PDB file

Hi,





How read pdb files using jchem api.


I would like to retrive the data from pdb file


Could u please give me an example.


I am able to retieve the data from sdf and rdf by getting property keys.





Thank u





regards,


richa

Hi,





some, though not all information are available in the MacroMolecule class: http://www.chemaxon.com/marvin/doc/api/chemaxon/marvin/modules/MacroMolecule.html.





Does this help?





Miklos

thank u for ur reply.





But I know this api.


I am not getting how to use this. And PDBReader also is there.





Regards,


richa

hi,





I want to use getAuthor in MacroMolecule. But I am not getting that.





Regarding api, I can read sdf, rdf files. But I am not able to follow this


MacroMolecule.





Please Help How to use this class.


Ex. I want to use getAuthor() method.





Thank u.





Regards,


richa

Hi, try sg like the code sample below:

Code:

public static void main( String[] args ) {         PDBReader p = new PDBReader();         try {             p.setInput( new MolInputStream( new FileInputStream( args[0]) ) );             MacroMolecule m = p.read();             System.out.println( "name = " + m.getName());             System.out.println( "header = " + m.getHeader() );             System.out.println( "title = " + m.getTitle() );             System.out.println( "source = " + m.getSource() );             System.out.println( "keywords = " + m.getKeywords() );             System.out.println( "exp. data = " + m.getExpData() );             System.out.println( "author = " + m.getAuthor() );         }         catch (Exception e) {             System.out.println("Error reading file " + args[0]);             e.printStackTrace();         }     }

Does this help?


Regards,


Miklos





Ps: Relevant API doc (beyong MacroMolecule that you are already familiar with): http://www.chemaxon.com/marvin/doc/api/chemaxon/marvin/modules/PDBReader.html

Hi Miklos,





Thank you for your Help!


I have tried all these the same way before posting the question. It is not finding the methods during compilation.


I am able to use macromolecule.component class but not


this.


Actually I want to retrieve the co-ordinates, triplet code of aminoacid, other records of a pdb file.





Once again thank you.





Waiting for your reply......





Regards,


Richa.

Hi Richa,

Quote:

I have tried all these the same way before posting the question. It is not finding the methods during compilation. I am able to use macromolecule.component class but not this.

Can you send us the error message you get during the compilation? The source code would also be useful, if you don't feel uncomfortable with this - you can send it in email (if not confidential) to support _at_ chemaxon.com.

Quote:

Actually I want to retrieve the co-ordinates, triplet code of aminoacid, other records of a pdb file.

Try the iterators embedded in the MacroMolecule class, e.g. http://www.chemaxon.com/marvin/doc/api/chemaxon/marvin/modules/MacroMolecule.Polymer.AtomIterator.html.








HTH


Miklos