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:[EMAIL PROTECTED] Sent: Friday, 11 July 2003 5:16 a.m.
To: Vasa Curcin
Cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] PDB file import
"Vasa" == Vasa Curcin <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> bioinformatics programming support - - Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -
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