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_HarmonicBondForce_addBond; 41 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_create; 42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_updateParametersInContext; 43 44 /** 45 * Harmonic Bond Force. 46 */ 47 public class HarmonicBondForce extends Force { 48 49 public HarmonicBondForce() { 50 pointer = OpenMM_HarmonicBondForce_create(); 51 } 52 53 /** 54 * Add a Harmonic Bond. 55 * 56 * @param i1 Index of the first atom. 57 * @param i2 Index of the second atom. 58 * @param length The equilibrium bond length. 59 * @param k The force constant. 60 */ 61 public void addBond(int i1, int i2, double length, double k) { 62 OpenMM_HarmonicBondForce_addBond(pointer, i1, i2, length, k); 63 } 64 65 /** 66 * Set the bond parameters. 67 * 68 * @param i The bond index. 69 * @param i1 Index of the first atom. 70 * @param i2 Index of the second atom. 71 * @param length The equilibrium bond length. 72 * @param k The force constant. 73 */ 74 public void setBondParameters(int i, int i1, int i2, double length, double k) { 75 OpenMM_HarmonicBondForce_addBond(pointer, i1, i2, length, k); 76 } 77 78 /** 79 * Update the parameters in the OpenMM Context. 80 * 81 * @param context The OpenMM Context. 82 */ 83 public void updateParametersInContext(Context context) { 84 if (context.hasContextPointer()) { 85 OpenMM_HarmonicBondForce_updateParametersInContext(pointer, context.getPointer()); 86 } 87 } 88 89 }