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The protein structure modules of BioJava.

There is a newer version: 7.1.3

package org.biojava.nbio.structure.contact;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Calc;
import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.xtal.CrystalTransform;
import org.biojava.nbio.structure.xtal.SpaceGroup;

import javax.vecmath.Point3d;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;

/**
 * A class containing methods to find interfaces in a given structure.
 * @author Jose Duarte
 * @since 5.4.0
 */
public class InterfaceFinder {

    public static final double DEFAULT_CONTACT_CUTOFF = 6;

    private static final CrystalTransform IDENTITY_TRANSFORM = new CrystalTransform((SpaceGroup) null);
    private static final boolean INCLUDE_HETATOMS = true;

    private List polyChains;
    private double cutoff;

    private BoundingBox[] boundingBoxes;

    public InterfaceFinder(Structure structure) {
        this.polyChains = new ArrayList<>(structure.getPolyChains());
        trimPolyChains();
        this.cutoff = DEFAULT_CONTACT_CUTOFF;
    }

    /**
     * Remove polymer chains with 0 atoms.
     */
    private void trimPolyChains() {
        polyChains.removeIf(chain -> {
            int count = chain.getAtomGroups().stream().map(Group::getAtoms).mapToInt(Collection::size).sum();
            return count == 0;
        });
    }

    /**
     * Set the contact distance cutoff.
     * @param cutoff the distance value in Angstroms
     */
    public void setCutoff(double cutoff) {
        this.cutoff = cutoff;
    }

    /**
     * Find all inter polymer-chain interfaces in the structure.
     * Two chains will be considered in contact if at least a pair of atoms (one from each chain) is within the
     * contact cutoff.
     * @return the list of all interfaces
     */
    public StructureInterfaceList getAllInterfaces() {
        initBoundingBoxes();

        StructureInterfaceList list = new StructureInterfaceList();

        for (int i = 0; i0) {
            interf = new StructureInterface(
                    StructureTools.getAllNonHAtomArray(chain1, INCLUDE_HETATOMS), StructureTools.getAllNonHAtomArray(chain2, INCLUDE_HETATOMS),
                    chain1.getName(), chain2.getName(),
                    graph,
                    IDENTITY_TRANSFORM, IDENTITY_TRANSFORM);
        }

        return interf;
    }
}