def test_overwritten_prm(self):
qprm = QPrm("amber", ignore_errors=True) # duplicates
qprm.read_amber_parm("data/ff-amber14/parm/parm10.dat")
ow = qprm.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
# check overwritten parm
assert ow[0].prm_id == "C N CX CT"
assert ow[0].fcs == [0.0, 0.4, 2.0, 2.0]
def test_amber_conversion(self):
qp_str = open("data/qamber14.prm", "r").read()
qp_str = re.sub("(\*|\!|#).*", "", qp_str)
qp_str = re.sub("\s+$", "", qp_str, 0, re.MULTILINE)
qp_str = re.sub("^\n", "", qp_str, 0, re.MULTILINE)
qprm = QPrm("amber", ignore_errors=True) # duplicates
qprm.read_amber_parm("data/ff-amber14/parm/parm10.dat")
ow = qprm.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
# add options section manually and compare with official lib
for line in """\
name Q-Amber14SB
type AMBER
vdw_rule arithmetic
scale_14 0.8333
switch_atoms off
improper_potential periodic
improper_definition explicit\
""".splitlines():
lf = line.split()
qprm.options[lf[0]] = " ".join(lf[1:])
qp_str2 = qprm.get_string()
qp_str2 = re.sub("\s+$", "", qp_str2, 0, re.MULTILINE)
qp_str2 = re.sub("^\n", "", qp_str2, 0, re.MULTILINE)
assert qp_str == qp_str2
def test_wrong_ff_fail(self):
qprm = QPrm("amber")
with pytest.raises(QPrmError):
qprm.read_ffld("data/ace_ash_nma.ffld11", None)
qprm = QPrm("oplsaa")
with pytest.raises(QPrmError):
qprm.read_amber_parm("data/ff-amber14/parm/parm10.dat")
with pytest.raises(QPrmError):
qprm.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
def test_read_amber_parm(self):
qprm = QPrm("amber")
qprm.read_amber_parm("data/gaff.dat")
assert len(qprm.atom_types) == 71
assert len(qprm.bonds) == 832
assert len(qprm.angles) == 4618
assert len(qprm.generic_torsions) == 587
assert len(qprm.torsions) == 66
assert len(qprm.generic_impropers) == 8
assert len(qprm.impropers) == 27
def test_overwritten_prm_fail(self):
qprm = QPrm("amber") # no ignore_errors
qprm.read_amber_parm("data/ff-amber14/parm/parm10.dat")
with pytest.raises(QPrmError):
qprm.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
def test_read_amber_parm_fail(self):
qprm = QPrm("amber")
with pytest.raises(QPrmError):
qprm.read_amber_parm("data/ff-amber14/parm/frcmod.ff14SB")
def test_ff14sb_conversion():
# Amber14FF to Qamber14
#
# Convert Amber14 lib (+prepin for impropers) and parm+frcmod to Q lib/prm
# Load the structure 'all_amino_acids.pdb' and build the topology
# Check the total bonding energy contributions and number of bonding terms
# and compare the library and parameter set with official qamber14.
#
qal = QLib("amber")
qap = QPrm("amber", ignore_errors=True) # duplicates
qal.read_amber_lib("data/ff-amber14/amber12_mod.lib")
qal.read_amber_lib("data/ff-amber14/arn.lib")
qal.read_prepin_impropers("data/ff-amber14/prep/amino12.in")
qal.read_prepin_impropers("data/ff-amber14/arn.prepi")
qap.read_amber_parm("data/ff-amber14/parm/parm10.dat")
qap.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
# add options to parameters
for line in """\
name Q-Amber14SB
type AMBER
vdw_rule arithmetic !vdW combination rule (geometric or arithmetic)
scale_14 0.8333 ! electrostatic 1-4 scaling factor
switch_atoms off
improper_potential periodic
improper_definition explicit\
""".splitlines():
lf = line.split()
qap.options[lf[0]] = " ".join(lf[1:])
# remove head from ACE and tail from NME
cons = qal.residue_dict["ACE"].connections
cons = [con for con in cons if "head" not in con]
qal.residue_dict["ACE"].connections = cons
cons = qal.residue_dict["NME"].connections
cons = [con for con in cons if "tail" not in con]
qal.residue_dict["NME"].connections = cons
qas1 = QStruct("data/all_amino_acids.pdb", "pdb", ignore_errors=True)
qat = QTopology(qal, qap, qas1)
q_tors = sum([len(list(tor.prm.get_prms())) for tor in qat.torsions])
assert len(qat.bonds) == 464
assert len(qat.angles) == 829
assert len(qat.torsions) == 1221
assert q_tors == 1950
assert len(qat.impropers) == 102
be = sum([bond.calc()[0] for bond in qat.bonds])
ae = sum([ang.calc()[0] for ang in qat.angles])
te = sum([tor.calc()[0] for tor in qat.torsions])
ie = sum([imp.calc()[0] for imp in qat.impropers])
assert is_close(be, 181.2572830)
assert is_close(ae, 212.8539304)
assert is_close(te, 417.2919960)
assert is_close(ie, 22.8171235)
# compare with official lib
qa14_lib = open("data/qamber14.lib", "r").read()
qa14_prm = open("data/qamber14.prm", "r").read()
assert qal.get_string() in qa14_lib
assert qap.get_string() in qa14_prm
qlib = QLib("amber", ignore_errors=args.ignore_errors)
qprm = QPrm("amber", ignore_errors=args.ignore_errors)
try:
qlib.read_mol2(args.mol2[0])
except QLibError as e:
print("FATAL! Problem with mol2: {}".format(str(e)))
sys.exit(1)
try:
qlib.read_prepin_impropers(args.prepi[0])
except QLibError as e:
print("FATAL! Problem with prepi: {}".format(str(e)))
sys.exit(1)
for parm in args.parms:
try:
qprm.read_amber_parm(parm)
except QPrmError as e:
print("FATAL! Problem with parm: {}".format(str(e)))
sys.exit(1)
for frcmod in args.frcmods:
try:
qprm.read_amber_frcmod(frcmod)
except QPrmError as e:
print("FATAL! Problem with frcmod: {}".format(str(e)))
sys.exit(1)
try:
qstruct = QStruct(args.mol2[0], "mol2")
except QStructError as e:
print("FATAL! Problem with mol2: {}".format(str(e)))
#
# Amber14FF to Qamber14
#
# Convert Amber14 lib (+prepin for impropers) and parm+frcmod to Q lib/prm
# Load all_amino_acids.pdb and all_amino_acids.mol2 and build topology
# separately.
#
# ignore_errors=True is needed because frcmod.ff14SB overwrites some parameters
#
qal = QLib("amber")
qap = QPrm("amber", ignore_errors=True)
qal.read_amber_lib("../Amber/ff-amber14/amber12_mod.lib")
qal.read_amber_lib("../Amber/ff-amber14/arn.lib")
qal.read_prepin_impropers("../Amber/ff-amber14/prep/amino12.in")
qal.read_prepin_impropers("../Amber/ff-amber14/arn.prepi")
log_dups(qap.read_amber_parm("../Amber/ff-amber14/parm/parm10.dat"))
log_dups(qap.read_amber_parm("../Amber/ff-amber14/parm/parm10.dat"))
log_dups(qap.read_amber_frcmod("../Amber/ff-amber14/parm/frcmod.ff14SB"))
# add options to parameters
for line in """name Q-Amber14SB
type AMBER
vdw_rule arithmetic !vdW combination rule (geometric or arithmetic)
scale_14 0.8333 ! electrostatic 1-4 scaling factor
switch_atoms off
improper_potential periodic
improper_definition explicit""".splitlines():
lf = line.split()
qap.options[lf[0]] = " ".join(lf[1:])
# remove head from ACE and tail from NME
