org.wallerlab.yoink.molecular.service.calculator.ClosestDistanceToMoleculeCalculator.java Source code

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Here is the source code for org.wallerlab.yoink.molecular.service.calculator.ClosestDistanceToMoleculeCalculator.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.molecular.service.calculator;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

import javax.annotation.Resource;

import org.springframework.stereotype.Service;
import org.wallerlab.yoink.api.model.molecular.Atom;
import org.wallerlab.yoink.api.model.molecular.Coord;
import org.wallerlab.yoink.api.model.molecular.Molecule;
import org.wallerlab.yoink.api.service.Calculator;
import org.wallerlab.yoink.api.service.math.Vector;

/**
 * This class is to calculate the closest distance between one point in space and a molecule
 * 
 * @author Min Zheng
 *
 */

@Service
public class ClosestDistanceToMoleculeCalculator implements Calculator<Double, Coord, Molecule> {

    @Resource
    private Calculator<Double, Coord, Atom> distanceCalculator;

    /**
     * calculate the distance minimum between a coordinate and a molecule.
     * 
     * @param gridCoord
     *            -{@link org.wallerlab.yoink.api.model.molecular.Coord}
     * @param molecule
     *            -{@link org.wallerlab.yoink.api.model.molecular.Molecule}
     * @return density -{@link java.lang.Double}
     * 
     */
    public Double calculate(Coord gridCoord, Molecule molecule) {
        List<Double> distances = new ArrayList<Double>();
        for (Atom atom : molecule.getAtoms()) {
            double tempdistance = distanceCalculator.calculate(gridCoord, atom);
            distances.add(tempdistance);
        }
        double distance = Collections.min(distances);
        return distance;
    }
}