Bioperl: Structure object?

Dr Nicolas Le Novere
Wed, 7 Jun 2000 10:16:44 +0100 (BST)

On Tue, 6 Jun 2000, Steve Chervitz wrote:

> Chuck Pearson writes:

>  > What is the status of the structure object?  I have an academic
>  > interest in being able to code some of the tasks (representations of
>  > atomic coordinates, constructing and editing coordinate sets,
>  > computations of charges and energy, etc.) and it would appear that
>  > successfully coding some of these tasks would fit well into the
>  > requirements for the structure object outlined on;
> Well, the quick answer is that the present Bioperl distribution or cvs
> repository does not contain any code for handling 3D structural data.
> However, I have written some Bioperl modules along these lines that
> can be used to create hierarchical structure objects (atom group,
> molecule, complex) and populate them from PDB files.
> The modules aren't fully functional and the PDB parser doesn't handle
> all record types, but this could be a good starting point for you to
> build on.
> I've been meaning to resuscitate this code and get it into Bioperl 
> before it disappears into the ether. I'll look into getting it into a

Just a quick message to encourage you to keep on. I know we are quite numerous 
to write our own scripts to manipulate PDB files and bioperl packages would be 
of obvious interest. Although I am a writer clean enough to write those pieces
of code, I will be happy to test them in the most extreme cases :-) 


Dr Nicolas Le Novère           
Dpt of Zoology, University of Cambridge, Downing street, Cambridge CB2 3EJ, UK
tel: +44 1223 336623       fax: +44 1223 336676    e-mail:

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