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.crystal;
39
40 import static org.apache.commons.math3.util.FastMath.floor;
41 import static org.apache.commons.math3.util.FastMath.max;
42 import static org.apache.commons.math3.util.FastMath.min;
43
44 /**
45 * The ReflectionSpline class represents a reflection spline basis.
46 *
47 * @author Timothy D. Fenn
48 * @see <a href="http://dx.doi.org/10.1107/S0021889802013420" target="_blank"> Cowtan, K. 2002.
49 * Generic representation and evaluation of properties as a function of position in reciprocal
50 * space. J. Appl. Cryst. 35:655-663. </a>
51 * @since 1.0
52 */
53 public class ReflectionSpline {
54
55 private final ReflectionList reflectionList;
56 private final int nParams;
57 private double f;
58 private int i0, i1, i2;
59 private double dfi0, dfi1, dfi2;
60
61 /**
62 * Constructor for ReflectionSpline.
63 *
64 * @param reflectionList a {@link ffx.crystal.ReflectionList} object.
65 * @param nParams an int.
66 */
67 public ReflectionSpline(ReflectionList reflectionList, int nParams) {
68 this.reflectionList = reflectionList;
69 this.nParams = nParams;
70 }
71
72 /**
73 * dfi0
74 *
75 * @return a double.
76 */
77 public double dfi0() {
78 return dfi0;
79 }
80
81 /**
82 * dfi1
83 *
84 * @return a double.
85 */
86 public double dfi1() {
87 return dfi1;
88 }
89
90 /**
91 * dfi2
92 *
93 * @return a double.
94 */
95 public double dfi2() {
96 return dfi2;
97 }
98
99 /**
100 * f
101 *
102 * @return a double.
103 */
104 public double f() {
105 return f;
106 }
107
108 /**
109 * Evaluate basis function and derivative at a given resolution
110 * <p>
111 * Equations 24 and 25 in Cowtan et al.
112 *
113 * @param invResSq resolution of desired spline interpolation
114 * @param params current spline parameters
115 * @return value at invResSq
116 */
117 public double f(double invResSq, double[] params) {
118 double s = nParams * reflectionList.ordinal(invResSq);
119 int i = (int) floor(s);
120 double ds = s - i - 0.5;
121 i0 = min(max(0, i - 1), nParams - 1);
122 i1 = min(max(0, i), nParams - 1);
123 i2 = min(max(0, i + 1), nParams - 1);
124
125 f =
126 params[i0] * 0.5 * (ds - 0.5) * (ds - 0.5)
127 + params[i1] * (0.75 - ds * ds)
128 + params[i2] * 0.5 * (ds + 0.5) * (ds + 0.5);
129
130 dfi0 = 0.5 * (ds - 0.5) * (ds - 0.5);
131 dfi1 = 0.75 - ds * ds;
132 dfi2 = 0.5 * (ds + 0.5) * (ds + 0.5);
133
134 return f;
135 }
136
137 /**
138 * i0
139 *
140 * @return an int.
141 */
142 public int i0() {
143 return i0;
144 }
145
146 /**
147 * i1
148 *
149 * @return an int.
150 */
151 public int i1() {
152 return i1;
153 }
154
155 /**
156 * i2
157 *
158 * @return an int.
159 */
160 public int i2() {
161 return i2;
162 }
163 }