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.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 }