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_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])
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_write_other_formats_like_mol2():
# mol2
pdb_out = 'out.mol2'
command = ['pdb4amber', '-i', pdb_fn, '-o', pdb_out]
with tempfolder():
subprocess.check_call(command)
with open(pdb_out) as fh:
assert fh.read().startswith('@<TRIPOS>MOLECULE')
def test_run_with_filename_log():
# default
logfile = 'pdb4amber.log'
with tempfolder():
run(arg_pdbout='out.pdb', arg_pdbin=get_fn('4lzt/4lzt_h.pdb'))
with open(logfile) as fh:
assert 'Summary of pdb4amber' in fh.read()
# given name
logfile = 'hello.log'
with tempfolder():
run(
arg_pdbout='out.pdb',
arg_pdbin=get_fn('4lzt/4lzt_h.pdb'),
arg_logfile=logfile)
with open(logfile) as fh:
assert 'Summary of pdb4amber' 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_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_run_with_StringIO_log():
stringio_file = StringIO()
with tempfolder():
run(
arg_pdbout='out.pdb',
arg_pdbin=get_fn('4lzt/4lzt_h.pdb'),
arg_logfile=stringio_file)
stringio_file.seek(0)
assert 'Summary of pdb4amber' in stringio_file.read()
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_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_run_with_stderr_stdout_log():
# dummy
with tempfolder():
subprocess.check_call([
'pdb4amber',
get_fn('4lzt/4lzt_h.pdb'),
'-o',
'out.pdb',
'--logfile=stderr',
])
with tempfolder():
subprocess.check_call([
'pdb4amber',
get_fn('4lzt/4lzt_h.pdb'),
'-o',
'out.pdb',
'--logfile=stdout',
])
def test_fetch_pdbid():
''' e.g: pdb4amber 1l2y --pdbid '''
pdb_fn = '1l2y'
command = ['pdb4amber', pdb_fn, '--pdbid']
with tempfolder():
output = subprocess.check_output(command).decode()
input_pdb = StringIO(output)
input_pdb.seek(0)
parm = pmd.read_PDB(input_pdb)
assert len(parm.atoms) == 304
def test_fetch_pdbid_and_use_reduce():
''' e.g: pdb4amber 1tsu --pdbid --reduce'''
pdb_fn = '1tsu'
command = ['pdb4amber', pdb_fn, '--pdbid', '--reduce']
with tempfolder():
output = subprocess.check_output(command).decode()
input_pdb = StringIO(output)
input_pdb.seek(0)
parm = pmd.read_PDB(input_pdb)
assert len(parm.atoms) == 3174
def test_simplest_command_pdb4amber_mypdb():
# pdb4amber my.pdb
pdb_fn = get_fn('2igd/2igd.pdb')
command = ['pdb4amber', pdb_fn]
with tempfolder():
output = subprocess.check_output(
' '.join(command), shell=True).decode()
input_pdb = StringIO(output)
input_pdb.seek(0)
parm = pmd.read_PDB(input_pdb)
assert len(parm.atoms) == 574
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_noter():
pdb_fh = get_fn('2igd/2igd.pdb')
parm = pmd.load_file(pdb_fh)
parm_gap = parm[':1,3']
with tempfolder():
fn = 'gap.pdb'
noter_fn = 'noter.pdb'
parm_gap.save(fn)
assert get_num_ters(fn) == 2
output = subprocess.check_output(
['pdb4amber', fn, '--noter', '-o', noter_fn])
assert get_num_ters(noter_fn) == 0
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_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_keep_altlocs():
''' e.g: pdb4amber 2igd.pdb --keep-altlocs --reduce'''
pdb_fn = get_fn('2igd/2igd.pdb')
command = ['pdb4amber', pdb_fn, '--keep-altlocs', '--reduce']
with tempfolder():
output = subprocess.check_output(command).decode()
input_pdb = StringIO(output)
input_pdb.seek(0)
parm = pmd.read_PDB(input_pdb)
res4 = parm.residues[4]
for atom in res4.atoms:
if atom.name.startswith('CB') or atom.name.startswith('CG'):
assert atom.other_locations
def test_find_gaps():
expected_line = 'gap of 4.134579 A between MET 1 and PRO 2'
pdb_fh = get_fn('2igd/2igd.pdb')
parm = pmd.load_file(pdb_fh)
parm_gap = parm[':1,3']
with tempfolder():
fn = 'gap.pdb'
parm_gap.save(fn)
# remove TER to have gap
subprocess.check_call(
'cat {} | sed "/TER/d" > new1.pdb'.format(fn), shell=True)
output = subprocess.check_output(
['pdb4amber', 'new1.pdb', '--logfile=stdout']).decode()
assert expected_line in output
def test_stdin_stdout_with_reduce():
''' e.g: cat my.pdb | pdb4amber --reduce '''
pdb_fn = get_fn('2igd/2igd.pdb')
command = ['cat', pdb_fn, '|', 'pdb4amber', '--reduce']
with tempfolder():
# use shell=True since check_output return exit 1 with |
# not sure why.
output = subprocess.check_output(
' '.join(command), shell=True).decode()
input_pdb = StringIO(output)
input_pdb.seek(0)
parm = pmd.read_PDB(input_pdb)
assert len(parm.atoms) == 1033
def test_mutation():
# mol2
pdb_fn = get_fn('2igd/2igd.pdb')
pdb_out = 'out.pdb'
# no whitespace
command = [
'pdb4amber', '-i', pdb_fn, '-o', pdb_out, '-m', '1-ALA,2-ALA,3-ALA'
]
with tempfolder():
subprocess.check_call(command)
parm = pmd.load_file(pdb_out)
assert set(res.name for res in parm.residues[:3]) == {"ALA"}
# with whitespace
command = [
'pdb4amber', '-i', pdb_fn, '-o', pdb_out, '-m', '1-ALA, 2-ALA, 3-ALA'
]
with tempfolder():
subprocess.check_call(command)
parm = pmd.load_file(pdb_out)
assert set(res.name for res in parm.residues[:3]) == {"ALA"}
def test_nab():
fn = 'nuc.pdb'
with tempfolder():
nab.run("""
molecule m;
m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );
putpdb("nuc.pdb", m, "-wwpdb");
""")
root = 'tmp_jamber'
assert not os.path.exists(root + '.nab')
assert not os.path.exists(root + '.c')
assert not os.path.exists(root + '.out')
parm = pmd.load_file(fn)
assert len(parm.atoms) == 638
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_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_noter_using_run_method():
pdb_fh = get_fn('2igd/2igd.pdb')
parm = pmd.load_file(pdb_fh)
parm_gap = parm[':1,3']
with tempfolder():
fn = 'gap.pdb'
noter_fn = 'noter.pdb'
parm_gap.save(fn)
assert get_num_ters(fn) == 2
pdb4amber.run(
noter_fn,
fn,
arg_elbow=True,
arg_reduce=False,
arg_logfile=sys.stderr,
arg_conect=False,
arg_noter=True, )
assert get_num_ters(noter_fn) == 0
def test_nab_adna():
with tempfolder():
parm = build_adna('AAAAAAAAAA')
assert len(parm.atoms) == 638
def test_nab_arna():
with tempfolder():
parm = build_arna('AAAAAAAAAA')
print(parm.atoms)
def test_simplest_command_pdb4amber():
command = ['pdb4amber']
with tempfolder():
output = subprocess.check_output(command).decode()
assert 'usage: pdb4amber' in output