def test_residue_iter(array):
centroid = [
struc.centroid(res).tolist() for res in struc.residue_iter(array)
]
ref_centroid = struc.apply_residue_wise(array,
array.coord,
np.average,
axis=0)
assert centroid == ref_centroid.tolist()
def test_coarse_grained(pdb_id):
# Multi atom SASA (ProtOr), compare with single atom SASA
# on residue level
file = mmtf.MMTFFile.read(join(data_dir("structure"), pdb_id + ".mmtf"))
array = mmtf.get_structure(file, model=1)
array = array[struc.filter_amino_acids(array)]
sasa = struc.apply_residue_wise(array, struc.sasa(array,
vdw_radii="ProtOr"),
np.nansum)
sasa_exp = struc.apply_residue_wise(array,
struc.sasa(array, vdw_radii="Single"),
np.nansum)
# Assert that more than 90% of atoms
# have less than 10% SASA difference
assert np.count_nonzero(np.isclose(sasa, sasa_exp, rtol=1e-1,
atol=1)) / len(sasa) > 0.9
# Assert that more than 98% of atoms
# have less than 40% SASA difference
assert np.count_nonzero(np.isclose(sasa, sasa_exp, rtol=4e-1,
atol=1)) / len(sasa) > 0.98
def test_apply_residue_wise(array):
data = struc.apply_residue_wise(array, np.ones(len(array)), np.sum)
assert data.tolist() == [
len(array[array.res_id == i]) for i in range(1, 21)
]
# Besides other parameters, you can choose between different
# Van-der-Waals radii sets:
# *Prot0r*, the default set, is a set that defines radii for
# non-hydrogen atoms, but determines the radius of an atom based on the
# assumed amount of hydrogen atoms connected to it.
# Therefore, *ProtOr* is suitable for structures with missing hydrogen
# atoms, like crystal structures.
# Since the structure of *TC5b* was elucidated via NMR, we can assign a
# radius to every single atom (including hydrogens), hence we use the
# *Single* set.
array = strucio.load_structure(file_path)[0]
# The following line calculates the atom-wise SASA of the atom array
atom_sasa = struc.sasa(array, vdw_radii="Single")
# Sum up SASA for each residue in atom array
res_sasa = struc.apply_residue_wise(array, atom_sasa, np.sum)
# Again plotting stuff
plt.plot(np.arange(1, 21), res_sasa)
plt.xlim(0, 20)
plt.xticks(np.arange(1, 21))
plt.xlabel("Residue")
plt.ylabel("SASA")
plt.show()
########################################################################
# Secondary structure determination
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
#
# *Biotite* can also be used to assign
# *secondary structure elements* (SSE) to a structure with the
# :func:`annotate_sse()` function.
