[Biojava-l] question about pdb reader

[Andreas Prlic]

Hi !

To me this looks like output from an old version of the parser. The one  
that is available in the current version
of BioJava version prints some warnings and shows the lines that can  
not be parsed, but it can read the rest of the file fine.

Jun: can you make sure you are on the latest version of BioJava?

The problems with both files is that the REMARK 2 line is not according  
to the PDB file spec. - This is unfortunately something
that happens in several of the PDB files, but the parser can deal with  
this.

Andreas

On 8 Jun 2007, at 15:11, Richard Holland wrote:

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> Hi there.
>
> The bug I mentioned was to do with more informative error messages,
> which indeed were implemented in the most recent code. However, it  
> seems
> your file either has a bad REMARK 2 block, or our parser is incorrectly
> treating REMARK 20-29 and REMARK 200-299 blocks as REMARK 2 blocks.
>
> ANDREAS - can you check to see that the code wouldn't accidentally pick
> up REMARK 20-29/200-299 blocks whilst looking for REMARK 2 blocks? If  
> it
> does, can you fix it?
>
> JUN GAO - can you open up your file in a text editor and locate all the
> REMARK 2 blocks to see if they conform to the pattern "REMARK 2
> RESOLUTION <some number> ANGSTROMS"? If they don't, can you post one to
> this list that doesn't conform?
>
> cheers,
> Richard
>
>
> Jun Gao wrote:
>> another one:
>>
>> 1mcr
>> java.lang.NumberFormatException: For input string: "E BEA"
>> 	at  
>> sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java: 
>> 1224)
>> 	at java.lang.Float.parseFloat(Float.java:394)
>> 	at  
>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBFil 
>> eParser.java:334)
>> 	at  
>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFileP 
>> arser.java:349)
>> 	at  
>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser. 
>> java:845)
>> 	at  
>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser. 
>> java:764)
>> 	at  
>> org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileRea 
>> der.java:189)
>>
>>
>> -----Original Message-----
>> From: Richard Holland [mailto:holland at ebi.ac.uk]
>> Sent: Fri 6/8/2007 5:54 AM
>> To: Jun Gao
>> Cc: biojava-l at lists.open-bio.org
>> Subject: Re: [Biojava-l] question about pdb reader
>>
>> Hi there.
>>
>> This bug has already been fixed in the most recent beta releases of
>> BioJava 1.5
>>
>> cheers,
>> Richard
>>
>>
>> Jun Gao wrote:
>>>> Hi all,
>>>>
>>>> when I use PDBFileReader to open pdbfile(PDB ID 1rei),I always get  
>>>> these exception:
>>>>
>>>> java.lang.NumberFormatException: For input string: "OMS A"
>>>> 	at  
>>>> sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java: 
>>>> 1224)
>>>> 	at java.lang.Float.parseFloat(Float.java:394)
>>>> 	at  
>>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBF 
>>>> ileParser.java:334)
>>>> 	at  
>>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFil 
>>>> eParser.java:349)
>>>> 	at  
>>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse 
>>>> r.java:845)
>>>> 	at  
>>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse 
>>>> r.java:764)
>>>> 	at  
>>>> org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileR 
>>>> eader.java:189)
>>>> java.lang.NumberFormatException: For input string: "OMS W"
>>>> 	at  
>>>> sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java: 
>>>> 1224)
>>>> 	at java.lang.Float.parseFloat(Float.java:394)
>>>> 	at  
>>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_2_Handler(PDBF 
>>>> ileParser.java:334)
>>>> 	at  
>>>> org.biojava.bio.structure.io.PDBFileParser.pdb_REMARK_Handler(PDBFil 
>>>> eParser.java:349)
>>>> 	at  
>>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse 
>>>> r.java:845)
>>>> 	at  
>>>> org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParse 
>>>> r.java:764)
>>>> 	at  
>>>> org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileR 
>>>> eader.java:189)
>>>>
>>>> Is this a bug of PDBFileReader?
>>>>
>>>> thanks!
>>>>
>>>> Jun
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>
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Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
			 +44 (0) 1223 49 6891

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