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.parsers;
39
40 import ffx.potential.MolecularAssembly;
41 import ffx.potential.bonded.Atom;
42 import ffx.potential.bonded.Bond;
43 import java.io.File;
44 import java.util.ArrayList;
45
46 /**
47 * The MergeFilter class allows Force Field X to treat merging of Systems just like opening a file
48 * from a hard disk or socket.
49 *
50 * @author Michael J. Schnieders
51 * @since 1.0
52 */
53 public class MergeFilter extends SystemFilter {
54
55 /**
56 * Constructor for MergeFilter.
57 *
58 * @param f a {@link ffx.potential.MolecularAssembly} object.
59 * @param a a {@link java.util.ArrayList} object.
60 * @param b a {@link java.util.ArrayList} object.
61 */
62 public MergeFilter(MolecularAssembly f, ArrayList<Atom> a, ArrayList<Bond> b) {
63 super(new File(""), f, null, null);
64 atomList = a;
65 bondList = b;
66 }
67
68 /** {@inheritDoc} */
69 @Override
70 public void closeReader() {
71 // logger.fine(" Reading trajectories not yet supported for MergeFilter");
72 // No logger set for MergeFilter.
73 }
74
75 /** {@inheritDoc} */
76 @Override
77 public boolean readFile() {
78 return true;
79 }
80
81 /** {@inheritDoc} */
82 @Override
83 public boolean readNext(boolean resetPosition) {
84 return false;
85 }
86
87 /** {@inheritDoc} */
88 @Override
89 public boolean readNext(boolean resetPosition, boolean print) {
90 return false;
91 }
92
93 /** {@inheritDoc} */
94 @Override
95 public boolean readNext(boolean resetPosition, boolean print, boolean parse) {
96 return false;
97 }
98
99 /** {@inheritDoc} */
100 @Override
101 public boolean readNext() {
102 return readNext(false);
103 }
104
105 /** {@inheritDoc} */
106 @Override
107 public boolean writeFile(File saveFile, boolean append, String[] extraLines) {
108 return false;
109 }
110 }