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.openmm; 39 40 import com.sun.jna.ptr.IntByReference; 41 import com.sun.jna.ptr.PointerByReference; 42 43 import java.nio.IntBuffer; 44 45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_append; 46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_create; 47 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_destroy; 48 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_get; 49 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_getSize; 50 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_resize; 51 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_set; 52 53 /** 54 * Bonds are specified by pairs of integers (the atom indices). 55 */ 56 public class BondArray { 57 58 private PointerByReference pointer; 59 60 /** 61 * Create a new bond array. 62 * 63 * @param size The size of the bond array. 64 */ 65 public BondArray(int size) { 66 pointer = OpenMM_BondArray_create(size); 67 } 68 69 /** 70 * Append a bond to the bond array. 71 * 72 * @param i1 The first atom index. 73 * @param i2 The second atom index. 74 */ 75 public void append(int i1, int i2) { 76 OpenMM_BondArray_append(pointer, i1, i2); 77 } 78 79 /** 80 * Set the bond at index to i1 and i2. 81 * 82 * @param index The index of the bond to set. 83 * @param i1 The first atom index. 84 * @param i2 The second atom index. 85 */ 86 public void set(int index, int i1, int i2) { 87 OpenMM_BondArray_set(pointer, index, i1, i2); 88 } 89 90 /** 91 * Get the size of the bond array. 92 * 93 * @return The size of the bond array. 94 */ 95 public int getSize() { 96 return OpenMM_BondArray_getSize(pointer); 97 } 98 99 /** 100 * Resize the bond array. 101 * 102 * @param size The new size of the bond array. 103 */ 104 public void resize(int size) { 105 OpenMM_BondArray_resize(pointer, size); 106 } 107 108 /** 109 * Get the bond at index. 110 * 111 * @param index The index of the bond to get. 112 * @param i1 The first atom index. 113 * @param i2 The second atom index. 114 */ 115 public void get(int index, IntBuffer i1, IntBuffer i2) { 116 OpenMM_BondArray_get(pointer, index, i1, i2); 117 } 118 119 /** 120 * Get the bond at index. 121 * 122 * @param index The index of the bond to get. 123 * @param i1 The first atom index. 124 * @param i2 The second atom index. 125 */ 126 public void get(int index, IntByReference i1, IntByReference i2) { 127 OpenMM_BondArray_get(pointer, index, i1, i2); 128 } 129 130 /** 131 * Get the pointer to the bond array. 132 * 133 * @return The pointer to the bond array. 134 */ 135 public PointerByReference getPointer() { 136 return pointer; 137 } 138 139 /** 140 * Destroy the bond array. 141 */ 142 public void destroy() { 143 if (pointer != null) { 144 OpenMM_BondArray_destroy(pointer); 145 pointer = null; 146 } 147 } 148 149 }