org.wallerlab.yoink.regionizer.partitioner.GridPointAssigner.java Source code

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Here is the source code for org.wallerlab.yoink.regionizer.partitioner.GridPointAssigner.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.regionizer.partitioner;

import java.util.Map;
import java.util.Set;

import javax.annotation.Resource;

import org.springframework.stereotype.Component;
import org.wallerlab.yoink.api.model.molecular.Coord;
import org.wallerlab.yoink.api.model.molecular.Molecule;
import org.wallerlab.yoink.api.model.regionizer.Region;
import org.wallerlab.yoink.api.service.Calculator;
import org.wallerlab.yoink.api.service.cube.Assigner;

/**
 * This class is to determine if a grid point is in the intersection region
 * between QM core and non-QM core in adaptiveSearch region.
 * 
 * @author Min Zheng
 *
 */
@Component
public class GridPointAssigner implements Assigner<Coord, Map<Region.Name, Region>, Region.Name> {

    @Resource
    private Calculator<Map<String, Object>, Coord, Set<Molecule>> voronoiCalculator;

    /**
     * for a grid point, get its two neighbours from Voronoi partitioning, if it
     * satisfies the criteria(two neighbours are different, not both in QM core
     * region or in non-QM core adaptive search region.), it will be used for
     * following calculation of density interaction analysis(like DORI and
     * SEDD).
     * 
     * @param tempCoord
     *            -{@link org.wallerlab.yoink.api.model.molecular.Coord}, the
     *            coordinate of the grid point
     * @param regions
     *            - a Map, Region.Name
     *            {@link org.wallerlab.yoink.api.model.regionizer.Region.Name }
     *            as key, Region
     *            {@link org.wallerlab.yoink.api.model.regionizer.Region} as
     *            value
     * @param cubeRegionName
     *            {@link org.wallerlab.yoink.api.model.regionizer.Region.Name}
     * @return properties - a Map, String {@link java.lang.String} as Key,
     *         Object {@link java.lang.Object} as value
     */
    public Map assign(Coord tempCoord, Map<Region.Name, Region> regions, Region.Name cubeRegionName) {
        Region qmCoreRegion = regions.get(Region.Name.QM_CORE);
        Region nonQmCoreRegion = regions.get(Region.Name.NONQM_CORE_ADAPTIVE_SEARCH);
        Map<String, Object> properties = voronoiCalculator.calculate(tempCoord,
                regions.get(cubeRegionName).getMolecules());
        Set<Molecule> moleculeSet = (Set<Molecule>) properties.get("twoClosestMolecules");
        boolean notNeighbourPair = (boolean) (moleculeSet.size() != 2);
        switch (cubeRegionName) {
        case SYSTEM:
            if (notNeighbourPair) {
                properties.clear();
            }
            break;
        default:
            boolean bothNeighboursAreInNonQmCore = nonQmCoreRegion.containsAll(moleculeSet);
            boolean bothNeighboursAreInQmCore = qmCoreRegion.containsAll(moleculeSet);
            if (notNeighbourPair || bothNeighboursAreInNonQmCore || bothNeighboursAreInQmCore) {
                properties.clear();
            }
        }
        return properties;
    }

}