Regarding the issue of finding H-bonds in PDB files:

Besides all the algorithmic suggestions already given, The problem may be even "smaller" than it looks. If your PDB file has water molecules and the protein labeled properly, you now have to consider only water atom-protein atom pairs, instead of every possible pair. And not even every protein atom, if you restrict your definition of H-bond to the typical O...H or N...H.

In reply to Re: Re: Re: Processing data with lot of math... by itub
in thread Processing data with lot of math... by qhayaal

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