Re: Optimizing PDB data structures

Incidentally, as best as I can see (you could double-check, though), BioPerl doesn't have a PDB parser or object model. I would strongly encourage you to contribute your work back, if at all possible.

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Re: Re: Optimizing PDB data structures by seaver (Pilgrim) on Sep 25, 2003 at 13:43 UTC
I did have a look at BioPerl in the hope fo finding a PDB parser. I haven't taken the time yet to investigate their requirements. As it happens, following a bit of Mark's advice, I've created data structures very specific to my project needs, and also have yet to test extensively against the variety of typos within the PDB. As it is, since I hope to run the parser on every file in the PDB, (creating my own database), I should be able to give BioPerl something very reliable, but not yet. Cheers Sam	[reply]

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Re: Re: Optimizing PDB data structures
by seaver (Pilgrim) on Sep 25, 2003 at 13:43 UTC

I haven't taken the time yet to investigate their requirements. As it happens, following a bit of Mark's advice, I've created data structures very specific to my project needs, and also have yet to test extensively against the variety of typos within the PDB.

As it is, since I hope to run the parser on every file in the PDB, (creating my own database), I should be able to give BioPerl something very reliable, but not yet.

Cheers
Sam

[reply]