1 // ****************************************************************************** 2 // 3 // Title: Force Field X. 4 // Description: Force Field X - Software for Molecular Biophysics. 5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2025. 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 }