Bioperl: Structure object?

Steve Chervitz (Steve A. Chervitz)
Tue, 6 Jun 2000 13:49:25 -0700 (PDT)

Chuck Pearson writes:
 > I am a newbie (both to Perl and to Bioperl), and I'm sensitive to
 > appearing as a newbie since I've dealt with newbies on other lists
 > before (flames to /dev/null, please), so I'll just start out simply:
 > 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;
 > however, I don't want to duplicate anything that anyone has already
 > done and that I'm simply too clueless to find.  8-)

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
contributable state in the near term. (Hmm. This would probably be a
good thing for me to present at the BOSC in August...)


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