def test_compute_chi():
"""Test that the proper chi angles are computed.
The "reference data" is manually computed with pymol.
"""
try:
from jinja2 import Template
except ImportError:
raise SkipTest("jinja2 is required for this test")
pymol_script = Template('''
import numpy as np
from pymol import cmd, CmdException
CHI1_ATOMS = [["N", "CA", "CB", "CG"],
["N", "CA", "CB", "CG1"],
["N", "CA", "CB", "SG"],
["N", "CA", "CB", "OG"],
["N", "CA", "CB", "OG1"]]
CHI2_ATOMS = [["CA", "CB", "CG", "CD"],
["CA", "CB", "CG", "CD1"],
["CA", "CB", "CG1", "CD1"],
["CA", "CB", "CG", "OD1"],
["CA", "CB", "CG", "ND1"]]
CHI3_ATOMS = [["CB", "CG", "CD", "NE"],
["CB", "CG", "CD", "CE"],
["CB", "CG", "CD", "OE1"],
["CB", "CG", "SD", "CE"]]
CHI4_ATOMS = [["CG", "CD", "NE", "CZ"],
["CG", "CD", "CE", "NZ"]]
for n, chi_atoms in enumerate([CHI1_ATOMS, CHI2_ATOMS, CHI3_ATOMS, CHI4_ATOMS]):
indices, angles = [], []
for r in range(1, cmd.count_atoms('name ca')+1):
r_indices, r_angles = None, None
for atoms in chi_atoms:
try:
selection = ['%d/%s' % (r, e) for e in atoms]
r_indices = [cmd.id_atom(s) - 1 for s in selection]
r_angles = cmd.get_dihedral(*selection) * np.pi / 180.0
except CmdException:
pass
if r_indices is not None:
indices.append(r_indices)
angles.append(r_angles)
np.savetxt("{{indices_fn}}.%d" % (n+1), indices, '%d')
np.savetxt("{{angles_fn}}.%d" % (n+1), angles)
cmd.quit()''')
pymol = find_executable('pymol')
if pymol is None:
try_paths = ['/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL']
for path in try_paths:
if os.path.exists(path):
pymol = path
continue
if pymol is None:
raise SkipTest("pymol executable not found")
try:
tempdir = tempfile.mkdtemp()
indices_fn = os.path.join(tempdir, 'indices')
angles_fn = os.path.join(tempdir, 'angles')
pymolscript_fn = os.path.join(tempdir, 'pymolscript.py')
with open(pymolscript_fn, 'w') as f:
f.write(pymol_script.render({'indices_fn': indices_fn,
'angles_fn': angles_fn}))
os.system('%s %s -cr %s' % (pymol, get_fn('2EQQ.pdb'), pymolscript_fn))
ref_indices = [np.loadtxt(indices_fn + '.%d' % i, dtype=int) for i in range(1,5)]
ref_angles = [np.loadtxt(angles_fn + '.%d' % i) for i in range(1,5)]
finally:
shutil.rmtree(tempdir)
indices, angles = zip(*[compute_chi1(traj, opt=False), compute_chi2(traj, opt=False),
compute_chi3(traj, opt=False), compute_chi4(traj, opt=False)])
indices_opt, angles_opt = zip(*[compute_chi1(traj, opt=True), compute_chi2(traj, opt=True),
compute_chi3(traj, opt=True), compute_chi4(traj, opt=True)])
for x, y in zip(indices, ref_indices):
eq(x, y)
for x, y in zip(indices_opt, ref_indices):
eq(x, y)
for x, y in zip(angles, ref_angles):
eq(x[0], y, decimal=4)
for x, y in zip(angles_opt, ref_angles):
eq(x[0], y, decimal=4)
def test_compute_chi():
"""Test that the proper chi angles are computed.
The "reference data" is manually computed with pymol.
"""
try:
from jinja2 import Template
except ImportError:
raise SkipTest("jinja2 is required for this test")
pymol_script = Template('''
import numpy as np
from pymol import cmd, CmdException
CHI1_ATOMS = [["N", "CA", "CB", "CG"],
["N", "CA", "CB", "CG1"],
["N", "CA", "CB", "SG"],
["N", "CA", "CB", "OG"],
["N", "CA", "CB", "OG1"]]
CHI2_ATOMS = [["CA", "CB", "CG", "CD"],
["CA", "CB", "CG", "CD1"],
["CA", "CB", "CG1", "CD1"],
["CA", "CB", "CG", "OD1"],
["CA", "CB", "CG", "ND1"]]
CHI3_ATOMS = [["CB", "CG", "CD", "NE"],
["CB", "CG", "CD", "CE"],
["CB", "CG", "CD", "OE1"],
["CB", "CG", "SD", "CE"]]
CHI4_ATOMS = [["CG", "CD", "NE", "CZ"],
["CG", "CD", "CE", "NZ"]]
for n, chi_atoms in enumerate([CHI1_ATOMS, CHI2_ATOMS, CHI3_ATOMS, CHI4_ATOMS]):
indices, angles = [], []
for r in range(1, cmd.count_atoms('name ca')+1):
r_indices, r_angles = None, None
for atoms in chi_atoms:
try:
selection = ['%d/%s' % (r, e) for e in atoms]
r_indices = [cmd.id_atom(s) - 1 for s in selection]
r_angles = cmd.get_dihedral(*selection) * np.pi / 180.0
except CmdException:
pass
if r_indices is not None:
indices.append(r_indices)
angles.append(r_angles)
np.savetxt("{{indices_fn}}.%d" % (n+1), indices, '%d')
np.savetxt("{{angles_fn}}.%d" % (n+1), angles)
cmd.quit()''')
pymol = find_executable('pymol')
if pymol is None:
try_paths = ['/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL']
for path in try_paths:
if os.path.exists(path):
pymol = path
continue
if pymol is None:
raise SkipTest("pymol executable not found")
try:
tempdir = tempfile.mkdtemp()
indices_fn = os.path.join(tempdir, 'indices')
angles_fn = os.path.join(tempdir, 'angles')
pymolscript_fn = os.path.join(tempdir, 'pymolscript.py')
with open(pymolscript_fn, 'w') as f:
f.write(
pymol_script.render({
'indices_fn': indices_fn,
'angles_fn': angles_fn
}))
os.system('%s %s -cr %s' % (pymol, get_fn('2EQQ.pdb'), pymolscript_fn))
ref_indices = [
np.loadtxt(indices_fn + '.%d' % i, dtype=int) for i in range(1, 5)
]
ref_angles = [np.loadtxt(angles_fn + '.%d' % i) for i in range(1, 5)]
finally:
shutil.rmtree(tempdir)
indices, angles = zip(*[
compute_chi1(traj, opt=False),
compute_chi2(traj, opt=False),
compute_chi3(traj, opt=False),
compute_chi4(traj, opt=False)
])
indices_opt, angles_opt = zip(*[
compute_chi1(traj, opt=True),
compute_chi2(traj, opt=True),
compute_chi3(traj, opt=True),
compute_chi4(traj, opt=True)
])
for x, y in zip(indices, ref_indices):
eq(x, y)
for x, y in zip(indices_opt, ref_indices):
eq(x, y)
for x, y in zip(angles, ref_angles):
eq(x[0], y, decimal=4)
for x, y in zip(angles_opt, ref_angles):
eq(x[0], y, decimal=4)
def test_compute_chi(get_fn, tmpdir, pymol, traj):
"""Test that the proper chi angles are computed.
The "reference data" is manually computed with pymol.
"""
try:
from jinja2 import Template
except ImportError:
pytest.skip("jinja2 is required for this test")
pymol_script = Template('''
import numpy as np
from pymol import cmd, CmdException
CHI1_ATOMS = [["N", "CA", "CB", "CG"],
["N", "CA", "CB", "CG1"],
["N", "CA", "CB", "SG"],
["N", "CA", "CB", "OG"],
["N", "CA", "CB", "OG1"]]
CHI2_ATOMS = [["CA", "CB", "CG", "CD"],
["CA", "CB", "CG", "CD1"],
["CA", "CB", "CG1", "CD1"],
["CA", "CB", "CG", "OD1"],
["CA", "CB", "CG", "ND1"],
["CA", "CB", "CG", "SD"]]
CHI3_ATOMS = [["CB", "CG", "CD", "NE"],
["CB", "CG", "CD", "CE"],
["CB", "CG", "CD", "OE1"],
["CB", "CG", "SD", "CE"]]
CHI4_ATOMS = [["CG", "CD", "NE", "CZ"],
["CG", "CD", "CE", "NZ"]]
CHI5_ATOMS = ["CD", "NE", "CZ", "NH1"]
for n, chi_atoms in enumerate([CHI1_ATOMS, CHI2_ATOMS, CHI3_ATOMS, CHI4_ATOMS, CHI5_ATOMS]):
indices, angles = [], []
for r in range(1, cmd.count_atoms('name ca')+1):
r_indices, r_angles = None, None
for atoms in chi_atoms:
try:
selection = ['%d/%s' % (r, e) for e in atoms]
r_indices = [cmd.id_atom(s) - 1 for s in selection]
r_angles = cmd.get_dihedral(*selection) * np.pi / 180.0
except CmdException:
pass
if r_indices is not None:
indices.append(r_indices)
angles.append(r_angles)
np.savetxt("{{indices_fn}}.%d" % (n+1), indices, '%d')
np.savetxt("{{angles_fn}}.%d" % (n+1), angles)
cmd.quit()''')
indices_fn = os.path.join(tmpdir, 'indices')
angles_fn = os.path.join(tmpdir, 'angles')
pymolscript_fn = os.path.join(tmpdir, 'pymolscript.py')
with open(pymolscript_fn, 'w') as f:
f.write(pymol_script.render({'indices_fn': indices_fn,
'angles_fn': angles_fn}))
os.system('%s %s -cr %s' % (pymol, get_fn('2EQQ.pdb'), pymolscript_fn))
ref_indices = [np.loadtxt(indices_fn + '.%d' % i, dtype=int) for i in range(1, 5)]
ref_angles = [np.loadtxt(angles_fn + '.%d' % i) for i in range(1, 5)]
indices, angles = zip(*[compute_chi1(traj, opt=False), compute_chi2(traj, opt=False),
compute_chi3(traj, opt=False), compute_chi4(traj, opt=False),
compute_chi5(traj, opt=False)])
indices_opt, angles_opt = zip(*[compute_chi1(traj, opt=True), compute_chi2(traj, opt=True),
compute_chi3(traj, opt=True), compute_chi4(traj, opt=True),
compute_chi5(traj, opt=True)])
for x, y in zip(indices, ref_indices):
eq(x, y)
for x, y in zip(indices_opt, ref_indices):
eq(x, y)
for x, y in zip(angles, ref_angles):
eq(x[0], y, decimal=4)
for x, y in zip(angles_opt, ref_angles):
eq(x[0], y, decimal=4)