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 }