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_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']