def test_replace_pattern_in_structure__in_uio66_replacing_linker_with_linker_does_not_change_positions():
with Path("tests/uio66/uio66.cif") as path:
structure = Atoms.load_cif(path)
with Path("tests/uio66/uio66-linker.cif") as path:
search_pattern = Atoms.load_cif(path)
with Path("tests/uio66/uio66-linker-fluorinated.cif") as path:
replace_pattern = Atoms.load_cif(path)
final_structure = replace_pattern_in_structure(structure, search_pattern, replace_pattern)
assert Counter(final_structure.elements) == {'C': 192, 'O': 120, 'F': 96, 'Zr': 24}
def test_atoms_load_cif__loads_elements():
with Path("tests/uio66/uio66-linker.cif").open() as fd:
atoms = Atoms.load_cif(fd)
assert atoms.elements == [
"C", "O", "O", "C", "C", "H", "H", "C", "C", "C", "C", "H", "H", "O",
"C", "O"
]
def hkust1_cif():
with Path("tests/hkust-1/hkust-1-with-bonds.cif") as path:
yield Atoms.load_cif(path)
def hkust1_3x3x3_cif():
with Path("tests/hkust-1/hkust-1-3x3x3.cif") as path:
yield Atoms.load_cif(path)
"""
Run and visualize with:
python -m cProfile -o hkustperf.pstats -s tottime hkustperf.py
snakeviz hkustperf.pstats
"""
import ase
import ase.io
import numpy as np
from mofun import find_pattern_in_structure, replace_pattern_in_structure, Atoms
hkust1_cif = Atoms.load_cif("../tests/hkust-1/hkust-1-with-bonds.cif")
benzene = Atoms.from_ase_atoms(ase.io.read("../tests/molecules/benzene.xyz"))
hkust1_repped = hkust1_cif.replicate(repldims=(3, 3, 3))
match_indices = find_pattern_in_structure(hkust1_repped, benzene)
