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1   // ******************************************************************************
2   //
3   // Title:       Force Field X.
4   // Description: Force Field X - Software for Molecular Biophysics.
5   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2021.
6   //
7   // This file is part of Force Field X.
8   //
9   // Force Field X is free software; you can redistribute it and/or modify it
10  // under the terms of the GNU General Public License version 3 as published by
11  // the Free Software Foundation.
12  //
13  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
14  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
15  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
16  // details.
17  //
18  // You should have received a copy of the GNU General Public License along with
19  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
20  // Place, Suite 330, Boston, MA 02111-1307 USA
21  //
22  // Linking this library statically or dynamically with other modules is making a
23  // combined work based on this library. Thus, the terms and conditions of the
24  // GNU General Public License cover the whole combination.
25  //
26  // As a special exception, the copyright holders of this library give you
27  // permission to link this library with independent modules to produce an
28  // executable, regardless of the license terms of these independent modules, and
29  // to copy and distribute the resulting executable under terms of your choice,
30  // provided that you also meet, for each linked independent module, the terms
31  // and conditions of the license of that module. An independent module is a
32  // module which is not derived from or based on this library. If you modify this
33  // library, you may extend this exception to your version of the library, but
34  // you are not obligated to do so. If you do not wish to do so, delete this
35  // exception statement from your version.
36  //
37  // ******************************************************************************
38  package ffx.potential.parameters;
39  
40  import static ffx.potential.parameters.ForceField.ForceFieldType.RELATIVESOLV;
41  import static java.lang.Double.parseDouble;
42  import static java.lang.String.format;
43  
44  import java.util.Comparator;
45  import java.util.Objects;
46  import java.util.logging.Level;
47  import java.util.logging.Logger;
48  
49  /**
50   * A BaseType for relative solvation energies (intended for nonstandard amino acids).
51   *
52   * @author Michael J. Schnieders
53   * @author Jacob M. Litman
54   * @since 1.0
55   */
56  public class RelativeSolvationType extends BaseType implements Comparator<String> {
57  
58    /** A Logger for the RelativeSolvationType class. */
59    private static final Logger logger = Logger.getLogger(RelativeSolvationType.class.getName());
60  
61    /** The residue name; */
62    private final String resName;
63    /** THe solvation energy. */
64    private final double solvEnergy;
65  
66    /**
67     * Constructor for RelativeSolvationType.
68     *
69     * @param resname a {@link java.lang.String} object.
70     * @param solvEnergy a double.
71     */
72    public RelativeSolvationType(String resname, double solvEnergy) {
73      super(RELATIVESOLV, resname);
74      this.resName = resname;
75      this.solvEnergy = solvEnergy;
76    }
77  
78    /**
79     * Construct a RelativeSolvationType from an input string.
80     *
81     * @param input The overall input String.
82     * @param tokens The input String tokenized.
83     * @return a RelativeSolvationType instance.
84     */
85    public static RelativeSolvationType parse(String input, String[] tokens) {
86      if (tokens.length < 3) {
87        logger.log(Level.WARNING, "Invalid RELATIVE_SOLVATION type:\n{0}", input);
88        return null;
89      }
90      String resName = tokens[1];
91      try {
92        double relSolvValue = parseDouble(tokens[2]);
93        return new RelativeSolvationType(resName, relSolvValue);
94      } catch (NumberFormatException ex) {
95        String message = "Exception parsing RELATIVE_SOLVATION type:\n" + input + "\n";
96        logger.log(Level.SEVERE, message, ex);
97      }
98      return null;
99    }
100 
101   /** {@inheritDoc} */
102   @Override
103   public int compare(String o1, String o2) {
104     return o1.compareTo(o2);
105   }
106 
107   /** {@inheritDoc} */
108   @Override
109   public boolean equals(Object o) {
110     if (o instanceof RelativeSolvationType) {
111       return ((RelativeSolvationType) o).getResName().equals(resName);
112     }
113     return false;
114   }
115 
116   /**
117    * Getter for the field <code>resName</code>.
118    *
119    * @return a {@link java.lang.String} object.
120    */
121   public String getResName() {
122     return resName;
123   }
124 
125   /**
126    * Getter for the field <code>solvEnergy</code>.
127    *
128    * @return a double.
129    */
130   public double getSolvEnergy() {
131     return solvEnergy;
132   }
133 
134   /** {@inheritDoc} */
135   @Override
136   public int hashCode() {
137     return Objects.hash(resName);
138   }
139 
140   /** {@inheritDoc} */
141   @Override
142   public String toString() {
143     return format("relative solvation %10s %8.5f", resName, solvEnergy);
144   }
145 }