On May 5, 2006, at 4:25 p, Bob Hanson wrote:
Timothy Driscoll wrote:
On May 5, 2006, at 2:28 p, Bob Hanson wrote:
Tim, the issue is simply this: It's unlikely that the Jmol team
would know, for example, that a specific user had used
"src" (just as an example). Are we to then consider asking all
users "Can we use 'src' for a command, or are you already using
it?" That's what I mean by being careful with your definitions.
Any user defining terms risks future breaks. That's all I'm
saying. I'm personally recommending tilde (not underscore)
because I know for a fact that it is not used in any Jmol
definition, and so that works.
I understand and can appreciate this. and I have little
experience with software development.
but from what I know, predefined terms often can be overridden by
the user without breaking things (perl comes to mind especially,
but this is also true in Rasmol and was in Chime). the term is
simply redefined in local context. then it is the author's
responsibility to make sure their application makes proper use of
the term. hopefully this is what Jmol will do.
Not yet, though.
ok; I can appreciate that. not all software con function the same
way. I imagine there are good reasons *not* to allow/accept this.
undoubtedly it is my ignorance showing, but I would expect Jmol
to know the difference between a keyword string and a token.
for example, from context? for example, I would never use a
defined set called 'connected' in the context 'select connected
(x)'; likewise, I could never use the token 'connected' in
'select connected' (or could I?).
The compiler isn't that smart. It first runs through the list
checking for known "tokens" assigning them their integer-based
identifier. When you define a term, that term is looked up in the
"known token" database. If the token is there, you are out of luck.
Full stop: "invalid expression token..."
So whether the term is followed by parentheses or not, that's not
the issue. "connected" is defined; you cannot reassign it.
ack. I did not fully understand that.
Now, SHOULD you be able to reassign it? That's a question Miguel
has to answer. I'm pretty sure he does not agree with me that the
user should be able to override tokens "locally" as you say is
possible in other scripting languages and, apparently in Chime and
RasMol. (I'm not so sure about that -- I see you can't, for
example, define "backbone" in RasMol.) It's just introduces too
much unpredictability into the application to let people do that.
I think 'override tokens' was the wrong language for me to use. I
was thinking about redefining predefined sets like protein and
nucleic. but in fact, in hindsight, I see the problem is with
tokens, and I can see how this may be undesirable. I do not use
definitions like 'backbone' or 'connected' myself, but I can see how
it would be quite easy to do so.
I have some thoughts about this, but I want to wait and bring them up
a little later. too far off-topic already. :-)
You have some great, very elaborate scripts there, Tim. I know you
have worked very very hard to make them do the most amazing things.
I think there are probably 4 or 5 people in the world with that
sort of extensive scripting base. I don't want to make more work
for you, and it worries me that we might introduce a capability like
select molecule=3
that would break your pages.
I appreciate the compliment, but I can see how this issue could bite
even a simple script. so we need some obvious way to tell an author
that he/she has used a token as a defined set. other than having the
script die, if possible. but we can discuss this another time.
thanks for the clarification, Bob,
tim
--
Timothy Driscoll em: [EMAIL PROTECTED]
Virginia Bioinformatics Institute ph: 540-231-3007
Bioinformatics I im: molvisions
Washington St., Blacksburg, VA 24061
"Anyone who considers arithmetical methods of producing random digits
is, of course, in a state of sin." - J von Neumann
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