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Proteins & Datastructures

Philippe Stas philstas at ultr5.vub.ac.be
Fri Feb 14 09:35:52 EST 1997

William Pitt (ubcg08l at mail.cryst.bbk.ac.uk) wrote:
: Thomas hamelryck wrote:
: > Are there any books or references dealing with the efficient representation
: > of a protein in a program?  Useful suggestions or programming tips are welcome
: > too.
: > 

: solve the Atom, Bond problem by creating Graph of Atoms within the
: Molecule class to hold the connectivity information. In this way Atom
: can   
: freed from their dependence on Bond. This also makes sense on a
: biological
: level: an atom can exist independently of any bonds but a bond must
: involve two atoms.

Indeed, the Graph seems the most efficient and easiest to adapt Datastructure
to implement atom connectivity. String and or bond-parameters can be linked 
with the node connections.

One should also consider if a molecule , or a subunit of a molecule, should
be implemented as a set of residues or a set of atoms. The residue
implementation should work faster when handling major parts of the molecule.
The set of atoms inplementation on the other hand has advantages for selecting
atoms rather than residues.

Philippe Stas

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