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 static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_addBond; 41 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_addGlobalParameter; 42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_addPerBondParameter; 43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_create; 44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_destroy; 45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_setBondParameters; 46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_updateParametersInContext; 47 48 /** 49 * Custom Bond Force. 50 */ 51 public class CustomBondForce extends Force { 52 53 /** 54 * Custom Bond Force Constructor. 55 * 56 * @param energy The definition of the Energy. 57 */ 58 public CustomBondForce(String energy) { 59 pointer = OpenMM_CustomBondForce_create(energy); 60 } 61 62 /** 63 * Add a bond to the OpenMM System. 64 * 65 * @param i1 The index of the first atom. 66 * @param i2 The index of the second atom. 67 * @param parameters The bond parameters. 68 */ 69 public void addBond(int i1, int i2, DoubleArray parameters) { 70 OpenMM_CustomBondForce_addBond(pointer, i1, i2, parameters.getPointer()); 71 } 72 73 /** 74 * Add a per-bond parameter to the CustomBondForce. 75 * 76 * @param name The name of the parameter. 77 */ 78 public void addPerBondParameter(String name) { 79 OpenMM_CustomBondForce_addPerBondParameter(pointer, name); 80 } 81 82 /** 83 * Add a global parameter to the CustomBondForce. 84 * 85 * @param name The name of the parameter. 86 * @param value The value of the parameter. 87 */ 88 public void addGlobalParameter(String name, double value) { 89 OpenMM_CustomBondForce_addGlobalParameter(pointer, name, value); 90 } 91 92 /** 93 * Set the parameters for one bond in the OpenMM System. 94 * 95 * @param index The index of the bond. 96 * @param i1 The index of the first atom. 97 * @param i2 The index of the second atom. 98 * @param parameters The bond parameters. 99 */ 100 public void setBondParameters(int index, int i1, int i2, DoubleArray parameters) { 101 OpenMM_CustomBondForce_setBondParameters(pointer, index, i1, i2, parameters.getPointer()); 102 } 103 104 /** 105 * Update the parameters in the OpenMM Context. 106 * 107 * @param context The OpenMM Context. 108 */ 109 public void updateParametersInContext(Context context) { 110 if (context.hasContextPointer()) { 111 OpenMM_CustomBondForce_updateParametersInContext(pointer, context.getPointer()); 112 } 113 } 114 115 /** 116 * Destroy the OpenMM CustomBondForce. 117 */ 118 public void destroy() { 119 if (pointer != null) { 120 OpenMM_CustomBondForce_destroy(pointer); 121 pointer = null; 122 } 123 } 124 125 }