def test_write_conect():
pdb_out = 'out.pdb'
pdb_fn = get_fn('1dwc.pdb')
command = ['-i', pdb_fn, '-o', pdb_out]
with tempfolder():
pdb4amber.main(command)
with open(pdb_out) as fh:
assert 'ATOM 1196 SG CYX H 148 55.729 28.382 19.687 1.00 10.07' in fh.read()
def test_strip_atoms():
pdb_fn = get_fn('2igd/2igd.cif')
pdb_out = 'out.pdb'
command = ['-i', pdb_fn, '-o', pdb_out, '--strip', ':3-500']
with tempfolder():
pdb4amber.main(command)
parm = pmd.load_file(pdb_out)
assert len(parm.residues) == 2
def test_keep_all_model():
orig_parm = pmd.download_PDB('1l2y')
pdb_out = 'out.pdb'
# default
with tempfolder():
pdb4amber.main(['1l2y', '--pdbid', '-o', pdb_out, '--model', '-1'])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (38, 304, 3)
def test_constantph():
option = '--constantph'
pdb_out = 'out.pdb'
command = ['-i', pdb_fn, '-o', pdb_out, option]
with tempfolder():
# just run to increase code coverage
# we already test in another file
pdb4amber.main(command)
def test_reduce_with_cif_input():
option = '--reduce'
pdb_fn = get_fn('2igd/2igd.cif')
pdb_out = 'out.pdb'
command = ['-i', pdb_fn, '-o', pdb_out, option]
with tempfolder():
pdb4amber.main(command)
parm = pmd.load_file(pdb_out)
atom_names = set(atom.name for atom in parm.atoms
if atom.atomic_number == 1)
assert atom_names
def test_noh(tmpdir):
inp_pdb = get_fn('nmr_struc_1.pdb')
with tmpdir.as_cwd():
parm_with_h = pmd.load_file(inp_pdb)
assert len(parm_with_h.atoms) == 304
assert len([
atom for atom in parm_with_h.atoms if atom.atomic_number == 1
]) == 150
pdb4amber.main([inp_pdb, '-y', '-o', 'out.pdb'])
parm = pmd.load_file('out.pdb')
assert not [atom for atom in parm.atoms if atom.atomic_number == 1]
assert len(parm.atoms) == 154
def test_write_sslink():
pdb_out = 'out.pdb'
pdb_fn = get_fn('4lzt/4lzt_h.pdb')
command = ['-i', pdb_fn, '-o', pdb_out]
sslink_name = 'out_sslink'
sslink_pair = [(6, 127), (30, 115), (64, 80), (76, 94)]
with tempfolder():
pdb4amber.main(command)
with open(sslink_name) as fh:
for index, line in enumerate(fh):
id0, idx1 = [int(i) for i in line.split()]
assert (id0, idx1) == sslink_pair[index]
def test_fetch_pdbid(tmpdir):
''' e.g: pdb4amber 1l2y --pdbid '''
pdb_fn = '1l2y'
with tmpdir.as_cwd():
with patch('parmed.download_PDB') as mock_download:
def effect(*args):
return pmd.load_file(get_fn('1l2y.pdb'))
mock_download.side_effect = effect
pdb4amber.main(['1l2y', '--pdbid', '-o', 'out.pdb'])
assert mock_download.called
def test_writing_renum():
pdb_fn = get_fn('2igd/2igd_2_residues.pdb')
pdb_out = 'out.pdb'
command = [pdb_fn]
expected_lines = """
MET 1 MET 1
PRO 3 PRO 2
""".strip().split('\n')
with tempfolder():
pdb4amber.main(command)
with open('stdout_renum.txt') as fh:
output_lines = [line.strip() for line in fh.readlines()]
assert expected_lines == output_lines
def test_write_model():
fname = get_fn('1l2y.pdb')
orig_parm = pmd.load_file(fname)
pdb_out = 'out.pdb'
# default
with tempfolder():
pdb4amber.main([fname, '-o', pdb_out])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (1, 304, 3)
# model 1
with tempfolder():
pdb4amber.main([fname, '-o', pdb_out, '--model', '1'])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (1, 304, 3)
np.testing.assert_almost_equal(parm.coordinates,
orig_parm.get_coordinates()[0])
# model 2
model = 2
with tempfolder():
pdb4amber.main([fname, '-o', pdb_out, '--model', str(model)])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (1, 304, 3)
np.testing.assert_almost_equal(parm.coordinates,
orig_parm.get_coordinates()[model - 1])
# keep all models
with tempfolder():
pdb_out = 'out.pdb'
pdb4amber.main([fname, '-o', pdb_out, '--model', '-1'])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (38, 304, 3)
def test_amber_compatible_residues(tmpdir):
option = '--amber-compatible-residues'
pdb_in = get_fn('3orn.pdb')
pdb_out = 'out.pdb'
command = ['-i', pdb_in, '-o', pdb_out, option]
with tmpdir.as_cwd():
pdb4amber.main(command)
parm = pmd.load_file(pdb_out)
res_names = set(res.name for res in parm.residues)
assert res_names == {
'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS',
'HOH', 'ILE', 'LEU', 'LYS', 'MET', 'MG', 'PHE', 'PRO', 'SER',
'THR', 'TRP', 'TYR', 'VAL'
}
def test_prot_only():
option = '--pro'
pdb_out = 'out.pdb'
command = ['-i', pdb_fn, '-o', pdb_out, option]
with tempfolder():
orig_parm = pmd.load_file(pdb_fn)
res_names = set(res.name for res in orig_parm.residues)
assert 'NO3' in res_names
assert 'HOH' in res_names
pdb4amber.main(command)
parm = pmd.load_file(pdb_out)
res_names = set(res.name for res in parm.residues)
assert 'NO3' not in res_names
assert 'HOH' not in res_names
def test_no_hydrogen():
option = '--nohyd'
pdb_out = 'out.pdb'
command = ['-i', pdb_fn, '-o', pdb_out, option]
with tempfolder():
orig_parm = pmd.load_file(pdb_fn)
atom_names = set(atom.name for atom in orig_parm.atoms
if atom.atomic_number == 1)
assert atom_names
pdb4amber.main(command)
parm = pmd.load_file(pdb_out)
atom_names = set(atom.name for atom in parm.atoms
if atom.atomic_number == 1)
assert not atom_names
def test_not_write_sslink_conect_record():
pdb_out = 'out.pdb'
pdb_fn = get_fn('4lzt/4lzt_h.pdb')
sslink_name = 'out_sslink'
# has conect
with tempfolder():
command = ['-i', pdb_fn, '-o', pdb_out]
pdb4amber.main(command)
with open(pdb_out) as fh:
assert 'CONECT' in fh.read()
# no conect
with tempfolder():
command = ['-i', pdb_fn, '-o', pdb_out, '--no-conect']
pdb4amber.main(command)
with open(pdb_out) as fh:
assert 'CONECT' not in fh.read()
def test_dry():
option = '--dry'
pdb_out = 'out.pdb'
command = ['-i', pdb_fn, '-o', pdb_out, option]
with tempfolder():
orig_parm = pmd.load_file(pdb_fn)
resnames = set(res.name for res in orig_parm.residues)
assert resnames.intersection(WATER_NAMES)
pdb4amber.main(command)
parm = pmd.load_file(pdb_out)
resnames = set(res.name for res in parm.residues)
assert not resnames.intersection(WATER_NAMES)
# water
water_parm = pmd.load_file('out_water.pdb')
assert set(res.name for res in water_parm.residues) == {'HOH'}
def test_write_model():
orig_parm = pmd.download_PDB('1l2y')
pdb_out = 'out.pdb'
# default
with tempfolder():
pdb4amber.main(['1l2y', '--pdbid', '-o', pdb_out])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (1, 304, 3)
# model 1
with tempfolder():
pdb4amber.main(['1l2y', '--pdbid', '-o', pdb_out, '--model', '1'])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (1, 304, 3)
np.testing.assert_almost_equal(parm.coordinates,
orig_parm.get_coordinates()[0])
# model 2
model = 2
with tempfolder():
pdb4amber.main(['1l2y', '--pdbid', '-o', pdb_out, '--model',
str(model)
])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (1, 304, 3)
np.testing.assert_almost_equal(parm.coordinates,
orig_parm.get_coordinates()[model - 1])
