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.potential.nonbonded; 39 40 /** 41 * By implementing the MaskingInterface interface, interaction pairs can be excluded during {@link 42 * ffx.potential.nonbonded.NeighborList} construction. 43 * 44 * <p>During non-bonded calculations, the interactions between bonded atoms (1-2, 1-3 or 1-4, for 45 * example) may be masked to zero. The interaction energy between excluded atoms is described by the 46 * bonded energy terms. 47 * 48 * @author Michael J. Schnieders 49 * @since 1.0 50 */ 51 public interface MaskingInterface { 52 53 /** 54 * Interactions with atom i that should not be included in the NeighborList should be set to 0. 55 * 56 * @param i The atom whose masking rules should be applied. 57 * @param is14 True if atom i and the current atom are 1-4 to each other. 58 * @param masks One or more masking arrays. 59 * @since 1.0 60 */ 61 void applyMask(final int i, final boolean[] is14, final double[]... masks); 62 63 /** 64 * After calling removeMask, all entries in the mask array should be 1 and is14 array false. 65 * 66 * @param i The atom whose masking rules should be removed. 67 * @param is14 True if atom i and the current atom are 1-4 to each other. 68 * @param masks One or more masking arrays. 69 * @since 1.0 70 */ 71 void removeMask(final int i, final boolean[] is14, final double[]... masks); 72 }