def test_scaled_cell_consistency(structure):
"""Test scaled_cell's PDB-designated validation: inverse of det(SCALE) = Volume of cell"""
# Manual calculation of volume = |a_1 . (a_2 x a_3)|
a_1 = structure.lattice_vectors[0]
a_2 = structure.lattice_vectors[1]
a_3 = structure.lattice_vectors[2]
a_mid_0 = a_2[1] * a_3[2] - a_2[2] * a_3[1]
a_mid_1 = a_2[2] * a_3[0] - a_2[0] * a_3[2]
a_mid_2 = a_2[0] * a_3[1] - a_2[1] * a_3[0]
volume_from_cellpar = abs(a_1[0] * a_mid_0 + a_1[1] * a_mid_1 + a_1[2] * a_mid_2)
scale = scaled_cell(structure.lattice_vectors)
volume_from_scale = 1 / numpy.linalg.det(scale)
assert volume_from_scale == pytest.approx(volume_from_cellpar)
def test_scaled_cell_and_fractional_coordinates(structures):
"""Make sure these two different calculations arrive at the same result"""
for structure in structures:
scale = scaled_cell(structure.lattice_vectors)
scale = numpy.asarray(scale)
cartesian_positions = numpy.asarray(structure.cartesian_site_positions)
scaled_fractional_positions = (scale.T @ cartesian_positions.T).T
for i in range(3):
scaled_fractional_positions[:, i] %= 1.0
scaled_fractional_positions[:, i] %= 1.0
scaled_fractional_positions = [
tuple(position) for position in scaled_fractional_positions
]
calculated_fractional_positions = fractional_coordinates(
cell=structure.lattice_vectors,
cartesian_positions=structure.cartesian_site_positions,
)
for scaled_position, calculated_position in zip(
scaled_fractional_positions, calculated_fractional_positions):
assert scaled_position == pytest.approx(calculated_position)
def get_pdb( # pylint: disable=too-many-locals
optimade_structure: OptimadeStructure, ) -> str:
""" Write Protein Data Bank (PDB) structure in the old PDB format from OPTIMADE structure
Inspired by `ase.io.proteindatabank.write_proteindatabank()` in the ASE package.
:param optimade_structure: OPTIMADE structure
:return: str
"""
if globals().get("np", None) is None:
warn(NUMPY_NOT_FOUND)
return None
pdb = ""
attributes = optimade_structure.attributes
rotation = None
if all(attributes.dimension_types):
currentcell = np.asarray(attributes.lattice_vectors)
cellpar = cell_to_cellpar(currentcell)
exportedcell = cellpar_to_cell(cellpar)
rotation = np.linalg.solve(currentcell, exportedcell)
# Setting Z-value = 1 and using P1 since we have all atoms defined explicitly
Z = 1
spacegroup = "P 1"
pdb += (
f"CRYST1{cellpar[0]:9.3f}{cellpar[1]:9.3f}{cellpar[2]:8.3f}"
f"{cellpar[3]:7.2f}{cellpar[4]:7.2f}{cellpar[5]:7.2f} {spacegroup:11s}{Z:4d}\n"
)
for i, vector in enumerate(scaled_cell(currentcell)):
pdb += f"SCALE{i + 1} {vector[0]:10.6f}{vector[1]:10.6f}{vector[2]:10.6f} {0:10.5f}\n"
# There is a limit of 5 digit numbers in this field.
pdb_maxnum = 100000
bfactor = 1.0
pdb += "MODEL 1\n"
species: Dict[str, OptimadeStructureSpecies] = {
species.name: species
for species in attributes.species
}
cartesian_site_positions, _ = pad_positions(
attributes.cartesian_site_positions)
sites = np.asarray(cartesian_site_positions)
if rotation is not None:
sites = sites.dot(rotation)
for site_number in range(attributes.nsites):
species_name = attributes.species_at_sites[site_number]
site = sites[site_number]
current_species = species[species_name]
for index, symbol in enumerate(current_species.chemical_symbols):
if symbol == "vacancy":
continue
label = species_name
if len(current_species.chemical_symbols) > 1:
if ("vacancy" in current_species.chemical_symbols
and len(current_species.chemical_symbols) == 2):
pass
else:
label = f"{symbol}{index + 1}"
pdb += (
f"ATOM {site_number % pdb_maxnum:5d} {label:4} MOL 1 "
f"{site[0]:8.3f}{site[1]:8.3f}{site[2]:8.3f}"
f"{current_species.concentration[index]:6.2f}"
f"{bfactor:6.2f} {symbol.upper():2} \n")
pdb += "ENDMDL\n"
return pdb