[Pipet Devel] updated model

J.W. Bizzaro bizzaro at bc.edu
Tue Dec 8 11:40:46 EST 1998

Konrad Hinsen wrote:
> I am not quite sure what you mean by that. XML can be used only between
> programs that understand XML, so very probably none of the existing
> analysis programs that we want to include. And CGI is a technique used
> for Web servers.

We are obviously seeing things differently.  I am not talking about algorithms
that plug into TULIP with *no* modification whatsoever.  (That would be where we
need PyExpect.)  I am assuming (1) most algorithms run through once, (2) they
communicate via stdin/stdout, and (3) the source code is available and can be
modified by us or by the author.  And considering this is the situation, these
algorithms can be changed from outputting plain text to outputting text with XML
markers.  *IF* they do this, we can make the core tools read XML, and tada! we
have communication.

It seems you and Thomas are considering tools not only with various languages
but with various GUI's, that can be added to TULIP without modification.  Unless
you have something else in mind, it will take Expect to do this...only if there
is stdin/stdout communication.  Otherwise, as you said Konrad, there may be no
reasonable solution for these whatsoever ;-)

> I don't really know what people *need*; I don't want to suppose that
> my needs are typical. But I do have Python implementations of most
> common structural analysis techniques, and can easily add more. Most
> techniques I know deal with comparing different conformations of the
> same protein, or of two closely related proteins.

Well, I don't work with the most common tools either.  I can take a quess at
what might be nice...some tools that allow someone to see a 3D structure,
manipulate it, and point out some residues maybe?  Anything else?

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/

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