def test_read_with_cclib():
"""Test if we can correctly read with cclib."""
main(["-g", "/tmp/fnord.Gaussian.gjf"])
main(["/tmp/fnord.Gaussian.gjf", "data/benzene.out"])
assert_equals(
open("data/benzene.gjf").read(),
"""#Put Keywords Here, check Charge and Multiplicity.
data/benzene.out
0 1
C 1.7458930000 1.7957530000 -1.0597530000
C 0.9484120000 2.8689700000 -1.4311180000
C 1.4480470000 1.0743490000 0.0876540000
C -0.1470660000 3.2206120000 -0.6552520000
C 0.3525690000 1.4259910000 0.8635200000
C -0.4449120000 2.4992080000 0.4921550000
H 2.5997410000 1.5203090000 -1.6651660000
H 1.1810280000 3.4311430000 -2.3262420000
H 2.0700040000 0.2375420000 0.3781170000
H -0.7690240000 4.0574200000 -0.9457150000
H 0.1199530000 0.8638180000 1.7586440000
H -1.2987600000 2.7746520000 1.0975680000
""",
)
def test_conformers():
cyclohexanol_conformers = conformers(cyclohexanol_mol)
assert_equals(len(cyclohexanol_conformers), 1)
pentane_conformers = conformers(pentane_mol)
assert_equals(len(pentane_conformers), 7)
output = pybel.Outputfile("xyz", "examples/pentane_conformers.xyz",
overwrite=True)
for mol in pentane_conformers:
output.write(mol)
output.close()
main(["examples/templates/opt.MOPAC.mop",
"examples/pentane_conformers.xyz"])
def test_example_fragments_orca():
main(["examples/templates/fragments.ORCA.inp", "examples/water_dimer.xyz"])
assert_equals(open("examples/water_dimer.inp").read(),
"""# examples/water_dimer.xyz
! Opt
* xyz 0 1
O(1) 0.12908 -0.26336 0.64798
H(1) 0.89795 0.28805 0.85518
H(1) 0.10833 -0.20468 -0.33302
O(2) 0.31020 0.07569 -2.07524
H(2) -0.26065 0.64232 -2.62218
H(2) 0.64083 -0.57862 -2.71449
*
""")
def _test_example_fragments_orca():
"""Test if fragmentation works with ORCA inputs."""
main(["pnictogen/repo/split.ORCA.inp", "data/water-dimer.xyz"])
assert_equals(
open("data/water-dimer.inp").read(),
"""# data/water-dimer.xyz
! Opt
* xyz 0 1
O(1) 0.12908 -0.26336 0.64798
H(1) 0.89795 0.28805 0.85518
H(1) 0.10833 -0.20468 -0.33302
O(2) 0.31020 0.07569 -2.07524
H(2) -0.26065 0.64232 -2.62218
H(2) 0.64083 -0.57862 -2.71449
*""",
)
def test_main():
for template in boilerplates:
main(["-g", template])
# One at a time
for xyz_file in example_xyz_files:
main([template, xyz_file])
# All at once
main([template] + list(example_xyz_files))
# Allow use of template in the parent directory
with cd("examples/boilerplates"):
main(["../templates/EDA.ADF.in", "../water_dimer.xyz"])
def test_update_data():
mol = pybel.readstring("smi", "[Ag+]")
assert_equals(mol.charge, 1)
assert_equals(mol.spin, 1)
update_data(mol, "spin=2 charge=0")
assert_equals(mol.charge, 0)
assert_equals(mol.spin, 2)
# Keywords in title
main(["-g", "examples/boilerplates/Gaussian.gjf"])
main(["examples/boilerplates/Gaussian.gjf", "examples/hydroxide.xyz"])
assert_equals(open("examples/hydroxide.gjf").read(),
"""#Put Keywords Here, check Charge and Multiplicity.
This guy has charge=-1 but its multiplicity spin=2 is incorrect
-1 2
O 0.05840 0.05840 0.00000
H 1.00961 -0.06802 0.00000
""")
def test_main():
"""Test if main works."""
for template in templates:
main(["-g", template])
# One at a time
for xyz_file in example_xyz_files:
main([template, xyz_file])
# All at once
main([template] + list(example_xyz_files))
# Allow use of template in the parent directory
with cd("data"):
main(["../pnictogen/repo/ADF.in", "water-dimer.xyz"])
def test_pnictogen():
"""Test if pnictogen works."""
for template in templates:
template_prefix, extension = os.path.splitext(template)
for xyz_file in example_xyz_files:
input_prefix, xyz_file_extension = os.path.splitext(xyz_file)
mol = Atoms(
cclib.bridge.cclib2openbabel.readfile(xyz_file,
xyz_file_extension[1:]))
written_files = pnictogen(mol, input_prefix, template,
extension[1:])
assert_equals(type(written_files), list)
for written_file in written_files:
assert_equals(type(written_file), str)
written_files2 = pnictogen(mol, input_prefix, template)
assert_equals(written_files, written_files2)
# Allow use of template in the parent directory
with cd("pnictogen/repo"):
mol = Atoms(
cclib.bridge.cclib2openbabel.readfile("../../data/water-dimer.xyz",
"xyz"))
written_files = pnictogen(mol, "../../data/water-dimer", "ADF.in",
"in")
assert_equals(written_files, ["../../data/water-dimer.in"])
main(["-g", "/tmp/hello.world.ORCA.inp"])
mol = Atoms(cclib.bridge.cclib2openbabel.readfile("data/co.xyz", "xyz"))
written_files = pnictogen(mol,
"data/co",
"/tmp/hello.world.ORCA.inp",
foo="bar")
assert_equals(written_files, ["data/co.inp"])
def test_render_templates():
"""Test if templates are correctly rendered."""
water_mol = Atoms(
cclib.bridge.cclib2openbabel.readfile("data/water.xyz", "xyz"))
if not water_mol.name:
water_mol.name = "data/water.xyz"
main(["-g", "/tmp/foo.ADF.in"])
main(["/tmp/foo.ADF.in", "data/water.xyz"])
assert_equals(
open("data/water.in").read().strip(),
"""TITLE data/water.xyz
CHARGE 0 0
Number of atoms
3
ATOMS Cartesian
O 0.0584027061 0.0584027059 0.0000000000
H 1.0096135406 -0.0680162466 0.0000000000
H -0.0680162466 1.0096135407 0.0000000000
End
Basis
End
Geometry
End""",
)
main(["-g", "/tmp/test.GAMESS.inp"])
main(["/tmp/test.GAMESS.inp", "data/water.xyz"])
assert_equals(
open("data/water.inp").read(),
""" $CONTRL COORD=CART UNITS=ANGS $END
$DATA
data/water.xyz
C1
O 8.0 0.0584027061 0.0584027059 0.0000000000
H 1.0 1.0096135406 -0.0680162466 0.0000000000
H 1.0 -0.0680162466 1.0096135407 0.0000000000
$END
""",
)
main(["-g", "/tmp/hello.GAMESSUK.inp"])
main(["/tmp/hello.GAMESSUK.inp", "data/water.xyz"])
assert_equals(open("data/water.inp").read(), water_mol.to_string("gukin"))
main(["-g", "/tmp/hello.world.Gaussian.gjf"])
main(["/tmp/hello.world.Gaussian.gjf", "data/water.xyz"])
assert_equals(
open("data/water.gjf").read(),
"""#Put Keywords Here, check Charge and Multiplicity.
data/water.xyz
0 1
O 0.0584027061 0.0584027059 0.0000000000
H 1.0096135406 -0.0680162466 0.0000000000
H -0.0680162466 1.0096135407 0.0000000000
""",
)
main(["-g", "/tmp/bar.Jaguar.in"])
main(["/tmp/bar.Jaguar.in", "data/water.xyz"])
assert_equals(open("data/water.in").read(), water_mol.to_string("jin"))
main(["-g", "/tmp/foo.Molpro.inp"])
main(["/tmp/foo.Molpro.inp", "data/water.xyz"])
assert_equals(open("data/water.inp").read(), water_mol.to_string("mp"))
main(["-g", "/tmp/example.MOPAC.mop"])
main(["/tmp/example.MOPAC.mop", "data/water.xyz"])
assert_equals(
open("data/water.mop").read(),
"""CHARGE=0 MS=0.0
data/water.xyz
O 0.05840 1 0.05840 1 0.00000 1
H 1.00961 1 -0.06802 1 0.00000 1
H -0.06802 1 1.00961 1 0.00000 1
""",
)
main(["-g", "/tmp/bar.MPQC.in"])
main(["/tmp/bar.MPQC.in", "data/water.xyz"])
assert_equals(open("data/water.in").read(), water_mol.to_string("mpqcin"))
main(["-g", "/tmp/foo.NWChem.nw"])
main(["/tmp/foo.NWChem.nw", "data/water.xyz"])
assert_equals(
open("data/water.nw").read(),
"""start molecule
title data/water.xyz
geometry units angstroms print xyz autosym
O 0.0584027061 0.0584027059 0.0000000000
H 1.0096135406 -0.0680162466 0.0000000000
H -0.0680162466 1.0096135407 0.0000000000
end
""",
)
main(["-g", "/tmp/example.ORCA.inp"])
main(["/tmp/example.ORCA.inp", "data/water.xyz"])
assert_equals(
open("data/water.inp").read(),
"""# data/water.xyz
! Opt
* xyz 0 1
O 0.0584027061 0.0584027059 0.0000000000
H 1.0096135406 -0.0680162466 0.0000000000
H -0.0680162466 1.0096135407 0.0000000000
*
""",
)
main(["-g", "/tmp/bar.Psi.dat"])
main(["/tmp/bar.Psi.dat", "data/water.xyz"])
assert_equals(
open("data/water.dat").read(),
"""# data/water.xyz
molecule {
0 1
O 0.0584027061 0.0584027059 0.0000000000
H 1.0096135406 -0.0680162466 0.0000000000
H -0.0680162466 1.0096135407 0.0000000000
units angstrom
}
optimize('scf')
""",
)
main(["-g", "/tmp/example.QChem.in"])
main(["/tmp/example.QChem.in", "data/water.xyz"])
assert_equals(open("data/water.in").read(), water_mol.to_string("qcin"))
main(["-g", "/tmp/foo.ZINDO.input"])
main(["/tmp/foo.ZINDO.input", "data/water.xyz"])
assert_equals(open("data/water.input").read(), water_mol.to_string("zin"))
def _test_example_eda_adf():
"""Test example for EDA in ADF."""
main(["pnictogen/repo/split.ADF.in", "data/water-dimer.xyz"])
assert_equals(
open("data/water-dimer_eda.in").read(),
"""TITLE data/water-dimer.xyz eda
CHARGE 0 0
Number of atoms
6
ATOMS Cartesian
O 0.12908 -0.26336 0.64798 f=f1
H 0.89795 0.28805 0.85518 f=f1
H 0.10833 -0.20468 -0.33302 f=f1
O 0.31020 0.07569 -2.07524 f=f2
H -0.26065 0.64232 -2.62218 f=f2
H 0.64083 -0.57862 -2.71449 f=f2
End
Fragments
f1 data/water-dimer_f1.t21
f2 data/water-dimer_f2.t21
End
Basis
End
Geometry
End
""",
)
assert_equals(
open("data/water-dimer_f1.in").read(),
"""TITLE data/water-dimer.xyz f1
CHARGE 0 0
Number of atoms
3
ATOMS Cartesian
O 0.12908 -0.26336 0.64798
H 0.89795 0.28805 0.85518
H 0.10833 -0.20468 -0.33302
End
Basis
End
Geometry
End
""",
)
assert_equals(
open("data/water-dimer_f2.in").read(),
"""TITLE data/water-dimer.xyz f2
CHARGE 0 0
Number of atoms
3
ATOMS Cartesian
O 0.31020 0.07569 -2.07524
H -0.26065 0.64232 -2.62218
H 0.64083 -0.57862 -2.71449
End
Basis
End
Geometry
End
""",
)
def test_render_boilerplates():
water_mol = list(pybel.readfile("xyz", "examples/water.xyz"))[0]
main(["-g", "examples/boilerplates/ADF.in"])
main(["examples/boilerplates/ADF.in", "examples/water.xyz"])
assert_equals(open("examples/water.in").read(), water_mol.write("adf"))
main(["-g", "examples/boilerplates/GAMESS.inp"])
main(["examples/boilerplates/GAMESS.inp", "examples/water.xyz"])
assert_equals(open("examples/water.inp").read(),
""" $CONTRL COORD=CART UNITS=ANGS $END
$DATA
PBE0-D3(BJ)/def2-TZVP @ ORCA 4.0.1.2
C1
O 8.0 0.0584027061 0.0584027059 0.0000000000
H 1.0 1.0096135406 -0.0680162466 0.0000000000
H 1.0 -0.0680162466 1.0096135407 0.0000000000
$END
""")
main(["-g", "examples/boilerplates/GAMESSUK.inp"])
main(["examples/boilerplates/GAMESSUK.inp", "examples/water.xyz"])
assert_equals(open("examples/water.inp").read(), water_mol.write("gukin"))
main(["-g", "examples/boilerplates/Gaussian.gjf"])
main(["examples/boilerplates/Gaussian.gjf", "examples/water.xyz"])
assert_equals(open("examples/water.gjf").read(),
"""#Put Keywords Here, check Charge and Multiplicity.
PBE0-D3(BJ)/def2-TZVP @ ORCA 4.0.1.2
0 1
O 0.05840 0.05840 0.00000
H 1.00961 -0.06802 0.00000
H -0.06802 1.00961 0.00000
""")
main(["-g", "examples/boilerplates/Jaguar.in"])
main(["examples/boilerplates/Jaguar.in", "examples/water.xyz"])
assert_equals(open("examples/water.in").read(), water_mol.write("jin"))
main(["-g", "examples/boilerplates/Molpro.inp"])
main(["examples/boilerplates/Molpro.inp", "examples/water.xyz"])
assert_equals(open("examples/water.inp").read(), water_mol.write("mp"))
main(["-g", "examples/boilerplates/MOPAC.mop"])
main(["examples/boilerplates/MOPAC.mop", "examples/water.xyz"])
assert_equals(open("examples/water.mop").read(),
"""CHARGE=0 MS=0.0
PBE0-D3(BJ)/def2-TZVP @ ORCA 4.0.1.2
O 0.05840 1 0.05840 1 0.00000 1
H 1.00961 1 -0.06802 1 0.00000 1
H -0.06802 1 1.00961 1 0.00000 1
""")
main(["-g", "examples/boilerplates/MPQC.in"])
main(["examples/boilerplates/MPQC.in", "examples/water.xyz"])
assert_equals(open("examples/water.in").read(), water_mol.write("mpqcin"))
main(["-g", "examples/boilerplates/NWChem.nw"])
main(["examples/boilerplates/NWChem.nw", "examples/water.xyz"])
assert_equals(open("examples/water.nw").read(), """start molecule
title PBE0-D3(BJ)/def2-TZVP @ ORCA 4.0.1.2
geometry units angstroms print xyz autosym
O 0.05840 0.05840 0.00000
H 1.00961 -0.06802 0.00000
H -0.06802 1.00961 0.00000
end
""")
main(["-g", "examples/boilerplates/ORCA.inp"])
main(["examples/boilerplates/ORCA.inp", "examples/water.xyz"])
assert_equals(open("examples/water.inp").read(),
"""# PBE0-D3(BJ)/def2-TZVP @ ORCA 4.0.1.2
! Opt
* xyz 0 1
O 0.05840 0.05840 0.00000
H 1.00961 -0.06802 0.00000
H -0.06802 1.00961 0.00000
*
""")
main(["-g", "examples/boilerplates/Psi.dat"])
main(["examples/boilerplates/Psi.dat", "examples/water.xyz"])
assert_equals(open("examples/water.dat").read(),
"""# PBE0-D3(BJ)/def2-TZVP @ ORCA 4.0.1.2
molecule {
0 1
O 0.05840 0.05840 0.00000
H 1.00961 -0.06802 0.00000
H -0.06802 1.00961 0.00000
units angstrom
}
optimize('scf')""")
main(["-g", "examples/boilerplates/QChem.in"])
main(["examples/boilerplates/QChem.in", "examples/water.xyz"])
assert_equals(open("examples/water.in").read(), water_mol.write("qcin"))
main(["-g", "examples/boilerplates/ZINDO.input"])
main(["examples/boilerplates/ZINDO.input", "examples/water.xyz"])
assert_equals(open("examples/water.input").read(), water_mol.write("zin"))
def test_example_eda_adf():
main(["examples/templates/EDA.ADF.in", "examples/water_dimer.xyz"])
assert_equals(open("examples/water_dimer_eda.in").read(),
"""TITLE examples/water_dimer.xyz
CHARGE 0 0
Number of atoms
6
ATOMS Cartesian
O 0.12908 -0.26336 0.64798 f=frag1
H 0.89795 0.28805 0.85518 f=frag1
H 0.10833 -0.20468 -0.33302 f=frag1
O 0.31020 0.07569 -2.07524 f=frag2
H -0.26065 0.64232 -2.62218 f=frag2
H 0.64083 -0.57862 -2.71449 f=frag2
End
Fragments
frag1 examples/water_dimer_frag1.t21
frag2 examples/water_dimer_frag2.t21
End
Basis
End
Geometry
End
""")
assert_equals(open("examples/water_dimer_frag1.in").read(),
"""TITLE frag1
CHARGE 0 0
Number of atoms
3
ATOMS Cartesian
O 0.12908 -0.26336 0.64798
H 0.89795 0.28805 0.85518
H 0.10833 -0.20468 -0.33302
End
Basis
End
Geometry
End
""")
assert_equals(open("examples/water_dimer_frag2.in").read(),
"""TITLE frag2
CHARGE 0 0
Number of atoms
3
ATOMS Cartesian
O 0.31020 0.07569 -2.07524
H -0.26065 0.64232 -2.62218
H 0.64083 -0.57862 -2.71449
End
Basis
End
Geometry
End
""")