Jobs fail silently if protonation_program_2=="none"

[Vassyli]

A test run with exactly 1 compound failed silently, despite having "store_queue_log_files" set to "all_uncompressed".

This bug consists of actually two bugs:

• one-queue.sh failes, because protonation_program_2 has been set to "none", despite the documentation saying that "none" is a valid choice.
• However, the run fails to copy the log files from the temporary directory to the "output-files" directory.

After some investigation, I can attribute the first issue due to an errornous check in one-queue.sh on line 975:

elif [[ "${protonation_program_2}" !=  "cxcalc" ]] && [[ "${protonation_program_2}" !=  "obabel" ]] && [[ "${protonation_program_2}" ==  "none" ]]; then

This raises an error if protonation_program_2 is "none", but not if its set to a non-valid character. The line should instead be:

elif [[ "${protonation_program_2}" !=  "cxcalc" ]] && [[ "${protonation_program_2}" !=  "obabel" ]] && [[ "${protonation_program_2}" !=  "none" ]]; then

line 1000 is even worse:

    elif [[ "${conformation_program_2}" !=  "molconvert" ]] && [[ "${conformation_program_2}" !=  "obabel" ]] && [[ "${protonation_program_2}" ==  "none" ]]; then

Here, the comparison makes the same issue - but additionally, the checked variable is wrong, too, as again protonation_program_2 is checked, instead of conformation_program_2. Correctly, it should be:

    elif [[ "${conformation_program_2}" !=  "molconvert" ]] && [[ "${conformation_program_2}" !=  "obabel" ]] && [[ "${conformation_program_2}" !=  "none" ]]; then