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.crystal;
39
40 import org.apache.commons.configuration2.CompositeConfiguration;
41
42 import static java.lang.String.format;
43 import static org.apache.commons.math3.util.FastMath.abs;
44
45 /**
46 * The Resolution class encapsulates the sampling limits and resolution limits for a given crystal
47 * and/or data set.
48 *
49 * @author Timothy D. Fenn
50 * @since 1.0
51 */
52 public class Resolution {
53
54 /**
55 * The sampling limit for the data set.
56 */
57 public final double sampling;
58 /**
59 * The resolution of the data set.
60 */
61 public final double resolution;
62 /**
63 * The inverse resolution squared of the data set.
64 */
65 private final double inverseResSq;
66
67 /**
68 * Constructor for Resolution.
69 *
70 * @param resolution a double.
71 * @param sampling a double.
72 */
73 public Resolution(double resolution, double sampling) {
74 this.resolution = resolution;
75 this.inverseResSq = 1.0 / (resolution * resolution);
76 this.sampling = sampling;
77 }
78
79 /**
80 * Constructor for Resolution.
81 *
82 * @param resolution a double.
83 */
84 public Resolution(double resolution) {
85 this(resolution, 1.0 / 1.5);
86 }
87
88 /**
89 * Returns a string representation of the Resolution object, including the resolution and sampling values.
90 *
91 * @return A formatted string containing the resolution and sampling values of the object.
92 */
93 @Override
94 public String toString() {
95 return format(" Resolution: %6.3f Sampling: %6.3f", resolution, sampling);
96 }
97
98 /**
99 * checkProperties
100 *
101 * @param properties a {@link org.apache.commons.configuration2.CompositeConfiguration} object.
102 * @param isNeutron If true, this is a neutron diffraction data set.
103 * @param defaultResolution The resolution from the reflection file.
104 * @return a {@link ffx.crystal.Resolution} object.
105 */
106 public static Resolution checkProperties(CompositeConfiguration properties,
107 boolean isNeutron, double defaultResolution) {
108 double resolution = properties.getDouble("resolution", defaultResolution);
109 if (isNeutron) {
110 resolution = properties.getDouble("neutron-resolution", resolution);
111 } else {
112 resolution = properties.getDouble("xray-resolution", resolution);
113 }
114 double sampling = properties.getDouble("sampling", 0.6);
115
116 if (resolution <= 0.0) {
117 return null;
118 }
119
120 return new Resolution(resolution, sampling);
121 }
122
123 /**
124 * inInverseResSqRange
125 *
126 * @param res a double.
127 * @return a boolean.
128 */
129 public boolean inInverseResSqRange(double res) {
130 if (abs(res - this.inverseResSq) < 1e-8) {
131 return true;
132 } else {
133 return res < this.inverseResSq;
134 }
135 }
136
137 /**
138 * inResolutionRange
139 *
140 * @param res a double.
141 * @return a boolean.
142 */
143 public boolean inResolutionRange(double res) {
144 if (abs(res - this.resolution) < 1e-8) {
145 return true;
146 } else {
147 return res > this.resolution;
148 }
149 }
150
151 /**
152 * inverseResSqLimit
153 *
154 * @return a double.
155 */
156 public double inverseResSqLimit() {
157 return inverseResSq;
158 }
159
160 /**
161 * resolutionLimit
162 *
163 * @return a double.
164 */
165 public double resolutionLimit() {
166 return resolution;
167 }
168
169 /**
170 * samplingLimit
171 *
172 * @return a double.
173 */
174 public double samplingLimit() {
175 return sampling;
176 }
177 }