internal virtual void addStructure(Structure structure)
{
if (structureCount == structures.Length)
{
structures = (Structure[])AtomSetCollectionReader.setLength(structures, structureCount + 32);
}
structures[structureCount++] = structure;
}
////////////////////////////////////////////////////////////////
// atomSet stuff
////////////////////////////////////////////////////////////////
internal virtual void newAtomSet()
{
// System.out.println("newAtomSet()");
currentAtomSetIndex = atomSetCount++;
if (atomSetCount > atomSetNumbers.Length)
{
atomSetNumbers = AtomSetCollectionReader.doubleLength(atomSetNumbers);
atomSetNames = AtomSetCollectionReader.doubleLength(atomSetNames);
atomSetAtomCounts = AtomSetCollectionReader.doubleLength(atomSetAtomCounts);
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.Properties' and 'System.Collections.Specialized.NameValueCollection' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
atomSetProperties = (System.Collections.Specialized.NameValueCollection[])AtomSetCollectionReader.doubleLength(atomSetProperties);
}
atomSetNumbers[currentAtomSetIndex] = atomSetCount;
}
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;
}
internal virtual void addAtom(Atom atom)
{
if (atomCount == atoms.Length)
{
atoms = (Atom[])AtomSetCollectionReader.doubleLength(atoms);
}
atoms[atomCount++] = atom;
if (atomSetCount == 0)
{
atomSetCount = 1;
currentAtomSetIndex = 0;
atomSetNumbers[0] = 1;
}
atom.atomSetIndex = currentAtomSetIndex;
++atomSetAtomCounts[currentAtomSetIndex];
/*
* System.out.println("addAtom ... after" +
* "\natomCount=" + atomCount +
* "\natomSetCount=" + atomSetCount +
* "\natomSetAtomCounts[" + (currentAtomSetIndex) + "]=" +
* atomSetAtomCounts[atomSetIndex]);
*/
}