>> So, there is no 'command line' version.
>
> There is no command line version, yet. But it is easy to do, and it will
> have smaller size than that of the GUI app. The command line app will
> just link to libghemical that contained the functionality but no file
> I/O.
OK, good.
>> Since it has a native file format, I would recommend using exactly
>> that format to send the data over the wire.
>
> Humm... I'm not sure about this one, please see below.
>
>> - we have to format the data some way to send
>> it over the wire
>
> Yes we have to format it someway. And the formatting could be pretty
> similar that that in the ghemical file format currently.
>
> But the problem is that the file format itself is not quite solid yet,
> and I might need to change it every now and then in future. So that's
> why using *exactly* same formats could cause problems in future.
So, maybe I missed something. You said 'I might need to change it'. Are
you part of the ghemical team?
>> - you can be assured of having full access to
>> ghemical functionality
>
> In fact we need to pass somewhat more information than the file format
> currently can handle. This is the information about method ("use
> molecular mechanics") and operation ("just calculate energy").
OK
>> - later on you may want to change the file
>> format that you send of the wire, but you
>> should take the simplest approach to get
>> started.
>
> Yep, I agree on this one.
>
> So perhaps the easiest way could be to more or less copy the
> current ghemical file format and add there the records for the needed
> extra information.
Yes, that sounds like where I would start.
>> That way, you can do 95% of your development and debugging without
>> involving the web server ... directly from the command line.
>
> Yep, this helps a lot! :)
>
>> The plugin will simply ask java to open this URL, with the POST data.
>
> Ok, if there is a ready method for this, that's the best choice.
Yes, it is trivial to do in Java.
>> Here is another big advantage of using a CGI and using the ghemical
>> file format ... You can do *all* of your testing from a web browser.
>> Your cgi will not be able to distinguish the JmolApplet from a web
>> browser. You can write a 10 line .html file that will use the POST
>> method to upload the contents of the form. Just Copy/Past a small
>> ghemical file into the form and hit submit ... your cgi will receive
>> the data and then send the results back to your web browser.
>
> Yep, I haven't started this yet, I don't even have a web server
> installed yet.
Do you need access to a webserver someplace?
What kind of system do you normally do development on?
> I thought that since it just uses standard input/output I
> could do initial testing just by running
>
> ./ghemical.cgi < testfile > output
>
> at console.
Yes, that is absolutely the way to get started and the right way to do the
development. Don't worry about the web server part ... especially since
you don't have one running.
Later on we will need to modify this a little bit in order to make it work
on the web server.
(Note: Although the CGI input will come from stdin, it will not be in
exactly the same format. In fact, what you get from stdin will be
form-encoded, in order to support multiple named parameters. But this is
not something that you should worry about at this time.)
> Ok, to summarize, using ghemical file format would be Ok otherwise,
> except it is still subject to change and this might cause unnecessary
> headaches at longer term. Therefore I would prefer a similar but still
> separate format that would also contain the "extra information".
Good.
Start with ghemical.
(For the future: Egon will encourage you to use XML. Given that you think
the ghemical format is not very stable, then I think I may agree with him.
)
Miguel
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