Subject: Re: CCL:Summary: Visualization of molecules and arbitrary geometric o bjects

From: Konrad Hinsen <[email-masked]>
Date: Thu, 9 Jul 1998 18:16:10 +0200 (DFT)

> This reminds me of a related feature I've always wanted to see in
> modeling packages.  I'd like to be able to select a subset of atoms in a
>...
> I think that quantifying the shape and size of molecular fragments
> (cavities) is an important, useful and often overlooked aspect of most
> molecular modeling packages.

The essential problem is the use of "packages", i.e. monolithic
programs, for molecular modelling. It is unlikely that any such
package will ever provide all features you want, and so in practice
you have to adapt your wishlist to what's available. Even if a program
is available in source code, few people are able to make substantial
modifications or additions, because the complexity of a big program
code requires significant programming experience and plenty of time.

During the last two years I have developed an alternative approach: a
molecular modelling toolkit, i.e. a library of useful operations in
molecular modelling, to be used with (and to a large part written in)
Python, a high-level general-purpose easy-to-learn programming
language. This library contains basic functions that are always needed
(system construction, import/export, geometric operations, etc.), plus
a large range of more specialized techniques. It even includes some of
the techniques that were asked for in the post I am replying to. With
this fundamental stuff out of the way, implementing additional
specialized methods becomes much easier. Moreover, it is not necessary
to understand or even look at any of the original code of the library,
even though this might be helpful in some cases. To give an example, I
was able to add a complete new forcefield (admittedly a simple one) in
an afternoon, including testing, and without modifying or even looking
at any of the original files.

For those who want to know more about this approach, have a look at

    http://starship.skyport.net/crew/hinsen/mmtk.html

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Konrad Hinsen                            | E-Mail: [email-masked]
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