[Biojava-l] PDB file import

[Schreiber, Mark]

I don't know is BioJava has a PDB reader, I know there is a PDB to XML
type of converter but it seems a shame to not have some way to read PDB
(it keeps us very sequence centric). Does anyone have one they want to
donate?

- Mark


> -----Original Message-----
> From: Keith James [mailto:kdj at sanger.ac.uk] 
> Sent: Friday, 11 July 2003 5:16 a.m.
> To: Vasa Curcin
> Cc: biojava-l at biojava.org
> Subject: Re: [Biojava-l] PDB file import
> 
> 
> >>>>> "Vasa" == Vasa Curcin <vc100 at doc.ic.ac.uk> writes:
> 
>     Vasa> Is PDB file import working?  Invoking:
> 
>     Vasa> SequenceFormat sf =
>     Vasa> SeqIOTools.getSequenceFormat(SeqIOConstants.PDB);
> 
>     Vasa> Returns:
> 
>     Vasa> org.biojava.bio.BioException: No SequenceFormat available
>     Vasa> for format/alphabet identifier '524309'
> 
> Hi,
> 
> In this case the exception message is true - there really is 
> no SequenceFormat available for PDB. I don't think that there 
> has ever been one.
> 
> SeqIOConstants was designed to allow identifiers for any/all 
> formats so that an application could still refer to an 
> unsupported format in a defined way. I'm afraid that PDB 
> falls into that category.
> 
> Keith
> 
> -- 
> 
> - Keith James <kdj at sanger.ac.uk> bioinformatics programming support -
> - Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -
> 
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> 
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