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PDBAtomCustomizer.java

/*  $RCSfile$
 *  $Author$
 *  $Date$
 *  $Revision$
 *
 *  Copyright (C) 2005-2007  The Chemistry Development Kit (CDK) project
 *
 *  Contact: cdk-devel@lists.sourceforge.net
 *
 *  This program is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public License
 *  as published by the Free Software Foundation; either version 2.1
 *  of the License, or (at your option) any later version.
 *  All we ask is that proper credit is given for our work, which includes
 *  - but is not limited to - adding the above copyright notice to the beginning
 *  of your source code files, and to any copyright notice that you may distribute
 *  with programs based on this work.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public License
 *  along with this program; if not, write to the Free Software
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package org.openscience.cdk.libio.cml;

import nu.xom.Attribute;
import nu.xom.Element;

import org.xmlcml.cml.element.CMLScalar;

import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.protein.data.PDBAtom;

/**
 * Customizer for the libio-cml Convertor to be able to export details for
 * PDBAtom's.
 *
 * @author        egonw
 * @cdk.created   2005-05-04
 * @cdk.module    pdbcml
 * @cdk.githash
 * @cdk.set       libio-cml-customizers
 * @cdk.require   java1.5+
 */
00053 public class PDBAtomCustomizer implements ICMLCustomizer {

00055     public void customize(IAtom atom, Object nodeToAdd) throws Exception {
      if (!(nodeToAdd instanceof Element))
            throw new CDKException("NodeToAdd must be of type nu.xom.Element!");
      
      Element element = (Element)nodeToAdd;
        if (atom instanceof PDBAtom) {
            PDBAtom pdbAtom = (PDBAtom)atom;
            if (pdbAtom.getAltLoc() != null) {
                  CMLScalar scalar = new CMLScalar();
                scalar.addAttribute(new Attribute("dictRef", "pdb:altLoc"));
                scalar.appendChild(pdbAtom.getAltLoc());
                element.appendChild(scalar);
            }
            
            if (pdbAtom.getChainID() != null) {
                Element scalar = new CMLScalar();
                scalar.addAttribute(new Attribute("dictRef", "pdb:chainID"));
                scalar.appendChild(pdbAtom.getChainID());
                element.appendChild(scalar);
            }
            
            {
                Element scalar = new CMLScalar();
                scalar.addAttribute(new Attribute("dictRef", "pdb:hetAtom"));
                scalar.appendChild(""+pdbAtom.getHetAtom());
                element.appendChild(scalar);
            }
            
            if (pdbAtom.getICode() != null) {
                Element scalar = new CMLScalar();
                scalar.addAttribute(new Attribute("dictRef", "pdb:iCode"));
                scalar.appendChild(pdbAtom.getICode());
                element.appendChild(scalar);
            }
            
            if (pdbAtom.getName() != null) {
                Element scalar = new Element("label");
                scalar.addAttribute(new Attribute("dictRef", "pdb:name"));
                scalar.appendChild(pdbAtom.getName());
                element.appendChild(scalar);
            }
            
            {
                Element scalar = new CMLScalar();
                scalar.addAttribute(new Attribute("dictRef", "pdb:oxt"));
                scalar.appendChild("" + pdbAtom.getOxt());
                element.appendChild(scalar);
            }
            
            if (pdbAtom.getRecord() != null) {
                Element scalar = new CMLScalar();
                scalar.addAttribute(new Attribute("dictRef", "pdb:record"));
                scalar.appendChild(pdbAtom.getRecord());
                element.appendChild(scalar);
            }
            
            if (pdbAtom.getResName() != null) {
                Element scalar = new CMLScalar();
                scalar.addAttribute(new Attribute("dictRef", "pdb:resName"));
                scalar.appendChild(pdbAtom.getResName());
                element.appendChild(scalar);
            }
            
            if (pdbAtom.getResSeq() != null) {
                Element scalar = new CMLScalar();
                scalar.addAttribute(new Attribute("dictRef", "pdb:resSeq"));
                scalar.appendChild(pdbAtom.getResSeq());
                element.appendChild(scalar);
            }
            
            if (pdbAtom.getSegID() != null) {
                Element scalar = new CMLScalar();
                scalar.addAttribute(new Attribute("dictRef", "pdb:segID"));
                scalar.appendChild(pdbAtom.getSegID());
                element.appendChild(scalar);
            }
            
            if (pdbAtom.getSerial() != 0) {
                Element scalar = new CMLScalar();
                scalar.addAttribute(new Attribute("dictRef", "pdb:serial"));
                scalar.appendChild("" + pdbAtom.getSerial());
                element.appendChild(scalar);
            }
            
            if (pdbAtom.getTempFactor() != -1.0) {
                Element scalar = new CMLScalar();
                scalar.addAttribute(new Attribute("dictRef", "pdb:tempFactor"));
                scalar.appendChild("" + pdbAtom.getTempFactor());
                element.appendChild(scalar);
            }
            
            element.addAttribute(new Attribute("occupancy", "" + pdbAtom.getOccupancy()));
        }
    }

00150     public void customize(IAtomContainer molecule, Object nodeToAdd) throws Exception {
        // nothing to do at this moment
    }

00154       public void customize(IBond bond, Object nodeToAdd) throws Exception {
            // nothing to do at this moment
      }
}


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