private void PrepareStereochemistry(int u, int prev)
{
Topology topology = g.TopologyOf(u);
if (topology != Topology.Unknown)
{
if (rings.TryGetValue(u, out IList <RingClosure> closures))
{
// most of time we only have a single closure, we can
// handle this easily by moving the ranks of the prev
// and curr atom back and using the curr rank for the
// ring
if (closures.Count == 1)
{
int ring = closures[0].Other(u);
int uAt = visitedAt[u];
int rAt = visitedAt[ring];
visitedAt[prev]--;
visitedAt[u]--;
visitedAt[ring] = uAt;
tokens[u].Configure(topology.ConfigurationOf(visitedAt));
// restore
visitedAt[prev]++;
visitedAt[u]++;
visitedAt[ring] = rAt;
}
else
{
// more complicated, we first move the other two atoms out
// the way then store and change the current ranks of the
// ring atoms. We restore all visitedAt once we exit
Trace.Assert(closures.Count <= 4);
visitedAt[prev] -= 4;
visitedAt[u] -= 4;
int rank = visitedAt[u];
for (int i = 0; i < closures.Count; ++i)
{
int v = closures[i].Other(u);
tmp[i] = visitedAt[v];
visitedAt[v] = ++rank;
}
tokens[u].Configure(topology.ConfigurationOf(visitedAt));
// restore
for (int i = 0; i < closures.Count; ++i)
{
visitedAt[closures[i].Other(u)] = tmp[i];
}
visitedAt[prev] += 4;
visitedAt[u] += 4;
}
}
else
{
tokens[u].Configure(topology.ConfigurationOf(visitedAt));
}
}
}
