public TokenizedExpression Tokenize(StringExpression exp)
{
TokenizedExpression ret = new TokenizedExpression();
ret.FunctionalGpTokens = exp.FunctionalGpTokens.Select((str) =>
{
if (Regex.IsMatch(str, @"^\d+$"))
{
return(new Token(Operators.number, int.Parse(str)));
}
else
{
return(new Token(dictAllFunctionalGps[str], 0));
}
}).ToList();
ret.ParentChainTokens = exp.ParentChainTokens.Select((str) =>
{
return(new Token(dictAllParentChain[str], 0));
}).ToList();
ret.TailTokens = exp.TailTokens.Select((str) =>
{
if (Regex.IsMatch(str, @"^\d+$"))
{
return(new Token(Operators.number, int.Parse(str)));
}
else
{
return(new Token(dictAllTail[str], 0));
}
}).ToList();
return(ret);
}
public void FromName(string name)
{
StringExpression exp = Lexer(name);
TokenizedExpression texp = Tokenize(exp);
GetRawMolecule(texp);
FixMolecule();
}
public Molecule GetRawMolecule(TokenizedExpression exp)
{
//Make parent chain
List <Node> parentChain = new List <Node>();
List <Bond> parentChainBonds = new List <Bond>();
for (int i = 0; i < (int)exp.ParentChainTokens[0].Type; i++)
{
Node tmp = new Node(Elements.Carbon);
Nodes.Add(tmp);
parentChain.Add(tmp);
}
for (int i = 0; i < parentChain.Count - 1; i++)
{
Bond tmp = new Bond(parentChain[i], parentChain[i + 1], BondType.Single, Orientation.Horizontal);
parentChainBonds.Add(tmp);
Bonds.Add(tmp);
}
//make bonds
int mode = 0;
List <int> numbers = new List <int>();
int engPreNum = 0;
bool ignoreHyphen = true;
for (int i = 0; i < exp.TailTokens.Count; i++)
{
Token t = exp.TailTokens[i];
if (mode == 0)
{
Operators op;
Suffixes suffix;
EngPrefixes engPre;
if (t.Type is Operators)
{
op = (Operators)t.Type;
if (op == Operators.number)
{
numbers.Add(t.data);
}
else if (op == Operators.comma)
{
}
else if (op == Operators.hyphen && !ignoreHyphen)
{
mode = 1;
}
}
else if (t.Type is EngPrefixes)
{
engPre = (EngPrefixes)t.Type;
engPreNum = (int)engPre;
}
else if (t.Type is Suffixes)
{
suffix = (Suffixes)t.Type;
if (suffix == Suffixes.oic_acid)
{
OicAcid(parentChain[0]);
if (engPreNum == 2)
{
OicAcid(parentChain.Last());
}
}
else if (suffix == Suffixes.carboxylic_acid)
{
CarboxylicAcid(parentChain[0]);
if (engPreNum == 2)
{
CarboxylicAcid(parentChain.Last());
}
}
else if (suffix == Suffixes.al)
{
Aldehyde(parentChain[0]);
if (engPreNum == 2)
{
Aldehyde(parentChain.Last());
}
}
else if (suffix == Suffixes.ol)
{
Alcohol(parentChain[0]);
if (engPreNum == 2)
{
Alcohol(parentChain.Last());
}
}
else if (suffix == Suffixes.one)
{
Ketone(parentChain[0]);
if (engPreNum == 2)
{
Ketone(parentChain.Last());
}
}
else if (suffix == Suffixes.amine)
{
Amine(parentChain[0]);
if (engPreNum == 2)
{
Amine(parentChain.Last());
}
}
numbers.Clear();
engPreNum = 0;
mode = 0;
}
else
{
//TODO: implicit bond location
ignoreHyphen = true;
}
}
else if (mode == 1)
{
EngPrefixes engPrefix;
Bonds btype;
Suffixes suffix;
if (t.Type is Operators && !ignoreHyphen)
{
throw new FormatException("Wrong token format at token #" + i);
}
else if (t.Type is EngPrefixes)
{
engPrefix = (EngPrefixes)t.Type;
//TODO: check prefix validity
}
else if (t.Type is Bonds)
{
btype = (Bonds)t.Type;
foreach (int k in numbers)
{
parentChainBonds[k - 1].Type = (BondType)(int)btype;
}
numbers.Clear();
engPreNum = 0;
mode = 0;
ignoreHyphen = true;
}
else if (t.Type is Suffixes)
{
suffix = (Suffixes)t.Type;
if (suffix == Suffixes.ol)
{
foreach (int k in numbers)
{
Alcohol(parentChain[k - 1]);
}
}
else if (suffix == Suffixes.carboxylic_acid)
{
foreach (int k in numbers)
{
CarboxylicAcid(parentChain[k - 1]);
}
}
else if (suffix == Suffixes.one)
{
foreach (int k in numbers)
{
Ketone(parentChain[k - 1]);
}
}
else if (suffix == Suffixes.amine)
{
foreach (int k in numbers)
{
Amine(parentChain[k - 1]);
}
}
numbers.Clear();
engPreNum = 0;
mode = 0;
ignoreHyphen = true;
}
}
if (ignoreHyphen && (t.Type is Operators && (Operators)t.Type == Operators.hyphen))
{
ignoreHyphen = false;
}
}
//make functional groups
mode = 0;
numbers = new List <int>();
engPreNum = 0;
ignoreHyphen = false;
for (int i = 0; i < exp.FunctionalGpTokens.Count; i++)
{
Token t = exp.FunctionalGpTokens[i];
if (mode == 0)
{
Operators op;
EngPrefixes engPre;
FunctionalGps fGp;
if (t.Type is Operators)
{
op = (Operators)t.Type;
if (op == Operators.number)
{
numbers.Add(t.data);
}
else if (op == Operators.comma)
{
}
else if (op == Operators.hyphen && !ignoreHyphen)
{
mode = 1;
}
}
else if (t.Type is EngPrefixes)
{
engPre = (EngPrefixes)t.Type;
engPreNum = (int)engPre;
}
else if (t.Type is FunctionalGps)
{
fGp = (FunctionalGps)t.Type;
if (fGp == FunctionalGps.cyclo)
{
if (parentChain.First() != parentChain.Last() && !GetOther(parentChain.First()).Select(b => b.GetOther(parentChain.First())).Contains(parentChain.Last()))
{
Bonds.Add(new Bond(parentChain.First(), parentChain.Last(), BondType.Single, Orientation.None));
}
}
//TODO: implicit functional group location
ignoreHyphen = true;
}
}
else if (mode == 1)
{
EngPrefixes engPrefix;
FunctionalGps ftype;
ChemPrefixes chemPrefix;
if (t.Type is Operators && !ignoreHyphen)
{
throw new FormatException("Wrong token format at token #" + i);
}
else if (t.Type is EngPrefixes)
{
engPrefix = (EngPrefixes)t.Type;
//TODO: check prefix validity
}
else if (t.Type is ChemPrefixes)
{
chemPrefix = (ChemPrefixes)t.Type;
if (i < exp.FunctionalGpTokens.Count - 1)
{
ftype = (FunctionalGps)exp.FunctionalGpTokens[i + 1].Type;
if (ftype == FunctionalGps.yl)
{
foreach (int k in numbers)
{
Alkane(parentChain[k - 1], (int)chemPrefix);
}
}
else if (ftype == FunctionalGps.oxy)
{
foreach (int k in numbers)
{
Ether(parentChain[k - 1], (int)chemPrefix);
}
}
}
numbers.Clear();
engPreNum = 0;
mode = 0;
ignoreHyphen = true;
}
else if (t.Type is FunctionalGps)
{
ftype = (FunctionalGps)t.Type;
if (ftype == FunctionalGps.bromo)
{
foreach (int k in numbers)
{
Bromine(parentChain[k - 1]);
}
}
if (ftype == FunctionalGps.oxo)
{
foreach (int k in numbers)
{
Ketone(parentChain[k - 1]);
}
}
else if (ftype == FunctionalGps.phenyl)
{
foreach (int k in numbers)
{
Phenyl(parentChain[k - 1]);
}
}
else if (ftype == FunctionalGps.chloro)
{
foreach (int k in numbers)
{
Chlorine(parentChain[k - 1]);
}
}
else if (ftype == FunctionalGps.fluoro)
{
foreach (int k in numbers)
{
Fluorine(parentChain[k - 1]);
}
}
else if (ftype == FunctionalGps.hydroxy)
{
foreach (int k in numbers)
{
Alcohol(parentChain[k - 1]);
}
}
numbers.Clear();
engPreNum = 0;
mode = 0;
ignoreHyphen = true;
}
}
if (ignoreHyphen && (t.Type is Operators && (Operators)t.Type == Operators.hyphen))
{
ignoreHyphen = false;
}
}
return(this);
}
