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.parsers;
39
40 import ffx.potential.MolecularAssembly;
41 import ffx.potential.bonded.Atom;
42 import ffx.potential.bonded.Bond;
43
44 import java.io.File;
45 import java.util.ArrayList;
46
47 /**
48 * The MergeFilter class allows Force Field X to treat merging of Systems just like opening a file
49 * from a hard disk or socket.
50 *
51 * @author Michael J. Schnieders
52 * @since 1.0
53 */
54 public class MergeFilter extends SystemFilter {
55
56 /**
57 * Constructor for MergeFilter.
58 *
59 * @param f a {@link ffx.potential.MolecularAssembly} object.
60 * @param a a {@link java.util.ArrayList} object.
61 * @param b a {@link java.util.ArrayList} object.
62 */
63 public MergeFilter(MolecularAssembly f, ArrayList<Atom> a, ArrayList<Bond> b) {
64 super(new File(""), f, null, null);
65 atomList = a;
66 bondList = b;
67 }
68
69 /** {@inheritDoc} */
70 @Override
71 public void closeReader() {
72 // logger.fine(" Reading trajectories not yet supported for MergeFilter");
73 // No logger set for MergeFilter.
74 }
75
76 /** {@inheritDoc} */
77 @Override
78 public boolean readFile() {
79 return true;
80 }
81
82 /** {@inheritDoc} */
83 @Override
84 public boolean readNext(boolean resetPosition) {
85 return false;
86 }
87
88 /** {@inheritDoc} */
89 @Override
90 public boolean readNext(boolean resetPosition, boolean print) {
91 return false;
92 }
93
94 /** {@inheritDoc} */
95 @Override
96 public boolean readNext(boolean resetPosition, boolean print, boolean parse) {
97 return false;
98 }
99
100 /** {@inheritDoc} */
101 @Override
102 public boolean readNext() {
103 return readNext(false);
104 }
105
106 /** {@inheritDoc} */
107 @Override
108 public boolean writeFile(File saveFile, boolean append, String[] extraLines) {
109 return false;
110 }
111 }