public static Modification2[] FromStrings(IList <string> modNames)
{
if (modNames == null)
{
return(new Modification2[0]);
}
Modification2[] result = new Modification2[modNames.Count];
for (int i = 0; i < result.Length; i++)
{
result[i] = new Modification2(modNames[i]);
}
return(result);
}
private static double GetDeltaMass(Modification2 mod, string sequence, bool isNterm, bool isCterm)
{
ModificationPosition pos = mod.Position;
double deltaMass = 0;
for (int i = 0; i < mod.AaCount; i++)
{
for (int j = 0; j < sequence.Length; j++)
{
if ((pos == ModificationPosition.notNterm || pos == ModificationPosition.notTerm) && j == 0)
{
continue;
}
if ((pos == ModificationPosition.notCterm || pos == ModificationPosition.notTerm) && j == sequence.Length - 1)
{
continue;
}
if (sequence[j] == mod.GetAaAt(i))
{
deltaMass += mod.DeltaMass;
}
}
}
if (pos == ModificationPosition.anyNterm)
{
deltaMass += mod.DeltaMass;
}
if (pos == ModificationPosition.anyCterm)
{
deltaMass += mod.DeltaMass;
}
if (pos == ModificationPosition.proteinNterm && isNterm)
{
deltaMass += mod.DeltaMass;
}
if (pos == ModificationPosition.proteinCterm && isCterm)
{
deltaMass += mod.DeltaMass;
}
return(deltaMass);
}
public static AminoAcid GetAminoAcidFromLabel(Modification2 m)
{
return(m.AaCount == 0 ? null : AminoAcids.FromLetter(m.GetAaAt(0)));
}
/// <summary>
/// Given string label, return corresponding AminoAcid object, or null for a terminal modiciation.
/// </summary>
/// <param name="label">string label, e.g. "DimethLys2"</param>
/// <returns>AminoAcid object, or null for a terminal modiciation</returns>
public static AminoAcid GetAminoAcidFromLabel(string label)
{
Modification2 m = new Modification2(label);
return(m.AaCount == 0 ? null : AminoAcids.FromLetter(m.GetAaAt(0)));
}
private static double GetDeltaMass(Modification2 mod, string sequence, bool isNterm, bool isCterm)
{
ModificationPosition pos = mod.Position;
double deltaMass = 0;
for (int i = 0; i < mod.AaCount; i++){
for (int j = 0; j < sequence.Length; j++){
if ((pos == ModificationPosition.notNterm || pos == ModificationPosition.notTerm) && j == 0){
continue;
}
if ((pos == ModificationPosition.notCterm || pos == ModificationPosition.notTerm) && j == sequence.Length - 1){
continue;
}
if (sequence[j] == mod.GetAaAt(i)){
deltaMass += mod.DeltaMass;
}
}
}
if (pos == ModificationPosition.anyNterm){
deltaMass += mod.DeltaMass;
}
if (pos == ModificationPosition.anyCterm){
deltaMass += mod.DeltaMass;
}
if (pos == ModificationPosition.proteinNterm && isNterm){
deltaMass += mod.DeltaMass;
}
if (pos == ModificationPosition.proteinCterm && isCterm){
deltaMass += mod.DeltaMass;
}
return deltaMass;
}
public static double GetFixedModificationMass(string sequence, Modification2[] modifications, bool isProteinNterm,
bool isProteinCterm)
{
double monoisotopicMass = 0;
foreach (Modification2 mod in modifications){
monoisotopicMass += GetDeltaMass(mod, sequence, isProteinNterm, isProteinCterm);
}
return monoisotopicMass;
}
public static Modification2[] FromStrings(IList<string> modNames)
{
if (modNames == null){
return new Modification2[0];
}
Modification2[] result = new Modification2[modNames.Count];
for (int i = 0; i < result.Length; i++){
result[i] = new Modification2(modNames[i]);
}
return result;
}
public static double CalcMonoisotopicMass(string sequence, Modification2[] modifications, bool isProteinNterm,
bool isProteinCterm)
{
double m = CalcMonoisotopicMass(sequence);
m += GetFixedModificationMass(sequence, modifications, isProteinNterm, isProteinCterm);
return m;
}
public static AminoAcid GetAminoAcidFromLabel(Modification2 m)
{
return m.AaCount == 0 ? null : AminoAcids.FromLetter(m.GetAaAt(0));
}
/// <summary>
/// Given string label, return corresponding AminoAcid object, or null for a terminal modiciation.
/// </summary>
/// <param name="label">string label, e.g. "DimethLys2"</param>
/// <returns>AminoAcid object, or null for a terminal modiciation</returns>
public static AminoAcid GetAminoAcidFromLabel(string label)
{
Modification2 m = new Modification2(label);
return m.AaCount == 0 ? null : AminoAcids.FromLetter(m.GetAaAt(0));
}