def test_mol_from_compound(self, value, identifier_type, expected):
compound = reaction_pb2.Compound()
compound.identifiers.add(value=value, type=identifier_type)
mol = message_helpers.mol_from_compound(compound)
self.assertEqual(Chem.MolToSmiles(mol), expected)
mol, identifier = message_helpers.mol_from_compound(
compound, return_identifier=True)
self.assertEqual(Chem.MolToSmiles(mol), expected)
self.assertEqual(identifier, compound.identifiers[0])
def _compound_svg(compound: reaction_pb2.Compound,
bond_length: int = 25) -> str:
"""Returns an SVG string for the given compound.
If the compound does not have a structural identifier, a sentinel value
is returned instead.
Args:
compound: Compound message.
bond_length: Bond length in pixels.
Returns:
String SVG or sentinel value.
"""
try:
mol = message_helpers.mol_from_compound(compound)
if mol:
svg = drawing.mol_to_svg(mol, bond_length=bond_length)
if svg is None:
return message_helpers.get_compound_smiles(
compound) or "[Compound]"
return svg
except ValueError:
pass
return message_helpers.get_compound_smiles(compound) or "[Compound]"
def render_compound():
"""Returns an HTML-tagged SVG for the given Compound."""
compound = reaction_pb2.Compound()
compound.ParseFromString(flask.request.get_data())
try:
mol = message_helpers.mol_from_compound(compound)
return flask.jsonify(drawing.mol_to_svg(mol))
except ValueError:
return ''
def _compound_png(compound):
"""Returns a PNG string for the given compound.
If the compound does not have a structural identifier, a sentinel value
is returned instead.
Args:
compound: Compound message.
Returns:
String PNG or sentinel value.
"""
try:
mol = message_helpers.mol_from_compound(compound)
if mol:
return drawing.mol_to_png(mol)
except ValueError:
pass
return '[Compound]'
def test_mol_from_compound_failures(self, value, identifier_type):
compound = reaction_pb2.Compound()
compound.identifiers.add(value=value, type=identifier_type)
with self.assertRaisesRegex(ValueError,
'invalid structural identifier'):
message_helpers.mol_from_compound(compound)