org.wallerlab.yoink.density.service.densityProperties.DensityOverlapRegionsIndicatorComputer.java Source code

Introduction

Here is the source code for org.wallerlab.yoink.density.service.densityProperties.DensityOverlapRegionsIndicatorComputer.java

Source

/*
 * 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.density.service.densityProperties;

import org.springframework.stereotype.Service;
import org.wallerlab.yoink.api.model.density.DensityPoint;

/**
 * This class is to get the density overlap regions indicator(DORI) value of a
 * grid point. For DORI,see:De Silva, Piotr, and Clmence Corminboeuf.
 * "Simultaneous Visualization of Covalent and Noncovalent Interactions Using Regions of Density Overlap."
 * Journal of chemical theory and computation 10.9 (2014): 3745-3756.
 * 
 * @author Min Zheng
 *
 */
@Service
public class DensityOverlapRegionsIndicatorComputer extends SilvaDensityComputer {

    /**
     * calculate dori value of a grid point
     * 
     * @param densityPoint
     *            -{@link org.wallerlab.yoink.api.model.density.DensityPoint}
     * @param doriValue
     *            , pre-calculated
     * @return doriValue, final-calculated
     * 
     */
    protected double getSilvaValue(DensityPoint densityPoint, double doriValue) {
        double gradient = densityPoint.getGradient();
        doriValue *= (4.0 / Math.pow(gradient, 3));
        doriValue /= (1.0 + doriValue);
        return doriValue;
    }

}