def test_find_missing_heavy_atoms():
fn = get_fn('2igd/2igd.pdb')
parm = pmd.load_file(fn)
parm2 = parm[':1-2&!@CB']
parm2.save("test.pdb", overwrite=True)
pdbfixer = AmberPDBFixer(parm2)
assert len(pdbfixer.find_missing_heavy_atoms()) == 2
assert 'CB' not in set(atom.name for atom in pdbfixer.parm.atoms)
def test_constructore_AmberPDBFixer():
fn = get_fn('4lzt/4lzt_h.pdb')
parm = pmd.load_file(fn)
fixer_0 = AmberPDBFixer(parm)
fixer_1 = AmberPDBFixer(fn)
assert len(fixer_0.parm.atoms) == len(fixer_1.parm.atoms)
def test_add_missing_atoms():
fname = get_fn('dna.pdb')
parm = pmd.load_file(fname)
parm = parm['!@H=']
assert len(parm['@H='].atoms) == 0
fixer = AmberPDBFixer(parm)
fixer.add_missing_atoms()
assert len(fixer.parm['@H='].atoms) > 0
def test_constph():
fn = get_fn('4lzt/4lzt_h.pdb')
parm = pmd.load_file(fn)
resnames_before = set(res.name for res in parm.residues)
pdbfixer = AmberPDBFixer(parm)
pdbfixer.constph()
resnames_after = set(res.name for res in pdbfixer.parm.residues)
assert sorted(resnames_after - resnames_before) == sorted(
{'HIP', 'AS4', 'GL4'})
def test_assign_histidine():
fn = get_fn('4lzt/4lzt_h.pdb')
parm = pmd.load_file(fn)
his_residues = [
res.name for res in parm.residues
if res.name in {'HIS', 'HIE', 'HID', 'HIP'}
]
assert his_residues == ['HIS']
pdbfixer = AmberPDBFixer(parm)
pdbfixer.assign_histidine()
his_residues = [
res.name for res in pdbfixer.parm.residues
if res.name in {'HIS', 'HIE', 'HID', 'HIP'}
]
assert his_residues == ['HID']
# Do not rename to HIS if this residue does not
# have hydrogen.
parm2 = pmd.Structure()
for resnum, resname in enumerate(['HIE', 'HID', 'HIS']):
atom = pmd.Atom(name='C', atomic_number=6)
parm2.add_atom(atom, resname, resnum=resnum, chain='A')
fixer2 = AmberPDBFixer(parm2)
fixer2.assign_histidine()
assert ['HIE', 'HID', 'HIS'] == [res.name for res in fixer2.parm.residues]
def test_packmol():
pdb_fh = get_fn('2igd/2igd.pdb')
parm = pmd.load_file(pdb_fh)
water = parm[':HOH'][':1']
parm.strip(':HOH')
pdbfixer = AmberPDBFixer(parm)
assert len([
res.name for res in pdbfixer.parm.residues
if res.name.startswith('HOH')
]) == 0
pdbfixer.pack(water, n_copies=100)
assert len([
res.name for res in pdbfixer.parm.residues
if res.name.startswith('HOH')
]) == 100
def test_assign_histidine():
fn = get_fn('4lzt/4lzt_h.pdb')
parm = pmd.load_file(fn)
his_residues = [
res.name for res in parm.residues
if res.name in {'HIS', 'HIE', 'HID', 'HIP'}
]
assert his_residues == ['HIS']
pdbfixer = AmberPDBFixer(parm)
pdbfixer.assign_histidine()
his_residues = [
res.name for res in pdbfixer.parm.residues
if res.name in {'HIS', 'HIE', 'HID', 'HIP'}
]
assert his_residues == ['HID']
def test_find_disulfide():
fn = get_fn('4lzt/4lzt_h.pdb')
parm = pmd.load_file(fn)
pdbfixer = AmberPDBFixer(parm)
cys_cys_set, _ = pdbfixer.find_disulfide()
assert sorted(cys_cys_set) == [(5, 126), (29, 114), (63, 79), (75, 93)]
one_cys_parm = parm[':CYS'][':1']
pdbfixer_2 = AmberPDBFixer(one_cys_parm)
assert not pdbfixer_2.find_disulfide()[0]
def test_mutate():
pdb_fh = get_fn('ala3_alpha.pdb')
parm = pmd.load_file(pdb_fh)
assert set(res.name for res in parm.residues) == {'ALA'}
pdbfixer = AmberPDBFixer(parm)
pdbfixer.mutate([
(1, 'ARG'),
])
pdbfixer.add_missing_atoms()
assert [res.name
for res in pdbfixer.parm.residues] == ['ALA', 'ARG', 'ALA']
assert ([
atom.name for atom in pdbfixer.parm.residues[1]
if atom.atomic_number == 6
] == ['CA', 'CB', 'CG', 'CD', 'CZ', 'C'])
def test_find_non_standard_resnames():
fn = get_fn('4lzt/4lzt_h.pdb')
parm = pmd.load_file(fn)
pdbfixer = AmberPDBFixer(parm)
assert pdbfixer.find_non_starndard_resnames() == {'NO3'}
def test_find_gaps_nogap():
pdb_fh = get_fn('2igd/2igd_4tleap_uc.pdb')
parm = pmd.load_file(pdb_fh)
pdbfixer = AmberPDBFixer(parm)
assert not pdbfixer.find_gaps()
def test_find_gaps():
pdb_fh = get_fn('2igd/2igd.pdb')
parm = pmd.load_file(pdb_fh)
parm_gap = parm[':1,3']
pdbfixer = AmberPDBFixer(parm_gap)
assert pdbfixer.find_gaps() == [(4.134579301452567, 'MET', 0, 'PRO', 1)]
def get_fixer(fname):
pdb_fh = get_fn(fname)
parm = pmd.load_file(pdb_fh)
return AmberPDBFixer(parm)