internal virtual void addStructure(Structure structure) { if (structureCount == structures.Length) { structures = (Structure[])AtomSetCollectionReader.setLength(structures, structureCount + 32); } structures[structureCount++] = structure; }
internal virtual void addBond(Bond bond) { /* * System.out.println("I see a bond:" + bond.atomIndex1 + "-" + * bond.atomIndex2 + ":" + bond.order); */ if (bond.atomIndex1 < 0 || bond.atomIndex2 < 0 || bond.order <= 0) { /* * System.out.println(">>>>>>BAD BOND:" + bond.atomIndex1 + "-" + * bond.atomIndex2 + ":" + bond.order); */ return; } if (bondCount == bonds.Length) { bonds = (Bond[])AtomSetCollectionReader.setLength(bonds, bondCount + 1024); } bonds[bondCount++] = bond; }