def lig(config, inp: str, center: int, out: click.File):
"""Get all substructures (or ligands) that are bound to the center atom."""
# setup reference molecular structure
ref = ksr.constructMolecule(geometry=inp, out=out)
nat = ref.get_number_of_atoms()
# get all covalent bonding partner in reference complex
covbonds = config.context.invoke(bonds, inp=inp)
from kallisto.rmsd import recursiveGetSubstructures
silentPrinter(config.silent,
"Write out substructures for {}".format(center), out)
substructures = recursiveGetSubstructures(nat, covbonds, center)
k = 0
for path in substructures:
silentPrinter(
config.silent,
"Substructure {}: {}".format(k, path),
out,
)
k += 1
def test_lig_neopentane():
center = 0
mol = neopentane()
nat = mol.get_number_of_atoms()
bonds = mol.get_bonds()
substructures = recursiveGetSubstructures(nat, bonds,
center) # type: ignore
assert 1 in substructures[0]
assert 6 in substructures[0]
assert 8 in substructures[0]
assert 12 in substructures[0]
center = 1
substructures = recursiveGetSubstructures(nat, bonds,
center) # type: ignore
assert 6 in substructures[1]
assert 8 in substructures[2]
assert 12 in substructures[3]