def test_set_name(fragment1_3heg_bax: Fragment):
name = '3HEG_BAX_frag1'
fragment1_3heg_bax.name = name
assert fragment1_3heg_bax.name == name
assert fragment1_3heg_bax.molecule.GetProp('_Name') == name
fragment1_3heg_bax.name = ''
def test_atom_names__when_fragment_is_part_ofligand(
fragment2_3heg_bax: Fragment):
names = set(fragment2_3heg_bax.atom_names())
expected = {
'C1', 'C13', 'C16', 'C17', 'C18', 'C19', 'C2', 'C20', 'C21', 'C23',
'C24', 'C25', 'C27', 'C28', 'C3', 'C4', 'C5', 'C6', 'C7', 'CL11',
'F10', 'F8', 'F9', 'N12', 'N14', 'N26', 'O15', 'O22'
}
assert names == expected
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_atom_names__when_fragment_is_whole_ligand(
fragment1_3heg_bax: Fragment):
names = fragment1_3heg_bax.atom_names()
expected = {
'C1',
'C13',
'C16',
'C17',
'C18',
'C19',
'C2',
'C20',
'C21',
'C23',
'C24',
'C25',
'C27',
'C28',
'C29',
'C3',
'C31',
'C4',
'C5',
'C6',
'C7',
'CL11',
'F10',
'F8',
'F9',
'N12',
'N14',
'N26',
'N30',
'O15',
'O22',
'O32',
}
assert set(names) == expected
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
def test_atom_names__of_small_fragment(fragment25_3heg_bax: Fragment):
names = set(fragment25_3heg_bax.atom_names())
expected = {'O32', 'N30', 'C29', 'C31'}
assert names == expected
def test_unprotonated_molecule(fragment1_3heg_bax: Fragment):
mol = fragment1_3heg_bax.unprotonated_molecule()
expected = 'CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(C(F)(F)F)c3)cc2)ccn1'
assert MolToSmiles(mol) == expected
def test_smiles(fragment1_3heg_bax: Fragment):
mol = fragment1_3heg_bax.smiles()
expected = '[H]c1nc(C(=O)N([H])C([H])([H])[H])c([H])c(Oc2c([H])c([H])c(N([H])C(=O)N([H])c3c([H])c([H])c(Cl)c(C(F)' \
'(F)F)c3[H])c([H])c2[H])c1[H]'
assert mol == expected
def test_hash_code__when_fragment_is_not_ligand(fragment2_3heg_bax: Fragment):
hash_code = fragment2_3heg_bax.hash_code()
expected_hash_code = '88d5b594a6326908206691a497bdbe19'
assert hash_code == expected_hash_code
def test_hash_code__when_fragment_is_ligand(fragment1_3heg_bax: Fragment):
hash_code = fragment1_3heg_bax.hash_code()
expected_hash_code = '51980afadf63a7e7c8e95ba4f5e412ee'
assert hash_code == expected_hash_code
def test_nr_r_groups(fragment2_3heg_bax: Fragment):
nr = fragment2_3heg_bax.nr_r_groups()
assert nr == 1