def test_time_limit(janitor):
molecule = ACTopol("KKK.pdb", chargeType="bcc", debug=True, timeTol=2)
with pytest.raises(Exception) as e_info:
molecule.createACTopol()
assert e_info.value.args[
0] == "Semi-QM taking too long to finish... aborting!"
janitor.append(molecule.absHomeDir)
janitor.append(molecule.tmpDir)
def test_smiles(janitor, base, msg):
smiles = "c1ccc2c(c1)C(=O)N(C2=O)C3CCC(=NC3=O)O"
molecule = ACTopol(smiles, basename=base, chargeType="gas", debug=True)
molecule.createACTopol()
molecule.createMolTopol()
assert molecule
assert molecule.inputFile == msg
assert len(molecule.molTopol.atoms) == 29
janitor.append(molecule.absHomeDir)
janitor.append(molecule.tmpDir)
os.remove(molecule.absInputFile)
def test_charge_user(janitor):
molecule = ACTopol("ADPMg.mol2", chargeType="user", debug=True)
molecule.createACTopol()
molecule.createMolTopol()
assert molecule
assert len(molecule.molTopol.atoms) == 39
assert len(molecule.molTopol.properDihedrals) == 128
assert len(molecule.molTopol.improperDihedrals) == 7
assert molecule.molTopol.atoms[0].charge == 0.1667
assert molecule.molTopol.atoms[15].charge == -0.517
janitor.append(molecule.absHomeDir)
janitor.append(molecule.tmpDir)
def test_ekFlag(janitor):
molecule = ACTopol(
"benzene.pdb",
ekFlag=
'''"qm_theory='AM1', grms_tol=0.0005, scfconv=1.d-10, ndiis_attempts=700, qmcharge=0"''',
gmx4=True,
)
molecule.createACTopol()
molecule.createMolTopol()
assert molecule
assert len(molecule.molTopol.atoms) == 12
janitor.append(molecule.absHomeDir)
janitor.append(molecule.tmpDir)
def test_charges_chiral(janitor):
molecule = ACTopol("KKK.mol2", chargeType="gas", debug=True, chiral=True)
molecule.createACTopol()
molecule.createMolTopol()
assert molecule
assert len(molecule.molTopol.atoms) == 69
assert len(molecule.molTopol.properDihedrals) == 218
assert len(molecule.molTopol.improperDihedrals) == 5
assert len(molecule.molTopol.chiralGroups) == 3
assert molecule.chargeVal == "3"
assert molecule.molTopol.totalCharge == 3
assert molecule.molTopol.chiralGroups[-1][-1] == approx(66.713290)
janitor.append(molecule.absHomeDir)
janitor.append(molecule.tmpDir)
def test_amber(janitor, force, at, ndih):
molecule = ACTopol("FFF.mol2",
chargeType="gas",
debug=True,
atomType=at,
force=force)
molecule.createACTopol()
molecule.createMolTopol()
assert molecule
assert len(molecule.molTopol.atoms) == 63
assert len(molecule.molTopol.properDihedrals) == ndih
assert len(molecule.molTopol.improperDihedrals) == 23
assert molecule.molTopol.atoms[0].__repr__(
) == "<Atom id=1, name=N, <AtomType=N3>>"
janitor.append(molecule.absHomeDir)
janitor.append(molecule.tmpDir)
def test_sqm_tleap(janitor, capsys, ct, ft, msg):
# check chargeType user with PDB -> use bcc
# .mol and .mdl are the same file type
molecule = ACTopol(f"benzene.{ft}", chargeType=ct, debug=True)
molecule.createACTopol()
molecule.createMolTopol()
captured = capsys.readouterr()
assert molecule
assert len(molecule.molTopol.atoms) == 12
assert len(molecule.molTopol.properDihedrals) == 24
assert len(molecule.molTopol.improperDihedrals) == 6
assert molecule.molTopol.atoms[0].charge == approx(-0.13)
assert molecule.molTopol.atoms[-1].charge == approx(0.13)
assert msg in captured.out
janitor.append(molecule.absHomeDir)
janitor.append(molecule.tmpDir)
def test_mol2_sorted(janitor, issorted, charge, msg):
molecule = ACTopol("AAA.mol2",
chargeType="gas",
debug=True,
is_sorted=issorted)
molecule.createACTopol()
molecule.createMolTopol()
assert molecule
assert molecule.molTopol.atomTypes[0].__repr__() == "<AtomType=nz>"
assert len(molecule.molTopol.atoms) == 33
assert len(molecule.molTopol.properDihedrals) == 98
assert len(molecule.molTopol.improperDihedrals) == 5
assert molecule.molTopol.totalCharge == 0
assert molecule.molTopol.atoms[0].charge == approx(charge)
assert molecule.molTopol.atoms[-1].__repr__() == msg
janitor.append(molecule.absHomeDir)
janitor.append(molecule.tmpDir)
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_pdb(janitor, capsys):
molecule = ACTopol("FFF.pdb", chargeType="gas", debug=True)
molecule.createACTopol()
molecule.createMolTopol()
assert len(molecule.molTopol.atoms) == 63
assert len(molecule.molTopol.properDihedrals) == 188
assert len(molecule.molTopol.improperDihedrals) == 23
assert molecule.molTopol.atoms[0].__repr__(
) == "<Atom id=1, name=N, <AtomType=nz>>"
# check gaff2 and force
molecule = ACTopol("FFF.pdb",
chargeType="gas",
debug=True,
atomType="gaff2",
force=True)
molecule.createACTopol()
molecule.createMolTopol()
captured = capsys.readouterr()
assert len(molecule.molTopol.atoms) == 63
assert len(molecule.molTopol.properDihedrals) == 188
assert len(molecule.molTopol.improperDihedrals) == 23
assert molecule.molTopol.atoms[0].__repr__(
) == "<Atom id=1, name=N, <AtomType=nz>>"
assert "==> Overwriting pickle file FFF.pkl" in captured.out
# check for already present
molecule = ACTopol("FFF.mol2", chargeType="gas", debug=True)
molecule.createACTopol()
molecule.createMolTopol()
captured = capsys.readouterr()
assert molecule
assert "==> Pickle file FFF.pkl already present... doing nothing" in captured.out
janitor.append(molecule.absHomeDir)
janitor.append(molecule.tmpDir)
def acpype_api(
inputFile,
chargeType="bcc",
chargeVal=None,
multiplicity="1",
atomType="gaff2",
force=False,
basename=None,
debug=False,
outTopol="all",
engine="tleap",
allhdg=False,
timeTol=MAXTIME,
qprog="sqm",
ekFlag=None,
verbose=True,
gmx4=False,
merge=False,
direct=False,
is_sorted=False,
chiral=False,
is_smiles=False,
):
at0 = time.time()
print(header)
if debug:
texta = "Python Version %s" % sys.version
print("DEBUG: %s" % while_replace(texta))
try:
molecule = ACTopol(
inputFile=inputFile,
chargeType=chargeType,
chargeVal=chargeVal,
debug=debug,
multiplicity=multiplicity,
atomType=atomType,
force=force,
outTopol=outTopol,
allhdg=allhdg,
basename=basename,
timeTol=timeTol,
qprog=qprog,
ekFlag=ekFlag,
verbose=verbose,
gmx4=gmx4,
merge=merge,
direct=direct,
is_sorted=is_sorted,
chiral=chiral,
)
molecule.createACTopol()
molecule.createMolTopol()
"Output in JSON format"
os.chdir(molecule.absHomeDir)
readFiles(molecule.baseName, chargeType, atomType)
output = {
"file_name": molecule.baseName,
"em_mdp": em_mdp.getvalue(),
"AC_frcmod": AC_frcmod.getvalue(),
"AC_inpcrd": AC_inpcrd.getvalue(),
"AC_lib": AC_lib.getvalue(),
"AC_prmtop": AC_prmtop.getvalue(),
"mol2": mol2.getvalue(),
"CHARMM_inp": CHARMM_inp.getvalue(),
"CHARMM_prm": CHARMM_prm.getvalue(),
"CHARMM_rtf": CHARMM_rtf.getvalue(),
"CNS_inp": CNS_inp.getvalue(),
"CNS_par": CNS_par.getvalue(),
"CNS_top": CNS_top.getvalue(),
"GMX_OPLS_itp": GMX_OPLS_itp.getvalue(),
"GMX_OPLS_top": GMX_OPLS_top.getvalue(),
"GMX_gro": GMX_gro.getvalue(),
"GMX_itp": GMX_itp.getvalue(),
"GMX_top": GMX_top.getvalue(),
"NEW_pdb": NEW_pdb.getvalue(),
"md_mdp": md_mdp.getvalue(),
}
except Exception:
_exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
print("ACPYPE FAILED: %s" % exceptionValue)
if debug:
traceback.print_tb(exceptionTraceback, file=sys.stdout)
output = {"file_name": f"ERROR: {str(exceptionValue)}"}
execTime = int(round(time.time() - at0))
if execTime == 0:
amsg = "less than a second"
else:
amsg = elapsedTime(execTime)
print("Total time of execution: %s" % amsg)
clearFileInMemory()
try:
shutil.rmtree(molecule.absHomeDir)
except Exception:
print("DEBUG: No folder left to be removed")
return json.dumps(output)
cType = "gas"
debug = True
water = " -water none"
print(f"usePymol: {usePymol}, ffType: {ffType}, cType: {cType}")
tmpDir = "/tmp/testAcpype"
delList = ["topol.top", "posre.itp"]
# create Dummy PDB
tpdb = "/tmp/tmp.pdb"
dummyLine = "ATOM 1 N ALA A 1 -1.188 -0.094 0.463 1.00 0.00 N\n"
open(tpdb, "w").writelines(dummyLine)
tempObj = ACTopol(tpdb, chargeVal=0, verbose=False)
# Binaries for ambertools
acExe = tempObj.acExe
tleapExe = tempObj.tleapExe
sanderExe = os.path.join(os.path.dirname(acExe), "sander")
ambpdbExe = os.path.join(os.path.dirname(acExe), "ambpdb")
exePymol = "/sw/bin/pymol"
# Binaries for gromacs
gpath = "/home/awilter/miniconda3/envs/acpype/"
gmxTopDir = gpath + "share"
pdb2gmx = gpath + "bin/gmx pdb2gmx"
grompp = gpath + "bin/gmx grompp"
mdrun = gpath + "bin/gmx mdrun"