public Molecule(string empiricalFormula)
{
if (empiricalFormula.Contains(".")){
string[] q = empiricalFormula.Split('.');
Molecule[] m = new Molecule[q.Length];
int[] w = new int[q.Length];
for (int i = 0; i < q.Length; i++){
m[i] = new Molecule(q[i]);
w[i] = 1;
}
Molecule x = Sum(m, w);
AtomType = x.AtomType;
AtomCount = x.AtomCount;
CalcMasses();
} else{
int[][] tc = ProcessEmpiricalFormula(empiricalFormula);
AtomType = tc[0];
AtomCount = tc[1];
CalcMasses();
}
}
public Molecule GetMolecule()
{
Molecule[] x = new Molecule[ModificationTypes.Length];
for (int i = 0; i < x.Length; i++){
Modification mod = Tables.ModificationList[ModificationTypes[i]];
x[i] = mod.GetMolecule();
}
return Molecule.Sum(x, ModificationCounts);
}
protected bool Equals(Molecule other)
{
return ArrayUtils.EqualArrays(AtomType, other.AtomType) && ArrayUtils.EqualArrays(AtomCount, other.AtomCount);
}
public static Molecule Sum(Molecule molecule1, Molecule molecule2)
{
return Sum(new[]{molecule1, molecule2});
}
//TODO: can probably be optimized. (not necessary to produce the full counts arrays.)
public bool Contains(Molecule other)
{
int[] counts = ToCountArray();
int[] otherCounts = other.ToCountArray();
for (int i = 0; i < counts.Length; i++){
if (otherCounts[i] > counts[i]){
return false;
}
}
return true;
}
public static Molecule Subtract(Molecule molecule1, Molecule molecule2)
{
int[] counts = new int[ChemElements.Elements.Length];
for (int j = 0; j < molecule1.AtomType.Length; j++){
counts[molecule1.AtomType[j]] += molecule1.AtomCount[j];
}
for (int j = 0; j < molecule2.AtomType.Length; j++){
counts[molecule2.AtomType[j]] -= molecule2.AtomCount[j];
}
int[] types = new int[counts.Length];
int count = 0;
for (int i = 0; i < counts.Length; i++){
if (counts[i] > 0){
types[count++] = i;
}
}
Array.Resize(ref types, count);
return new Molecule(types, ArrayUtils.SubArray(counts, types));
}
public static Molecule Max(Molecule x, Molecule y)
{
int[] counts1 = new int[ChemElements.Elements.Length];
for (int j = 0; j < x.AtomType.Length; j++){
counts1[x.AtomType[j]] = x.AtomCount[j];
}
int[] counts2 = new int[ChemElements.Elements.Length];
for (int j = 0; j < y.AtomType.Length; j++){
counts2[y.AtomType[j]] = y.AtomCount[j];
}
int[] counts = new int[ChemElements.Elements.Length];
for (int i = 0; i < ChemElements.Elements.Length; i++){
counts[i] = Math.Max(counts1[i], counts2[i]);
}
int[] types = new int[counts.Length];
int count = 0;
for (int i = 0; i < counts.Length; i++){
if (counts[i] > 0){
types[count++] = i;
}
}
Array.Resize(ref types, count);
return new Molecule(types, ArrayUtils.SubArray(counts, types));
}
public static Tuple<Molecule, Molecule> GetDifferences(Molecule molecule1, Molecule molecule2)
{
int[] counts1 = new int[ChemElements.Elements.Length];
for (int j = 0; j < molecule1.AtomType.Length; j++){
counts1[molecule1.AtomType[j]] = molecule1.AtomCount[j];
}
int[] counts2 = new int[ChemElements.Elements.Length];
for (int j = 0; j < molecule2.AtomType.Length; j++){
counts2[molecule2.AtomType[j]] = molecule2.AtomCount[j];
}
for (int i = 0; i < counts1.Length; i++){
if (counts1[i] > counts2[i]){
counts1[i] -= counts2[i];
counts2[i] = 0;
} else{
counts2[i] -= counts1[i];
counts1[i] = 0;
}
}
int[] types1 = new int[counts1.Length];
int count1 = 0;
for (int i = 0; i < counts1.Length; i++){
if (counts1[i] > 0){
types1[count1++] = i;
}
}
Array.Resize(ref types1, count1);
Molecule diff1 = new Molecule(types1, ArrayUtils.SubArray(counts1, types1));
int[] types2 = new int[counts2.Length];
int count2 = 0;
for (int i = 0; i < counts2.Length; i++){
if (counts2[i] > 0){
types2[count2++] = i;
}
}
Array.Resize(ref types2, count2);
Molecule diff2 = new Molecule(types2, ArrayUtils.SubArray(counts2, types2));
return new Tuple<Molecule, Molecule>(diff1, diff2);
}
protected bool Equals(Molecule other)
{
return(ArrayUtils.EqualArrays(AtomType, other.AtomType) && ArrayUtils.EqualArrays(AtomCount, other.AtomCount));
}
public static Molecule Sum(Molecule molecule1, Molecule molecule2)
{
return(Sum(new[] { molecule1, molecule2 }));
}