Running mk_prepare_ligand.py on some unsupported ligands like [Sr+2] fails. This is fine, however the script returns a success exit code (0) which makes it difficult to detect the failure.
echo "
RDKit 3D
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 Sr 0 0 0 0 0 15 0 0 0 0 0 0
M CHG 1 1 2
M END
$$$$
" > test.sdf
mk_prepare_ligand.py -i test.sdf -o test.pdbqt
The script fails and prints the following output:
[16:04:31] Warning: molecule is tagged as 3D, but all Z coords are zero
[16:04:31] ERROR: Problems encountered parsing data fields
[16:04:31] ERROR: moving to the beginning of the next molecule
atom number 0 has None type, mol name:
However it returns a status code of 0 which makes it difficult to detect that something failed:
echo $?
0
It would be very nice if mk_prepare_ligand.py could return a non-0 exit code to indicate a failure occurred.
Running mk_prepare_ligand.py on some unsupported ligands like [Sr+2] fails. This is fine, however the script returns a success exit code (0) which makes it difficult to detect the failure.
The script fails and prints the following output:
However it returns a status code of 0 which makes it difficult to detect that something failed:
It would be very nice if mk_prepare_ligand.py could return a non-0 exit code to indicate a failure occurred.