Examples with ChainImpl org.biojava.nbio.structure.ChainImpl used on opensource projects

Example 1 with ChainImpl

use of org.biojava.nbio.structure.ChainImpl in project mm-dev by sbl-sdsc.

the class BiojavaAligner method getCAAtoms.

/**
 * Converts an array of points representing C-alpha position to a minimal BioJava data structure.
 *
 * @param points coordinates of C-alpha atoms
 * @return BioJava atom array
 */
private static Atom[] getCAAtoms(Point3d[] points) {
    Chain c = new ChainImpl();
    c.setId("A");
    // create dummy BioJava atoms for each C-alpha coordinate
    Atom[] atoms = new Atom[points.length];
    for (int i = 0; i < points.length; i++) {
        atoms[i] = new AtomImpl();
        atoms[i].setName(CA_NAME);
        Group g = new AminoAcidImpl();
        g.setPDBName(GROUP_NAME);
        g.setResidueNumber("A", i, ' ');
        g.addAtom(atoms[i]);
        c.addGroup(g);
        atoms[i].setX(points[i].x);
        atoms[i].setY(points[i].y);
        atoms[i].setZ(points[i].z);
    }
    return atoms;
}