bool IsInChain(BondingAtom b, int parentIndex)
{
if (b.Element != Element.C) return false;
if (parentIndex != 0 && b == chain[parentIndex - 1]) return true;
if (parentIndex != chain.Length - 1 && b == chain[parentIndex + 1]) return true;
return false;
}
static string AlkylSMILES(BondingAtom b, BondingAtom parent)
{
string smiles = b.Element.ToString();
foreach (BondingAtom child in b)
{
if (child != parent) smiles += AlkylSMILES(child, b);
}
return smiles;
}
private void AddChildren(BondingAtom b, BondingAtom parent)
{
foreach (BondingAtom child in b)
{
if (child != parent)
{
atoms.Add(child);
AddChildren(child, b);
}
}
}
int AlkylLength(BondingAtom b, BondingAtom parent)
{
foreach (BondingAtom child in b)
{
if (child != parent) return AlkylLength(child, b) + 1;
}
return 1;
}
public OrganicMolecule(BondingAtom a)
: this(new Molecule(a))
{
}
public OrganicMoleculeNamer(BondingAtom[] chain, Group highest)
{
this.chain = chain;
this.highest = highest;
prefixes = new Dictionary<string, List<int>>();
suffixes = new Dictionary<string, List<int>>();
EnumerateChain();
}
int LongestChildChain(BondingAtom b, BondingAtom parent)
{
int max = 0;
foreach (BondingAtom child in b)
{
if (child != parent && child.Element == Element.C)
{
max = Math.Max(max, LongestChildChain(child, b) + 1);
}
}
return max;
//return b.Where(child => child != parent && child.Element == Element.C).Max<BondingAtom, int>(child => LongestChildChain(child, b) + 1);
}
bool IsEnd(BondingAtom b)
{
int bondedCInChain = 0;
foreach (BondingAtom atom in b)
{
if (chain.Contains(atom)) bondedCInChain++;
}
return bondedCInChain < 2;
//return b.Count(atom => chain.Contains(atom)) < 2;
}
bool HasNonAlkylChild(BondingAtom b, BondingAtom parent)
{
foreach (Bond bond in b.Bonds)
{
if (bond.Target != parent)
{
if (bond.Target.Element != Element.C || bond.Order != 1) return true;
if (HasNonAlkylChild(bond.Target, b)) return true;
}
}
return false;
//return b.Bonds.Where(bond => bond.Target != parent).Any(
// bond => bond.Target.Element != Element.C || bond.Order != 1 || HasNonAlkylChild(bond.Target, b));
}
BondingAtom ChildWithLongestChain(BondingAtom b, BondingAtom parent)
{
int max = 0;
BondingAtom maxChild = null;
foreach (BondingAtom child in b)
{
if (child != parent && child.Element == Element.C)
{
int childChainLength = LongestChildChain(child, b) + 1;
if (childChainLength > max) maxChild = child;
max = Math.Max(max, childChainLength);
}
}
return maxChild;
}
void AssignChildren(BondingAtom b, BondingAtom parent)
{
foreach (BondingAtom child in b)
{
if (child != parent && child.Element == Element.C)
{
if (HasNonAlkylChild(child, b))
{
chain.Add(child);
AssignChildren(child, b);
return;
}
}
}
//what if all children were alkyl?
BondingAtom child2 = ChildWithLongestChain(b, parent);
if (child2 != null)
{
chain.Add(child2);
AssignChildren(child2, b);
}
}
public BondingAtom[] GetChain()
{
BondingAtom[] bAs = new BondingAtom[chain.Count];
bAs[0] = chain.Find((BondingAtom b) => IsEnd(b));
BondingAtom parent = null;
for (int i = 1; i < bAs.Length; i++)
{
foreach (BondingAtom b in bAs[i - 1])
{
if (b.Element == Element.C && b != parent && chain.Contains(b))
{
parent = bAs[i - 1];
bAs[i] = b;
break;
}
}
}
return bAs;
}
public Molecule(BondingAtom b)
{
atoms = new List<BondingAtom>();
atoms.Add(b);
AddChildren(b, null);
}