org.wallerlab.yoink.adaptive.smooth.smoothfunction.BrooksSmoothFunction.java Source code

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Here is the source code for org.wallerlab.yoink.adaptive.smooth.smoothfunction.BrooksSmoothFunction.java

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/*
 * Copyright 2014-2015 the original author or authors.
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.wallerlab.yoink.adaptive.smooth.smoothfunction;

import org.springframework.stereotype.Service;
import org.wallerlab.yoink.api.service.adaptive.SmoothFunction;

/**
 * this class is smooth function used in Hot-spot. the original smooth function
 * is from:
 * "CHARMM: A program for macromolecular energy, minimization, and dynamics calculations"
 * 
 * @author Min Zheng
 *
 */
@Service("brooksSmoothFunction")
public class BrooksSmoothFunction implements SmoothFunction {
    /**
     * this smooth function is used in hot-spot method. for details please see:
     * "A QM/MM simulation method applied to the solution of Li+ in liquid ammonia."
     * Chemical physics 211.1 (1996): 313-323.
     * 
     * @param currentValue, currentValue(variable) in smooth function
     * @param min, minimum value in smooth function
     * @param max, maximum value in smooth function
     * @return smooth factor
     */
    public double evaluate(double currentValue, double min, double max) {
        double smoothFactor;
        if (currentValue > max) {
            smoothFactor = 0;
        } else if (currentValue <= min) {
            smoothFactor = 1;
        } else {
            smoothFactor = Math.pow((Math.pow(max, 2) - Math.pow(currentValue, 2)), 2);
            smoothFactor = smoothFactor * (Math.pow(max, 2) + 2 * Math.pow(currentValue, 2) - 3 * Math.pow(min, 2));
            smoothFactor = smoothFactor / Math.pow((max * max - min * min), 3);
        }
        return smoothFactor;
    }

}