[Biojava-l] Reading meta data in PDB file?

[Andreas Prlic]

if you mean residues that have been mentioned in the REMARK section,
then those won't get parsed at the present. but you can have a look at
the following page to see how it deals with SEQRES and ATOM records:
http://biojava.org/wiki/BioJava:CookBook:PDB:seqres

Andreas

On Thu, Mar 12, 2009 at 8:50 AM, Anant Jain <anantpossible at gmail.com> wrote:
> Greetings,
>
> Even i want to retrieve position of missing residues but i am not getting
> any method, should i try regex in java for the given problem..
>
>
> On 3/12/09, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>>
>> Hi Ashika,
>>
>> actually some of the data is available via the Compound class, but for
>> the other parts of your query that is not there you would need to add
>> additional methods to the parser. if you have a patch, would be great
>> if you could post it to the list...
>>
>> Andreas
>>
>>
>>
>> 2009/3/12 Ashika Umanga Umagiliya <aumanga at biggjapan.com>:
>> > I assume there is no way to read these information and I have to modify
>> > the
>> > PDB parser ?
>> >
>> >
>> > Ashika Umanga Umagiliya wrote:
>> >>
>> >> Greetings all,
>> >> I want to read following information.I noticed that most of them are
>> >> stored under REMARK tag in PDB.Can I read them using BioJava PDB
>> >> Parser?
>> >>
>> >> Thanks in Advance,
>> >> Umanga.
>> >> ------------------------------
>> >>
>> >> Unit Cell:
>> >> a,b,c,alpha,beta,gamma values (I assume they are stored in CRYST1 tab?
>> >> )
>> >>
>> >> Molecular Description Asymetric Unit:
>> >> Polymer , Molecule , Chains
>> >>
>> >> Classification
>> >>
>> >> Source:
>> >> Polymer,Scientific Name
>> >>
>> >> Ligand Chemical Component :
>> >> Identifier , Name , Formula
>> >>
>> >> Diffraction Detector:
>> >> Detector,Type,Collection Data
>> >>
>> >> Diffration Radiation:
>> >> Monochromator,Diffraction Protocol,Wavelength,Wavelenth List
>> >>
>> >
>> >
>> > --
>> > $B%"%7%+(B $B%&%^%s%,(B $B%&%^%.%j%d(B
>> > $B-j9q:]%P%$%*%$%s%U%)%^%F%#%/%98&5f=j!J(BBiGG)
>> > $B")(B140-0001
>> > $BEl5~ETIJ at n6hKLIJ@n(B3-6-9 $B%"%s%I%&%S%k(B8F
>> > TEL:03-6679-8763
>> > FAX:03-6679-8764
>> >
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>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>>
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>
>