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_CustomCompoundBondForce_addBond; 41 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_addGlobalParameter; 42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_addPerBondParameter; 43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_create; 44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_destroy; 45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_setBondParameters; 46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_updateParametersInContext; 47 48 /** 49 * Custom Compound Bond Force. 50 */ 51 public class CustomCompoundBondForce extends Force { 52 53 public CustomCompoundBondForce(int i, String energy) { 54 pointer = OpenMM_CustomCompoundBondForce_create(i, energy); 55 } 56 57 /** 58 * Add a per-bond parameter to the OpenMM System. 59 * 60 * @param name The name of the parameter. 61 */ 62 public void addPerBondParameter(String name) { 63 OpenMM_CustomCompoundBondForce_addPerBondParameter(pointer, name); 64 } 65 66 /** 67 * Add a global parameter. 68 * 69 * @param name The parameter name. 70 * @param value The parameter value. 71 */ 72 public void addGlobalParameter(String name, double value) { 73 OpenMM_CustomCompoundBondForce_addGlobalParameter(pointer, name, value); 74 } 75 76 /** 77 * Add a Custom Compound Bond to the OpenMM System. 78 * 79 * @param particles The indices of the particles. 80 * @param parameters The bond parameters. 81 */ 82 public void addBond(IntArray particles, DoubleArray parameters) { 83 OpenMM_CustomCompoundBondForce_addBond(pointer, particles.getPointer(), parameters.getPointer()); 84 } 85 86 /** 87 * Set the parameters for a Custom Compound Bond. 88 * 89 * @param index The index of the bond. 90 * @param particles The indices of the particles. 91 * @param parameters The bond parameters. 92 */ 93 public void setBondParameters(int index, IntArray particles, DoubleArray parameters) { 94 OpenMM_CustomCompoundBondForce_setBondParameters(pointer, index, particles.getPointer(), parameters.getPointer()); 95 } 96 97 /** 98 * Update the parameters in the OpenMM Context. 99 * 100 * @param context The OpenMM Context. 101 */ 102 public void updateParametersInContext(Context context) { 103 if (context.hasContextPointer()) { 104 OpenMM_CustomCompoundBondForce_updateParametersInContext(pointer, context.getPointer()); 105 } 106 } 107 108 /** 109 * Clean up. 110 */ 111 public void destroy() { 112 OpenMM_CustomCompoundBondForce_destroy(pointer); 113 } 114 115 }