[Biojava-l] PDB file import

[Matthew Pocock]

Schreiber, Mark wrote:
> 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

Can we write a PDB-xml -> sequenceIO adaptor? It should not be an 
insurmountable problem. If anybody is keen to try this, there will be 
some biojava coder guys in IRC chat at irc.freenode.net in #biojava and 
we'll be pleased to hold your hand.

Matthew

> 
> 
> 
>>-----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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>>Biojava-l mailing list  -  Biojava-l at biojava.org 
>>http://biojava.org/mailman/listinfo/biojava-l
>>
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