Deleting Single Bonded Atoms

Dear All,





I just want to know if anybody can help me in a program which deletes all the atoms bonded to a single atom. I have attached here a sample mole file which contains the original structure and the structure(output) i wanted.





Thanks in advance





Aniraj

The easiest to achieve this with Standardizer.





See the second example on page 2 of the Standardizer poster.





Let me know if you prefer Java code.

Dear Sir,





I am presently going through the File you have mentioned but i think the java code for the same would be a great help in quick understanding. I woul like to have the java code Sir.





Thanks in Advance





Aniraj

See the code below. I modified the code for SimpleConverter from the Marvin Beans examples: http://www.chemaxon.com/marvin/examples/index.html





This page contains the API documentation of the used classes and methods: http://www.chemaxon.com/marvin/doc/api/

Code:

/*  * Copyright (c) 1998-2005 ChemAxon Ltd. All Rights Reserved.  *  * This software is the confidential and proprietary information of  * ChemAxon. You shall not disclose such Confidential Information  * and shall use it only in accordance with the terms of the agreements  * you entered into with ChemAxon.  *  */ package test; import chemaxon.formats.MolImporter; import chemaxon.struc.Molecule; import chemaxon.struc.MolAtom; import java.io.OutputStream; import java.io.FileOutputStream; /**  * Simple molecule file converter.  */ public class OneBondAtomRemover {     public static void main(String[] args) throws Exception {         if(args.length < 1) {             System.out.println(                 "Usage: OneBondAtomRemover input_file format\n"+                 "Example: OneBondAtomRemover caffeine.mol");             System.exit(0);         }         MolImporter importer = new MolImporter(args[0]);         Molecule mol = importer.read();         removeOneBondAtoms(mol);         String format = "mol";         byte[] data = mol.toBinFormat(format);         if(data == null) {             System.err.println("Cannot export molecule in \""                                 + format + "\" format.");             System.exit(1);         }         String outfile = "output."+format;         OutputStream out = new FileOutputStream(outfile);         out.write(data);         out.close();         System.out.println("Output written to file " + outfile);         System.exit(0);     }     private static void removeOneBondAtoms(Molecule mol) {         int i = findOneBondAtom(mol);         while(i != -1) {             mol.removeNode(i);             i = findOneBondAtom(mol);         }     }     private static int findOneBondAtom(Molecule mol) {         for (int i = 0; i < mol.getAtomCount(); i++) {             MolAtom ma = mol.getAtom(i);             if (ma.getBondCount() == 1) {                 return i;             }         }//end for(i)         return -1;     } }

Thanks for the same and it really works so good, i have the small idea of removing the single boded atoms but i am not able to put the code properly. I can use this for writing a big program which is very useful for me.





Thanks once again for the quick response.





Thanks and regards





Aniraj