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.numerics.estimator;
39
40 import static java.util.Arrays.stream;
41 import static org.apache.commons.math3.util.FastMath.sqrt;
42
43 /**
44 * The BootstrappableEstimator interface describes a StatisticalEstimator which can use bootstrap
45 * sampling as an additional method of calculating free energy and uncertainty. These will generally
46 * perform non-bootstrap estimation on construction, with estimateDG(true) called to reset the dG and
47 * uncertainty estimates using bootstrapping.
48 *
49 * @author Michael J. Schnieders
50 * @author Jacob M. Litman
51 * @since 1.0
52 */
53 public interface BootstrappableEstimator extends StatisticalEstimator {
54
55 /**
56 * Return a copy of this Estimator. Each implementation should specify its own type as the return
57 * type. Intended to make parallelization of bootstrapping easy.
58 *
59 * @return A copy of this Estimator.
60 */
61 BootstrappableEstimator copyEstimator();
62
63 /**
64 * Re-calculates free energy and enthalpy.
65 *
66 * @param randomSamples Whether to draw random samples with replacement (one bootstrap trial).
67 */
68 void estimateDG(final boolean randomSamples);
69
70 /**
71 * Re-calculates free energy and enthalpy without bootstrapping.
72 */
73 default void estimateDG() {
74 estimateDG(false);
75 }
76
77 /**
78 * Obtains bootstrap total free energy difference.
79 * The default implementation sums by-bin free energies.
80 *
81 * <p>May be over-ridden by non-sequential estimators like MBAR.
82 *
83 * @param freeEnergyDifferences By-bin bootstrap results.
84 * @return Overall free energy change.
85 */
86 default double getTotalFreeEnergyDifference(final double[] freeEnergyDifferences) {
87 return stream(freeEnergyDifferences).sum();
88 }
89
90 /**
91 * Obtains bootstrap free energy difference uncertainty.
92 * The default implementation is square root of summed variances.
93 *
94 * <p>May be over-ridden by non-sequential estimators like MBAR.
95 *
96 * @param variances Variance (not uncertainty) in by-bin bootstrap results.
97 * @return Overall uncertainty.
98 */
99 default double getTotalFEDifferenceUncertainty(final double[] variances) {
100 return sqrt(stream(variances).sum());
101 }
102
103 /**
104 * Obtains bootstrap total enthalpy change. The default implementation sums by-bin enthalpies.
105 *
106 * <p>May be over-ridden by non-sequential estimators like MBAR.
107 *
108 * @param enthalpyDifferences By-bin bootstrap results.
109 * @return Overall enthalpy.
110 */
111 default double getTotalEnthalpyDifference(final double[] enthalpyDifferences) {
112 return stream(enthalpyDifferences).sum();
113 }
114
115 /**
116 * Obtains bootstrap enthalpy uncertainty. The default implementation is square root of summed enthalpy
117 * variances.
118 *
119 * <p>May be over-ridden by non-sequential estimators like MBAR.
120 *
121 * @param enthalpyVariances Variance (not uncertainty) in by-bin bootstrap results.
122 * @return Overall enthalpy uncertainty.
123 */
124 default double getTotalEnthalpyUncertainty(final double[] enthalpyVariances) {
125 return sqrt(stream(enthalpyVariances).sum());
126 }
127 }