void deleteLigandBonds() { List<CMLAtom> atomList = this.getAtoms(); for (CMLAtom atom : atomList) { deleteLigandBonds(atom); } }
/** * removes a atom. * * @param atom * @return deleted atom or null */ public CMLAtom removeAtom(CMLAtom atom) { CMLAtom deletedAtom = null; if (this.equals(atom.getParent())) { super.removeChild(atom); if (atomMap != null) { atomMap.remove(atom.getId()); } deleteLigandBonds(atom); deletedAtom = atom; } return deletedAtom; }