def test_simple(self):
"""Simple complete run of get_glyc_restraint"""
with utils.temporary_directory() as tmpdir:
with open(os.path.join(tmpdir, 'test-allosmod.py'), 'w') as fh:
fh.write("""line 1
def special_patches(self, aln):
self.patch(residue_type='NGLB', residues=(self.residues['1:A'],
self.residues['2:B']))
line 2
""")
with open(os.path.join(tmpdir, 'test.pdb'), 'w') as fh:
fh.write("""
ATOM 1 N ALA A 1 17.807 17.608 5.019 1.00 17.18 N
ATOM 2 CA ALA A 1 17.121 17.162 6.197 1.00 15.60 C
ATOM 3 C ALA A 1 18.085 17.018 7.343 1.00 14.54 C
ATOM 4 O ALA A 1 19.244 16.654 7.119 1.00 15.42 O
HETATM 5 O1 BMA B 2 19.244 16.654 7.119 1.00 15.42 O
HETATM 6 C1 BMA B 2 19.244 16.654 7.119 1.00 15.42 O
""")
out = check_output(['allosmod', 'get_glyc_restraint', 'test.pdb',
'test-allosmod.py'], stderr=subprocess.STDOUT,
retcode=0, universal_newlines=True, cwd=tmpdir)
# One restraint between CA and C1:
self.assertEqual(out, 'R 3 1 1 1 2 2 1 '
'2 6 5.0000 0.0350\n')
# special_patches should have been removed from .py file:
with open(os.path.join(tmpdir, 'test-allosmod.py')) as fh:
contents = fh.read()
self.assertEqual(contents, 'line 1\nline 2\n')
def test_simple(self):
"""Simple complete run of bin_data"""
with utils.temporary_directory() as tmpdir:
testdata = os.path.join(tmpdir, 'test.data')
with open(testdata, 'w') as fh:
fh.write("""1.0 10
1.1 10
1.2 10
1.2 10
2.0\t20
3.0 30
4.0 40
5.0 50
6.0 60
""")
out = check_output(['allosmod', 'bin_data', 'test.data', '0', 'm1',
'10', '20'],
universal_newlines=True, cwd=tmpdir)
self.assertEqual(out, """0.92500 0.44444 4.00000
2.02500 0.11111 1.00000
3.12500 0.11111 1.00000
4.22500 0.11111 1.00000
4.77500 0.11111 1.00000
5.87500 0.11111 1.00000
""")
out = check_output(['allosmod', 'bin_data', 'test.data', '1', 'm1',
'10', '20'],
universal_newlines=True, cwd=tmpdir)
self.assertEqual(out, "9.72500 1.00000 4.00000\n")
def test_insert_fail(self):
"""Test align.insert_gap() failure"""
with utils.temporary_directory() as tmpdir:
ali = os.path.join(tmpdir, 'test_insert.ali')
with open(ali, 'w') as fh:
fh.write(TEST_ALIGNMENT)
self.assertRaises(ValueError, allosmod.util.align.insert_gap,
ali, 1, 97, 99)
def test_make_ligand_file(self):
"""Test make_ligand_file() function"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'ligands.ids')
cryptosite.patch_mapper.make_ligand_file(fname)
with open(fname) as fh:
lines = fh.readlines()
self.assertEqual(len(lines), 16)
def test_make_ligand_file(self):
"""Test make_ligand_file() function"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'ligands.ids')
cryptosite.patch_mapper.make_ligand_file(fname)
with open(fname) as fh:
lines = fh.readlines()
self.assertEqual(len(lines), 16)
def test_simple(self):
"""Simple complete run of count_alignments"""
with utils.temporary_directory() as tmpdir:
self.setup_inputs(tmpdir)
out = check_output(['allosmod', 'count_alignments',
'align.ali', 'templates', 'pm.pdb'],
universal_newlines=True, cwd=tmpdir)
self.assertEqual(out.rstrip('\r\n'), "2")
def test_detect_invalid_residue_types_ok(self):
"""Test _detect_invalid_residue_types() with OK sequence"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
with open(fname, 'w') as fh:
fh.write(pdb_line + '\n')
e = modeller.environ()
m = modeller.model(e, file=fname)
cleaning._detect_invalid_residue_types(m)
def test_count_alignments(self):
"""Test count_alignments function"""
from allosmod.count_alignments import count_alignments
with utils.temporary_directory() as tmpdir:
self.setup_inputs(tmpdir)
num_align, num_res = count_alignments(
os.path.join(tmpdir, "align.ali"),
"pm.pdb", ["5fd1", "1bqx"])
self.assertEqual(num_align, 113)
self.assertEqual(num_res, 57)
def test_insert(self):
"""Test align.insert_gap()"""
with utils.temporary_directory() as tmpdir:
ali = os.path.join(tmpdir, 'test_insert.ali')
with open(ali, 'w') as fh:
fh.write(TEST_ALIGNMENT)
s_out = StringIO()
allosmod.util.align.insert_gap(ali, 1, 7, 9, s_out)
out_lines = s_out.getvalue().split('\n')
self.assertEqual(out_lines[2], 'N/T--TVFQG---VAGQSLQ')
self.assertEqual(out_lines[6], 'NT-TV/F-QGVAG---QSLQ')
def test_simple_docking_example(self):
"""Test simple-docking example"""
with utils.temporary_directory() as tmpdir:
subprocess.check_call([sys.executable,
get_example_path("simple-docking.py")],
cwd=tmpdir)
# Make sure that a complete output file was produced
with open(os.path.join(tmpdir, 'output.cif')) as fh:
contents = fh.readlines()
self.assertEqual(len(contents), 271)
def test_duplicate_datasets_details(self):
"""Datasets with differing details should be considered duplicates"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
_make_test_file(fname)
l1 = ihm.location.InputFileLocation(fname, details='test details')
d1 = ihm.dataset.PDBDataset(l1)
l2 = ihm.location.InputFileLocation(fname, details='other details')
d2 = ihm.dataset.PDBDataset(l2)
self.assertEqual(l1, l2)
def test_duplicate_datasets_details(self):
"""Datasets with differing details should be considered duplicates"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
_make_test_file(fname)
l1 = ihm.location.InputFileLocation(fname, details='test details')
d1 = ihm.dataset.PDBDataset(l1)
l2 = ihm.location.InputFileLocation(fname, details='other details')
d2 = ihm.dataset.PDBDataset(l2)
self.assertEqual(l1, l2)
def _read_cif(self, cif, real_file, category_handlers):
if real_file:
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test')
with open(fname, 'w') as fh:
fh.write(cif)
with open(fname) as fh:
r = ihm.format.CifReader(fh, category_handlers)
r.read_file()
else:
r = ihm.format.CifReader(StringIO(cif), category_handlers)
r.read_file()
def _read_cif(self, cif, real_file, category_handlers):
if real_file:
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test')
with open(fname, 'w') as fh:
fh.write(cif)
with open(fname) as fh:
r = ihm.format.CifReader(fh, category_handlers)
r.read_file()
else:
r = ihm.format.CifReader(StringIO(cif), category_handlers)
r.read_file()
def test_file_location_local(self):
"""Test InputFileLocation with a local file"""
# Make tmpdir under current directory, as it's not always possible to
# get a relative path from cwd to /tmp (e.g. on Windows where they may
# be on different drives)
with utils.temporary_directory('.') as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
_make_test_file(fname)
l = ihm.location.InputFileLocation(fname)
self.assertEqual(l.path, os.path.abspath(fname))
self.assertIsNone(l.repo)
self.assertEqual(l.file_size, 8)
def test_file_location_local(self):
"""Test InputFileLocation with a local file"""
# Make tmpdir under current directory, as it's not always possible to
# get a relative path from cwd to /tmp (e.g. on Windows where they may
# be on different drives)
with utils.temporary_directory('.') as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
_make_test_file(fname)
l = ihm.location.InputFileLocation(fname)
self.assertEqual(l.path, os.path.abspath(fname))
self.assertEqual(l.repo, None)
self.assertEqual(l.file_size, 8)
def test_simple_docking_example(self):
"""Test simple-docking example"""
with utils.temporary_directory() as tmpdir:
subprocess.check_call(
[sys.executable,
get_example_path("simple-docking.py")],
cwd=tmpdir)
# Make sure that a complete output file was produced
with open(os.path.join(tmpdir, 'output.cif')) as fh:
contents = fh.readlines()
self.assertEqual(len(contents), 271)
def _check_bad_cif(self, cif, real_file, category_handlers={}):
"""Ensure that the given bad cif results in a parser error"""
if real_file:
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test')
with open(fname, 'w') as fh:
fh.write(cif)
with open(fname) as fh:
r = ihm.format.CifReader(fh, category_handlers)
self.assertRaises(ihm.format.CifParserError, r.read_file)
else:
r = ihm.format.CifReader(StringIO(cif), category_handlers)
self.assertRaises(ihm.format.CifParserError, r.read_file)
def test_simple(self):
"""Simple complete run of getavgpdb"""
with utils.temporary_directory() as tmpdir:
with open(os.path.join(tmpdir, 'align.ali'), 'w') as fh:
fh.write(ALIGN_ALI)
out = check_output(['allosmod', 'getavgpdb',
os.path.join(test_dir, 'input',
'asite_pdb1.pdb'),
os.path.join(test_dir, 'input',
'asite_pdb2.pdb'),
'pdb1', 'pdb2'], cwd=tmpdir)
self.assertEqual(sorted(os.listdir(tmpdir)),
['align.ali', 'avgpdb.pdb', 'list', 'run.log'])
def _check_bad_cif(self, cif, real_file, category_handlers={}):
"""Ensure that the given bad cif results in a parser error"""
if real_file:
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test')
with open(fname, 'w') as fh:
fh.write(cif)
with open(fname) as fh:
r = ihm.format.CifReader(fh, category_handlers)
self.assertRaises(ihm.format.CifParserError, r.read_file)
else:
r = ihm.format.CifReader(StringIO(cif), category_handlers)
self.assertRaises(ihm.format.CifParserError, r.read_file)
def test_opts(self):
"""Complete run of get_pm_initialstruct using different options"""
from allosmod.get_pm_initialstruct import get_pm_initialstruct
with utils.temporary_directory() as tmpdir:
self.setup_inputs(tmpdir, seq='A/W')
os.mkdir(os.path.join(tmpdir, 'pred_1fdx'))
check_output(['allosmod', 'get_pm_initialstruct', '--target', 'foo',
'--restraints-only', 'test.aln', 'templates',
'.', '1', 'fast'], cwd=tmpdir)
for f in ('1fdx', 'family.mat', 'foo.ini', 'test.aln',
'test.aln.ali', 'foo.rsr'):
os.unlink(os.path.join(tmpdir, 'pred_1fdx', f))
def test_simple(self):
"""Simple test of pdb2ali"""
with utils.temporary_directory() as tmpdir:
with open(os.path.join(tmpdir, 'test.pdb'), 'w') as fh:
fh.write(test_pdb)
for out in (check_output(['allosmod', 'pdb2ali', 'test.pdb'],
universal_newlines=True, cwd=tmpdir),
check_output(['python', '-m', 'allosmod.pdb2ali',
'test.pdb'], universal_newlines=True,
cwd=tmpdir)):
self.assertEqual(out, """>P1;test.pdb
structureX:test.pdb: 1 :A:+12:B:::-1.00:-1.00
CMYh./CMY-frh.*
""")
def test_nochdir(self):
"""Complete run of get_pm_initialstruct using --no-chdir"""
from allosmod.get_pm_initialstruct import get_pm_initialstruct
with utils.temporary_directory() as tmpdir:
os.mkdir(os.path.join(tmpdir, 'pred_1fdx'))
self.setup_inputs(tmpdir, seq='A/W', subdir='pred_1fdx')
check_output(['allosmod', 'get_pm_initialstruct', '--target', 'foo',
'--restraints-only', '--no-chdir', '--csrfile',
'test.rsr', 'test.aln', '../templates', '.', '1',
'fast'], cwd=os.path.join(tmpdir, 'pred_1fdx'))
for f in ('1fdx', 'family.mat', 'foo.ini', 'test.aln',
'test.aln.ali'):
os.unlink(os.path.join(tmpdir, 'pred_1fdx', f))
def test_get_qioft(self):
"""Test get_qioft() function"""
inputs = os.path.join(TOPDIR, 'test', 'input')
with utils.temporary_directory() as tmpdir:
subdir = os.path.join(tmpdir, 'XXX.pdb_14')
os.mkdir(subdir)
for f in ('list', 'pm.pdb.B10010001.pdb', 'pm_XXX.pdb'):
shutil.copy(os.path.join(inputs, f), subdir)
cryptosite.analysis.get_qioft(tmpdir)
with open(os.path.join(subdir, 'qioft_pm_XXX.pdb_11sc.dat')) as fh:
e = fh.readlines()
self.assertEqual(e, ['0.2205 0.3422 0.5290 0.3791 0.2468 '
'0.4816 0.3841 0.5149 0.4896 0.0971 0.3187 0.0189 \n'])
def test_dcd_writer_framesize_mismatch(self):
"""Test DCDWriter class with framesize mismatch"""
m1 = ihm.model.Model(None, None, None)
m1._atoms = [ihm.model.Atom(None, None, None, None, x=1,y=2,z=3),
ihm.model.Atom(None, None, None, None, x=4,y=5,z=6)]
m2 = ihm.model.Model(None, None, None)
m2._atoms = [ihm.model.Atom(None, None, None, None, x=1,y=2,z=3)]
with utils.temporary_directory() as tmpdir:
dcd = os.path.join(tmpdir, 'out.dcd')
with open(dcd, 'wb') as fh:
d = ihm.model.DCDWriter(fh)
d.add_model(m1)
self.assertRaises(ValueError, d.add_model, m2)
def test_get_pdb_seq(self):
"""Test get_pdb_seq()"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
with open(fname, 'w') as fh:
fh.write("""
ATOM 1 N CYS A 1 18.511 -1.416 15.632 1.00 6.84 C
ATOM 2 C CYS A 1 18.511 -1.416 15.632 1.00 6.84 C
ATOM 3 N GLY A 2 18.511 -1.416 15.632 1.00 6.84 C
ATOM 4 C GLY A 2 18.511 -1.416 15.632 1.00 6.84 C
ATOM 5 N TYR B 3 18.511 -1.416 15.632 1.00 6.84 C
ATOM 6 C TYR B 3 18.511 -1.416 15.632 1.00 6.84 C
""")
seq = cleaning.get_pdb_seq(fname, 'A')
self.assertEqual(seq, 'CG')
def test_get_pdb_seq(self):
"""Test get_pdb_seq()"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
with open(fname, 'w') as fh:
fh.write("""
ATOM 1 N CYS A 1 18.511 -1.416 15.632 1.00 6.84 C
ATOM 2 C CYS A 1 18.511 -1.416 15.632 1.00 6.84 C
ATOM 3 N GLY A 2 18.511 -1.416 15.632 1.00 6.84 C
ATOM 4 C GLY A 2 18.511 -1.416 15.632 1.00 6.84 C
ATOM 5 N TYR B 3 18.511 -1.416 15.632 1.00 6.84 C
ATOM 6 C TYR B 3 18.511 -1.416 15.632 1.00 6.84 C
""")
seq = cleaning.get_pdb_seq(fname, 'A')
self.assertEqual(seq, 'CG')
def test_dcd_writer_framesize_mismatch(self):
"""Test DCDWriter class with framesize mismatch"""
m1 = ihm.model.Model(None, None, None)
m1._atoms = [ihm.model.Atom(None, None, None, None, x=1,y=2,z=3),
ihm.model.Atom(None, None, None, None, x=4,y=5,z=6)]
m2 = ihm.model.Model(None, None, None)
m2._atoms = [ihm.model.Atom(None, None, None, None, x=1,y=2,z=3)]
with utils.temporary_directory() as tmpdir:
dcd = os.path.join(tmpdir, 'out.dcd')
with open(dcd, 'wb') as fh:
d = ihm.model.DCDWriter(fh)
d.add_model(m1)
self.assertRaises(ValueError, d.add_model, m2)
def test_simple(self):
"""Simple test of getcofm"""
with utils.temporary_directory() as tmpdir:
with open(os.path.join(tmpdir, 'test.pdb'), 'w') as fh:
fh.write(test_pdb)
for out in (check_output(['allosmod', 'getcofm', 'test.pdb'],
cwd=tmpdir),
check_output(['python', '-m', 'allosmod.getcofm',
'test.pdb'], cwd=tmpdir)):
x = float(out[:8])
y = float(out[9:17])
z = float(out[18:26])
self.assertAlmostEqual(x, 2.214, places=3)
self.assertAlmostEqual(y, 1.733, places=3)
self.assertAlmostEqual(z, 1.067, places=3)
def test_get_qioft(self):
"""Test get_qioft() function"""
inputs = os.path.join(TOPDIR, 'test', 'input')
with utils.temporary_directory() as tmpdir:
subdir = os.path.join(tmpdir, 'XXX.pdb_14')
os.mkdir(subdir)
for f in ('list', 'pm.pdb.B10010001.pdb', 'pm_XXX.pdb'):
shutil.copy(os.path.join(inputs, f), subdir)
cryptosite.analysis.get_qioft(tmpdir)
with open(os.path.join(subdir, 'qioft_pm_XXX.pdb_11sc.dat')) as fh:
e = fh.readlines()
self.assertEqual(e, [
'0.2205 0.3422 0.5290 0.3791 0.2468 '
'0.4816 0.3841 0.5149 0.4896 0.0971 0.3187 0.0189 \n'
])
def test_rewrite_chain(self):
"""Make sure that pdb2ali rewrites empty chain IDs"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
with open(fname, 'w') as fh:
fh.write(test_pdb.replace(' A ', ' '))
out = check_output(['allosmod', 'pdb2ali', 'test.pdb'],
universal_newlines=True, cwd=tmpdir)
self.assertEqual(out, """>P1;test.pdb
structureX:test.pdb: 1 :@:+12:B:::-1.00:-1.00
CMYh./CMY-frh.*
""")
with open(fname) as fh:
lines = fh.readlines()
# Empty chain should have been reassigned as '@'
self.assertEqual(lines[1][21], '@')
def test_rmf_em2d_restraint_provenance(self):
"""Test _RMFEM2DRestraintProvenance class"""
rmf_node = MockRMFNode("r1", 1)
with utils.temporary_directory() as tmpdir:
pgm = os.path.join(tmpdir, 'test.pgm2')
with open(pgm, 'w'):
pass
p = src.io._RMFEM2DRestraintProvenance(rmf_node, pgm, 4.0)
self.assertEqual(
p.name, 'EM class average from test.pgm2')
mock_session = make_session()
mock_session.logger = MockLogger()
model = src.io._RMFModel(mock_session, 'fname')
# Should be a noop since pgm2 isn't a known map format
p.load(mock_session, model)
def test_wrap(self):
"""Make sure that long sequences from pdb2ali are wrapped"""
with utils.temporary_directory() as tmpdir:
with open(os.path.join(tmpdir, 'test.pdb'), 'w') as fh:
for i in range(100):
fh.write("ATOM 1 N CYS A %-4d 1.453 "
"0.000 0.000 0.00 0.00 C\n" % (i+1))
fh.write(test_pdb)
out = check_output(['allosmod', 'pdb2ali', 'test.pdb'],
universal_newlines=True, cwd=tmpdir)
self.assertEqual(out,
""">P1;test.pdb
structureX:test.pdb: 1 :A:+112:B:::-1.00:-1.00
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCMYh./CMY-frh.*
""")
def test_cdensity_even_cutoff_positive(self):
"""Test contpres with even charge density, positive cutoff"""
with utils.temporary_directory() as tmpdir:
break_dat = os.path.join(tmpdir, 'break.dat')
with open(break_dat, 'w') as fh:
fh.write("foo\nbar\n")
out = check_output(['allosmod', 'contpres', '--cdensity_cutoff',
'1.0', os.path.join(test_dir, 'input',
'contpres_evencd.rsr'),
os.path.join(test_dir, 'input',
'contpres_evencd.pdb'), '50.0'],
cwd=tmpdir)
with open(break_dat) as fh:
content = fh.read()
self.assertEqual(content, "foo\nbar\n")
os.unlink(break_dat)
os.unlink(os.path.join(tmpdir, 'contpres.dat'))
def test_detect_invalid_residue_types_bad(self):
"""Test _detect_invalid_residue_types() with bad sequence"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
with open(fname, 'w') as fh:
fh.write("""
ATOM 1 N CYS A 1 18.511 -1.416 15.632 1.00 6.84 C
ATOM 2 C CYS A 1 18.511 -1.416 15.632 1.00 6.84 C
ATOM 3 N HIE A 2 18.511 -1.416 15.632 1.00 6.84 C
ATOM 4 C HIE A 2 18.511 -1.416 15.632 1.00 6.84 C
ATOM 5 N HSD B 3 18.511 -1.416 15.632 1.00 6.84 C
ATOM 6 C HSD B 3 18.511 -1.416 15.632 1.00 6.84 C
""")
e = modeller.environ()
m = modeller.model(e, file=fname)
self.assertRaises(cleaning.InvalidResiduesError,
cleaning._detect_invalid_residue_types, m)
def test_cdensity(self):
"""Simple contpres in cdensity mode"""
with utils.temporary_directory() as tmpdir:
break_dat = os.path.join(tmpdir, 'break.dat')
with open(break_dat, 'w') as fh:
fh.write("foo\nbar\n")
out = check_output(['allosmod', 'contpres', '--cdensity_cutoff',
'1.0', os.path.join(test_dir, 'input',
'test_contpres.rsr'),
os.path.join(test_dir, 'input',
'test_contpres.pdb'), '50.0'],
cwd=tmpdir)
with open(break_dat) as fh:
content = fh.read()
self.assertEqual(content, "foo\nbar\n2 50.0\n")
os.unlink(break_dat)
os.unlink(os.path.join(tmpdir, 'contpres.dat'))
def test_dcd_writer(self):
"""Test DCDWriter class"""
m1 = ihm.model.Model(None, None, None)
m1._atoms = [ihm.model.Atom(None, None, None, None, x=1,y=2,z=3),
ihm.model.Atom(None, None, None, None, x=4,y=5,z=6)]
with utils.temporary_directory() as tmpdir:
dcd = os.path.join(tmpdir, 'out.dcd')
with open(dcd, 'wb') as fh:
d = ihm.model.DCDWriter(fh)
d.add_model(m1)
d.add_model(m1)
with open(dcd, 'rb') as fh:
contents = fh.read()
self.assertEqual(len(contents), 452)
def test_dcd_writer(self):
"""Test DCDWriter class"""
m1 = ihm.model.Model(None, None, None)
m1._atoms = [ihm.model.Atom(None, None, None, None, x=1,y=2,z=3),
ihm.model.Atom(None, None, None, None, x=4,y=5,z=6)]
with utils.temporary_directory() as tmpdir:
dcd = os.path.join(tmpdir, 'out.dcd')
with open(dcd, 'wb') as fh:
d = ihm.model.DCDWriter(fh)
d.add_model(m1)
d.add_model(m1)
with open(dcd, 'rb') as fh:
contents = fh.read()
self.assertEqual(len(contents), 452)
def test_repository(self):
"""Test Repository"""
# Make tmpdir under current directory, as it's not always possible to
# get a relative path from cwd to /tmp (e.g. on Windows where they may
# be on different drives)
with utils.temporary_directory(os.getcwd()) as tmpdir:
subdir = os.path.join(tmpdir, 'subdir')
subdir2 = os.path.join(tmpdir, 'subdir2')
os.mkdir(subdir)
_make_test_file(os.path.join(subdir, 'bar'))
s = ihm.location.Repository(doi='10.5281/zenodo.46266',
root=os.path.relpath(tmpdir),
url='foo',
top_directory='baz')
self.assertEqual(s._root, tmpdir)
self.assertEqual(s.url, 'foo')
self.assertEqual(s.top_directory, 'baz')
loc = ihm.location.InputFileLocation(
os.path.relpath(os.path.join(subdir, 'bar')))
self.assertIsNone(loc.repo)
ihm.location.Repository._update_in_repos(loc, [s])
self.assertEqual(loc.repo.doi, '10.5281/zenodo.46266')
self.assertEqual(loc.path, os.path.join('subdir', 'bar'))
# Shouldn't touch locations that are already in repos
loc = ihm.location.InputFileLocation(repo='foo', path='bar')
self.assertEqual(loc.repo, 'foo')
ihm.location.Repository._update_in_repos(loc, [s])
self.assertEqual(loc.repo, 'foo')
# Shortest match should win
loc = ihm.location.InputFileLocation(
os.path.relpath(os.path.join(subdir, 'bar')))
s2 = ihm.location.Repository(doi='10.5281/zenodo.46280',
root=os.path.relpath(subdir),
url='foo',
top_directory='baz')
# Repositories that aren't above the file shouldn't count
s3 = ihm.location.Repository(doi='10.5281/zenodo.56280',
root=os.path.relpath(subdir2),
url='foo',
top_directory='baz')
ihm.location.Repository._update_in_repos(loc, [s2, s3, s])
self.assertEqual(loc.repo.doi, '10.5281/zenodo.46280')
self.assertEqual(loc.path, 'bar')
def test_modify_patch_dock_params(self):
"""Test _modify_patch_dock_params() function"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'params.txt')
with open(fname, 'w') as fh:
fh.write("""
protLib /chem.lib
ligandSeg 5.0 15.0 0.1 1 1 1 5
clusterParams 0.05 2 1.0 2.0
""")
cryptosite.patch_mapper._modify_patch_dock_params(fname)
with open(fname) as fh:
contents = fh.read()
self.assertEqual(contents, """
protLib /chem.lib
ligandSeg 5.0 15.0 0.5 1 1 0 5
clusterParams 0.1 3 1.0 2.0
""")
def test_simple(self):
"""Simple complete run of get_pm_initialstruct"""
from allosmod.get_pm_initialstruct import get_pm_initialstruct
with utils.temporary_directory() as tmpdir:
self.setup_inputs(tmpdir)
check_output(['allosmod', 'get_pm_initialstruct', '--target', 'foo',
'--keep-alignment', 'test.aln', 'templates',
'.', '1', 'slow'], cwd=tmpdir)
e = modeller.environ()
m = modeller.model(e, file=os.path.join(tmpdir, 'pred_1fdx',
'foo.B99990001.pdb'))
self.assertEqual([x.code for x in m.residues], ['A', 'W'])
self.assertEqual(m.chains[0].name, 'A')
for f in ('1fdx', 'foo.B99990001.pdb', 'foo.ini', 'foo.sch',
'test.aln', 'foo.D00000001', 'foo.rsr',
'foo.V99990001'):
os.unlink(os.path.join(tmpdir, 'pred_1fdx', f))
def test_simple(self):
"""Simple complete run of contpres"""
with utils.temporary_directory() as tmpdir:
break_dat = os.path.join(tmpdir, 'break.dat')
with open(break_dat, 'w') as fh:
fh.write("foo\nbar\n")
out = check_output(['allosmod', 'contpres',
os.path.join(test_dir, 'input',
'test_contpres.rsr'),
os.path.join(test_dir, 'input',
'test_contpres.pdb'), '50.0'],
cwd=tmpdir)
with open(break_dat) as fh:
content = fh.read()
self.assertEqual(content, "foo\nbar\n1 50.0\n3 50.0\n")
with open(os.path.join(tmpdir, 'contpres.dat')) as fh:
content = fh.read()
self.assertEqual(content, "1 4\n2 0\n3 4\n")
def test_duplicate_locations(self):
"""Datasets with same location should be considered duplicates"""
with utils.temporary_directory() as tmpdir:
fname1 = os.path.join(tmpdir, 'test1.pdb')
fname2 = os.path.join(tmpdir, 'test2.pdb')
_make_test_file(fname1)
_make_test_file(fname2)
loc1 = ihm.location.InputFileLocation(fname1)
loc2 = ihm.location.InputFileLocation(fname2)
# Identical datasets in the same location aren't duplicated
pdb1 = ihm.dataset.PDBDataset(loc1)
pdb2 = ihm.dataset.PDBDataset(loc1)
self.assertEqual(pdb1, pdb2)
# Datasets in different locations are OK
pdb1 = ihm.dataset.PDBDataset(loc1)
pdb2 = ihm.dataset.PDBDataset(loc2)
self.assertNotEqual(pdb1, pdb2)
def test_repository(self):
"""Test Repository"""
# Make tmpdir under current directory, as it's not always possible to
# get a relative path from cwd to /tmp (e.g. on Windows where they may
# be on different drives)
with utils.temporary_directory(os.getcwd()) as tmpdir:
subdir = os.path.join(tmpdir, 'subdir')
subdir2 = os.path.join(tmpdir, 'subdir2')
os.mkdir(subdir)
_make_test_file(os.path.join(subdir, 'bar'))
s = ihm.location.Repository(doi='10.5281/zenodo.46266',
root=os.path.relpath(tmpdir),
url='foo', top_directory='baz')
self.assertEqual(s._root, tmpdir)
self.assertEqual(s.url, 'foo')
self.assertEqual(s.top_directory, 'baz')
loc = ihm.location.InputFileLocation(
os.path.relpath(os.path.join(subdir, 'bar')))
self.assertEqual(loc.repo, None)
ihm.location.Repository._update_in_repos(loc, [s])
self.assertEqual(loc.repo.doi, '10.5281/zenodo.46266')
self.assertEqual(loc.path, os.path.join('subdir', 'bar'))
# Shouldn't touch locations that are already in repos
loc = ihm.location.InputFileLocation(repo='foo', path='bar')
self.assertEqual(loc.repo, 'foo')
ihm.location.Repository._update_in_repos(loc, [s])
self.assertEqual(loc.repo, 'foo')
# Shortest match should win
loc = ihm.location.InputFileLocation(
os.path.relpath(os.path.join(subdir, 'bar')))
s2 = ihm.location.Repository(doi='10.5281/zenodo.46280',
root=os.path.relpath(subdir),
url='foo', top_directory='baz')
# Repositories that aren't above the file shouldn't count
s3 = ihm.location.Repository(doi='10.5281/zenodo.56280',
root=os.path.relpath(subdir2),
url='foo', top_directory='baz')
ihm.location.Repository._update_in_repos(loc, [s2, s3, s])
self.assertEqual(loc.repo.doi, '10.5281/zenodo.46280')
self.assertEqual(loc.path, 'bar')
def test_get_energy(self):
"""Test get_energy() function"""
inputs = os.path.join(TOPDIR, 'test', 'input')
with utils.temporary_directory() as tmpdir:
subdir = os.path.join(tmpdir, 'XXX.pdb_14')
os.mkdir(subdir)
touch(os.path.join(subdir, 'pm.pdb.B10010001.pdb'))
touch(os.path.join(subdir, 'pm.pdb.B10020001.pdb'))
touch(os.path.join(subdir, 'pm.pdb.B99990001.pdb'))
shutil.copy(os.path.join(inputs, 'pm.pdb.D00000001'), subdir)
e = cryptosite.analysis.get_energy(tmpdir)
with open(os.path.join(subdir, 'energy.dat')) as fh:
e = fh.readlines()
self.assertEqual(e,
[' 1000 13478.55371 0.0280 0.0836 '
'3374.72437 499.52283\n',
' 1000 13580.25098 0.0279 0.0794 '
'3332.75293 493.31027\n'])
def test_modify_patch_dock_params(self):
"""Test _modify_patch_dock_params() function"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'params.txt')
with open(fname, 'w') as fh:
fh.write("""
protLib /chem.lib
ligandSeg 5.0 15.0 0.1 1 1 1 5
clusterParams 0.05 2 1.0 2.0
""")
cryptosite.patch_mapper._modify_patch_dock_params(fname)
with open(fname) as fh:
contents = fh.read()
self.assertEqual(
contents, """
protLib /chem.lib
ligandSeg 5.0 15.0 0.5 1 1 0 5
clusterParams 0.1 3 1.0 2.0
""")
def test_get_energy(self):
"""Test get_energy() function"""
inputs = os.path.join(TOPDIR, 'test', 'input')
with utils.temporary_directory() as tmpdir:
subdir = os.path.join(tmpdir, 'XXX.pdb_14')
os.mkdir(subdir)
touch(os.path.join(subdir, 'pm.pdb.B10010001.pdb'))
touch(os.path.join(subdir, 'pm.pdb.B10020001.pdb'))
touch(os.path.join(subdir, 'pm.pdb.B99990001.pdb'))
shutil.copy(os.path.join(inputs, 'pm.pdb.D00000001'), subdir)
e = cryptosite.analysis.get_energy(tmpdir)
with open(os.path.join(subdir, 'energy.dat')) as fh:
e = fh.readlines()
self.assertEqual(e, [
' 1000 13478.55371 0.0280 0.0836 '
'3374.72437 499.52283\n',
' 1000 13580.25098 0.0279 0.0794 '
'3332.75293 493.31027\n'
])
def test_first_data_block(self):
"""Only information from the first data block should be read"""
cif = """
_foo.var1 test1
data_model
_foo.var2 test2
data_model2
_foo.var3 test3
"""
h = GenericHandler()
r = ihm.format.CifReader(StringIO(cif), {'_foo': h})
self._check_first_data(r, h)
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test')
with open(fname, 'w') as fh:
fh.write(cif)
with open(fname) as fh:
h = GenericHandler()
r = ihm.format.CifReader(fh, {'_foo': h})
self._check_first_data(r, h)
def test_rmf_em_restraint_provenance(self):
"""Test _RMFEMRestraintProvenance class"""
rmf_node = MockRMFNode("r1", 1)
# Test with non-existent GMM file
p = src.io._RMFEMRestraintGMMProvenance(rmf_node, '/does/notexist')
self.assertEqual(p.name, 'Gaussian Mixture Model from notexist')
self.assertIsNone(p.previous)
p.load(None, None) # noop
# Test with GMM file containing no metadata
with utils.temporary_file(suffix='.gmm') as fname:
with open(fname, 'w') as fh:
pass
p = src.io._RMFEMRestraintGMMProvenance(rmf_node, fname)
self.assertIsNone(p.previous)
# Test with GMM file containing valid metadata
with utils.temporary_directory() as tmpdir:
gmm = os.path.join(tmpdir, 'test.gmm')
mrc = os.path.join(tmpdir, 'test.mrc2')
with open(gmm, 'w') as fh:
fh.write("""# Created by create_gmm.py
# data_fn: test.mrc2
# ncenters: 50
""")
with open(mrc, 'w') as fh:
pass
p = src.io._RMFEMRestraintGMMProvenance(rmf_node, gmm)
prev = p.previous
self.assertEqual(prev.filename, mrc)
self.assertEqual(p.name, 'Gaussian Mixture Model from test.gmm')
self.assertEqual(prev.name, 'EM map from test.mrc2')
mock_session = make_session()
mock_session.logger = MockLogger()
model = src.io._RMFModel(mock_session, 'fname')
# Should be a noop since mrc2 isn't a known map format
prev.load(mock_session, model)
def test_file_location_local_not_exist(self):
"""Test InputFileLocation with a local file that doesn't exist"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
self.assertRaises(ValueError, ihm.location.InputFileLocation,
fname)
