1 // ****************************************************************************** 2 // 3 // Title: Force Field X. 4 // Description: Force Field X - Software for Molecular Biophysics. 5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2024. 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.realspace; 39 40 /** 41 * RealSpaceRefinementData class. 42 * 43 * @author Timothy D. Fenn 44 * @since 1.0 45 */ 46 public class RealSpaceRefinementData { 47 48 private final int[] origin; 49 private final int[] extent; 50 private final int[] ni; 51 private double[] data; 52 private double densityScore; 53 private boolean periodic; 54 55 /** Constructor for RealSpaceRefinementData. */ 56 RealSpaceRefinementData() { 57 origin = new int[3]; 58 extent = new int[3]; 59 ni = new int[3]; 60 periodic = false; 61 } 62 63 /** 64 * Getter for the field <code>data</code>. 65 * 66 * @return the data 67 */ 68 public double[] getData() { 69 return data; 70 } 71 72 /** 73 * Setter for the field <code>data</code>. 74 * 75 * @param data the data to set 76 */ 77 public void setData(double[] data) { 78 this.data = data; 79 } 80 81 /** 82 * Getter for the field <code>ni</code>. 83 * 84 * @return the ni 85 */ 86 public int[] getNi() { 87 return ni; 88 } 89 90 /** 91 * Getter for the field <code>origin</code>. 92 * 93 * @return the origin 94 */ 95 public int[] getOrigin() { 96 return origin; 97 } 98 99 /** 100 * Setter for the field <code>extent</code>. 101 * 102 * @param x a int. 103 * @param y a int. 104 * @param z a int. 105 */ 106 public void setExtent(int x, int y, int z) { 107 extent[0] = x; 108 extent[1] = y; 109 extent[2] = z; 110 } 111 112 /** 113 * setNI. 114 * 115 * @param x a int. 116 * @param y a int. 117 * @param z a int. 118 */ 119 public void setNI(int x, int y, int z) { 120 ni[0] = x; 121 ni[1] = y; 122 ni[2] = z; 123 } 124 125 /** 126 * Setter for the field <code>origin</code>. 127 * 128 * @param x a int. 129 * @param y a int. 130 * @param z a int. 131 */ 132 public void setOrigin(int x, int y, int z) { 133 origin[0] = x; 134 origin[1] = y; 135 origin[2] = z; 136 } 137 138 /** 139 * getDataIndex 140 * 141 * @param x a int. 142 * @param y a int. 143 * @param z a int. 144 * @return a double. 145 */ 146 double getDataIndex(int x, int y, int z) { 147 int index = x + extent[0] * (y + extent[1] * z); 148 return data[index]; 149 } 150 151 /** 152 * Getter for the field <code>extent</code>. 153 * 154 * @return the extent 155 */ 156 int[] getExtent() { 157 return extent; 158 } 159 160 /** 161 * Getter for the field <code>densityScore</code>. 162 * 163 * @return the densityScore 164 */ 165 double getDensityScore() { 166 return densityScore; 167 } 168 169 /** 170 * Setter for the field <code>densityScore</code>. 171 * 172 * @param densityScore the densityScore to set 173 */ 174 void setDensityScore(double densityScore) { 175 this.densityScore = densityScore; 176 } 177 178 /** 179 * isPeriodic. 180 * 181 * @return the periodic 182 */ 183 boolean isPeriodic() { 184 return periodic; 185 } 186 187 /** 188 * Setter for the field <code>periodic</code>. 189 * 190 * @param periodic the periodic to set 191 */ 192 void setPeriodic(boolean periodic) { 193 this.periodic = periodic; 194 } 195 }