def condense_structure(self, structure: Structure) -> Dict[str, Any]:
"""Condenses the structure into an intermediate dict representation.
Args:
structure: A pymatgen structure object.
Returns:
The condensed structure information. The data is formatted as a
:obj:`dict` with a fixed set of keys. An up-to-date example of the,
the condensed representation of MoS2 given in the documentation.
See: ``robocrystallographer/docs_rst/source/format.rst`` or
https://hackingmaterials.lbl.gov/robocrystallographer/format.html
"""
# sort so we can give proper symmetry labels
structure = structure.get_sorted_structure()
# wrap all site coords into unit cell
structure.translate_sites(range(structure.num_sites), [1, 1, 1])
sga = SpacegroupAnalyzer(structure, symprec=self.symprec)
if self.use_conventional_cell:
structure = sga.get_conventional_standard_structure()
else:
structure = sga.get_symmetrized_structure()
bonded_structure = self.near_neighbors.get_bonded_structure(structure)
components = get_structure_components(
bonded_structure,
inc_orientation=True,
inc_site_ids=True,
inc_molecule_graph=True,
)
dimensionality = max(c["dimensionality"] for c in components)
mineral = self._condense_mineral(structure, components)
formula = self._condense_formula(structure, components)
structure_data = {
"formula": formula,
"spg_symbol": sga.get_space_group_symbol(),
"crystal_system": sga.get_crystal_system(),
"mineral": mineral,
"dimensionality": dimensionality,
}
site_analyzer = SiteAnalyzer(
bonded_structure,
symprec=self.symprec,
use_symmetry_equivalent_sites=self.use_symmetry_equivalent_sites,
)
structure_data["sites"] = site_analyzer.get_all_site_summaries()
structure_data[
"distances"] = site_analyzer.get_all_bond_distance_summaries()
structure_data[
"angles"] = site_analyzer.get_all_connectivity_angle_summaries()
structure_data[
"nnn_distances"] = site_analyzer.get_all_nnn_distance_summaries()
component_summary, component_makeup = self._condense_components(
components, sga, site_analyzer)
structure_data["components"] = component_summary
structure_data["component_makeup"] = component_makeup
if components_are_vdw_heterostructure(components):
hs_info = get_vdw_heterostructure_information(
components,
use_iupac_formula=self.use_iupac_formula,
use_common_formulas=self.use_common_formulas,
)
else:
hs_info = None
structure_data["vdw_heterostructure_info"] = hs_info
return structure_data
def test_get_all_nnn_distance_summaries(self):
sa = SiteAnalyzer(self.tin_dioxide)
data = sa.get_all_nnn_distance_summaries()
self.assertEqual(len(data[0][0]['corner']), 8)
self.assertEqual(len(data[0][0]['edge']), 2)
self.assertAlmostEqual(data[0][0]['edge'][0], 3.24322132)
