def test_wrong_ff_fail(self):
qlib = QLib("amber", ignore_errors=True)
with pytest.raises(QLibError):
qlib.read_ffld("data/ace_ash_nma.ffld11", None)
qlib = QLib("oplsaa", ignore_errors=True)
with pytest.raises(QLibError):
qlib.read_amber_lib("data/ff-amber14/lib/amino12.lib")
with pytest.raises(QLibError):
qlib.read_prepin_impropers("data/ff-amber14/lib/amino12.lib")
with pytest.raises(QLibError):
qlib.read_mol2("data/all_amino_acids.mol2")
def test_read_ffld(self):
qlib = QLib("oplsaa")
qstruct = QStruct("data/ace_ash_nma.pdb", "pdb")
qlib.read_ffld("data/ace_ash_nma.ffld11", qstruct)
assert len(qlib.residue_dict) == 3
assert len(qlib.residue_dict["ACE"].atoms) == 6
assert len(qlib.residue_dict["ASH"].atoms) == 13
assert len(qlib.residue_dict["NMA"].atoms) == 6
ash = qlib.residue_dict["ASH"]
assert ash.atoms[1].atom_type == "ash.CA"
assert is_close(ash.atoms[1].charge, 0.14)
assert "tail C" in ash.connections
assert "head N" in ash.connections
try:
qstruct = QStruct(args.pdb, "pdb", ignore_errors=args.ignore_errors)
except QStructError as err:
print "FATAL! Problem with pdb: {}".format(err)
sys.exit(1)
try:
qprm.read_ffld(args.ffld_output, qstruct)
except QPrmError as err:
print "FATAL! Problem with ffld file: {}".format(err)
sys.exit(1)
try:
qlib.read_ffld(args.ffld_output, qstruct)
except QLibError as err:
print "FATAL! Problem with ffld file: {}".format(err)
sys.exit(1)
try:
qtop = QTopology(qlib, qprm, qstruct)
except QTopologyError as err:
print "FATAL! Problem building the topology: {}".format(err)
sys.exit(1)
#
# get total and max energies and number of parameters
#
data, total_e, max_e, nprm = {}, {}, {}, {}
def test_read_ffld_wrong_order_fail(self):
# see if it fails with PDB with wrong atom-order
qlib = QLib("oplsaa")
qstruct = QStruct("data/ace_ash_nma_bad.pdb", "pdb")
with pytest.raises(QLibError):
qlib.read_ffld("data/ace_ash_nma.ffld11", qstruct)
def test_read_ffld_fail(self):
# no residues found
qlib = QLib("oplsaa")
qstruct = QStruct("data/ace_ash_nma.pdb", "pdb")
with pytest.raises(QLibError):
qlib.read_ffld("data/ace_ash_nma.pdb", qstruct)
def test_convert_oplsaa(self):
qlib = QLib("oplsaa")
qstruct = QStruct("data/ace_ash_nma.pdb", "pdb")
qlib.read_ffld("data/ace_ash_nma.ffld11", qstruct)
ql_str = qlib.get_string()
assert ql_str == open("data/ace_ash_nma.lib").read()