def test_makeopenbabel(self):
import openbabel
atomnos = numpy.array([1, 8, 1], "i")
atomcoords = numpy.array([[[-1., 1., 0.], [0., 0., 0.], [1., 1., 0.]]])
obmol = cclib2openbabel.makeopenbabel(atomcoords, atomnos)
obconversion = openbabel.OBConversion()
formatok = obconversion.SetOutFormat("inchi")
assert obconversion.WriteString(obmol).strip() == "InChI=1S/H2O/h1H2"
def test_makeopenbabel_and_makecclib(self):
"""Ensure that makeopenbabel and makecclib are inverse of each other"""
atomnos = numpy.array([1, 8, 1], "i")
atomcoords = numpy.array([[[-1., 1., 0.], [0., 0., 0.], [1., 1., 0.]]])
# makecclib(makeopenbabel(...))
obmol = cclib2openbabel.makeopenbabel(atomcoords, atomnos)
data = cclib2openbabel.makecclib(obmol)
numpy.testing.assert_allclose(data.atomcoords, atomcoords)
numpy.testing.assert_allclose(data.atomnos, atomnos)
# makeopenbabel(makecclib(...))
obmol = cclib2openbabel.makeopenbabel(data.atomcoords, data.atomnos)
data = cclib2openbabel.makecclib(
obmol) # this line is just to make the test easier
numpy.testing.assert_allclose(data.atomcoords, atomcoords)
numpy.testing.assert_allclose(data.atomnos, atomnos)
def test_makeopenbabel(self):
import openbabel
atomnos = numpy.array([1, 8, 1], "i")
atomcoords = numpy.array([[[-1., 1., 0.], [0., 0., 0.], [1., 1., 0.]]])
obmol = cclib2openbabel.makeopenbabel(atomcoords, atomnos)
obconversion = openbabel.OBConversion()
formatok = obconversion.SetOutFormat("inchi")
assert obconversion.WriteString(obmol).strip() == "InChI=1S/H2O/h1H2"
def get_InChI(attr):
try:
params = {
"atomcoords": np.asarray(attr["atomcoords"]),
"atomnos": attr["atomnos"],
"charge": attr["charge"],
"mult": attr["mult"]
}
mol = makeopenbabel(**params)
obconversion = ob.OBConversion()
obconversion.SetOutFormat("inchi")
ob.obErrorLog.StopLogging()
inchi = obconversion.WriteString(mol).strip()
if inchi.startswith("InChI="):
inchi = inchi.replace("InChI=", "")
return inchi
except:
return None
def generate_svg(res, inserted_id):
dir_path = "flaskapp/static/svg/"
if not os.path.isdir(dir_path):
os.mkdir(dir_path)
try:
params = {
"atomcoords": np.asarray(res["atomcoords"]),
"atomnos": np.asarray(res["atomnos"]),
"charge": res["charge"],
"mult": res["mult"]
}
except:
pass
try:
# Save the SVG file with filename same as mongodb document id
file_path = dir_path + inserted_id + ".svg"
print("Creating SVG : " + file_path)
mol = makeopenbabel(**params)
obconversion = ob.OBConversion()
obconversion.SetOutFormat("svg")
ob.obErrorLog.StopLogging()
obconversion.WriteFile(mol, file_path)
except:
pass