def test_amb2gmx_no_bins(janitor, capsys):
binaries = {"ac_bin": "no_ac", "obabel_bin": "no_obabel"}
argv = ["-x", "Base.inpcrd", "-p", "Base.prmtop"]
temp_base = "vir_temp"
cli.init_main(argv=argv + ["-b", temp_base], binaries=binaries)
captured = capsys.readouterr()
assert "Total time of execution:" in captured.out
_getoutput(f"rm -vfr {temp_base}* .*{temp_base}*")
def test_args_wrong_inputs(janitor, capsys, argv, code, msg):
with pytest.raises(SystemExit) as e_info:
init_main(argv=argv)
captured = capsys.readouterr()
assert msg in captured.err + captured.out
assert e_info.typename == "SystemExit"
assert e_info.value.code == code
_getoutput("rm -vfr vir_temp* .*vir_temp*")
def test_no_obabel(janitor, capsys, inp, msg):
binaries = {"ac_bin": "antechamber", "obabel_bin": "no_obabel"}
with pytest.raises(SystemExit) as e_info:
cli.init_main(argv=["-di", inp, "-c", "gas"], binaries=binaries)
captured = capsys.readouterr()
assert msg in captured.out
assert e_info.typename == "SystemExit"
assert e_info.value.code == 19
def test_no_ac(janitor, capsys):
binaries = {"ac_bin": "no_ac", "obabel_bin": "obabel"}
msg = f"ERROR: no '{binaries['ac_bin']}' executable... aborting!"
inp = "AAA.mol2"
with pytest.raises(SystemExit) as e_info:
cli.init_main(argv=["-di", inp, "-c", "gas"], binaries=binaries)
captured = capsys.readouterr()
assert msg in captured.out
assert e_info.typename == "SystemExit"
assert e_info.value.code == 19
def test_only_ac(janitor, capsys):
binaries = {"ac_bin": "antechamber", "obabel_bin": "no_obabel"}
msg1 = f"WARNING: no '{binaries['obabel_bin']}' executable, no PDB file can be used as input!"
msg2 = "Total time of execution:"
msg3 = "WARNING: No Openbabel python module, no chiral groups"
inp = "AAA.mol2"
temp_base = "vir_temp"
cli.init_main(argv=["-di", inp, "-c", "gas", "-b", temp_base],
binaries=binaries)
captured = capsys.readouterr()
assert msg1 in captured.out
assert msg2 in captured.out
assert msg3 in captured.out
_getoutput(f"rm -vfr {temp_base}* .*{temp_base}*")
def test_inputs(janitor, capsys, argv, msg):
temp_base = "vir_temp"
init_main(argv=argv)
captured = capsys.readouterr()
assert msg in captured.out
_getoutput(f"rm -vfr {temp_base}* .*{temp_base}* smiles_molecule.acpype")
#!/usr/bin/env python3
import re
import sys
from acpype.cli import init_main
if __name__ == "__main__":
sys.argv[0] = re.sub(r"(-script\.pyw?|\.exe)?$", "", sys.argv[0])
sys.exit(init_main())