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.ui.commands;
39
40 import java.io.Serializable;
41
42 /**
43 * The SimulationDefinition class is a serializable wrapper that specifies an FFX simulation.
44 *
45 * @author Michael J. Schnieders
46 */
47 public class SimulationDefinition implements Serializable {
48
49 private static final long serialVersionUID = 1L;
50 public boolean read = true;
51 // System definition
52 public int numatoms;
53 public int numkeys;
54 public String file;
55 public String forcefield;
56 public String[] keywords;
57 public double[][] coordinates;
58 public int[][] connectivity;
59 public int[] types;
60 public String[] name;
61 public String[] story;
62 public double[] charge;
63 public double[] mass;
64 public int[] atomic;
65
66 /**
67 * Constructor that allocates space for a simulation definition.
68 *
69 * @param a The number of atoms
70 * @param k The number of keywords
71 */
72 public SimulationDefinition(int a, int k) {
73 numatoms = a;
74 numkeys = k;
75 keywords = new String[k];
76 coordinates = new double[3][a];
77 connectivity = new int[4][a];
78 types = new int[a];
79 name = new String[a];
80 story = new String[a];
81 charge = new double[a];
82 mass = new double[a];
83 atomic = new int[a];
84 }
85
86 /** print */
87 public void print() {
88 System.out.println(this);
89 }
90
91 /**
92 * toString
93 *
94 * @return a {@link java.lang.String} object.
95 */
96 public String toString() {
97 return new String("Atoms: " + numatoms + " Keywords: " + numkeys);
98 }
99 }