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 <[email protected]> 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 <[email protected]> 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 <[email protected]>: >> > 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 >> >> >> > >> > >> > -- >> > アシカ ウマンガ ウマギリヤ >> > ㈱国際バイオインフォマティクス研究所（BiGG) >> > 〒140-0001 >> > 東京都品川区北品川3-6-9 アンドウビル8F >> > TEL:03-6679-8763 >> > FAX:03-6679-8764 >> > >> > _______________________________________________ >> > Biojava-l mailing list - [email protected] >> > http://lists.open-bio.org/mailman/listinfo/biojava-l >> > >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > >
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