public static double calMHmass(string _sequence,
AminoacidList[] _aminoacids,
isotList[][] _isotopes)
{
double protonMass = 1.007276; //proton Mass in Da (or amu).
double mass = 0.0;
Comb.compStrt[] composition;
if (_aminoacids.Length > 0)
{
composition = AminoacidList.calComposition(_sequence, _aminoacids);
}
else
{
return(0.0);
}
foreach (Comb.compStrt element in composition)
{
for (int i = 0; i < _isotopes.GetUpperBound(0); i++)
{
if (element.Elem == _isotopes[i][0].Elem)
{
mass += (double)element.Nats * _isotopes[i][0].Mass;
break;
}
}
}
//Add a proton
// Not correct
//string H = "H";
//for (int i = 0; i < _isotopes.GetUpperBound(0); i++)
//{
// if (_isotopes[i][0].Elem==H)
// {
// mass += _isotopes[i][0].Mass;
// break;
// }
//}
mass += protonMass;
return(mass);
}
/// <summary>
/// Reads a XML file with the aminoacids' list
/// </summary>
/// <param name="fileXml">XML with the aminoacids' list</param>
/// <returns>(AminoacidList[])</returns>
public static AminoacidList[] readXML(string fileXml)
{
//Initialize necessary objets for XML reading
XmlTextReader reader = new XmlTextReader(fileXml);
XmlNodeType nType = reader.NodeType;
XmlDocument xmldoc = new XmlDocument();
xmldoc.Load(reader);
//Initialize the AminoacidList[] tAaList
XmlNodeList xmlnodeAminoacid = xmldoc.GetElementsByTagName("aminoacid");
AminoacidList[] tAaList = new AminoacidList[xmlnodeAminoacid.Count];
XmlNodeList xmlnodeElement = xmldoc.GetElementsByTagName("Element");
//for each <aminoacid> entry
for (int i = 0; i < xmlnodeAminoacid.Count; i++)
{
//for each child node of the <aminoacid> entry
for (int j = 0; j < xmlnodeAminoacid[i].ChildNodes.Count; j++)
{
string sNode = xmlnodeAminoacid[i].ChildNodes[j].Name.ToString();
if (sNode == "Formula")
{
int nElements = 0;
//Count in <Formula> entry the Element values.
for (int k = 0; k < xmlnodeAminoacid[i].ChildNodes[j].ChildNodes.Count; k++)
{
string sElement = xmlnodeAminoacid[i].ChildNodes[j].ChildNodes[k].Name.ToString();
if (sElement == "Element")
{
nElements++;
}
}
//Initialize the class tAaList[i] with the correct number of elements
tAaList[i] = new AminoacidList(nElements);
//Search in <Formula> entry for the Element values.
for (int k = 0; k < xmlnodeAminoacid[i].ChildNodes[j].ChildNodes.Count; k++)
{
string sElement = xmlnodeAminoacid[i].ChildNodes[j].ChildNodes[k].Name.ToString();
if (sElement == "Element")
{
string sElem = xmlnodeAminoacid[i].ChildNodes[j].ChildNodes[k].Attributes["id"].Value.ToString();
//Search for the number of atoms
int iNatoms = 0;
for (int l = 0; l < xmlnodeAminoacid[i].ChildNodes[j].ChildNodes[k].ChildNodes.Count; l++)
{
string sAtoms = xmlnodeAminoacid[i].ChildNodes[j].ChildNodes[k].ChildNodes[l].Name.ToString();
if (sAtoms == "Natoms")
{
iNatoms = int.Parse(xmlnodeAminoacid[i].ChildNodes[j].ChildNodes[k].ChildNodes[l].InnerText.ToString(), System.Globalization.CultureInfo.InvariantCulture);
}
}
Comb.compStrt tElement = new Comb.compStrt(sElem, iNatoms);
tAaList[i].insert(tElement);
}
}
}
}
//Once you have initialized correctly the class, you can search for the <Name> tag, and so on
for (int j = 0; j < xmlnodeAminoacid[i].ChildNodes.Count; j++)
{
if (xmlnodeAminoacid[i].ChildNodes[j].Name.ToString() == "Name")
{
tAaList[i].name = xmlnodeAminoacid[i].ChildNodes[j].InnerText.ToString();
}
if (xmlnodeAminoacid[i].ChildNodes[j].Name.ToString() == "Code1")
{
tAaList[i].code1 = xmlnodeAminoacid[i].ChildNodes[j].InnerText.ToString();
}
if (xmlnodeAminoacid[i].ChildNodes[j].Name.ToString() == "Code3")
{
tAaList[i].code3 = xmlnodeAminoacid[i].ChildNodes[j].InnerText.ToString();
}
if (xmlnodeAminoacid[i].ChildNodes[j].Name.ToString() == "equivalent")
{
tAaList[i].equivalent = xmlnodeAminoacid[i].ChildNodes[j].InnerText.ToString();
}
}
}
return(tAaList);
}
