void generateFileInThread()
{
List <int[]> hbonds = RNAView.findHbonds();
PlotManager.Instance.PlotAdd("NHBonds", hbonds.Count);
int sequenceLength = MoleculeModel.sequence.Count();
string structure = VARNA.generateStructureString(sequenceLength, hbonds);
varnaProcess = VARNA.generateImage(MoleculeModel.sequence, structure, outputDirectory, "test.png");
varnaProcess.Exited += new EventHandler(varnaProcess_Exited);
varnaProcess.Start();
}
static void BuildHireRnaHydrogenBondsStructures()
{
foreach (KeyValuePair <int, ArrayList> entry in MoleculeModel.residues)
{
int nbOfAtoms = entry.Value.Count;
int i = 0;
while (i != nbOfAtoms)
{
int atomIndex = (int)entry.Value[i];
string atomName = MoleculeModel.atomsNamelist[atomIndex];
if (atomName == "C1" || atomName == "G2" || atomName == "U1" || atomName == "A2")
{
MoleculeModel.baseIdx.Add(atomIndex);
i = nbOfAtoms;
}
else
{
i++;
}
}
}
StreamReader sr = new StreamReader(GUIDisplay.directorypath + "/scale_RNA.dat");
string s;
// Debug.Log ("------------");
float num;
int t = 0;
string substr;
while ((s = sr.ReadLine()) != null)
{
substr = s.Substring(7, 10);
// Debug.Log(substr);
num = float.Parse(substr);
// Debug.Log ("Scale RNA " + t + " " + num);
MoleculeModel.scale_RNA.Add(num);
t++;
}
Debug.Log(MoleculeModel.scale_RNA.Count);
RNAView.RNAView_init();
// Debug.Log ("------------");
}