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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.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    /** Re-calculates free energy and enthalpy without bootstrapping. */
71    void estimateDG();
72  
73    /**
74     * Obtains bootstrap free energy. Default implementation sums by-bin free energies.
75     *
76     * <p>May be over-ridden by non-sequential estimators like MBAR.
77     *
78     * @param freeEnergyDifferences By-bin bootstrap results.
79     * @return Overall free energy change.
80     */
81    default double sumBootstrapResults(double[] freeEnergyDifferences) {
82      return stream(freeEnergyDifferences).sum();
83    }
84  
85    /**
86     * Obtains bootstrap enthalpy. Default implementation sums by-bin enthalpies.
87     *
88     * <p>May be over-ridden by non-sequential estimators like MBAR.
89     *
90     * @param totalEnthalpy By-bin bootstrap results.
91     * @return Overall enthalpy.
92     */
93    default double sumEnthalpyBootstrapResults(double[] totalEnthalpy) {
94      return stream(totalEnthalpy).sum();
95    }
96  
97    /**
98     * Obtains bootstrap uncertainty. Default implementation is square root of summed variances.
99     *
100    * <p>May be over-ridden by non-sequential estimators like MBAR.
101    *
102    * @param variances Variance (not uncertainty) in by-bin bootstrap results.
103    * @return Overall uncertainty.
104    */
105   default double sumBootstrapUncertainty(double[] variances) {
106     return sqrt(stream(variances).sum());
107   }
108 
109   /**
110    * Obtains bootstrap enthalpy uncertainty. Default implementation is square root of summed enthalpy
111    * variances.
112    *
113    * <p>May be over-ridden by non-sequential estimators like MBAR.
114    *
115    * @param enthalpyVariances Variance (not uncertainty) in by-bin bootstrap results.
116    * @return Overall enthalpy uncertainty.
117    */
118   default double sumBootstrapEnthalpyUncertainty(double[] enthalpyVariances) {
119     return sqrt(stream(enthalpyVariances).sum());
120   }
121 }