def test_from_string(self):
ans = """5
H4 C1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000"""
xyz = XYZ.from_string(ans)
mol = xyz.molecule
sp = ["C", "H", "H", "H", "H"]
for i, site in enumerate(mol):
self.assertEqual(site.species_string, sp[i])
self.assertEqual(len(site.coords), 3)
if i == 0:
self.assertTrue(all([c == 0 for c in site.coords]))
mol_str = """2
Random
C 2.39132145462 -0.700993488928 -7.22293142224e-06
C 1.16730636786 -1.38166622735 -2.77112970359e-06
"""
xyz = XYZ.from_string(mol_str)
mol = xyz.molecule
self.assertTrue(abs(mol[0].z) < 1e-5)
self.assertTrue(abs(mol[1].z) < 1e-5)
def test_from_string(self):
ans = """5
H4 C1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000"""
xyz = XYZ.from_string(ans)
mol = xyz.molecule
sp = ["C", "H", "H", "H", "H"]
for i, site in enumerate(mol):
self.assertEqual(site.species_string, sp[i])
self.assertEqual(len(site.coords), 3)
if i == 0:
self.assertTrue(all([c == 0 for c in site.coords]))
mol_str = """2
Random
C 2.39132145462 -0.700993488928 -7.22293142224e-06
C 1.16730636786 -1.38166622735 -2.77112970359e-06
"""
xyz = XYZ.from_string(mol_str)
mol = xyz.molecule
self.assertTrue(abs(mol[0].z) < 1e-5)
self.assertTrue(abs(mol[1].z) < 1e-5)
def test_from_string(self):
ans = """5
H4 C1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000"""
xyz = XYZ.from_string(ans)
mol = xyz.molecule
sp = ["C", "H", "H", "H", "H"]
for i, site in enumerate(mol):
self.assertEqual(site.species_string, sp[i])
self.assertEqual(len(site.coords), 3)
if i == 0:
self.assertTrue(all([c == 0 for c in site.coords]))
mol_str = """2
Random
C 2.39132145462 -0.700993488928 -7.22293142224e-06
C 1.16730636786 -1.38166622735 -2.77112970359e-06
"""
xyz = XYZ.from_string(mol_str)
mol = xyz.molecule
self.assertTrue(abs(mol[0].z) < 1e-5)
self.assertTrue(abs(mol[1].z) < 1e-5)
mol_str = """3
Random
C 0.000000000000E+00 2.232615992397E+01 0.000000000000E+00
C -2.383225420567E-31 1.116307996198E+01 1.933502166311E+01
C -4.440892098501D-01 -1.116307996198d+01 1.933502166311E+01
"""
xyz = XYZ.from_string(mol_str)
mol = xyz.molecule
self.assertAlmostEqual(mol[0].x, 0)
self.assertAlmostEqual(mol[1].y, 11.16307996198)
self.assertAlmostEqual(mol[2].x, -0.4440892098501)
self.assertAlmostEqual(mol[2].y, -11.16307996198)
# self.assertTrue(abs(mol[1].z) < 1e-5)
mol_str = """ 5
C32-C2-1
C 2.70450 1.16090 -0.14630 1 3 23 2
C 1.61930 1.72490 -0.79330 2 1 5 26
C 2.34210 1.02670 1.14620 3 1 8 6
C -0.68690 2.16170 -0.13790 4 5 18 7
C 0.67160 2.15830 0.14350 5 4 2 6
"""
xyz = XYZ.from_string(mol_str)
mol = xyz.molecule
self.assertAlmostEqual(mol[0].x, 2.70450)
self.assertAlmostEqual(mol[1].y, 1.72490)
self.assertAlmostEqual(mol[2].x, 2.34210)
self.assertAlmostEqual(mol[3].z, -0.13790)
def insert_solvents(coll):
names = """THF
monoglyme
Dimethylacetamide
propylene carbonate
ethylene carbonate
dimethylcarbonate
DMSO
ACN
Diethylcarbonate
propyl glyme
ethyl glyme
ethyl diglyme
diglyme
Butyldiglyme
tetraglyme
Pentaethylene glycol diethyl ether
Tetraethylene glycol diethyl ether
Tetraethylene glycol dibutyl ether
Butyldiglyme"""
for n in names.split("\n"):
response = requests.get(
"http://cactus.nci.nih.gov/chemical/structure/{}/file?format=xyz".
format(n))
if response.status_code == 200:
xyz = XYZ.from_string(response.text)
clean_mol = xyz.molecule
bb = BabelMolAdaptor(clean_mol)
pbmol = pb.Molecule(bb.openbabel_mol)
smiles = pbmol.write("smi").split()[0]
can = pbmol.write("can").split()[0]
inchi = pbmol.write("inchi")
svg = pbmol.write("svg")
d = {"molecule": clean_mol.as_dict()}
comp = clean_mol.composition
d["pretty_formula"] = comp.reduced_formula
d["formula"] = comp.formula
d["composition"] = comp.as_dict()
d["elements"] = list(comp.as_dict().keys())
d["nelements"] = len(comp)
d["charge"] = clean_mol.charge
d["spin_multiplicity"] = clean_mol.spin_multiplicity
d["smiles"] = smiles
d["can"] = can
d["inchi"] = inchi
# d["names"] = get_nih_names(smiles)
d["svg"] = svg
d["xyz"] = str(xyz)
d["tags"] = ["Solvents"]
coll.update(
{
"inchi": inchi,
"charge": clean_mol.charge,
"spin_multiplicity": clean_mol.spin_multiplicity
}, {"$set": d},
upsert=True)
else:
print("{} not found.\n".format(n))
def test_from_string(self):
ans = """5
H4 C1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000"""
xyz = XYZ.from_string(ans)
mol = xyz.molecule
sp = ["C", "H", "H", "H", "H"]
for i, site in enumerate(mol):
self.assertEqual(site.species_string, sp[i])
self.assertEqual(len(site.coords), 3)
if i == 0:
self.assertTrue(all([c == 0 for c in site.coords]))
mol_str = """2
Random
C 2.39132145462 -0.700993488928 -7.22293142224e-06
C 1.16730636786 -1.38166622735 -2.77112970359e-06
"""
xyz = XYZ.from_string(mol_str)
mol = xyz.molecule
self.assertTrue(abs(mol[0].z) < 1e-5)
self.assertTrue(abs(mol[1].z) < 1e-5)
mol_str = """3
Random
C 0.000000000000E+00 2.232615992397E+01 0.000000000000E+00
C -2.383225420567E-31 1.116307996198E+01 1.933502166311E+01
C -4.440892098501D-01 -1.116307996198d+01 1.933502166311E+01
"""
xyz = XYZ.from_string(mol_str)
mol = xyz.molecule
self.assertAlmostEqual(mol[0].x, 0)
self.assertAlmostEqual(mol[1].y, 11.16307996198)
self.assertAlmostEqual(mol[2].x, -0.4440892098501)
self.assertAlmostEqual(mol[2].y, -11.16307996198)
def set_struct_fromxyz(self, xyzstr):
self.xyz = xyzstr
self.struct = XYZ.from_string(xyzstr).molecule.as_dict()
self.boundary = "0d"