def test_init(self):
"""Test initialising MoleculeNamer."""
mn = MoleculeNamer()
self.assertTrue(mn)
mn = MoleculeNamer(use_online_pubchem=False)
self.assertTrue(mn)
def test_get_name_from_molecule_graph(self):
"""Test getting a molecule name from the molecule graph."""
mn = MoleculeNamer()
name = mn.get_name_from_molecule_graph(self.methylammonium)
self.assertEqual(name, "methylammonium")
# test iupac naming source
mn = MoleculeNamer(name_preference=("iupac", ))
name = mn.get_name_from_molecule_graph(self.methylammonium)
self.assertEqual(name, "methylazanium")
def _condense_components(
self,
components: List[Component],
spacegroup_analyzer: SpacegroupAnalyzer,
site_analyzer: SiteAnalyzer,
) -> Tuple[Dict[int, Any], List[int]]:
"""Condenses the component data.
Args:
components: A list of structure components, generated using
:obj:`pymatgen.analysis.dimensionality.get_structure_components`
site_analyzer: A site analyzer object for the structure containing
the components.
spacegroup_analyzer: A space group analyzer object for the structure
containing the components.
Returns:
The condensed component data and the component makeup of the
structure. The condensed components have the form::
{
0: {
'formula': 'MoS2',
'sites': [0, 2]
'dimensionality': 2,
'molecule_name': None,
'orientation': (0, 0, 1)
}
}
Where the ``0`` key is the component identifier. The ``sites``
key gives a :obj:`list` of the indexes of the inequivalent sites
in the structure. If the component is zero-dimensional and
is a known molecule, the ``molecule_name`` key will be a :obj:`str`
with the molecule name. The ``orientation`` key is the miller
index (for two-dimensional components) or direction of propagation
(for one-dimensional components).
"""
if self.use_symmetry_equivalent_sites:
inequiv_components = get_sym_inequiv_components(
components, spacegroup_analyzer)
else:
inequiv_components = get_structure_inequiv_components(components)
molecule_namer = MoleculeNamer()
components = {}
component_makeup = []
for i, component in enumerate(inequiv_components):
formula = get_component_formula(
component,
use_iupac_formula=self.use_iupac_formula,
use_common_formulas=self.use_common_formulas,
)
sites = site_analyzer.get_inequivalent_site_indices(
component["site_ids"])
if component["dimensionality"] == 0:
molecule_name = molecule_namer.get_name_from_molecule_graph(
component["molecule_graph"])
else:
molecule_name = None
components[i] = {
"formula": formula,
"dimensionality": component["dimensionality"],
"orientation": component["orientation"],
"molecule_name": molecule_name,
"sites": sites,
}
component_makeup.extend([i] * component["count"])
return components, component_makeup
def test_get_name_from_pubchem(self):
"""Test downloading the molecule name from Pubchem."""
mn = MoleculeNamer()
name = mn.get_name_from_pubchem("C[NH3]")
self.assertEqual(name, "methylammonium")
def test_molecule_graph_to_smiles(self):
"""Test converting a molecule graph to SMILES string."""
smiles = MoleculeNamer.molecule_graph_to_smiles(self.methylammonium)
self.assertEqual(smiles, "C[NH3]")