def test_glycam(janitor):
molecule = MolTopol(acFileTop="glycam_exe.prmtop", acFileXyz="glycam_exe.inpcrd", debug=True, amb2gmx=True)
molecule.writeGromacsTopolFiles()
molecule.writeCnsTopolFiles()
assert molecule
assert molecule.topo14Data.hasNondefault14()
assert len(molecule.topo14Data.scnb_scale_factor) == 31
janitor.append(molecule.absHomeDir)
def test_merge(janitor, merge, gaff, n_at, acoef, bcoef, msg):
molecule = MolTopol(acFileTop=f"ComplexG{gaff}.prmtop", acFileXyz=f"ComplexG{gaff}.inpcrd", debug=True, merge=merge)
molecule.writeGromacsTopolFiles()
assert molecule
assert len(molecule.atomTypesGromacs) == n_at
assert molecule.atomTypesGromacs[31].ACOEF == acoef
assert molecule.atomTypesGromacs[31].BCOEF == bcoef
assert molecule.atomTypesGromacs[31].__repr__() == msg
janitor.append(molecule.absHomeDir)
def test_ildn(janitor, mol, n1, n2, n3, n4, n5, msg):
molecule = MolTopol(acFileTop=f"{mol}.prmtop", acFileXyz=f"{mol}.inpcrd", debug=True)
molecule.writeGromacsTopolFiles()
assert molecule
assert len(molecule.atoms) == n1
assert len(molecule.properDihedrals) == n2
assert len(molecule.improperDihedrals) == n3
assert molecule.totalCharge == n4
assert len(molecule.atomTypes) == n5
assert molecule.atomTypes[23].__repr__() == msg
janitor.append(molecule.absHomeDir)
def test_amb2gmx(janitor, dd, g4, ntext):
# oct box with water and ions
# modified from https://ambermd.org/tutorials/basic/tutorial7/index.php
# using addIonsRand separated for each ion and TIP3PBOX
molecule = MolTopol(acFileTop="RAMP1_ion.prmtop", acFileXyz="RAMP1_ion.inpcrd", debug=True, direct=dd, gmx4=g4)
molecule.writeGromacsTopolFiles()
assert molecule
assert len(molecule.topText) == ntext
assert not molecule.topo14Data.hasNondefault14()
assert molecule.atoms[1300].__repr__() == "<Atom id=1301, name=NA+, <AtomType=Na+>>"
assert molecule.atoms[1310].__repr__() == "<Atom id=1311, name=CL-, <AtomType=Cl->>"
assert len(molecule.atoms) == 18618
janitor.append(molecule.absHomeDir)
def init_main(binaries: Dict[str, str] = binaries,
argv: Optional[List[str]] = None):
"""
Orchestrate the command line usage for ACPYPE with its all input arguments.
Args:
binaries (Dict[str, str], optional): Mostly used for debug and testing. Defaults to ``acpype.params.binaries``.
argv (Optional[List[str]], optional): Mostly used for debug and testing. Defaults to None.
Returns:
SystemExit(status): 0 or 19 (failed)
"""
_chk_py_ver()
if argv is None:
argv = sys.argv[1:]
parser = get_option_parser()
args = parser.parse_args(argv)
at0 = time.time()
amb2gmxF = False
if args.version:
print(header)
sys.exit(0)
level = 20
if not args.verboseless:
level = 100
if args.debug:
level = 10
logger(level).info(header)
if not args.input:
amb2gmxF = True
if not args.inpcrd or not args.prmtop:
parser.error("missing input files")
elif args.inpcrd or args.prmtop:
parser.error("either '-i' or ('-p', '-x'), but not both")
logger(level).debug(f"CLI: {' '.join(argv)}")
texta = f"Python Version {sys.version}"
logger(level).debug(while_replace(texta))
if args.direct and not amb2gmxF:
parser.error(
"option -u is only meaningful in 'amb2gmx' mode (args '-p' and '-x')"
)
acpypeFailed = False
if amb2gmxF:
logger(level).info("Converting Amber input files to Gromacs ...")
try:
molecule: AbstractTopol = MolTopol(
acFileXyz=args.inpcrd,
acFileTop=args.prmtop,
amb2gmx=True,
debug=args.debug,
basename=args.basename,
verbose=args.verboseless,
gmx4=args.gmx4,
merge=args.merge,
direct=args.direct,
is_sorted=args.sorted,
chiral=args.chiral,
)
except Exception:
acpypeFailed = _handle_exception(level)
if not acpypeFailed:
try:
molecule.writeGromacsTopolFiles()
molecule.printDebug("prmtop and inpcrd files parsed")
except Exception:
acpypeFailed = _handle_exception(level)
else:
try:
molecule = ACTopol(
args.input,
binaries=binaries,
chargeType=args.charge_method,
chargeVal=args.net_charge,
debug=args.debug,
multiplicity=args.multiplicity,
atomType=args.atom_type,
force=args.force,
outTopol=args.outtop,
allhdg=args.cnstop,
basename=args.basename,
timeTol=args.max_time,
qprog=args.qprog,
ekFlag=f'''"{args.keyword}"''',
verbose=args.verboseless,
gmx4=args.gmx4,
merge=args.merge,
direct=args.direct,
is_sorted=args.sorted,
chiral=args.chiral,
amb2gmx=False,
)
except Exception:
acpypeFailed = _handle_exception(level)
if not acpypeFailed:
try:
molecule.createACTopol()
except Exception:
acpypeFailed = _handle_exception(level)
if not acpypeFailed:
try:
molecule.createMolTopol()
except Exception:
acpypeFailed = _handle_exception(level)
execTime = int(round(time.time() - at0))
if execTime == 0:
amsg = "less than a second"
else:
amsg = elapsedTime(execTime)
logger(level).info(f"Total time of execution: {amsg}")
if args.ipython:
try:
import IPython
IPython.embed(colors="neutral")
except ModuleNotFoundError:
logger(level).exception("No 'ipython' installed")
if not args.debug:
try:
rmtree(molecule.tmpDir)
except Exception:
logger(level).debug("No tmp folder left to be removed")
else:
try:
if molecule.tmpDir:
logger(level).debug(
f"Keeping folder '{molecule.tmpDir}' for possible helping debugging"
)
except Exception:
logger(level).debug("No tmp folder left to be removed")
try:
copy_log(molecule)
except UnboundLocalError:
print(f"Log tmp location: {tmpLogFile}")
if acpypeFailed:
sys.exit(19)
os.chdir(molecule.rootDir)
if not amb2gmxF and molecule.obabelExe:
if molecule.checkSmiles():
afile = "smiles_molecule.mol2"
if os.path.exists(afile):
os.remove(afile)
def test_wrong_input(janitor):
with pytest.raises(Exception) as e_info:
MolTopol(acFileTop="nope.prmtop", acFileXyz="ILDN.inpcrd", debug=True, gmx4=True)
assert e_info.value.args == (2, "No such file or directory")
def test_ildn_gmx4_fail(janitor):
molecule = MolTopol(acFileTop="ILDN.prmtop", acFileXyz="ILDN.inpcrd", debug=True, gmx4=True)
with pytest.raises(Exception) as e_info:
molecule.writeGromacsTopolFiles()
assert e_info.value.args[0] == "Likely trying to convert ILDN to RB, DO NOT use option '-z'"
janitor.append(molecule.absHomeDir)