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.xray;
39
40 import static ffx.numerics.math.DoubleMath.sub;
41
42 import ffx.numerics.math.DoubleMath;
43 import ffx.potential.bonded.Atom;
44 import ffx.xray.RefinementMinimize.RefinementMode;
45
46 /**
47 * SolventBinaryFormFactor class.
48 *
49 * @author Timothy D. Fenn
50 * @since 1.0
51 */
52 public final class SolventBinaryFormFactor implements FormFactor {
53
54 private final double[] xyz = new double[3];
55 private final double[] dxyz = new double[3];
56 private final double probeRad;
57
58 /**
59 * Constructor for SolventBinaryFormFactor.
60 *
61 * @param atom a {@link ffx.potential.bonded.Atom} object.
62 * @param probeRad a double.
63 */
64 public SolventBinaryFormFactor(Atom atom, double probeRad) {
65 this(atom, probeRad, atom.getXYZ(null));
66 }
67
68 /**
69 * Constructor for SolventBinaryFormFactor.
70 *
71 * @param atom a {@link ffx.potential.bonded.Atom} object.
72 * @param probeRad a double.
73 * @param xyz an array of double.
74 */
75 public SolventBinaryFormFactor(Atom atom, double probeRad, double[] xyz) {
76 this.probeRad = probeRad;
77
78 update(xyz);
79 }
80
81 /** {@inheritDoc} */
82 @Override
83 public double rho(double f, double lambda, double[] xyz) {
84 sub(this.xyz, xyz, dxyz);
85 return rho(f, lambda, DoubleMath.length(dxyz));
86 }
87
88 /**
89 * rho
90 *
91 * @param f a double.
92 * @param lambda a double.
93 * @param ri a double.
94 * @return a double.
95 */
96 public double rho(double f, double lambda, double ri) {
97 if (ri <= probeRad) {
98 return 0.0;
99 } else {
100 return f;
101 }
102 }
103
104 /**
105 * Derivatives are zero or infinite for the binary model.
106 *
107 * <p>{@inheritDoc}
108 */
109 @Override
110 public void rhoGrad(double[] xyz, double dfc, RefinementMode refinementmode) {}
111
112 /** {@inheritDoc} */
113 @Override
114 public void update(double[] xyz) {
115 update(xyz, 0.0);
116 }
117
118 /** {@inheritDoc} */
119 @Override
120 public void update(double[] xyz, double badd) {
121 this.xyz[0] = xyz[0];
122 this.xyz[1] = xyz[1];
123 this.xyz[2] = xyz[2];
124 }
125 }