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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 ffx.potential.MolecularAssembly;
41  import ffx.potential.Utilities.FileType;
42  import ffx.potential.bonded.Atom;
43  import ffx.potential.bonded.Bond;
44  import ffx.potential.parameters.AtomType;
45  import ffx.potential.parsers.SystemFilter;
46  import java.io.File;
47  import java.util.ArrayList;
48  import java.util.Hashtable;
49  import java.util.Vector;
50  
51  /**
52   * The SimulationFilter class parses system data sent by FFXServer to FFXClient.
53   *
54   * @author Michael J. Schnieders
55   */
56  public final class SimulationFilter extends SystemFilter {
57  
58    SimulationDefinition system;
59    Hashtable<Integer, AtomType> atomTypes = new Hashtable<Integer, AtomType>();
60  
61    /**
62     * Constructor for SimulationFilter.
63     *
64     * @param sys a {@link ffx.ui.commands.SimulationDefinition} object.
65     * @param m a {@link ffx.potential.MolecularAssembly} object.
66     */
67    public SimulationFilter(SimulationDefinition sys, MolecularAssembly m) {
68      super(new File(""), m, null, null);
69      system = sys;
70      fileType = FileType.SIM;
71      fileRead = false;
72    }
73  
74    @Override
75    public void closeReader() {
76      // logger.fine(" Reading trajectories not yet supported for MergeFilter");
77      // No logger set for SimulationFilter.
78    }
79  
80    /** {@inheritDoc} */
81    @Override
82    public boolean readFile() {
83      // Create Molecular Mechanics Data Objects from the SimulationDefinition
84      // information
85      for (int i = 0; i < system.numatoms; i++) {
86        AtomType atomType = atomTypes.get(system.types[i]);
87        if (atomType == null) {
88          atomType =
89              new AtomType(
90                  system.types[i],
91                  -1,
92                  system.name[i],
93                  system.story[i],
94                  system.atomic[i],
95                  system.mass[i],
96                  0);
97          atomTypes.put(system.types[i], atomType);
98        }
99      }
100     atomList = new ArrayList<Atom>();
101     Vector<Integer> bonds1 = new Vector<Integer>();
102     Vector<Integer> bonds2 = new Vector<Integer>();
103     double[] d = new double[3];
104     int[] b = new int[4];
105     for (int i = 0; i < system.numatoms; i++) {
106       d[0] = system.coordinates[0][i];
107       d[1] = system.coordinates[1][i];
108       d[2] = system.coordinates[2][i];
109       String s = "" + system.types[i];
110       AtomType atomType = atomTypes.get(s);
111       Atom a = new Atom(i + 1, "" + atomType.type, atomType, d);
112       atomList.add(a);
113       int b1 = i + 1;
114       b[0] = system.connectivity[0][i];
115       b[1] = system.connectivity[1][i];
116       b[2] = system.connectivity[2][i];
117       b[3] = system.connectivity[3][i];
118       int j = 0;
119       while (j < 4 && b[j] != 0) {
120         int b2 = b[j];
121         bonds1.add(b1);
122         bonds2.add(b2);
123         j++;
124       }
125     }
126     bondList = new ArrayList<Bond>();
127     for (int i = 0; i < bonds1.size(); i++) {
128       int a1 = bonds1.get(i);
129       int a2 = bonds2.get(i);
130       if (a1 < a2) {
131         Atom atom1 = atomList.get(a1 - 1);
132         Atom atom2 = atomList.get(a2 - 1);
133         bondList.add(new Bond(atom1, atom2));
134       }
135     }
136     setFileRead(true);
137     return true;
138   }
139 
140   @Override
141   public boolean readNext(boolean resetPosition) {
142     return false;
143   }
144 
145   @Override
146   public boolean readNext(boolean resetPosition, boolean print) {
147     return false;
148   }
149 
150   @Override
151   public boolean readNext(boolean resetPosition, boolean print, boolean parse) {
152     return false;
153   }
154 
155   @Override
156   public boolean readNext() {
157     return readNext(false);
158   }
159 
160   /** {@inheritDoc} */
161   @Override
162   public boolean writeFile(File saveFile, boolean append, String[] extraLines) {
163     return false;
164   }
165 }