====== Unialign

===== Usage Manual

You can specify options or commands through the command line. You can also run the program in an interactive mode where you can type commands. The command line format is as follows:
<code>
unialign.exe "option1 value1" "option2 value2" "command1" "command2 argument2 argument3" ...
</code>
Equivalently, you can type the same commands in interactive mode:
<code>
unialign.exe "cmdmode 1"
> option1 value1
> option2 value2
> command1
> command2 argument2 argument3
</code>

==== Available Options and Commands
^ command ^ description ^
| help | print options and their current values |
| cmdmode [0|1] | run in interactive mode -- only effective if provided in command line |
| (q)uit | exit the program |
| datadir /path/to/datadir | set the data directory where the pdb files reside |
| align pdbfile1 pdbfile2 | align two protein structures |