenTextures(3, textures)
except RuntimeError as e:
assert not show_diff(
str(e), """\
Argument "textures" has one or more elements of the wrong type.""")
else:
raise Exception_expected
def exercise():
verbose = "--verbose" in sys.argv[1:]
list_cif = server.mon_lib_list_cif()
srv = server.server(list_cif=list_cif)
open("tmp.cif", "w").write(tmp_cif)
srv.process_cif(file_name="tmp.cif")
comp_comp_id = srv.get_comp_comp_id_direct(comp_id="tst")
motif = comp_comp_id.as_geometry_restraints_motif()
out = StringIO()
motif.show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), expected_out_tst_comp)
for link_link_id in srv.link_link_id_list:
out = StringIO()
link_link_id.as_geometry_restraints_motif_manipulation().show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
if (link_link_id.chem_link.id == "tst_lnk"):
assert not show_diff(out.getvalue(), expected_out_tst_lnk)
for mod_mod_id in srv.mod_mod_id_list:
out = StringIO()
mod_mod_id.as_geometry_restraints_motif_manipulation().show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
if (mod_mod_id.chem_mod.id == "tst_mod"):
assert not show_diff(out.getvalue(), expected_out_tst_mod)
print "OK"
def run_and_compare_implementations(this_script, n, m, iprint):
outputs = []
for impl in ["fortran", "raw_reference", "raw"]:
if impl == "fortran" and not have_lbfgs_fem:
continue
cmd = 'scitbx.python "%s" %s %d %d %d %d' % (this_script, impl, n, m,
iprint[0], iprint[1])
out = run_cmd(cmd=cmd)
if impl == "fortran":
out = out.replace("D-", "E-").replace("D+", "E+")
out = replace_e0dd_with_edd(out=out)
out = out.replace("E-00", "E+00")
out = truncate_floats(out=out)
outputs.append(out)
assert len(outputs) >= 2
a = outputs[0]
for b in outputs[1:]:
if sys.platform != 'darwin':
assert a == b, show_diff(b, a)
elif a != b:
show_diff(b, a)
# We need this to cover up test failure with Xcode >=7.3
for lia, lib in zip(a.splitlines(), b.splitlines()):
if lia != lib:
gnorma = lia.split()[3]
gnormb = lib.split()[3]
assert abs(float(gnorma) - float(gnormb)) <= 1e-6
def exercise_cablam():
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/pdb103l.ent",
test=os.path.isfile) #This is the same file used for tst_kinemage.py
if (regression_pdb is None):
print "Skipping exercise_cablam(): input pdb (pdb103l.ent) not available"
return
#-----
pdb_io = pdb.input(regression_pdb)
pdbid = os.path.basename(regression_pdb)
hierarchy = pdb_io.construct_hierarchy()
oneline_test = cablam_test_string()
cablam_validate.oneline(hierarchy, peptide_cutoff=0.05,
peptide_bad_cutoff=0.01, ca_cutoff=0.005, pdbid=pdbid,
writeto=oneline_test)
text_test = cablam_test_string()
outliers = cablam_validate.analyze_pdb(hierarchy, outlier_cutoff=0.05, pdbid=pdbid)
cablam_validate.give_text(outliers, writeto=text_test)
#print '|',oneline_test.output,'|'
#print '|',ref_cablam_give_oneline,'|'
#print '|',text_test.output,'|'
#print '|',ref_cablam_give_text,'|'
assert not show_diff(oneline_test.output , ref_cablam_give_oneline)
assert not show_diff(text_test.output , ref_cablam_give_text)
def exercise():
verbose = "--verbose" in sys.argv[1:]
list_cif = server.mon_lib_list_cif()
srv = server.server(list_cif=list_cif)
open("tmp.cif", "w").write(tmp_cif)
srv.process_cif(file_name="tmp.cif")
comp_comp_id = srv.get_comp_comp_id_direct(comp_id="tst")
motif = comp_comp_id.as_geometry_restraints_motif()
out = StringIO()
motif.show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), expected_out_tst_comp)
for link_link_id in srv.link_link_id_list:
out = StringIO()
link_link_id.as_geometry_restraints_motif_manipulation().show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
if (link_link_id.chem_link.id == "tst_lnk"):
assert not show_diff(out.getvalue(), expected_out_tst_lnk)
for mod_mod_id in srv.mod_mod_id_list:
out = StringIO()
mod_mod_id.as_geometry_restraints_motif_manipulation().show(out=out)
if (verbose): sys.stdout.write(out.getvalue())
if (mod_mod_id.chem_mod.id == "tst_mod"):
assert not show_diff(out.getvalue(), expected_out_tst_mod)
print "OK"
def exercise_str_repr():
sgi = sgtbx.space_group_info('P1')
uc = sgi.any_compatible_unit_cell(volume=1000)
cs = crystal.symmetry(unit_cell=None, space_group=None)
assert eval(repr(cs)).is_similar_symmetry(cs)
assert not show_diff(str(cs), """\
Unit cell: None
Space group: None""")
cs = crystal.symmetry(unit_cell=uc, space_group=None)
assert eval(repr(cs)).is_similar_symmetry(cs, 1e-8, 1e-3)
assert not show_diff(
str(cs), """\
Unit cell: (8.52593, 11.0837, 14.4941, 83, 109, 129)
Space group: None""")
cs = crystal.symmetry(unit_cell=None, space_group=sgi.group())
assert eval(repr(cs)).is_similar_symmetry(cs, 1e-8, 1e-3)
assert not show_diff(str(cs), """\
Unit cell: None
Space group: P 1 (No. 1)""")
cs = crystal.symmetry(unit_cell=uc, space_group=sgi.group())
assert eval(repr(cs)).is_similar_symmetry(cs, 1e-8, 1e-3)
assert not show_diff(
str(cs), """\
Unit cell: (8.52593, 11.0837, 14.4941, 83, 109, 129)
Space group: P 1 (No. 1)""")
def exercise_cablam():
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/pdb103l.ent",
test=os.path.isfile) #This is the same file used for tst_kinemage.py
if (regression_pdb is None):
print "Skipping exercise_cablam(): input pdb (pdb103l.ent) not available"
return
#-----
pdb_io = pdb.input(regression_pdb)
pdbid = os.path.basename(regression_pdb)
hierarchy = pdb_io.construct_hierarchy()
output_holder = cablam_test_string()
cablamalyze = cablam.cablamalyze(
pdb_hierarchy = hierarchy,
outliers_only=False,
out=output_holder,
quiet=False)
cablamalyze.as_oneline()
assert not show_diff(output_holder.output , ref_cablam_oneline)
output_holder.output = ""
cablamalyze.as_text()
assert not show_diff(output_holder.output , ref_cablam_text)
def exercise_cablam():
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/pdb103l.ent",
test=os.path.isfile) #This is the same file used for tst_kinemage.py
if (regression_pdb is None):
print "Skipping exercise_cablam(): input pdb (pdb103l.ent) not available"
return
#-----
pdb_io = pdb.input(regression_pdb)
pdbid = os.path.basename(regression_pdb)
hierarchy = pdb_io.construct_hierarchy()
output_holder = cablam_test_string()
cablamalyze = cablam.cablamalyze(pdb_hierarchy=hierarchy,
outliers_only=False,
out=output_holder,
quiet=False)
cablamalyze.as_oneline()
assert not show_diff(output_holder.output, ref_cablam_oneline)
output_holder.output = ""
cablamalyze.as_text()
assert not show_diff(output_holder.output, ref_cablam_text)
def exercise_adopt_phil():
master_phil = libtbx.phil.parse("""\
scope1 {
a = 1
.type = int
b = 2
.type = int
}
""")
working_phil = libtbx.phil.parse("""\
scope1.a = 3
scope1.b = 4
""")
i = libtbx.phil.interface.index(master_phil=master_phil,
working_phil=working_phil,
fetch_new=True)
params = i.get_python_object()
other_master_phil = libtbx.phil.parse("""\
scope1 {
c = 3
.type = int
}
scope2 {
subscope2 {
d = 4
.type = int
}
e = 5
.type = int
}
""")
i.adopt_phil(phil_object=other_master_phil)
scope1 = i.get_scope_by_name("scope1")
s = StringIO()
scope1.show(out=s)
assert not show_diff(s.getvalue(), """\
scope1 {
a = 3
b = 4
c = 3
}
""")
s = StringIO()
i.working_phil.show(out=s)
assert not show_diff(
s.getvalue(), """\
scope1 {
a = 3
b = 4
c = 3
}
scope2 {
subscope2 {
d = 4
}
e = 5
}
""")
def exercise(args):
verbose = "--verbose" in args
if (verbose):
log = sys.stdout
else:
log = None
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
ncs_dir = libtbx.env.find_in_repositories(
relative_path="phenix_regression/ncs",
test=os.path.isdir)
if (ncs_dir is None):
print "Skipping exercise(): input files not available"
else:
for file_name in ["simple.pdb", "ambiguous_alignment.pdb"]:
model = get_model(os.path.join(ncs_dir, file_name))
group = ncs.restraints.group.from_atom_selections(
model = model,
reference_selection_string=None,
selection_strings=["chain A", "chain B"],
coordinate_sigma=None,
b_factor_weight=None,
special_position_warnings_only=False)
assert len(group.selection_pairs) == 1
assert list(group.selection_pairs[0][0]) == [0,1,2,3]
if (file_name == "simple.pdb"):
assert list(group.selection_pairs[0][1]) == [4,5,6,7]
else:
assert list(group.selection_pairs[0][1]) == [4,6,7,8]
model = get_model(os.path.join(ncs_dir, "no_match.pdb"))
try:
ncs.restraints.group.from_atom_selections(
model=model,
reference_selection_string=None,
selection_strings=["chain A", "chain B"],
coordinate_sigma=None,
b_factor_weight=None,
special_position_warnings_only=False)
except Sorry, e:
assert not show_diff(str(e), '''\
NCS restraints selections do not produce any pairs of matching atoms:
Reference selection: "chain A"
Other selection: "chain B"''')
else: raise Exception_expected
try:
ncs.restraints.group.from_atom_selections(
model=model,
reference_selection_string=None,
selection_strings=["chain A", "chain C"],
coordinate_sigma=None,
b_factor_weight=None,
special_position_warnings_only=False)
except Sorry, e:
assert not show_diff(str(e), '''\
NCS restraints selections produce only one pair of matching atoms:
Reference selection: "chain A"
Other selection: "chain C"''')
def exercise_miller_export_as_shelx_hklf():
s = """\
1 2 -1 23.34 4.56
2 -3 9 12.45 6.12
99999999999999999.9999999.99
-999-999-999-9999.99-9999.99
3 4 5999999.99999999.
3 4 5-99999.9-999999.
"""
ma = hklf.reader(file_object=StringIO(s)).as_miller_arrays()[0]
sio = StringIO()
ma.export_as_shelx_hklf(file_object=sio)
ma2 = hklf.reader(file_object=StringIO(sio.getvalue())).as_miller_arrays()[0]
assert approx_equal(ma.indices(), ma2.indices())
assert approx_equal(ma.data(), ma2.data())
assert approx_equal(ma.sigmas(), ma2.sigmas())
#
ma = ma.select(flex.size_t([0]))
def check(d, s, f):
if (s is not None): s = flex.double([s])
ma2 = ma.array(data=flex.double([d]), sigmas=s)
sio = StringIO()
ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True)
assert not show_diff(sio.getvalue(), """\
1 2 -1%s
0 0 0 0.00 0.00
""" % f)
try: ma2.export_as_shelx_hklf(sio)
except RuntimeError: pass
else: raise Exception_expected
check(-12345678, 1, "-999999. 0.08")
check(-12345678, None, "-999999. 0.00")
check(2, -12345678, " 0.16-999999.")
check(123456789, 30, "9999999. 2.43")
check(123456789, None, "9999999. 0.00")
check(40, 123456789, " 3.249999999.")
check(-23456789, 123456789, "-999999.5263153.")
check(123456789, -23456789, "5263153.-999999.")
#
ma = hklf.reader(file_object=StringIO(s)).as_miller_arrays()[0]
ma = ma.select(flex.size_t([0,1]))
ma2 = ma.array(data=flex.double([123456789, -23456789]))
sio = StringIO()
ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True)
assert not show_diff(sio.getvalue(), """\
1 2 -15263153. 0.00
2 -3 9-999999. 0.00
0 0 0 0.00 0.00
""")
ma2 = ma.array(data=flex.double([-23456789, 823456789]))
sio = StringIO()
ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True)
assert not show_diff(sio.getvalue(), """\
1 2 -1-284858. 0.00
2 -3 99999999. 0.00
0 0 0 0.00 0.00
""")
def exercise_adopt_phil():
master_phil = libtbx.phil.parse("""\
scope1 {
a = 1
.type = int
b = 2
.type = int
}
""")
working_phil = libtbx.phil.parse("""\
scope1.a = 3
scope1.b = 4
""")
i = libtbx.phil.interface.index(master_phil=master_phil,
working_phil=working_phil,
fetch_new=True)
params = i.get_python_object()
other_master_phil = libtbx.phil.parse("""\
scope1 {
c = 3
.type = int
}
scope2 {
subscope2 {
d = 4
.type = int
}
e = 5
.type = int
}
""")
i.adopt_phil(phil_object=other_master_phil)
scope1 = i.get_scope_by_name("scope1")
s = StringIO()
scope1.show(out=s)
assert not show_diff(s.getvalue(), """\
scope1 {
a = 3
b = 4
c = 3
}
""")
s = StringIO()
i.working_phil.show(out=s)
assert not show_diff(s.getvalue(), """\
scope1 {
a = 3
b = 4
c = 3
}
scope2 {
subscope2 {
d = 4
}
e = 5
}
""")
def exercise_basic():
a = flex.double((10, 20))
p = flex.double((-25, 355))
c = flex.polar(a, p, True)
f = flex.double((0.3, 0.9))
s = miller.set(crystal_symmetry=crystal.symmetry(unit_cell=(10, 10, 10, 90,
90, 90),
space_group_symbol="P1"),
indices=flex.miller_index([(1, 2, 3), (-3, 4, -6)]),
anomalous_flag=False)
out = StringIO()
s.array(data=c).as_phases_phs(out=out)
assert not show_diff(
out.getvalue(), """\
1 2 3 4999.99 1.00 -25.00
-3 4 -6 9999.99 1.00 -5.00
""")
out = StringIO()
s.array(data=c).as_phases_phs(out=out, scale_amplitudes=False)
assert not show_diff(
out.getvalue(), """\
1 2 3 10.00 1.00 -25.00
-3 4 -6 20.00 1.00 -5.00
""")
for phases in [s.array(data=p), p]:
out = StringIO()
s.array(data=c).amplitudes().as_phases_phs(out=out,
phases=phases,
phases_deg=True)
assert not show_diff(
out.getvalue(), """\
1 2 3 4999.99 1.00 -25.00
-3 4 -6 9999.99 1.00 355.00
""")
for phases in [s.array(data=p * (math.pi / 180)), p * (math.pi / 180)]:
out = StringIO()
s.array(data=c).amplitudes().as_phases_phs(out=out,
phases=phases,
phases_deg=False)
assert not show_diff(
out.getvalue(), """\
1 2 3 4999.99 1.00 -25.00
-3 4 -6 9999.99 1.00 355.00
""")
for figures_of_merit in [s.array(data=f), f]:
out = StringIO()
s.array(data=c).as_phases_phs(out=out,
figures_of_merit=figures_of_merit)
assert not show_diff(
out.getvalue(), """\
1 2 3 4999.99 0.30 -25.00
-3 4 -6 9999.99 0.90 -5.00
""")
def run():
import os
import shutil
import fileinput
import libtbx.load_env
from libtbx import easy_run
from libtbx.test_utils import show_diff
try:
dials_regression = libtbx.env.dist_path('dials_regression')
except KeyError:
print 'FAIL: dials_regression not configured'
exit(0)
path = os.path.join(dials_regression,
"experiment_test_data/experiment_1.json")
newpath = os.path.join(os.getcwd(), 'experiments.json')
shutil.copyfile(path, newpath)
for line in fileinput.FileInput(newpath, inplace=True):
if '$DIALS_REGRESSION' in line:
line = line.replace('$DIALS_REGRESSION', dials_regression)
print line
cmd = "dials.export format=mosflm %s" % newpath
result = easy_run.fully_buffered(cmd).raise_if_errors()
assert os.path.exists("mosflm/index.mat")
with open("mosflm/index.mat", "rb") as f:
lines = f.read()
assert not show_diff(
lines, """\
-0.01210200 -0.01954526 0.00309519
-0.00416605 -0.00080573 -0.02427340
0.01931593 -0.01241956 -0.00329641
0.000 0.000 0.000
-0.52228050 -0.84350975 0.12535704
-0.17980379 -0.03477015 -0.98308781
0.83360283 -0.53598726 -0.13350648
42.2717 42.2720 39.6704 90.0001 89.9993 89.9998
0.000 0.000 0.000
""")
assert os.path.exists("mosflm/mosflm.in")
with open("mosflm/mosflm.in", "rb") as f:
lines = f.read()
assert lines.startswith("DIRECTORY")
assert not show_diff(
"\n".join(lines.split("\n")[1:]), """\
TEMPLATE centroid_####.cbf
SYMMETRY 89
BEAM 220.002 212.478
DISTANCE 190.1800
MATRIX index.mat
""")
def exercise_pair_sym_table_tidy_and_full_connectivity():
def check_one_way(pst):
for sym_pair in pst.iterator():
i_seq, j_seq = sym_pair.i_seqs()
assert i_seq <= j_seq
assert len(pst[i_seq][j_seq]) > 0
if (i_seq != j_seq):
assert i_seq not in pst[j_seq]
def check_two_way(pst):
for sym_pair in pst.iterator():
i_seq, j_seq = sym_pair.i_seqs()
assert len(pst[i_seq][j_seq]) > 0
assert len(pst[j_seq][i_seq]) > 0
pst_extracted = bond_sym_table.tidy(
site_symmetry_table=structure.site_symmetry_table())
check_one_way(pst_extracted)
sio_extracted = StringIO()
structure.pair_sym_table_show(pst_extracted, out=sio_extracted)
pst = pst_extracted.tidy(
site_symmetry_table=structure.site_symmetry_table())
check_one_way(pst)
sio = StringIO()
structure.pair_sym_table_show(pst, out=sio)
assert not show_diff(sio.getvalue(), sio_extracted.getvalue())
pst = pst_extracted.full_connectivity()
check_two_way(pst)
pst_full = pst_extracted.full_connectivity(
site_symmetry_table=structure.site_symmetry_table())
check_two_way(pst_full)
sio = StringIO()
structure.pair_sym_table_show(pst_full,
is_full_connectivity=True,
out=sio)
assert sio.getvalue().find("sym. equiv.") < 0
pst = pst_full.tidy(
site_symmetry_table=structure.site_symmetry_table())
check_one_way(pst)
sio = StringIO()
structure.pair_sym_table_show(pst, out=sio)
assert not show_diff(sio.getvalue(), sio_extracted.getvalue())
pst_full2 = pst_full.full_connectivity(
site_symmetry_table=structure.site_symmetry_table())
check_two_way(pst_full2)
pst = pst_full2.tidy(
site_symmetry_table=structure.site_symmetry_table())
check_one_way(pst)
sio = StringIO()
structure.pair_sym_table_show(pst, out=sio)
assert not show_diff(sio.getvalue(), sio_extracted.getvalue())
def tst_to_cif_sheet():
pdb_str1 = """\
SHEET 1 AA1 4 ILE A 7 PRO A 10 0
SHEET 2 AA1 4 MET A 92 THR A 99 1 O LEU A 95 N ILE A 7
SHEET 3 AA1 4 THR A 73 SER A 82 -1 N LEU A 76 O ILE A 94
SHEET 4 AA1 4 VAL A 34 THR A 39 -1 N PHE A 35 O VAL A 81
SHEET 1 AA2 3 LYS A 19 GLN A 23 0
SHEET 2 AA2 3 TRP A 59 VAL A 62 -1 O LEU A 60 N VAL A 22
SHEET 3 AA2 3 PHE A 51 ILE A 53 -1 N ILE A 52 O LYS A 61"""
ann = annotation.from_records(pdb_str1.split("\n"))
cif_loops = ann.as_cif_loops()
assert len(cif_loops) == 4, len(cif_loops)
out = StringIO()
cif_block = iotbx.cif.model.block()
for loop in cif_loops:
loop.show(out)
cif_block.add_loop(loop)
v = out.getvalue()
# print "\"%s\"" % v
ann_back = annotation.from_cif_block(cif_block)
assert ann_back.get_n_helices() == 0
assert ann_back.get_n_sheets() == 2
assert [len(x.strands) for x in ann_back.sheets] == [4, 3]
# print ann_back.as_pdb_str()
assert not show_diff(ann_back.as_pdb_str(), pdb_str1)
pdb_str2 = """\
SHEET 1 AA1 4 ILE A 7 PRO A 10 0
SHEET 2 AA1 4 MET A 92 THR A 99 1 O LEU A 95 N ILE A 7
SHEET 3 AA1 4 THR A 73 SER A 82 -1 N LEU A 76 O ILE A 94
SHEET 4 AA1 4 VAL A 34 THR A 39 -1 N PHE A 35 O VAL A 81"""
ann = annotation.from_records(pdb_str2.split("\n"))
cif_loops = ann.as_cif_loops()
assert len(cif_loops) == 4, len(cif_loops)
out = StringIO()
cif_block = iotbx.cif.model.block()
for loop in cif_loops:
loop.show(out)
cif_block.add_loop(loop)
v = out.getvalue()
# print "\"%s\"" % v
ann_back = annotation.from_cif_block(cif_block)
assert ann_back.get_n_helices() == 0
assert ann_back.get_n_sheets() == 1
assert [len(x.strands) for x in ann_back.sheets] == [4]
# print ann_back.as_pdb_str()
assert not show_diff(ann_back.as_pdb_str(), pdb_str2)
def exercise_pair_sym_table_tidy_and_full_connectivity():
def check_one_way(pst):
for sym_pair in pst.iterator():
i_seq, j_seq = sym_pair.i_seqs()
assert i_seq <= j_seq
assert len(pst[i_seq][j_seq]) > 0
if (i_seq != j_seq):
assert i_seq not in pst[j_seq]
def check_two_way(pst):
for sym_pair in pst.iterator():
i_seq, j_seq = sym_pair.i_seqs()
assert len(pst[i_seq][j_seq]) > 0
assert len(pst[j_seq][i_seq]) > 0
pst_extracted = bond_sym_table.tidy(
site_symmetry_table=structure.site_symmetry_table())
check_one_way(pst_extracted)
sio_extracted = StringIO()
structure.pair_sym_table_show(pst_extracted, out=sio_extracted)
pst = pst_extracted.tidy(
site_symmetry_table=structure.site_symmetry_table())
check_one_way(pst)
sio = StringIO()
structure.pair_sym_table_show(pst, out=sio)
assert not show_diff(sio.getvalue(), sio_extracted.getvalue())
pst = pst_extracted.full_connectivity()
check_two_way(pst)
pst_full = pst_extracted.full_connectivity(
site_symmetry_table=structure.site_symmetry_table())
check_two_way(pst_full)
sio = StringIO()
structure.pair_sym_table_show(
pst_full, is_full_connectivity=True, out=sio)
assert sio.getvalue().find("sym. equiv.") < 0
pst = pst_full.tidy(
site_symmetry_table=structure.site_symmetry_table())
check_one_way(pst)
sio = StringIO()
structure.pair_sym_table_show(pst, out=sio)
assert not show_diff(sio.getvalue(), sio_extracted.getvalue())
pst_full2 = pst_full.full_connectivity(
site_symmetry_table=structure.site_symmetry_table())
check_two_way(pst_full2)
pst = pst_full2.tidy(
site_symmetry_table=structure.site_symmetry_table())
check_one_way(pst)
sio = StringIO()
structure.pair_sym_table_show(pst, out=sio)
assert not show_diff(sio.getvalue(), sio_extracted.getvalue())
def exercise_03():
answer_phil_str = """\
protein.sheet {
sheet_id = " 3"
first_strand = chain 'A' and resid 157 through 161
strand {
selection = chain 'A' and resid 114 through 122
sense = antiparallel
bond_start_current = None
bond_start_previous = None
}
strand {
selection = chain 'A' and resid 193 through 201
sense = parallel
bond_start_current = None
bond_start_previous = None
}
}"""
annot = ss.annotation.from_records(records=ann_3.split('\n'))
assert len(annot.helices) == 0
assert len(annot.sheets) == 1
ann_sheet = annot.sheets[0]
assert ann_sheet.n_strands == 3
assert ann_sheet.registrations == [None]*3
only_sheet = annot.sheets[0]
phil_string = annot.as_restraint_groups()
assert not test_utils.show_diff(phil_string, answer_phil_str,
strip_trailing_whitespace=True)
def run(args):
assert len(args) == 0
import libtbx.load_env
import os
op = os.path
cbf = libtbx.env.under_dist(
module_name="cbflib",
path="examples/fit2d_data.cbf")
assert op.isfile(cbf)
from cbflib_adaptbx.command_line import dump
from cStringIO import StringIO
sio = StringIO()
dump.process(file_name=cbf, out=sio)
from libtbx.test_utils import show_diff
assert not show_diff(sio.getvalue(), """\
File name: %s
Number of blocks: 1
Block name: image_1
Number of categories: 12
Category name: diffrn
Category name: diffrn_source
Category name: diffrn_radiation
Category name: diffrn_radiation_wavelength
Category name: diffrn_measurement
Category name: diffrn_detector
Category name: diffrn_detector_element
Category name: diffrn_data_frame
Category name: array_structure_list
Category name: array_element_size
Category name: array_intensities
Category name: array_data
""" % cbf)
print "OK"
def exercise_03():
answer_phil_str = """\
protein.sheet {
sheet_id = " 3"
first_strand = chain 'A' and resid 157 through 161
strand {
selection = chain 'A' and resid 114 through 122
sense = antiparallel
bond_start_current = None
bond_start_previous = None
}
strand {
selection = chain 'A' and resid 193 through 201
sense = parallel
bond_start_current = None
bond_start_previous = None
}
}"""
annot = ss.annotation.from_records(records=ann_3.split('\n'))
assert len(annot.helices) == 0
assert len(annot.sheets) == 1
ann_sheet = annot.sheets[0]
assert ann_sheet.n_strands == 3
assert ann_sheet.registrations == [None] * 3
only_sheet = annot.sheets[0]
phil_string = annot.as_restraint_groups()
assert not test_utils.show_diff(
phil_string, answer_phil_str, strip_trailing_whitespace=True)
def exercise_heavy () :
from mmtbx.regression import make_fake_anomalous_data
from mmtbx.command_line import validate_waters
import mmtbx.ions.utils
from iotbx.file_reader import any_file
file_base = "tst_validate_waters_1"
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(file_base=file_base)
mtz_file = make_fake_anomalous_data.generate_mtz_file(
file_base="tst_validate_waters_1",
d_min=1.5,
anomalous_scatterers=[
group_args(selection="element CD", fp=-0.29, fdp=2.676),
group_args(selection="element CL", fp=0.256, fdp=0.5),
])
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = mmtbx.ions.utils.anonymize_ions(hierarchy, log=null_out())
hierarchy.write_pdb_file("%s_start.pdb" % file_base,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
args = ["tst_validate_waters_1_start.pdb", "tst_validate_waters_1.mtz",
"skip_twin_detection=True"]
results = validate_waters.run(args=args, out=null_out())
out = StringIO()
results.show(out=out)
s = easy_pickle.dumps(results)
r2 = easy_pickle.loads(s)
out2 = StringIO()
r2.show(out=out2)
assert not show_diff(out.getvalue(), out2.getvalue())
assert (results.n_bad >= 1) and (results.n_heavy == 2)
def run_and_compare_implementations(this_script, n, m, iprint):
outputs = []
for impl in ["fortran", "raw_reference", "raw"]:
if (impl == "fortran" and not have_lbfgs_fem):
continue
cmd = 'scitbx.python "%s" %s %d %d %d %d' % (
this_script, impl, n, m, iprint[0], iprint[1])
out = run_cmd(cmd=cmd)
if (impl == "fortran"):
out = out.replace("D-", "E-").replace("D+", "E+")
out = replace_e0dd_with_edd(out=out)
out = out.replace("E-00", "E+00")
out = truncate_floats(out=out)
outputs.append(out)
assert len(outputs) >= 2
a = outputs[0]
for i in xrange(1, len(outputs)):
b = outputs[i]
if show_diff(a, b):
# We need this to cover up test failure with Xcode 7.3
for lia, lib in zip(a.splitlines(), b.splitlines()):
if lia != lib:
gnorma = lia.split()[3]
gnormb = lib.split()[3]
assert abs(float(gnorma) - float(gnormb)) <= 1e-7
def exercise_pro_missing_hd1(mon_lib_srv):
pdb_inp = iotbx.pdb.input(source_info=None, lines="""\
ATOM 110 N PRO A 263 0.453 -20.680 -39.256 1.00 53.34 N
ATOM 111 CA PRO A 263 0.444 -22.054 -39.751 1.00 50.42 C
ATOM 112 C PRO A 263 0.860 -22.998 -38.645 1.00 52.10 C
ATOM 113 O PRO A 263 1.693 -22.614 -37.817 1.00 48.32 O
ATOM 114 CB PRO A 263 1.491 -22.052 -40.887 1.00 53.30 C
ATOM 115 CG PRO A 263 2.012 -20.645 -40.990 1.00 57.05 C
ATOM 116 CD PRO A 263 1.586 -19.897 -39.782 1.00 53.45 C
ATOM 117 HA PRO A 263 -0.437 -22.302 -40.100 1.00 60.51 H
ATOM 118 HB2 PRO A 263 2.210 -22.664 -40.664 1.00 63.96 H
ATOM 119 HB3 PRO A 263 1.066 -22.318 -41.718 1.00 63.96 H
ATOM 120 HG2 PRO A 263 2.980 -20.669 -41.043 1.00 68.45 H
ATOM 121 HG3 PRO A 263 1.645 -20.229 -41.786 1.00 68.45 H
ATOM 122 HD2 PRO A 263 1.267 -19.021 -40.049 1.00 64.14 H
""")
pdb_hierarchy = pdb_inp.construct_hierarchy()
residue = pdb_hierarchy.only_residue()
rotamer_iterator = mon_lib_srv.rotamer_iterator(
comp_id=residue.resname,
atom_names=residue.atoms().extract_name(),
sites_cart=residue.atoms().extract_xyz())
assert not show_diff(
rotamer_iterator.problem_message,
'resname=PRO: missing atom "HD1" for tor_id "hh3"')
def exercise_group_args():
from libtbx import group_args
from cStringIO import StringIO
out = StringIO()
a = group_args(a=1, b=2, c=3)
assert a.a == 1
assert a.b == 2
assert a.c == 3
b = group_args(d='d', e='e')
assert b.d == 'd'
assert b.e == 'e'
print >> out, a
v = out.getvalue()
assert not show_diff(
v, """group_args
a : 1
b : 2
c : 3\n""")
a.merge(b)
assert a.a == 1
assert a.b == 2
assert a.c == 3
assert a.d == 'd'
assert a.e == 'e'
assert b.d == 'd'
assert b.e == 'e'
c = group_args(a=11, b=12)
a.merge(c)
assert a.a == 11
assert a.b == 12
assert a.c == 3
assert c.a == 11
assert c.b == 12
def exercise_heavy():
from mmtbx.regression import make_fake_anomalous_data
from mmtbx.command_line import validate_waters
import mmtbx.ions.utils
from iotbx.file_reader import any_file
file_base = "tst_validate_waters_1"
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(
file_base=file_base)
mtz_file = make_fake_anomalous_data.generate_mtz_file(
file_base="tst_validate_waters_1",
d_min=1.5,
anomalous_scatterers=[
group_args(selection="element CD", fp=-0.29, fdp=2.676),
group_args(selection="element CL", fp=0.256, fdp=0.5),
])
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = mmtbx.ions.utils.anonymize_ions(hierarchy, log=null_out())
hierarchy.write_pdb_file(
"%s_start.pdb" % file_base,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
args = [
"tst_validate_waters_1_start.pdb", "tst_validate_waters_1.mtz",
"skip_twin_detection=True"
]
results = validate_waters.run(args=args, out=null_out())
out = StringIO()
results.show(out=out)
s = easy_pickle.dumps(results)
r2 = easy_pickle.loads(s)
out2 = StringIO()
r2.show(out=out2)
assert not show_diff(out.getvalue(), out2.getvalue())
assert (results.n_bad >= 1) and (results.n_heavy == 2)
def run():
import os
import libtbx.load_env
from libtbx import easy_run
from libtbx.test_utils import show_diff
try:
dials_regression = libtbx.env.dist_path('dials_regression')
except KeyError:
print 'FAIL: dials_regression not configured'
exit(0)
path = os.path.join(dials_regression, "refinement_test_data",
"i04_weak_data")
cmd = "dials.compare_orientation_matrices %s/experiments.json %s/regression_experiments.json" % (
path, path)
result = easy_run.fully_buffered(cmd).raise_if_errors()
out = "\n".join(result.stdout_lines[7:])
out = out.replace("-0", "0")
assert not show_diff(
out, """\
Change of basis op: a,b,c
Rotation matrix to transform crystal 1 to crystal 2:
{{1.000, 0.000, 0.000},
{0.000, 1.000, 0.000},
{0.000, 0.000, 1.000}}
Rotation of 0.002 degrees about axis (0.916, 0.081, 0.393)
""")
def check_tls_params(params1, params2):
for tls1, tls2 in zip(params1, params2):
assert approx_equal(tls1.t, tls2.t)
assert approx_equal(tls1.l, tls2.l)
assert approx_equal(tls1.s, tls2.s)
assert approx_equal(tls1.origin, tls2.origin)
assert not show_diff(tls1.selection_string, tls2.selection_string)
def exercise_1(prefix="tst_model_remove_alternative_conformations_1"):
""" Make sure that CA in SER3 gets to the right position. """
inp = iotbx.pdb.input(lines=tst_pdb_str, source_info=None)
model = mmtbx.model.manager(model_input=inp)
model.remove_alternative_conformations(always_keep_one_conformer=False)
assert not show_diff(
model.model_as_pdb(), """\
ATOM 1 N PHE L 2 201.672 235.270 272.436 1.00 33.60 N
ATOM 2 CA PHE L 2 201.753 236.596 271.840 1.00 33.60 C
ATOM 3 C PHE L 2 200.597 237.520 272.192 1.00 33.60 C
ATOM 4 O PHE L 2 200.835 238.721 272.367 1.00 33.60 O
ATOM 5 CB PHE L 2 201.883 236.467 270.321 1.00 32.90 C
ATOM 6 CG PHE L 2 201.850 237.775 269.616 1.00 32.90 C
ATOM 7 CD1 PHE L 2 202.865 238.689 269.797 1.00 32.90 C
ATOM 8 CD2 PHE L 2 200.820 238.083 268.748 1.00 32.90 C
ATOM 9 CE1 PHE L 2 202.829 239.908 269.166 1.00 32.90 C
ATOM 10 CE2 PHE L 2 200.799 239.290 268.089 1.00 32.90 C
ATOM 11 CZ PHE L 2 201.803 240.201 268.300 1.00 32.90 C
ATOM 12 N SER L 3 199.357 236.979 272.328 1.00 34.28 N
ATOM 13 CA SER L 3 198.124 237.714 272.618 1.00 34.28 C
ATOM 14 C SER L 3 197.907 238.857 271.631 1.00 34.28 C
ATOM 15 O SER L 3 198.129 240.024 271.974 1.00 34.28 O
ATOM 16 CB SER L 3 198.121 238.241 274.053 1.00 35.83 C
ATOM 17 OG SER L 3 198.875 239.432 274.158 1.00 35.83 O
ATOM 18 N PRO L 4 197.482 238.564 270.395 1.00 33.41 N
ATOM 19 CA PRO L 4 197.440 239.596 269.355 1.00 33.41 C
ATOM 20 C PRO L 4 196.353 240.646 269.519 1.00 33.41 C
ATOM 21 O PRO L 4 196.212 241.494 268.633 1.00 33.41 O
ATOM 22 CB PRO L 4 197.209 238.776 268.079 1.00 33.14 C
ATOM 23 CG PRO L 4 196.474 237.597 268.538 1.00 33.14 C
ATOM 24 CD PRO L 4 197.000 237.268 269.901 1.00 33.14 C
TER
END
""")
def tst_1(prefix="tst_split_data_cif_1"):
with open(prefix + '.cif', 'w') as f:
f.write(sf_5r82)
easy_run.fully_buffered('iotbx.split_data_cif %s.cif' % prefix)
original_model = iotbx.cif.reader(input_string=sf_5r82).model()
block_names = original_model.keys()
for bn in block_names:
assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn))
assert os.path.isfile('%s.cif_%s_000.cif' % (prefix, bn))
# testing output cif
for bn in block_names:
m = iotbx.cif.reader(file_path='%s.cif_%s_000.cif' %
(prefix, bn)).model()
for k in original_model[bn].keys():
assert approx_equal(m[bn][k], original_model[bn][k])
# testing output mtz
for bn in block_names:
mtz_obj = iotbx.mtz.object('%s.cif_%s_000.mtz' % (prefix, bn))
# print('working with', '%s.cif_%s_000.mtz' % (prefix, bn))
strio = StringIO()
mtz_obj.show_summary(out=strio)
# mtz_obj.show_column_data(out=strio)
val = strio.getvalue()
assert not show_diff(val, sf_5r82_mtz_results[bn])
def make_geo_pickle_unpickle(geometry, xrs, prefix):
init_out = StringIO.StringIO()
from_file_out = StringIO.StringIO()
geometry.show_sorted(
sites_cart=xrs.sites_cart(),
site_labels=xrs.scatterers().extract_labels(),
f=init_out)
t0 = time()
pklfile = open("%s.pkl" % prefix, 'wb')
#import code, traceback; code.interact(local=locals(), banner="".join( traceback.format_stack(limit=10) ) )
pickle.dump(geometry, pklfile)
pklfile.close()
t1 = time()
pklfile = open("%s.pkl" % prefix, 'rb')
grm_from_file = pickle.load(pklfile)
pklfile.close()
t2 = time()
print "Time pickling/unpickling: %.4f, %.4f" % (t1-t0, t2-t1)
grm_from_file.show_sorted(
sites_cart=xrs.sites_cart(),
site_labels=xrs.scatterers().extract_labels(),
f=from_file_out)
# print "INITIAL"
init_v = init_out.getvalue()
# print init_v
# print "="*50
# print "From disc"
from_file_v = from_file_out.getvalue()
# print from_file_v
# STOP()
assert not show_diff(init_v, from_file_v)
def run(args):
assert args in [[], ["--forever"]]
verbose = True
while True:
if (flex.int().as_numpy_array(optional=True) is None):
try:
flex.int().as_numpy_array()
except RuntimeError, e:
assert not show_diff(str(e), "numpy API not available")
else:
raise Exception_expected
else:
for flex_type in [
flex.bool,
flex.int,
flex.long,
flex.float,
flex.double,
flex.complex_double,
flex.size_t]:
exercise_basic(flex_type, verbose)
exercise_int()
if (len(args) == 0):
break
verbose = False
def make_geo_pickle_unpickle(geometry, xrs, prefix):
init_out = StringIO()
from_file_out = StringIO()
geometry.show_sorted(sites_cart=xrs.sites_cart(),
site_labels=xrs.scatterers().extract_labels(),
f=init_out)
energy_original = geometry.energies_sites(sites_cart=xrs.sites_cart())
t0 = time()
#import code, traceback; code.interact(local=locals(), banner="".join( traceback.format_stack(limit=10) ) )
pklstr = pickle.dumps(geometry)
t1 = time()
grm_from_file = pickle.loads(pklstr)
t2 = time()
# Fails here:
energy_from_pickle = grm_from_file.energies_sites(
sites_cart=xrs.sites_cart())
assert approx_equal(energy_original.target, energy_from_pickle.target)
print("Time pickling/unpickling: %.4f, %.4f" % (t1 - t0, t2 - t1))
grm_from_file.show_sorted(sites_cart=xrs.sites_cart(),
site_labels=xrs.scatterers().extract_labels(),
f=from_file_out)
# print "INITIAL"
init_v = init_out.getvalue()
# print init_v
# print "="*50
# print "From disc"
from_file_v = from_file_out.getvalue()
# print from_file_v
# STOP()
assert not show_diff(init_v, from_file_v)
return grm_from_file
def exercise_show_summary():
from scitbx.graph import test_cases_tardy_pdb
tcs = test_cases_tardy_pdb.select_test_cases(
tags_or_indices=["ZINC03847120"])
assert len(tcs) == 1
tt = tcs[0].tardy_tree_construct()
for vl,cb in [(None, ("10", "11")),
(list("ABCDEFGHIKLMNO"), ("L", "M"))]:
sio = StringIO()
assert tt.show_summary(vertex_labels=vl, out=sio, prefix="&") is tt
assert not show_diff(sio.getvalue(), """\
&number of vertices: 14
&number of edges: 15
&find cluster loops: 0 repeats
&number of fixed vertex lists: 0
&number of fixed vertices: 0
&number of clusters: 1
&merge clusters with multiple connections: 1 pass
&number of hinge edges: 1
&number of loop edges: 0
&number of loop edge bendings: 0
&number of fixed hinges: 1
&tardy fixed hinge: %s
& %s
""" % cb)
def check(text):
if (file_name == "intrinsics_extra.f"):
check_intrinsics_extra(text)
return
if (file_name == "sf.f"):
text = text.replace(" -0.620088", " -0.620087")
elif (file_name == "unformatted_experiments.f"):
if (sys.byteorder == "big"):
text = text \
.replace(
" 1234 5678",
" 5678 1234") \
.replace(
" 18558553691448",
" 23330262356193")
have_diffs = show_diff(text, "\n".join(info.out_lines))
def assert_not_have_diffs():
if (opts.keep_going):
print "WARNING: --keep-going after show_diff:", exe_name
else:
assert not have_diffs
if (have_diffs):
if (exe_name is fem_exe_name):
assert_not_have_diffs()
elif (exe_name is ifort_exe_name):
if ( not info.ifort_diff_behavior
and not info.ifort_diff_floating_point_format):
assert_not_have_diffs()
else:
raise AssertionError
def tst_run(args=[]):
assert len(args) == 0
import libtbx.load_env
import os
op = os.path
cbf = libtbx.env.under_dist(module_name="cbflib",
path="examples/fit2d_data.cbf")
assert op.isfile(cbf)
from cbflib_adaptbx.command_line import dump
from six.moves import cStringIO as StringIO
sio = StringIO()
dump.process(file_name=cbf, out=sio)
from libtbx.test_utils import show_diff
assert not show_diff(
sio.getvalue(), """\
File name: %s
Number of blocks: 1
Block name: image_1
Number of categories: 12
Category name: diffrn
Category name: diffrn_source
Category name: diffrn_radiation
Category name: diffrn_radiation_wavelength
Category name: diffrn_measurement
Category name: diffrn_detector
Category name: diffrn_detector_element
Category name: diffrn_data_frame
Category name: array_structure_list
Category name: array_element_size
Category name: array_intensities
Category name: array_data
""" % cbf)
print "OK"
def exercise_001(file_name="tst_mtrix_biomt_cmdl_001.pdb"):
"""
Make sure SS gets populated by MTRIX
"""
of = open(file_name, "w")
print(pdb_str_2b, file=of)
of.close()
easy_run.call("phenix.pdb.mtrix_reconstruction %s" % file_name)
pdb_inp = iotbx.pdb.input(
file_name="tst_mtrix_biomt_cmdl_001_MTRIX_expanded.pdb")
a = pdb_inp.extract_secondary_structure()
assert a.get_n_helices() == 3, a.get_n_helices()
assert a.get_n_sheets() == 3, "%d" % a.get_n_sheets()
# checking chain ids. If this part is failing, then something is changed in
# chain expanding which made chain ids in hierarchy.py:join_roots()
# not compatible with those used in secondary_structure.py:multiply_to_asu
chain_ids = [h.start_chain_id for h in a.helices]
assert chain_ids == ['A', 'C', 'E'], chain_ids
# checking sheets
assert not show_diff(
a.as_pdb_str(), """\
HELIX 1 1 THR A 1 THR A 2 1 6
HELIX 2 2 THR C 1 THR C 2 1 6
HELIX 3 3 THR E 1 THR E 2 1 6
SHEET 1 1 2 THR A 1 THR A 3 0
SHEET 2 1 2 THR B 4 THR B 5 -1 O THR B 4 N THR A 2
SHEET 1 2 2 THR C 1 THR C 3 0
SHEET 2 2 2 THR D 4 THR D 5 -1 O THR D 4 N THR C 2
SHEET 1 3 2 THR E 1 THR E 3 0
SHEET 2 3 2 THR F 4 THR F 5 -1 O THR F 4 N THR E 2""")
def exercise_mixed_read_write(opts):
tmp = "exercise_mixed_read_write.tmp"
tst_f = "exercise_mixed_read_write.f"
open(tst_f, "w").write("""\
program prog
open(
& unit=1,
& file='%s',
& status='old')
read(1, '(i2)') num
write(6, '(i2)') num*2
write(1, '(i2)') 78
end
""" % tmp)
for cmd in build_cmds(tst_f=tst_f, opts=opts):
if (opts.verbose): print cmd
open(tmp, "wb").write("""\
12
34
56
""")
stdout = easy_run.fully_buffered(
command=cmd).raise_if_errors().stdout_lines
assert stdout == ["24"]
tmp_text = open(tmp, "rb").read()
assert not show_diff(tmp_text, """\
12
78
""")
def test_1():
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/2qxs.pdb", test=os.path.isfile)
pdb_inp = iotbx.pdb.input(file_name=regression_pdb)
h = pdb_inp.construct_hierarchy()
stats = mmtbx.model.statistics.geometry(pdb_hierarchy=h)
out = StringIO()
stats.show(log=out)
assert not show_diff(
out.getvalue(), """
GEOMETRY RESTRAINTS LIBRARY: NONE
DEVIATIONS FROM IDEAL VALUES.
BOND : 0.000 0.000 0
ANGLE : 0.000 0.000 0
CHIRALITY : 0.000 0.000 0
PLANARITY : 0.000 0.000 0
DIHEDRAL : 0.000 0.000 0
MIN NONBONDED DISTANCE : 0.000
MOLPROBITY STATISTICS.
ALL-ATOM CLASHSCORE : 7.78
RAMACHANDRAN PLOT:
OUTLIERS : 0.68 %
ALLOWED : 0.90 %
FAVORED : 98.42 %
ROTAMER OUTLIERS : 4.35 %
CBETA DEVIATIONS : 0.87 %
PEPTIDE PLANE:
CIS-PROLINE : 7.14 %
CIS-GENERAL : 0.00 %
TWISTED PROLINE : 0.00 %
TWISTED GENERAL : 0.42 %
""")
def exercise():
atom_names = ["CA", "C", "C", "X", "HB1", "HB2", "HB3"]
matched = interpreters["LEU"].match_atom_names(atom_names)
s = StringIO()
matched.show_problems(out=s, prefix=">")
assert not show_diff(
s.getvalue(), """\
>unexpected atom names: "X"
>multiple matches: expected pattern=C names="C", "C"
>mutually exclusive: 1hB 3hB
""")
ala_names = ["N", "CA", "C", "O", "CB"]
ala_missing_names = ["CA", "CB", "O"]
ala_with_h = ["N", "CA", "C", "O", "CB", "HA", "HB1", "HB2", "HB3", "H"]
ala_matched = interpreters["ALA"].match_atom_names(ala_names)
ala_missing = interpreters["ALA"].match_atom_names(ala_missing_names)
ala_h = interpreters["ALA"].match_atom_names(ala_with_h)
assert ala_matched.missing_atom_names(ignore_hydrogen=True) == set(())
assert ala_missing.missing_atom_names(ignore_hydrogen=True) == set(
("C", "N"))
assert ala_h.missing_atom_names(ignore_hydrogen=False) == set(())
print "OK"
def exercise_pro_missing_hd1(mon_lib_srv):
pdb_inp = iotbx.pdb.input(source_info=None, lines="""\
ATOM 110 N PRO A 263 0.453 -20.680 -39.256 1.00 53.34 N
ATOM 111 CA PRO A 263 0.444 -22.054 -39.751 1.00 50.42 C
ATOM 112 C PRO A 263 0.860 -22.998 -38.645 1.00 52.10 C
ATOM 113 O PRO A 263 1.693 -22.614 -37.817 1.00 48.32 O
ATOM 114 CB PRO A 263 1.491 -22.052 -40.887 1.00 53.30 C
ATOM 115 CG PRO A 263 2.012 -20.645 -40.990 1.00 57.05 C
ATOM 116 CD PRO A 263 1.586 -19.897 -39.782 1.00 53.45 C
ATOM 117 HA PRO A 263 -0.437 -22.302 -40.100 1.00 60.51 H
ATOM 118 HB2 PRO A 263 2.210 -22.664 -40.664 1.00 63.96 H
ATOM 119 HB3 PRO A 263 1.066 -22.318 -41.718 1.00 63.96 H
ATOM 120 HG2 PRO A 263 2.980 -20.669 -41.043 1.00 68.45 H
ATOM 121 HG3 PRO A 263 1.645 -20.229 -41.786 1.00 68.45 H
ATOM 122 HD2 PRO A 263 1.267 -19.021 -40.049 1.00 64.14 H
""")
pdb_hierarchy = pdb_inp.construct_hierarchy()
residue = pdb_hierarchy.only_residue()
rotamer_iterator = mon_lib_srv.rotamer_iterator(
comp_id=residue.resname,
atom_names=residue.atoms().extract_name(),
sites_cart=residue.atoms().extract_xyz())
assert not show_diff(
rotamer_iterator.problem_message,
'resname=PRO: missing atom "HD1" for tor_id "hh3"')
def check_tls_params(params1, params2):
for tls1, tls2 in zip(params1, params2):
assert approx_equal(tls1.t, tls2.t)
assert approx_equal(tls1.l, tls2.l)
assert approx_equal(tls1.s, tls2.s)
assert approx_equal(tls1.origin, tls2.origin)
assert not show_diff(tls1.selection_string, tls2.selection_string)
def exercise_set_seg_id () :
input_pdb = """\
ATOM 1 O GLY A 3 1.434 1.460 2.496 1.00 6.04 O
ATOM 2 O CYS A 7 2.196 4.467 3.911 1.00 4.51 O
ATOM 3 O CYS A 1 -1.433 4.734 5.405 1.00 7.85 O
TER
ATOM 4 O SER B 4 0.297 0.843 7.226 1.00 7.65 O
ATOM 5 OG ASER B 4 -2.625 1.057 4.064 0.50 5.46 O
ATOM 6 OG BSER B 4 -0.885 0.189 3.843 0.50 11.74 O
TER
ATOM 7 O LEU 0 5.613 12.448 6.864 1.00 7.32 O
TER
END
"""
open("tmp_seg_id.pdb", "w").write(input_pdb)
easy_run.call("phenix.pdbtools tmp_seg_id.pdb set_seg_id_to_chain_id=True --quiet")
pdb_out_1 = open("tmp_seg_id.pdb_modified.pdb").read()
assert not show_diff(pdb_out_1, """\
ATOM 1 O GLY A 3 1.434 1.460 2.496 1.00 6.04 A O
ATOM 2 O CYS A 7 2.196 4.467 3.911 1.00 4.51 A O
ATOM 3 O CYS A 1 -1.433 4.734 5.405 1.00 7.85 A O
TER
ATOM 4 O SER B 4 0.297 0.843 7.226 1.00 7.65 B O
ATOM 5 OG ASER B 4 -2.625 1.057 4.064 0.50 5.46 B O
ATOM 6 OG BSER B 4 -0.885 0.189 3.843 0.50 11.74 B O
TER
ATOM 7 O LEU 0 5.613 12.448 6.864 1.00 7.32 O
TER
END
""")
easy_run.call("phenix.pdbtools tmp_seg_id.pdb_modified.pdb clear_seg_id=True --quiet")
pdb_out_2 = open("tmp_seg_id.pdb_modified.pdb_modified.pdb").read()
assert (pdb_out_2 == input_pdb)
def exercise_input_pickling():
pdb_inp = pdb.pdb_input(source_info="file/name",
lines=pdb_string_all_sections)
s = pickle.dumps(pdb_inp, 1)
l = pickle.loads(s)
assert not show_diff(l.as_pdb_string(), pdb_inp.as_pdb_string())
assert l.source_info() == "pickle"
for section in pdb.input_sections:
assert not show_diff("\n".join(getattr(l, section)()), "\n".join(
getattr(pdb_inp, section)()))
s = "\n".join(l.__getinitargs__()[1])
d = hashlib.md5(s).hexdigest()
if (pdb.hierarchy.atom.has_siguij()):
assert d == "bf987c40cc8672e2f2324d91d6de3e2b"
else:
assert d == "7375e96fd52794a785284580730de20c"
def exercise():
atom_names = ["CA", "C", "C", "X", "HB1", "HB2", "HB3"]
matched = interpreters["LEU"].match_atom_names(atom_names)
s = StringIO()
matched.show_problems(out=s, prefix=">")
assert not show_diff(
s.getvalue(),
"""\
>unexpected atom names: "X"
>multiple matches: expected pattern=C names="C", "C"
>mutually exclusive: 1hB 3hB
""",
)
ala_names = ["N", "CA", "C", "O", "CB"]
ala_missing_names = ["CA", "CB", "O"]
ala_with_h = ["N", "CA", "C", "O", "CB", "HA", "HB1", "HB2", "HB3", "H"]
ala_matched = interpreters["ALA"].match_atom_names(ala_names)
ala_missing = interpreters["ALA"].match_atom_names(ala_missing_names)
ala_h = interpreters["ALA"].match_atom_names(ala_with_h)
assert ala_matched.missing_atom_names(ignore_hydrogen=True) == set(())
assert ala_missing.missing_atom_names(ignore_hydrogen=True) == set(("C", "N"))
assert ala_h.missing_atom_names(ignore_hydrogen=False) == set(())
print "OK"
def exercise_mixed_read_write(opts):
tmp = "exercise_mixed_read_write.tmp"
tst_f = "exercise_mixed_read_write.f"
open(tst_f, "w").write("""\
program prog
open(
& unit=1,
& file='%s',
& status='old')
read(1, '(i2)') num
write(6, '(i2)') num*2
write(1, '(i2)') 78
end
""" % tmp)
for cmd in build_cmds(tst_f=tst_f, opts=opts):
if (opts.verbose): print(cmd)
open(tmp, "w").write("""\
12
34
56
""")
stdout = easy_run.fully_buffered(
command=cmd).raise_if_errors().stdout_lines
assert stdout == ["24"]
tmp_text = open(tmp, "rb").read()
assert not show_diff(
tmp_text, b"""\
12
78
""".replace(b"\n", os.linesep.encode("latin-1")))
def run_and_check(cmd, pdbs_file, expected_out):
abs_paths = []
for rel_path in open(op.join(dd, pdbs_file)).read().splitlines():
abs_paths.append(op.normpath(op.join(dd, rel_path)))
list_of_pdbs = "list_of_pdbs_%d" % run_serial.next()
print >> open(list_of_pdbs, "w"), "\n".join(abs_paths)
cmd = cmd % list_of_pdbs
if (valgrind):
cmd = "valgrind " + cmd
print cmd
remove_files("out")
if (not valgrind):
buffers = easy_run.fully_buffered(command=cmd).raise_if_errors()
if (expected_out is None):
return buffers.stdout_lines
else:
easy_run.call(command=cmd)
if (expected_out is None):
return None
filtered_lines = []
for line in open("out").read().splitlines():
sw = line.startswith
if (sw("pole") or sw("members") or sw("min: ") or sw("max: ")):
filtered_lines.append(line)
assert not show_diff("\n".join(filtered_lines)+"\n", expected_out)
print "OK"
def exercise_make_atom_with_labels():
awl = pdb.make_atom_with_labels()
assert not show_diff(
awl.format_atom_record_group(siguij=False),
"""\
ATOM 0.000 0.000 0.000 0.00 0.00""",
)
awl = pdb.make_atom_with_labels(
xyz=(1, 2, 3),
sigxyz=(4, 5, 6),
occ=7,
sigocc=8,
b=9,
sigb=10,
uij=(11, 12, 13, 14, 15, 16),
siguij=(17, 18, 19, 20, 21, 22),
hetero=True,
serial="ABCDE",
name="FGHI",
segid="JKLM",
element="NO",
charge="PQ",
model_id="RSTU",
chain_id="VW",
resseq="XYZa",
icode="b",
altloc="c",
resname="def",
)
expected = """\
HETATMABCDE FGHIcdefVWXYZab 1.000 2.000 3.000 7.00 9.00 JKLMNOPQ
SIGATMABCDE FGHIcdefVWXYZab 4.000 5.000 6.000 8.00 10.00 JKLMNOPQ
ANISOUABCDE FGHIcdefVWXYZab 110000 120000 130000 140000 150000 160000 JKLMNOPQ
"""[
:-1
]
assert not show_diff(awl.format_atom_record_group(siguij=False), expected)
if pdb.hierarchy.atom.has_siguij():
assert not show_diff(
awl.format_atom_record_group(),
expected
+ """
SIGUIJABCDE FGHIcdefVWXYZab 170000 180000 190000 200000 210000 220000 JKLMNOPQ
"""[
:-1
],
)
def exercise_strip_spaces_separate_strings():
from fable.read import Error, source_line, strip_spaces_separate_strings
import itertools
global_line_index_generator = itertools.count()
def slc(cmbnd):
return [
source_line(
global_line_index_generator=global_line_index_generator,
file_name="str",
line_number=i+1,
text=" "+line)
for i,line in enumerate(cmbnd.splitlines())]
def check(cmbnd, expected_code, expected_strings):
for cmbnd_work,expected_strings_work in [
(cmbnd, expected_strings),
(cmbnd.replace("'", '"'), [s.replace("'", '"')
for s in expected_strings])]:
ssl = strip_spaces_separate_strings(source_line_cluster=slc(cmbnd_work))
assert not show_diff(ssl.code, expected_code)
assert len(ssl.strings) == len(ssl.string_indices)
assert ssl.strings == expected_strings_work
expected_string_indices = []
for i,c in enumerate(expected_code):
if (c == "'" or c == '"'):
expected_string_indices.append(i)
assert ssl.string_indices == expected_string_indices
if (cmbnd.find('"') > 0):
break
check("a = 0", "a=0", [])
check("a = ''", "a='", [""])
check("a = '\"'", "a='", ["\""])
check("a = \"'\"", "a='", ["'"])
check("a = 'x'", "a='", ["x"])
check("a = ' x ' ", "a='", [" x "])
check("a = ''''", "a='", ["'"])
check("call foo('')", "callfoo(')", [""])
check("call foo('''')", "callfoo(')", ["'"])
check("c a l l f o o ( '''' ) ", "callfoo(')", ["'"])
check(" c a l l f o o ( '''' ) ", "callfoo(')", ["'"])
check(" C A L LF O O ( ' abc '''' def ''' , ' g''h''i''' , X ) ",
"callfoo(',',x)", [" abc '' def '", " g'h'i'"])
check("a = '\n'", "a='", [""])
check("a = 'x\n'", "a='", ["x"])
check("a = '\ny'", "a='", ["y"])
check("a = 'x\ny'", "a='", ["xy"])
check("a = '''\n'", "a='", ["'"])
check("a = '\n'''", "a='", ["'"])
check("a = '''\n'''", "a='", ["''"])
#
for cmbnd,q,nd in [("'abc", "'", 9), ('x="', '"', 11)]:
try:
strip_spaces_separate_strings(source_line_cluster=slc(cmbnd))
except Error, e:
assert not show_diff(str(e), """\
Missing terminating %s character:
at str(1):
| %s|
%s^""" % (q, cmbnd, "-"*nd))
else: raise Exception_expected
def exercise_input_pickling():
pdb_inp = pdb.pdb_input(source_info="file/name", lines=pdb_string_all_sections)
for p in [pickle, cPickle]:
s = p.dumps(pdb_inp, 1)
l = p.loads(s)
assert not show_diff(l.as_pdb_string(), pdb_inp.as_pdb_string())
assert l.source_info() == "pickle"
for section in pdb.input_sections:
assert not show_diff(
"\n".join(getattr(l, section)()),
"\n".join(getattr(pdb_inp, section)()))
s = "\n".join(l.__getinitargs__()[1])
d = hashlib_md5(s).hexdigest()
if (pdb.hierarchy.atom.has_siguij()):
assert d == "bf987c40cc8672e2f2324d91d6de3e2b"
else:
assert d == "7375e96fd52794a785284580730de20c"
def run_and_compare_sdrive_fem(this_script):
sdrive_fem = libtbx.env.under_build(path="scitbx/lbfgs/sdrive_fem")
if (not os.path.isfile(sdrive_fem)):
return
outputs = []
for cmd in [sdrive_fem, 'scitbx.python "%s" fortran 100 5 1 0' % this_script]:
outputs.append(run_cmd(cmd=cmd))
assert not show_diff(outputs[0], outputs[1])
def exercise_basic():
a = flex.double((10,20))
p = flex.double((-25,355))
c = flex.polar(a, p, True)
f = flex.double((0.3,0.9))
s = miller.set(
crystal_symmetry=crystal.symmetry(
unit_cell=(10,10,10,90,90,90),
space_group_symbol="P1"),
indices=flex.miller_index([(1,2,3),(-3,4,-6)]),
anomalous_flag=False)
out = StringIO()
s.array(data=c).as_phases_phs(out=out)
assert not show_diff(out.getvalue(), """\
1 2 3 4999.99 1.00 -25.00
-3 4 -6 9999.99 1.00 -5.00
""")
out = StringIO()
s.array(data=c).as_phases_phs(out=out, scale_amplitudes=False)
assert not show_diff(out.getvalue(), """\
1 2 3 10.00 1.00 -25.00
-3 4 -6 20.00 1.00 -5.00
""")
for phases in [s.array(data=p), p]:
out = StringIO()
s.array(data=c).amplitudes().as_phases_phs(
out=out, phases=phases, phases_deg=True)
assert not show_diff(out.getvalue(), """\
1 2 3 4999.99 1.00 -25.00
-3 4 -6 9999.99 1.00 355.00
""")
for phases in [s.array(data=p*(math.pi/180)), p*(math.pi/180)]:
out = StringIO()
s.array(data=c).amplitudes().as_phases_phs(
out=out, phases=phases, phases_deg=False)
assert not show_diff(out.getvalue(), """\
1 2 3 4999.99 1.00 -25.00
-3 4 -6 9999.99 1.00 355.00
""")
for figures_of_merit in [s.array(data=f), f]:
out = StringIO()
s.array(data=c).as_phases_phs(out=out, figures_of_merit=figures_of_merit)
assert not show_diff(out.getvalue(), """\
1 2 3 4999.99 0.30 -25.00
-3 4 -6 9999.99 0.90 -5.00
""")
def exercise_weighting_schemes():
unit_weighting = least_squares.unit_weighting()
assert unit_weighting.type() == "unit"
assert str(unit_weighting) == "w=1"
shelx_weighting = least_squares.mainstream_shelx_weighting(0.1234, 0.5678)
assert shelx_weighting.type() == "calc"
assert not show_diff(
str(shelx_weighting),
"w=1/[\s^2^(Fo^2^)+(0.1234P)^2^+0.5678P] where P=(Fo^2^+2Fc^2^)/3")
def exercise(space_group_info, anomalous_flag,
d_min=1.0, reflections_per_bin=200, n_bins=10, verbose=0):
elements = ("N", "C", "C", "O") * 5
structure_factors = random_structure.xray_structure(
space_group_info,
elements=elements,
volume_per_atom=50.,
min_distance=1.5,
general_positions_only=True,
use_u_aniso=False,
u_iso=adptbx.b_as_u(10)
).structure_factors(
anomalous_flag=anomalous_flag, d_min=d_min, algorithm="direct")
if (0 or verbose):
structure_factors.xray_structure().show_summary()
asu_contents = dicts.with_default_value(0)
for elem in elements: asu_contents[elem] += 1
f_calc = abs(structure_factors.f_calc())
f_calc.setup_binner(
auto_binning=True,
reflections_per_bin=reflections_per_bin,
n_bins=n_bins)
if (0 or verbose):
f_calc.binner().show_summary()
for k_given in [1,0.1,0.01,10,100]:
f_obs = miller.array(
miller_set=f_calc,
data=f_calc.data()*k_given).set_observation_type_xray_amplitude()
f_obs.use_binner_of(f_calc)
wp = statistics.wilson_plot(f_obs, asu_contents, e_statistics=True)
if (0 or verbose):
print "wilson_k, wilson_b:", wp.wilson_k, wp.wilson_b
print "space group:", space_group_info.group().type().hall_symbol()
print "<E^2-1>:", wp.mean_e_sq_minus_1
assert 0.8 < wp.wilson_k/k_given < 1.2
assert 0.64 < wp.wilson_intensity_scale_factor/(k_given*k_given) < 1.44
assert 9 < wp.wilson_b < 11
assert wp.xy_plot_info().fit_correlation == wp.fit_correlation
if space_group_info.group().is_centric():
assert 0.90 < wp.mean_e_sq_minus_1 < 1.16
assert 3.15 < wp.percent_e_sq_gt_2 < 6.5
else:
assert 0.65 < wp.mean_e_sq_minus_1 < 0.90
assert 1.0 < wp.percent_e_sq_gt_2 < 3.15
assert wp.normalised_f_obs.size() == f_obs.size()
f_obs = f_calc.array(data=flex.double(f_calc.indices().size(), 0))
f_obs.use_binner_of(f_calc)
n_bins = f_obs.binner().n_bins_used()
try:
statistics.wilson_plot(f_obs, asu_contents)
except RuntimeError, e:
assert not show_diff(str(e), """\
wilson_plot error: %d empty bins:
Number of bins: %d
Number of f_obs > 0: 0
Number of f_obs <= 0: %d""" % (n_bins, n_bins, f_obs.indices().size()))
def exercise_01():
import libtbx.load_env
if not libtbx.env.has_module("reduce"):
print "Reduce not installed, needed for model.add_hydrogens(). skipping"
return
pdb_file_name = "add_h_to_hoh.pdb"
tmp_f = open(pdb_file_name, "w")
tmp_f.write(input_model)
tmp_f.close()
processed_pdb_files_srv = mmtbx.utils.process_pdb_file_srv(log=StringIO())
processed_pdb_file, pdb_inp = processed_pdb_files_srv.process_pdb_files(pdb_file_names=[pdb_file_name])
xray_structure = processed_pdb_file.xray_structure()
#
geometry = processed_pdb_file.geometry_restraints_manager(show_energies=False, assume_hydrogens_all_missing=True)
restraints_manager = mmtbx.restraints.manager(geometry=geometry)
#
model = mmtbx.model.manager(
refinement_flags=None,
processed_pdb_files_srv=processed_pdb_files_srv,
restraints_manager=restraints_manager,
xray_structure=xray_structure,
pdb_hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy,
log=None,
)
####
model.add_hydrogens(correct_special_position_tolerance=1.0)
result = StringIO()
model.write_pdb_file(out=result)
result = result.getvalue().splitlines()
####
result1 = []
for r1 in result:
if r1.startswith("ATOM") or r1.startswith("HETATM"):
result1.append(r1)
result2 = []
for r2 in expected_result.splitlines():
if r2.startswith("ATOM") or r2.startswith("HETATM"):
result2.append(r2)
assert len(result1) == len(result2)
for r1, r2 in zip(result1, result2):
r1 = r1[:30] + r1[60:]
r2 = r2[:30] + r2[60:]
assert not show_diff(r1, r2)
####
cntr = 0
xrs1 = iotbx.pdb.pdb_input(
source_info=None, lines=flex.std_string(expected_result.splitlines())
).xray_structure_simple()
xrs2 = iotbx.pdb.pdb_input(source_info=None, lines=flex.std_string(result)).xray_structure_simple()
for s1, s2 in zip(xrs1.scatterers(), xrs2.scatterers()):
if s1.element_symbol().strip() not in ["H", "D"]:
assert s1.element_symbol().strip() == s2.element_symbol().strip()
assert approx_equal(s1.site, s2.site)
cntr += 1
assert cntr == 19
def recycle(expected_column_data): mtz_obj = ma.as_mtz_dataset(column_root_label="X").mtz_object() sio = StringIO() mtz_obj.show_column_data_human_readable(out=sio) from libtbx.test_utils import show_diff if (verbose): sys.stdout.write(sio.getvalue()) assert not show_diff(sio.getvalue(), expected_column_data) ma_2 = only_element(mtz_obj.as_miller_arrays()) assert_equal_data_and_sigmas(ma, ma_2)