def test_site__fragment2_3heg_bax(fragment2_3heg_bax: Fragment):
site = fragment2_3heg_bax.site()
site_ligand = site.ligand()
assert len(site_ligand.atoms()) == 28
assert site_ligand.name() == 'fragment of BAX'
seq_nrs = seq_nrs_of_site(site)
expected = {
30, 35, 36, 38, 51, 53, 55, 70, 71, 74, 75, 78, 83, 84, 86, 104, 106,
107, 108, 109, 110, 138, 140, 141, 146, 147, 148, 149, 151, 155, 157,
166, 167, 168, 169
}
assert expected == seq_nrs
def test_site__fragment1_3heg_bax(fragment1_3heg_bax: Fragment):
site = fragment1_3heg_bax.site()
seq_nrs = seq_nrs_of_site(site)
"""Expected seq nrs was calculated using Yasara script::
LoadPDB tests/fixtures/3HEG.prepped.pdb,Center=No,Correct=No
DelRes HOH
DelRes protein with distance > 6 from bax
DelRes BAX
SavePDB 1,tests/fixtures/3heg_BAX_frag1.prepped.site.pdb,Format=PDB,Transform=No
and the Python snippet::
from atomium.files import pdb_from_file
p = pdb_from_file('3heg_BAX_frag1.prepped.site.pdb').model()
seq_nrs = sorted([int(r.residue_id().replace('A', '')) for r in p.residues()])
"""
expected = {
30, 35, 36, 38, 40, 51, 53, 55, 70, 71, 74, 75, 78, 83, 84, 86, 104,
106, 107, 108, 109, 110, 111, 138, 140, 141, 146, 147, 148, 149, 151,
155, 157, 166, 167, 168, 169
}
assert expected == seq_nrs