Python QLib.read_mol2の例

コード例 #1

ファイル: qlibrary_test.py プロジェクト: acmnpv/qtools

    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")

コード例 #2

ファイル: q_amber2q.py プロジェクト: acmnpv/qtools

for k, v in six.iteritems(vars(args)):
    if k in ["mol2", "prepi", "parm", "frcmods"]:
        for fn in v:
            if not os.path.lexists(fn):
                print("File '{}' doesn't exist.".format(fn))
                sys.exit(1)

#
# create QLib, QPrm, QStruct and QTopology objects
#

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)