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.openmm; 39 40 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCentroidBondForce_addBond; 41 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCentroidBondForce_addGroup; 42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCentroidBondForce_addPerBondParameter; 43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCentroidBondForce_create; 44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCentroidBondForce_destroy; 45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCentroidBondForce_setUsesPeriodicBoundaryConditions; 46 47 /** 48 * Custom Centroid Bond Force. 49 */ 50 public class CentroidBondForce extends Force { 51 52 /** 53 * OpenMM CustomCentroidBondForce constructor. 54 * 55 * @param nGroups The number of particles in the bond. 56 * @param energy The energy expression. 57 */ 58 public CentroidBondForce(int nGroups, String energy) { 59 pointer = OpenMM_CustomCentroidBondForce_create(nGroups, energy); 60 } 61 62 /** 63 * Add a per bond parameters 64 * 65 * @param name The parameter name. 66 */ 67 public void addPerBondParameter(String name) { 68 OpenMM_CustomCentroidBondForce_addPerBondParameter(pointer, name); 69 } 70 71 /** 72 * Add a atoms of atoms to the force. 73 * 74 * @param atoms The group of atoms. 75 * @param weight The weight of each atom. 76 */ 77 public void addGroup(IntArray atoms, DoubleArray weight) { 78 OpenMM_CustomCentroidBondForce_addGroup(pointer, atoms.getPointer(), weight.getPointer()); 79 } 80 81 /** 82 * Add a bond between two groups to the force. 83 * 84 * @param groups The two groups. 85 * @param parameters The parameters of each groups. 86 */ 87 public void addBond(IntArray groups, DoubleArray parameters) { 88 OpenMM_CustomCentroidBondForce_addBond(pointer, groups.getPointer(), parameters.getPointer()); 89 } 90 91 /** 92 * Set whether to use periodic boundary conditions. 93 * 94 * @param periodic 1 if periodic boundary conditions should be used, 0 if not. 95 */ 96 public void setUsesPeriodicBoundaryConditions(int periodic) { 97 OpenMM_CustomCentroidBondForce_setUsesPeriodicBoundaryConditions(pointer, periodic); 98 } 99 100 /** 101 * Destroy the OpenMM CustomCentroidBondForce. 102 */ 103 public void destroy() { 104 OpenMM_CustomCentroidBondForce_destroy(pointer); 105 } 106 107 }