/*
 * Copyright (c) 2005, Stanford University. All rights reserved. 
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 * modification, are permitted provided that the following conditions
 * are met: 
 *  - Redistributions of source code must retain the above copyright 
 *    notice, this list of conditions and the following disclaimer. 
 *  - Redistributions in binary form must reproduce the above copyright 
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 *    documentation and/or other materials provided with the distribution. 
 *  - Neither the name of the Stanford University nor the names of its 
 *    contributors may be used to endorse or promote products derived 
 *    from this software without specific prior written permission. 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS 
 * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE 
 * COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
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 * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
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/*
 * Created on May 1, 2005
 *
 */
package org.simtk.molecularstructure.nucleicacid;

import java.util.*;

/** 
 * @author Christopher Bruns
 * 
 * 
 */
public class Pyrimidine extends Nucleotide {
    public Pyrimidine(char olc, String tlc, String name) {
        super(olc, tlc, name);
    }
//    public Pyrimidine() {
//        super('Y', "PYR", "(unidentified pyrimidine)");
//    }
    
    @Override
    protected void addGenericBonds() {
        super.addGenericBonds();
        // Note - sugar-base linkage depends upon nucleotide type
        // addGenericBond(" C1*", " N9 ");
        addGenericBond(" C1*", " N1 ");
    }

    @Override
    public Set<String> getHydrogenBondAcceptorAtomNames() {
        Set<String> answer = super.getHydrogenBondAcceptorAtomNames();
        answer.add(" N1 ");
        return answer;
    }
}