Examples with Atom org.biojava.bio.structure.Atom used on opensource projects

Example 6 with Atom

use of org.biojava.bio.structure.Atom in project ffx by mjschnie.

the class PDBFileMatcher method getMatchingAtom.

/**
 * Searches for atom1's match in atoms2; first checks for an equivalent
 * atom, then performs a search over all atoms in atoms2.
 *
 * @param atom1 An Atom.
 * @param atoms2 An Atom[] to search.
 * @return atom1's match in atom2.
 * @throws IllegalArgumentException If no match could be found.
 */
private Atom getMatchingAtom(Atom atom1, Atom[] atoms2) throws IllegalArgumentException {
    Atom atom2 = atoms2[0];
    Structure structure2 = atom2.getGroup().getChain().getParent();
    try {
        atom2 = getMatchingAtom(atom1, structure2, false);
        return atom2;
    } catch (IllegalArgumentException ex) {
        for (Atom atom : atoms2) {
            if (compareAtoms(atom1, atom)) {
                return atom;
            }
        }
    }
    throw new IllegalArgumentException(String.format("No matching atom for %s found", atom1.toString()));
}