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:[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 - > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
